bluuebunny/crossref_metadata_2025 huggingface dataset:
Retaining cell–cell contact enables preparation and culture of spheroids composed of pure primary cancer cells from colorectal cancer
Authors: Kondo Jumpei , Endo Hiroko , Okuyama Hiroaki , Ishikawa Osamu , Iishi Hiroyasu , Tsujii Masahiko , Ohue Masayuki , Inoue Masahiro
Published: March 2011

Primary culture of the cancer cells from patients’ tumors can provide crucial information of individual tumors, yet the technology has not been optimized until now. We developed an innovative culture method for primary colorectal cancer cells, based on the principle that cell–cell contact of cancer cells was maintained throughout the process. When tumor tissue was dissociated into cell clusters, in which cell–cell contact was retained, they rapidly formed spheroids that we termed cancer tissue-originated spheroids (CTOSs). CTOSs of colorectal cancer consisted of highly purified and viable cancer cells, and they were prepared with high efficiency. In immunodeficient mice, CTOSs formed xenograft tumors that retained the features of the parental tumors. Moreover, CTOSs were able to be cultured and expanded in vitro using a 3D culture system and stem cell culture medium. This method allowed evaluation of chemosensitivity and signal pathway activation in cancer cells from individual patients. Easy preparation and culture of pure primary cancer cells provides an innovative platform for studying cancer biology and developing personalized medicine.
Natural dissociation of olivine to (Mg,Fe)SiO
3
perovskite and magnesiowüstite in a shocked Martian meteorite
Authors: Miyahara Masaaki , Ohtani Eiji , Ozawa Shin , Kimura Makoto , El Goresy Ahmed , Sakai Takeshi , Nagase Toshiro , Hiraga Kenji , Hirao Naohisa , Ohishi Yasuo
Published: March 2011

We report evidence for the natural dissociation of olivine in a shergottite at high-pressure and high-temperature conditions induced by a dynamic event on Mars. Olivine (Fa
34-41
) adjacent to or entrained in the shock melt vein and melt pockets of Martian meteorite olivine-phyric shergottite Dar al Gani 735 dissociated into (Mg,Fe)SiO
3
perovskite (Pv)+magnesiowüstite (Mw), whereby perovskite partially vitrified during decompression. Transmission electron microscopy observations reveal that microtexture of olivine dissociation products evolves from lamellar to equigranular with increasing temperature at the same pressure condition. This is in accord with the observations of synthetic samples recovered from high-pressure and high-temperature experiments. Equigranular (Mg,Fe)SiO
3
Pv and Mw have 50–100 nm in diameter, and lamellar (Mg,Fe)SiO
3
Pv and Mw have approximately 20 and approximately 10 nm in thickness, respectively. Partitioning coefficient,
K
Pv/Mw
 = [FeO/MgO]/[FeO/MgO]
Mw
, between (Mg,Fe)SiO
3
Pv and Mw in equigranular and lamellar textures are approximately 0.15 and approximately 0.78, respectively. The dissociation of olivine implies that the pressure and temperature conditions recorded in the shock melt vein and melt pockets during the dynamic event were approximately 25 GPa but 700 °C at least.
The long shadow cast by childhood physical and mental problems on adult life
Authors: Goodman Alissa , Joyce Robert , Smith James P.
Published: March 2011

In this article we assess and compare long-term adult socioeconomic status impacts from having experienced psychological and physical health problems in childhood. To do so, we use unique prospective data from the British National Child Development Study, a continuing panel study of a cohort of 17,634 children born in Great Britain during a single week in March 1958. To date there have been nine waves for this birth cohort to monitor their physical, educational, and social development, during childhood (at birth and 7, 11, and 16 y) and adulthood (age 23, 33, 42, 46, and 50 y). Excellent contemporaneous information exists throughout childhood on physical and psychological health, captured by doctor and nurse-led medical examinations and detailed parental and teacher questionnaires. This information is combined with a wealth of contemporaneous information on adult health and economic experiences collected from cohort members. Information includes their economic circumstances (earnings, labor supply, and other sources of family income), physical and psychological health, and relationship status. Large effects are found due to childhood psychological problems on the ability of affected children to work and earn as adults and on intergenerational and within-generation social mobility. Adult family incomes are reduced by 28% by age 50 y, with sustained impacts on labor supply, marriage stability, and the conscientiousness and agreeableness components of the “Big Five” personality traits. Effects of psychological health disorders during childhood are far more important over a lifetime than physical health problems.
Rather than resonance, flapping wing flyers may play on aerodynamics to improve performance
Authors: Ramananarivo Sophie , Godoy-Diana Ramiro , Thiria Benjamin
Published: March 2011

Saving energy and enhancing performance are secular preoccupations shared by both nature and human beings. In animal locomotion, flapping flyers or swimmers rely on the flexibility of their wings or body to passively increase their efficiency using an appropriate cycle of storing and releasing elastic energy. Despite the convergence of many observations pointing out this feature, the underlying mechanisms explaining how the elastic nature of the wings is related to propulsive efficiency remain unclear. Here we use an experiment with a self-propelled simplified insect model allowing to show how wing compliance governs the performance of flapping flyers. Reducing the description of the flapping wing to a forced oscillator model, we pinpoint different nonlinear effects that can account for the observed behavior—in particular a set of cubic nonlinearities coming from the clamped-free beam equation used to model the wing and a quadratic damping term representing the fluid drag associated to the fast flapping motion. In contrast to what has been repeatedly suggested in the literature, we show that flapping flyers optimize their performance not by especially looking for resonance to achieve larger flapping amplitudes with less effort, but by tuning the temporal evolution of the wing shape (i.e., the phase dynamics in the oscillator model) to optimize the aerodynamics.
Virophage control of antarctic algal host–virus dynamics
Authors: Yau Sheree , Lauro Federico M. , DeMaere Matthew Z. , Brown Mark V. , Thomas Torsten , Raftery Mark J. , Andrews-Pfannkoch Cynthia , Lewis Matthew , Hoffman Jeffrey M. , Gibson John A. , Cavicchioli Ricardo
Published: March 2011

Viruses are abundant ubiquitous members of microbial communities and in the marine environment affect population structure and nutrient cycling by infecting and lysing primary producers. Antarctic lakes are microbially dominated ecosystems supporting truncated food webs in which viruses exert a major influence on the microbial loop. Here we report the discovery of a virophage (relative of the recently described Sputnik virophage) that preys on phycodnaviruses that infect prasinophytes (phototrophic algae). By performing metaproteogenomic analysis on samples from Organic Lake, a hypersaline meromictic lake in Antarctica, complete virophage and near-complete phycodnavirus genomes were obtained. By introducing the virophage as an additional predator of a predator–prey dynamic model we determined that the virophage stimulates secondary production through the microbial loop by reducing overall mortality of the host and increasing the frequency of blooms during polar summer light periods. Virophages remained abundant in the lake 2 y later and were represented by populations with a high level of major capsid protein sequence variation (25–100% identity). Virophage signatures were also found in neighboring Ace Lake (in abundance) and in two tropical lakes (hypersaline and fresh), an estuary, and an ocean upwelling site. These findings indicate that virophages regulate host–virus interactions, influence overall carbon flux in Organic Lake, and play previously unrecognized roles in diverse aquatic ecosystems.
Identification of a bioactive 51-membered macrolide complex by activation of a silent polyketide synthase in
Streptomyces ambofaciens
Authors: Laureti Luisa , Song Lijiang , Huang Sheng , Corre Christophe , Leblond Pierre , Challis Gregory L. , Aigle Bertrand
Published: March 2011

There is a constant need for new and improved drugs to combat infectious diseases, cancer, and other major life-threatening conditions. The recent development of genomics-guided approaches for novel natural product discovery has stimulated renewed interest in the search for natural product-based drugs. Genome sequence analysis of
Streptomyces ambofaciens
ATCC23877 has revealed numerous secondary metabolite biosynthetic gene clusters, including a giant type I modular polyketide synthase (PKS) gene cluster, which is composed of 25 genes (nine of which encode PKSs) and spans almost 150 kb, making it one of the largest polyketide biosynthetic gene clusters described to date. The metabolic product(s) of this gene cluster are unknown, and transcriptional analyses showed that it is not expressed under laboratory growth conditions. The constitutive expression of a regulatory gene within the cluster, encoding a protein that is similar to Large ATP binding of the LuxR (LAL) family proteins, triggered the expression of the biosynthetic genes. This led to the identification of four 51-membered glycosylated macrolides, named stambomycins A–D as metabolic products of the gene cluster. The structures of these compounds imply several interesting biosynthetic features, including incorporation of unusual extender units into the polyketide chain and in
trans
hydroxylation of the growing polyketide chain to provide the hydroxyl group for macrolide formation. Interestingly, the stambomycins possess promising antiproliferative activity against human cancer cell lines. Database searches identify genes encoding LAL regulators within numerous cryptic biosynthetic gene clusters in actinomycete genomes, suggesting that constitutive expression of such pathway-specific activators represents a powerful approach for novel bioactive natural product discovery.
IL-15 transpresentation promotes both human T-cell reconstitution and T-cell–dependent antibody responses in vivo
Authors: Huntington Nicholas D. , Alves Nuno L. , Legrand Nicolas , Lim Annick , Strick-Marchand Helene , Mention Jean-Jacques , Plet Ariane , Weijer Kees , Jacques Yannick , Becker Pablo D. , Guzman Carlos , Soussan Patrick , Kremsdorf Dina , Spits Hergen , Di Santo James P.
Published: March 2011

Cytokine immunotherapies targeting T lymphocytes are attractive clinical interventions against viruses and tumors. In the mouse, the homeostasis of memory α/β CD8+T cells and natural killer (NK) cells is significantly improved with increased IL-15 bioavailability. In contrast, the role of “transpresented” IL-15 on human T-cell development and homeostasis in vivo is unknown. We found that both CD8 and CD4 T cells in human immune system (HIS) mice are highly sensitive to transpresented IL-15 in vivo, with both naïve (CD62L+CD45RA+) and memory phenotype (CD62L−CD45RO+) subsets being significantly increased following IL-15 “boosting.” The unexpected global improvement in human T-cell homeostasis involved enhanced proliferation and survival of both naïve and memory phenotype peripheral T cells, which potentiated B-cell responses by increasing the frequency of antigen-specific responses following immunization. Transpresented IL-15 did not modify T-cell activation patterns or alter the global T-cell receptor (TCR) repertoire diversity. Our results indicate an unexpected effect of IL-15 on human T cells in vivo, in particular on CD4+T cells. As IL-15 promotes human peripheral T-cell homeostasis and increases the frequency of neutralizing antibody responses in HIS mice, IL-15 immunotherapy could be envisaged as a unique approach to improve vaccine responses in the clinical setting.
Mutation that blocks ATP binding creates a pseudokinase stabilizing the scaffolding function of kinase suppressor of Ras, CRAF and BRAF
Authors: Hu Jiancheng , Yu Haiyang , Kornev Alexandr P. , Zhao Jianping , Filbert Erin L. , Taylor Susan S. , Shaw Andrey S.
Published: March 2011

Because mutations in RAS and BRAF represent the most common mutations found in human tumors, identification of inhibitors has been a major goal. Surprisingly, new oncogenic BRAF specific inhibitors inhibit cells transformed with mutated BRAF but paradoxically stimulate the growth of cells transformed with RAS. Here, we show that the mechanism for activation is via drug-induced dimer formation between CRAF and kinase suppressor of Ras (KSR)1. To understand the function of KSR1, we generated a KSR1 mutant that cannot bind ATP but stabilizes the closed, active conformation of KSR1. Molecular modeling suggested that the mutant stabilizes the two hydrophobic spines critical for the closed active conformation. We, therefore, could use the mutant to discriminate between the scaffold versus kinase functions of KSR1. The KSR1 mutant bound constitutively to RAF and mitogen-activated protein kinase kinase (MEK) but could not reconstitute activity suggesting that the catalytic activity of KSR1 is required for its function. Analogous mutations in BRAF and CRAF allowed us to test the generality of the model. The mutation induced changes consistent with the active, closed conformation of both kinases and confirmed that BRAF functions distinctly from CRAF in the MAP kinase pathway. Not only does this work suggest that KSR1 may function as a kinase, we anticipate that the mutation that we generated may be broadly applicable to stabilize the closed conformation of other kinases many of which may also form dimers.
Social rejection shares somatosensory representations with physical pain
Authors: Kross Ethan , Berman Marc G. , Mischel Walter , Smith Edward E. , Wager Tor D.
Published: March 2011

How similar are the experiences of social rejection and physical pain? Extant research suggests that a network of brain regions that support the affective but not the sensory components of physical pain underlie both experiences. Here we demonstrate that when rejection is powerfully elicited—by having people who recently experienced an unwanted break-up view a photograph of their ex-partner as they think about being rejected—areas that support the sensory components of physical pain (secondary somatosensory cortex; dorsal posterior insula) become active. We demonstrate the overlap between social rejection and physical pain in these areas by comparing both conditions in the same individuals using functional MRI. We further demonstrate the specificity of the secondary somatosensory cortex and dorsal posterior insula activity to physical pain by comparing activated locations in our study with a database of over 500 published studies. Activation in these regions was highly diagnostic of physical pain, with positive predictive values up to 88%. These results give new meaning to the idea that rejection “hurts.” They demonstrate that rejection and physical pain are similar not only in that they are both distressing—they share a common somatosensory representation as well.
Tidal surge in the M2 proton channel, sensed by 2D IR spectroscopy
Authors: Ghosh Ayanjeet , Qiu Jade , DeGrado William F. , Hochstrasser Robin M.
Published: March 2011

The M2 proton channel from influenza A virus transmits protons across membranes via a narrow aqueous pore lined by water and a proton sensor, His37. Near the center of the membrane, a water cluster is stabilized by the carbonyl of Gly34 and His37, the properties of which are modulated by protonation of His37. At low pH (5–6), where M2 conducts protons, this region undergoes exchange processes on the microsecond to second timescale. Here, we use 2D IR to examine the instantaneous conformational distribution and hydration of G34, and the evolution of the ensemble on the femtosecond to picosecond timescale. The channel water is strongly pH dependent as gauged by 2D IR which allows recording of the vibrational frequency autocorrelation function of a
13
C = 
18
O Gly34 probe. At pH 8, where entry and exit of protons within the channel are very slow, the carbonyl groups appear to adopt a single conformation/environment. The high-pH conformer does not exhibit spectral dynamics near the Gly34, and water in the channel must form a relatively rigid ice-like structure. By contrast, two vibrational forms of G34 are seen at pH 6.2, neither of which is identical to the high-pH form. In at least one of these low-pH forms, the probe is immersed in a very mobile, bulk-like aqueous environment having a correlation time
ca.
1.3 ps at pH 6.2. Thus, protonation of His37 at low pH causes liquid-like water molecules to flow into the neighborhood of the Gly34.
WORK, LIFE COURSE, AND GENDER
Authors: Nilsen Ann
Published: March 2011

Since Norwegian family-friendly policies are gender neutral while the division of labour in families is gendered, some argue that the generous state support for families may end up upholding the status quo; it may perpetuate the existing inequitable division of labour between mothers and fathers in the home and in the labour market in which some women take long maternity leave and work part-time. Since many gender equality measures are intended to increase the percentage of women in male-dominated occupations and positions, they are aimed at occupations with upwardly mobile trajectories. A typological distinction between ‘career’ and ‘non-career’ work is made in the analysis of biographical cases of men and women in two different organisational settings. Their thoughts and actions in relation to their occupational trajectories over the life course are examined in different layers of context in order to understand how a complex set of factors affects ways of adjusting to the phase of being parents of young children. The paper concludes that the relationship between gender equality measures and family-friendly policies is not necessarily characterised by tensions, but must rather be considered in relation to a complex set of circumstances in men's and women's life courses that include family, education, and occupation as well as organisational settings that for the many do not involve career jobs.
Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice
Authors: Nakagawa Shinichi , Naganuma Takao , Shioi Go , Hirose Tetsuro
Published: March 2011

Nuclei of higher organisms are well structured and have multiple, distinct nuclear compartments or nuclear bodies. Paraspeckles are recently identified mammal-specific nuclear bodies ubiquitously found in most cells cultured in vitro. To investigate the physiological role of paraspeckles, we examined the in vivo expression patterns of two long noncoding RNAs, NEAT1_1 and NEAT1_2, which are essential for the architectural integrity of nuclear bodies. Unexpectedly, these genes were only strongly expressed in a particular subpopulation of cells in adult mouse tissues, and prominent paraspeckle formation was observed only in the cells highly expressing NEAT1_2. To further investigate the cellular functions of paraspeckles, we created an animal model lacking NEAT1 by gene targeting. These knockout mice were viable and fertile under laboratory growth conditions, showing no apparent phenotypes except for the disappearance of paraspeckles. We propose that paraspeckles are nonessential, subpopulation-specific nuclear bodies formed secondary to particular environmental triggers.
ARH cooperates with AP-1B in the exocytosis of LDLR in polarized epithelial cells
Authors: Kang Richard S. , Fölsch Heike
Published: March 2011

The autosomal recessive hypercholesterolemia protein (ARH) is well known for its role in clathrin-mediated endocytosis of low-density lipoprotein receptors (LDLRs). During uptake, ARH directly binds to the FxNPxY signal in the cytoplasmic tail of LDLR. Interestingly, the same FxNPxY motif is used in basolateral exocytosis of LDLR from recycling endosomes (REs), which is facilitated by the epithelial-specific clathrin adaptor AP-1B. However, AP-1B directly interacts with neither the FxNPxY motif nor the second more distally located YxxØ sorting motif of LDLR. Here, we show that ARH colocalizes and cooperates with AP-1B in REs. Knockdown of ARH in polarized epithelial cells leads to specific apical missorting of truncated LDLR, which encodes only the FxNPxY motif (LDLR-CT27). Moreover, a mutation in ARH designed to disrupt the interaction of ARH with AP-1B specifically abrogates exocytosis of LDLR-CT27. We conclude that in addition to its role in endocytosis, ARH cooperates with AP-1B in basolateral exocytosis of LDLR from REs.
Viral infection prevents diabetes by inducing regulatory T cells through NKT cell–plasmacytoid dendritic cell interplay
Authors: Diana Julien , Brezar Vedran , Beaudoin Lucie , Dalod Marc , Mellor Andrew , Tafuri Anna , von Herrath Matthias , Boitard Christian , Mallone Roberto , Lehuen Agnès
Published: March 2011

Type 1 diabetes (T1D) is an autoimmune disease resulting from T cell–mediated destruction of insulin-producing β cells, and viral infections can prevent the onset of disease. Invariant natural killer T cells (iNKT cells) exert a regulatory role in T1D by inhibiting autoimmune T cell responses. As iNKT cell–plasmacytoid dendritic cell (pDC) cooperation controls viral replication in the pancreatic islets, we investigated whether this cellular cross talk could interfere with T1D development during viral infection. Using both virus-induced and spontaneous mouse models of T1D, we show that upon viral infection, iNKT cells induce TGF-β–producing pDCs in the pancreatic lymph nodes (LNs). These tolerogenic pDCs convert naive anti-islet T cells into Foxp3+ CD4+ regulatory T cells (T reg cells) in pancreatic LNs. T reg cells are then recruited into the pancreatic islets where they produce TGF-β, which dampens the activity of viral- and islet-specific CD8+ T cells, thereby preventing T1D development in both T1D models. These findings reveal a crucial cooperation between iNKT cells, pDCs, and T reg cells for prevention of T1D by viral infection.
Spectroscopy of the electronic states of the Heusler compounds Co2FeAl and Co2Cr0.6Fe0.4Al and the influence of oxidation
Authors: Jourdan Martin , Große-Schulte Fabian , Hahn Michaela , Schönhense Gerd
Published: March 2011

The band structures of the Heusler compounds Co2Cr0.6Fe0.4Al and Co2FeAl were investigated in situ by angle-resolved ultraviolet photoemission spectroscopy. The samples were prepared by a sputtering process optimized for tunnelling junction preparation, the photoemission process in the normal direction of the (0 0 1)-oriented thin films was excited by a helium gas discharge lamp (hν = 21.2 eV and hν = 40.8 eV). The spectra of clean samples are compared with calculations of the total and partial bulk density of states and are evaluated within the three-step model of photoemission. Basic agreement with theoretical predictions of the bulk band structure is concluded. At oxygen exposures of the thin films of only 1 Langmuir a chemisorption phase with significant changes in the valence-band spectrum near the Fermi energy is observed. At 10 L oxygen the spectra are indicative of an oxide within the UPS probing depth.
Swift heavy ion irradiation of Pt nanocrystals: II. Structural changes and H desorption
Authors: Giulian R , Araujo L L , Kluth P , Sprouster D J , Schnohr C S , Byrne A P , Ridgway M C
Published: March 2011

The structural properties and H desorption from embedded Pt nanocrystals (NCs) following irradiation with swift heavy ions were investigated as a function of energy and fluence. From x-ray absorption near-edge spectroscopy analysis, Pt–H bonding was identified in NCs annealed in a forming gas (95% N2 + 5% H2) ambient. The H content decreased upon irradiation and the desorption process was NC-size dependent such that larger NCs required a higher fluence to achieve a H-free state. Pt–H bonding and NC dissolution both perturbed the NC structural parameters (coordination number, bond-length and mean-square relative displacement) as determined with extended x-ray absorption fine structure measurements.
Growth mechanisms for doped clusters
Authors: Janssens Ewald , Lievens Peter
Published: March 2011

Structural growth mechanisms for metal doped nanoclusters are investigated in combined experimental and theoretical studies. In particular, silicon, copper and gold clusters incorporating a transition metal dopant atom are investigated:SinX(X=Cu, V),CunSc+andAunY+withn< 20. The doped clusters are produced with a dual-target dual-laser vaporization source. Structural information about the doped nanoclusters is provided by infrared multi-photon dissociation spectroscopy. Their size and composition dependent stability is studied with photofragmentation and mass spectrometry. A detailed understanding of the role of the dopant atom in the structural growth and in the electronic structure of the clusters is obtained by comparison with quantum chemical computations using density functional theory.
The effect of Ku on telomere replication time is mediated by telomere length but is independent of histone tail acetylation
Authors: Lian Hui-Yong , Robertson E. Douglas , Hiraga Shin-ichiro , Alvino Gina M. , Collingwood David , McCune Heather J. , Sridhar Akila , Brewer Bonita J. , Raghuraman M. K. , Donaldson Anne D.
Published: March 2011

DNA replication in Saccharomyces cerevisiae proceeds according to a temporal program. We have investigated the role of the telomere-binding Ku complex in specifying late replication of telomere-proximal sequences. Genome-wide analysis shows that regions extending up to 80 kb from telomeres replicate abnormally early in a yku70 mutant. We find that Ku does not appear to regulate replication time by binding replication origins directly, nor is its effect on telomere replication timing mediated by histone tail acetylation. We show that Ku instead regulates replication timing through its effect on telomere length, because deletion of the telomerase regulator Pif1 largely reverses the short telomere defect of a yku70 mutant and simultaneously rescues its replication timing defect. Consistent with this conclusion, deleting the genome integrity component Elg1 partially rescued both length and replication timing of yku70 telomeres. Telomere length–mediated control of replication timing requires the TG1–3repeat-counting component Rif1, because a rif1 mutant replicates telomeric regions early, despite having extended TG1–3tracts. Overall, our results suggest that the effect of Ku on telomere replication timing results from its impact on TG1–3repeat length and support a model in which Rif1 measures telomere repeat length to ensure that telomere replication timing is correctly programmed.
Degradation of Alzheimer's amyloid fibrils by microglia requires delivery of ClC-7 to lysosomes
Authors: Majumdar Amitabha , Capetillo-Zarate Estibaliz , Cruz Dana , Gouras Gunnar K. , Maxfield Frederick R.
Published: March 2011

Incomplete lysosomal acidification in microglia inhibits the degradation of fibrillar forms of Alzheimer's amyloid β peptide (fAβ). Here we show that in primary microglia a chloride transporter, ClC-7, is not delivered efficiently to lysosomes, causing incomplete lysosomal acidification. ClC-7 protein is synthesized by microglia but it is mistargeted and appears to be degraded by an endoplasmic reticulum–associated degradation pathway. Activation of microglia with macrophage colony-stimulating factor induces trafficking of ClC-7 to lysosomes, leading to lysosomal acidification and increased fAβ degradation. ClC-7 associates with another protein, Ostm1, which plays an important role in its correct lysosomal targeting. Expression of both ClC-7 and Ostm1 is increased in activated microglia, which can account for the increased delivery of ClC-7 to lysosomes. Our findings suggest a novel mechanism of lysosomal pH regulation in activated microglia that is required for fAβ degradation.
Btn3 is a negative regulator of Btn2-mediated endosomal protein trafficking and prion curing in yeast
Authors: Kanneganti Vydehi , Kama Rachel , Gerst Jeffrey E.
Published: March 2011

Yeast Btn2 facilitates the retrieval of specific proteins from late endosomes (LEs) to the Golgi, a process that may be adversely affected in Batten disease patients. We isolated the putative yeast orthologue of a human complex I deficiency gene, designated here as BTN3, as encoding a Btn2-interacting protein and negative regulator. First, yeast overexpressing BTN3 phenocopy the deletion of BTN2 and mislocalize certain trans-Golgi proteins, like Kex2 and Yif1, to the LE and vacuole, respectively. In contrast, the deletion of BTN3 results in a tighter pattern of protein localization to the Golgi. Second, BTN3 overexpression alters Btn2 localization from the IPOD compartment, which correlates with a sharp reduction in Btn2-mediated [URE3] prion curing. Third, Btn3 and the Snc1 v-SNARE compete for the same binding domain on Btn2, and this competition controls Btn2 localization and function. The inhibitory effects upon protein retrieval and prion curing suggest that Btn3 sequesters Btn2 away from its substrates, thus down-regulating protein trafficking and aggregation. Therefore Btn3 is a novel negative regulator of intracellular protein sorting, which may be of importance in the onset of complex I deficiency and Batten disease in humans.
The peroxin Pex34p functions with the Pex11 family of peroxisomal divisional proteins to regulate the peroxisome population in yeast
Authors: Tower Robert J. , Fagarasanu Andrei , Aitchison John D. , Rachubinski Richard A.
Published: March 2011

Peroxisomes are ubiquitous organelles involved in diverse metabolic processes, most notably the metabolism of lipids and the detoxification of reactive oxygen species. Peroxisomes are highly dynamic and change in size and number in response to both intra- and extracellular cues. In the yeast Saccharomyces cerevisiae, peroxisome growth and division are controlled by both the differential import of soluble matrix proteins and a specialized divisional machinery that includes peroxisome-specific factors, such as members of the Pex11 protein family, and general organelle divisional factors, such as the dynamin-related protein Vps1p. Global yeast two-hybrid analyses have demonstrated interactions between the product of the S. cerevisiae gene of unknown function, YCL056c, and Pex proteins involved in peroxisome biogenesis. Here we show that the protein encoded by YCL056c, renamed Pex34p, is a peroxisomal integral membrane protein that acts independently and also in concert with the Pex11 protein family members Pex11p, Pex25p, and Pex27p to control the peroxisome populations of cells under conditions of both peroxisome proliferation and constitutive peroxisome division. Yeast two-hybrid analysis showed that Pex34p interacts physically with itself and with Pex11p, Pex25p, and Pex27p but not with Vps1p. Pex34p can act as a positive effector of peroxisome division as its overexpression leads to increased numbers of peroxisomes in wild type and pex34Δ cells. Pex34p requires the Pex11 family proteins to promote peroxisome division. Our discovery of Pex34p as a protein involved in the already complex control of peroxisome populations emphasizes the necessity of cells to strictly regulate their peroxisome populations to be able to respond appropriately to changing environmental conditions.
Quantifying causes of discard variability: an indispensable assistance to discard estimation and a paramount need for policy measures
Authors: Depestele Jochen , Vandemaele Sofie , Vanhee Willy , Polet Hans , Torreele Els , Leirs Herwig , Vincx Magda
Published: March 2011

Depestele, J., Vandemaele, S., Vanhee, W., Polet, H., Torreele, E., Leirs, H., and Vincx, M. 2011. Quantifying causes of discard variability: an indispensable assistance to discard estimation and a paramount need for policy measures. – ICES Journal of Marine Science, 68: 1719–1725. Fishery-dependent data underpin the scientific advice given to fishery managers. However, discard estimates are often imprecise as a result of limited sampling coverage. Estimating discard rates from length frequency distributions (LFDs) in commercial catches may complement information from observer trips. The accuracy of estimates depends greatly on careful investigation of the discard variability. Here, the impact of three essential factors was quantified for beam-trawl fisheries in the southern North Sea: (i) market prices, (ii) landings per trip (LPT) limitations, and (iii) selectivity of the commercial fishing gear. Observed discard rates for cod, plaice, sole, and whiting were compared with estimates based on length frequency data, taking account of the variability attributable to LPT limitations and market price. Observed discard estimates of cod and whiting differed significantly from LFD-derived estimates because of highgrading. The results indicate that LFD-derived discard estimates are only reliable if the crucial driving factors are quantified. LFDs can be collected from research vessels or by fishers in partnership with scientists. Based upon many of these LFDs and the discard-variability factors identified in observer programmes, discard rates can be estimated better.
Patient Safety
Authors: Ambrose Lucy
Published: March 2011

‘First do no harm’ is a central premise of medicine believed to originate from Hippocrates and is the opening statement in many articles relating to patient safety. It focuses the great challenge for current and future practitioners to minimize risk to our patients. Over the last two decades, it has been demonstrated that we do harm to our patients on a regular basis. Evidence has emerged from across the world, which demonstrates the level of harm that patients' experience during their journeys through health care systems. Between 10 and 20% of all health care encounters result in harm to patients. A worldwide movement has emerged in response to these figures, which aims to improve safety and includes all involved in health care across primary and secondary care.
The Ageing Population
Authors: Wale Anita
Published: March 2011

Our population is getting larger and older and with this, the burden of disease is predicted to increase. In addition, the issue of age discrimination is becoming increasingly relevant. This article provides an overview of how our population is changing, the effect this is likely to have and an overview of age discrimination. In addition, it aims to highlight the significant issues that will directly affect general practice and how these may be addressed.
Germ‐Derived FAN as Nitrogen Source for Corn Endosperm Fermentation
Authors: Vidal Bernardo C. , Johnston David B. , Rausch Kent D. , Tumbleson M. E. , Singh Vijay
Published: March 2011

Corn endosperm separated by dry fractionation could exhibit poor fermentation performance due to loss of germ components beneficial for yeast growth. Inorganic nitrogen and other nutritional supplementations are used to overcome slow fermentation rates. We investigated the use of a protease in generating free amino nitrogen (FAN) from germ as an alternative to exogenous nitrogen sources. Up to 300% more FAN can be generated from germ in 6 hr of incubation with protease than without protease. Protease incubation also resulted in higher dry solids (ds) and total glucose contents in the germ hydrolyzates. During fermentation without urea addition, ethanol yields were dependent on mash FAN concentrations. Ethanol yields increased to a maximum when FAN level was 80–90 mg of FAN/100 g ds. At half the optimal FAN level (≈40 mg of FAN/100 g ds), nitrogen limitation occurred, as indicated by high residual glucose concentrations. However, germ FAN did not increase the ethanol yields compared to urea supplementation, likely because germ FAN resulted in lower substrate consumption compared to urea supplementation. Lower substrate consumption correlated to the increase in residual maltose with increase in initial FAN. Ethanol productivity in 0–24 hr of fermentation was higher with germ FAN than with urea, thus decreasing overall fermentation time.
Phosphoproteome Analysis of Lotus japonicus Roots Reveals Shared and Distinct Components of Symbiosis and Defense
Authors: Serna-Sanz Antonio , Parniske Martin , Peck Scott C.
Published: March 2011

Plant roots form an intracellular symbiosis with nitrogen-fixing bacteria while maintaining the capacity for defending themselves against bacterial pathogens. To investigate the molecular relationship between these opposing cellular responses, we compared changes in the root phosphoproteome of the legume Lotus japonicus occurring within minutes after perception of nodulation factor (NF), a symbiotic signaling molecule, to those elicited by flagellin peptide (flg22), a conserved pathogen-associated peptide motif present in flagellar protein of a wide range of bacteria. Phosphoproteins were visualized by autoradiography of two-dimensional polyacrylamide gels after in vivo labeling with 33P-orthophosphate. Comparisons of NF- and flg22-induced phosphoprotein patterns revealed signal-specific responses but also a surprisingly large overlap. Specificity of the responses was observed because the NF receptor kinases NFR1 and NFR5 were both required for NF- but not for flg22-mediated changes in the phosphoproteome. Moreover, NF did not stimulate an oxidative burst or activation of mitogen-activated protein kinases, two common markers for early defense responses that were induced by flg22. Inhibitor studies revealed that phosphorylation of at least some of the proteins in response to NF requires phospholipase D (PLD) whereas regulation of the flg22 phosphoproteome is PLD-independent. Although plant signal transduction during symbiosis and defense utilizes distinct components, phosphorylation of overlapping sets of proteins is achieved.
Efficacy of Four Soil Treatments Against Fusarium oxysporum f. sp. vasinfectum Race 4 on Cotton
Authors: Bennett R. S. , Spurgeon D. W. , DeTar W. R. , Gerik J. S. , Hutmacher R. B. , Hanson B. D.
Published: March 2011

Fusarium wilt, caused by race 4 of Fusarium oxysporum f. sp. vasinfectum, is a critically important disease problem in California cotton (Pima, Gossypium barbadense; Upland, G. hirsutum). Because few cultivars with resistance to race 4 are available, alternative management strategies for this disease are needed. Four soil treatments (50:50 methyl-bromide + chloropicrin as a positive control; 60:40 chloropicrin + 1,3-dichloropropene; 6 weeks of solarization; and metam-sodium) were evaluated for efficacy against race 4 in a naturally infested, heavy clay soil. Treatments were evaluated based on plant mortality, height, number of mainstem nodes, vascular discoloration ratings, and soil counts of F. oxysporum. Two cultivars each of Pima and Upland cotton varying in resistance to race 4 were used. Plant mortality was lowest in methyl-bromide + chloropicrin, solarization, and chloropicrin + 1,3-dichloropropene treatments, and highest in the nontreated and metam-sodium treatments. Although most plant mortality occurred within 5 weeks after planting, substantial mortality of the susceptible Pima cultivar DP 744 accumulated for up to 10 weeks. Seven to eight weeks after planting, plants in methyl-bromide + chloropicrin and chloropicrin + 1,3-dichloropropene treatments were taller and had more mainstem nodes than in other treatments. Vascular discoloration was reduced in methyl-bromide + chloropicrin and solarization treatments compared with the nontreated control, metam-sodium, and chloropicrin + 1,3-dichloropropene treatments. Soil counts of F. oxysporum were significantly reduced only in the methylbromide + chloropicrin, chloropicrin + 1,3-dichloropropene, and solarization treatments. Six weeks of solarization and 60:40 chloropicrin + 1,3-dichloropropene (295 liters a.i./ha) proved effective for reducing Fusarium wilt of cotton in heavy clay soil.
Fodinibius salinus gen. nov., sp. nov., a moderately halophilic bacterium isolated from a salt mine
Authors: Wang Yong-Xia , Liu Ji-Hui , Xiao Wei , Zhang Xiao-Xia , Li Yi-Qing , Lai Yong-Hong , Ji Kai-Yan , Wen Meng-Liang , Cui Xiao-Long
Published: March 2011

A novel, moderately halophilic, rod-shaped bacterium, designated strain YIM D17T, was isolated from a sample of sediment from a salt mine in Yunnan, south-western China. The taxonomy of strain YIM D17T was investigated using a polyphasic approach. Strain YIM D17T was Gram-stain-negative, strictly aerobic and non-motile and formed pink colonies on marine agar. Optimal growth occurred at 37 °C, pH 7.5–8.0 and in the presence of 10–15 % (w/v) NaCl. The major menaquinone was MK-7. The polar lipid profile was composed predominantly of diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, one phospholipid, one glycolipid and one aminolipid. Minor amounts of other lipids were also detectable. The predominant cellular fatty acids were iso-C17 : 1ω9c/10-methyl-C16 : 0 (24.0 %), iso-C15 : 0 (23.6 %) and C16 : 1ω7c/C16 : 1ω6c (13.8 %). The DNA G+C content was 43.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the isolate formed a distinct clade with the genera Gracilimonas and Balneola (both in the phylum Bacteroidetes) and was related to the species Gracilimonas tropica, Balneola vulgaris and Balneola alkaliphila, with sequence similarities of 85.6 %, 83.0 % and 82.8 % to the respective type strains. On the basis of its phenotypic, chemotaxonomic and phylogenetic features, strain YIM D17T represents a novel species of a new genus, for which the name Fodinibius salinus gen. nov., sp. nov. is proposed. The type strain is YIM D17T ( = ACCC 10716T = DSM 21935T).
Idiomarina maris sp. nov., a marine bacterium isolated from sediment
Authors: Zhang Yan-Jiao , Zhang Xi-Ying , Zhao Hui-Lin , Zhou Ming-Yang , Li Hui-Juan , Gao Zhao-Ming , Chen Xiu-Lan , Dang Hong-Yue , Zhang Yu-Zhong
Published: March 2011

A protease-producing marine bacterium, designated CF12-14T, was isolated from sediment of the South China Sea. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain CF12-14T formed a separate lineage within the genus Idiomarina (Gammaproteobacteria). The isolate showed the highest 16S rRNA gene sequence similarity with Idiomarina salinarum ISL-52T (94.7 %), Idiomarina seosinensis CL-SP19T (94.6 %) and other members of the genus Idiomarina (91.9–94.6 %). Cells were Gram-negative, aerobic, flagellated, straight or slightly curved, and often formed buds and prosthecae. Strain CF12-14T grew at 4–42 °C (optimum 30–35 °C) and with 0.1–15 % (w/v) NaCl (optimum 2–3 %). The isolate reduced nitrate to nitrite and hydrolysed DNA, but did not produce acids from sugars. The predominant cellular fatty acids were iso-C15 : 0 (27.4 %), iso-C17 : 0 (16.0 %) and iso-C17 : 1ω9c (15.8 %). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major respiratory quinone was ubiquinone 8. The DNA G+C content was 50.4 mol%. The phylogenetic, phenotypic and chemotaxonomic data supported the conclusion that CF12-14T represents a novel species of the genus Idiomarina, for which the name Idiomarina maris sp. nov. is proposed. The type strain is CF12-14T ( = CCTCC AB 208166T = KACC 13974T).
Phylogenetic analysis and taxonomic distinction of six genera of pathogenic scuticociliates (Protozoa, Ciliophora) inferred from small-subunit rRNA gene sequences
Authors: Gao Feng , Strüder-Kypke Michaela , Yi Zhenzhen , Miao Miao , Al-Farraj Saleh A. , Song Weibo
Published: March 2011

Pathogenic scuticociliates, which are common in the haemolymph or tissues of maricultured animals and often cause serious diseases, are a species-rich assemblage with mostly unresolved systematic relationships, especially in some less-studied groups. In the present study, we sequenced the small-subunit rRNA gene of six species of scuticociliates, Uronemella parafilificum, Metanophrys sinensis, Parauronema longum, Cohnilembus verminus, Porpostoma notata and Ancistrum crassum, the last two of which have not been studied previously using molecular analyses. Phylogenetic trees were constructed using Bayesian inference, maximum-likelihood and maximum-parsimony methods to assess the inter- and intra-generic relationships of scuticociliates. Results revealed the following: 1) Porpostoma did not cluster with the Philasteridae, Cohnilembidae or any other family of the order Philasterida; 2) sequences of Uronemella parafilificum and Uronemella filificum showed a difference of 1.02 % (15 nt sites), revealing a close relationship between them; 3) the approximately unbiased test rejected monophyly of both Metanophrys and Parauronema, indicating that the terminal position of the anterior end of the paroral membrane and the structure of membranelle 1 are unreliable characters for distinction of genera in this group of scuticociliates; 4) Ancistrum crassum grouped with Boveria subcylindrica, showing a close phylogenetic relationship between the orders Thigmotrichida and Pleuronematida; and 5) Parauronema longum, Cyclidium plouneouri and Cyclidium porcatum should be removed from their currently assigned genera.
Classification of avian haemolytic Actinobacillus-like organisms (Bisgaard taxon 26) associated with anseriforme birds as Actinobacillus anseriformium sp. nov.
Authors: Bisgaard M. , Christensen H.
Published: March 2011

Avian haemolytic Actinobacillus-like organisms have tentatively been named Bisgaard taxon 26. Phenotypic information has been published on 65 strains of this taxon. In the current study, 31 isolates were selected for genotypic characterization. Thirty strains had the same rpoB sequence and only one strain diverged in 1 nt. The highest rpoB similarity to members of other taxa was 89.7 % to the type strain of Actinobacillus equuli subsp. haemolyticus and the similarity to the type strain of the type species, Actinobacillus lignieresii, was 88.2 %. The lowest 16S rRNA gene sequence similarity between strains of the group was determined in previous investigations to be 99.6 % and the highest similarities of 96.4 and 96.2 % outside the group were obtained to the reference strain of Actinobacillus genomospecies 2 and to the type strain of A. equuli subsp. equuli, respectively; 95.8–95.3 % similarity was obtained with the type strain of A. lignieresii. recN gene sequence similarities within the group were from 99.5 % (strains F66T and F64) to 99.8 % (strains F66T and F67) corresponding to genome similarities of 93.9–94.6 %, which are near the upper limit for species compared with other members of the Pasteurellaceae. The highest recN similarity outside the group (83.4 %) was observed to the type strain of Actinobacillus capsulatus, whereas the similarity to the type strain of A. lignieresii was 80.9 %, corresponding to genome similarities of 57.7 and 52.0 %, respectively. All isolates meet the phenotypic characters outlined for Actinobacillus (urease-, phosphatase- and porphyrin-positive, indole-negative, acid production from fructose, sucrose, maltose and dextrin). β-Haemolysis of bovine blood is observed and isolates may demonstrate in vitro satellitic growth, referred to as V-factor or NAD requirement. Isolates have been obtained from the upper respiratory tract of web-footed birds in which they may cause sinusitis, conjunctivitis and septicaemia. Based on the characterization reported, it is proposed that the isolates belong to a novel species, Actinobacillus anseriformium sp. nov., which includes taxon 26 and a V-factor-dependent strain. The major fatty acids of the type strain are C16 : 1ω7c, C14 : 0, C16 : 0 and C14 : 0 3-OH and/or iso-C16 : 1 I, corresponding to the profile observed for the type strain of A. lignieresii. Five to 12 characters separate A. anseriformium from other taxa of Actinobacillus, with Actinobacillus ureae being most closely related; A. anseriformium can be differentiated from A. ureae based on haemolysis, β-glucosidase, and production of acid from (−)-d-sorbitol, trehalose and glycosides. The type strain of A. anseriformium is F66T ( = CCUG 60324T = CCM 7846T), which was isolated from conjunctivitis in a White Pekin duck.