bluuebunny/crossref_metadata_2025 huggingface dataset:
Signal sequence–independent SRP-SR complex formation at the membrane suggests an alternative targeting pathway within the SRP cycle
Authors: Braig David , Mircheva Miryana , Sachelaru Ilie , van der Sluis Eli O. , Sturm Lukas , Beckmann Roland , Koch Hans-Georg
Published: May 2011

Protein targeting by the signal recognition particle (SRP) and the bacterial SRP receptor FtsY requires a series of closely coordinated steps that monitor the presence of a substrate, the membrane, and a vacant translocon. Although the influence of substrate binding on FtsY-SRP complex formation is well documented, the contribution of the membrane is largely unknown. In the current study, we found that negatively charged phospholipids stimulate FtsY-SRP complex formation. Phospholipids act on a conserved positively charged amphipathic helix in FtsY and induce a conformational change that strongly enhances the FtsY-lipid interaction. This membrane-bound, signal sequence–independent FtsY-SRP complex is able to recruit RNCs to the membrane and to transfer them to the Sec translocon. Significantly, the same results were also observed with an artificial FtsY-SRP fusion protein, which was tethered to the membrane via a transmembrane domain. This indicates that substrate recognition by a soluble SRP is not essential for cotranslational targeting in Escherichia coli. Our findings reveal a remarkable flexibility of SRP-dependent protein targeting, as they indicate that substrate recognition can occur either in the cytosol via ribosome-bound SRP or at the membrane via a preassembled FtsY-SRP complex.
Exposed hydrophobicity is a key determinant of nuclear quality control degradation
Authors: Fredrickson Eric K. , Rosenbaum Joel C. , Locke Melissa N. , Milac Thomas I. , Gardner Richard G.
Published: May 2011

Protein quality control (PQC) degradation protects the cell by preventing the toxic accumulation of misfolded proteins. In eukaryotes, PQC degradation is primarily achieved by ubiquitin ligases that attach ubiquitin to misfolded proteins for proteasome degradation. To function effectively, PQC ubiquitin ligases must distinguish misfolded proteins from their normal counterparts by recognizing an attribute of structural abnormality commonly shared among misfolded proteins. However, the nature of the structurally abnormal feature recognized by most PQC ubiquitin ligases is unknown. Here we demonstrate that the yeast nuclear PQC ubiquitin ligase San1 recognizes exposed hydrophobicity in its substrates. San1 recognition is triggered by exposure of as few as five contiguous hydrophobic residues, which defines the minimum window of hydrophobicity required for San1 targeting. We also find that the exposed hydrophobicity recognized by San1 can cause aggregation and cellular toxicity, underscoring the fundamental protective role for San1-mediated PQC degradation of misfolded nuclear proteins.
Boulder ALignment Editor (ALE): a web-based RNA alignment tool
Authors: Stombaugh Jesse , Widmann Jeremy , McDonald Daniel , Knight Rob
Published: May 2011

Summary: The explosion of interest in non-coding RNAs, together with improvements in RNA X-ray crystallography, has led to a rapid increase in RNA structures at atomic resolution from 847 in 2005 to 1900 in 2010. The success of whole-genome sequencing has led to an explosive growth of unaligned homologous sequences. Consequently, there is a compelling and urgent need for user-friendly tools for producing structure-informed RNA alignments. Most alignment software considers the primary sequence alone; some specialized alignment software can also include Watson–Crick base pairs, but none adequately addresses the needs introduced by the rapid influx of both sequence and structural data. Therefore, we have developed the Boulder ALignment Editor (ALE), which is a web-based RNA alignment editor, designed for editing and assessing alignments using structural information. Some features of BoulderALE include the annotation and evaluation of an alignment based on isostericity of Watson–Crick and non-Watson–Crick base pairs, along with the collapsing (horizontally and vertically) of the alignment, while maintaining the ability to edit the alignment.

Availability:  http://www.microbio.me/boulderale.

Contact:  jesse.stombaugh@colorado.edu
Molecular signatures database (MSigDB) 3.0
Authors: Liberzon Arthur , Subramanian Aravind , Pinchback Reid , Thorvaldsdóttir Helga , Tamayo Pablo , Mesirov Jill P.
Published: May 2011

Motivation: Well-annotated gene sets representing the universe of the biological processes are critical for meaningful and insightful interpretation of large-scale genomic data. The Molecular Signatures Database (MSigDB) is one of the most widely used repositories of such sets.

Results: We report the availability of a new version of the database, MSigDB 3.0, with over 6700 gene sets, a complete revision of the collection of canonical pathways and experimental signatures from publications, enhanced annotations and upgrades to the web site.

Availability and Implementation: MSigDB is freely available for non-commercial use at http://www.broadinstitute.org/msigdb.

Contact:  gsea@broadinstitute.org
famCNV: copy number variant association for quantitative traits in families
Authors: Eleftherohorinou Hariklia , Andersson-Assarsson Johanna C. , Walters Robin G. , El-Sayed Moustafa Julia S. , Coin Lachlan , Jacobson Peter , Carlsson Lena M. S. , Blakemore Alexandra I. F. , Froguel Philippe , Walley Andrew J. , Falchi Mario
Published: May 2011

Summary: A program package to enable genome-wide association of copy number variants (CNVs) with quantitative phenotypes in families of arbitrary size and complexity. Intensity signals that act as proxies for the number of copies are modeled in a variance component framework and association with traits is assessed through formal likelihood testing.

Availability and implementation: The Java package is made available at www.imperial.ac.uk/medicine/people/m.falchi/.

Contact:  m.falchi@imperial.ac.uk
APOLLO: a quality assessment service for single and multiple protein models
Authors: Wang Zheng , Eickholt Jesse , Cheng Jianlin
Published: May 2011

Summary: We built a web server named APOLLO, which can evaluate the absolute global and local qualities of a single protein model using machine learning methods or the global and local qualities of a pool of models using a pair-wise comparison approach. Based on our evaluations on 107 CASP9 (Critical Assessment of Techniques for Protein Structure Prediction) targets, the predicted quality scores generated from our machine learning and pair-wise methods have an average per-target correlation of 0.671 and 0.917, respectively, with the true model quality scores. Based on our test on 92 CASP9 targets, our predicted absolute local qualities have an average difference of 2.60 Å with the actual distances to native structure.

Availability:  http://sysbio.rnet.missouri.edu/apollo/. Single and pair-wise global quality assessment software is also available at the site.

Contact:  chengji@missouri.edu
Climate impacts on eastern Bering Sea foodwebs: a synthesis of new data and an assessment of the Oscillating Control Hypothesis
Authors: Hunt George L. , Coyle Kenneth O. , Eisner Lisa B. , Farley Edward V. , Heintz Ron A. , Mueter Franz , Napp Jeffrey M. , Overland James E. , Ressler Patrick H. , Salo Sigrid , Stabeno Phyllis J.
Published: May 2011

Hunt, G. L., Coyle, K. O., Eisner, L. B., Farley, E. V., Heintz, R. A., Mueter, F., Napp, J. M., Overland, J. E., Ressler, P. H., Salo, S., and Stabeno, P. J. 2011. Climate impacts on eastern Bering Sea foodwebs: a synthesis of new data and an assessment of the Oscillating Control Hypothesis. – ICES Journal of Marine Science, 68: 1230–1243. Walleye pollock (Theragra chalcogramma) is an important component of the eastern Bering Sea ecosystem and subject to major fisheries. The Oscillating Control Hypothesis (OCH) predicted that recruitment of pollock year classes should be greatest in years with early ice retreat and late blooms in warm water, because more energy would flow into the pelagic (vs. benthic) community. The OCH further predicted that, with pollock population growth, there should be a shift from bottom-up to top-down regulation. New data support the predictions that in those years with early ice retreat, more primary production accrues to the pelagic compartment and that large numbers of age-0 pollock survive to summer. However, in these years, production of large crustacean zooplankton is reduced, depriving age-0 pollock of lipid-rich prey in summer and autumn. Consequently, age-0 pollock energy reserves (depot lipids) are low and predation on them is increased as fish switch to age-0 pollock from zooplankton. The result is weak recruitment of age-1 recruits the following year. A revised OCH indicates bottom-up constraints on pollock recruitment in very warm periods. Prolonged warm periods with decreased ice cover will likely cause diminished pollock recruitment and catches relative to recent values.
Enhancing Your CV
Authors: Rolfe Alix
Published: May 2011

Although finishing training might seem like a distant dream, by the end of your third year of specialist training (ST3), thoughts will be turning to the real prospect of finding a job. It is never too early to start thinking about your future career and specializing in general practice can lead to many interesting and varied opportunities from partnerships to expedition medicine or even becoming a media doctor. This article focuses on ways to enhance your curriculum vitae (CV) to open doors to your chosen jobs.
Phosphorylation of the epidermal growth factor receptor (EGFR) is essential for interleukin-8 release from intestinal epithelial cells in response to challenge with Escherichia coli O157 : H7 flagellin
Authors: Fraser-Pitt Douglas J. , Cameron Pamela , McNeilly Tom N. , Boyd Amanda , Manson Erin D. T. , Smith David G. E.
Published: May 2011

Enterohaemorrhagic Escherichia coli O157 : H7 is a major foodborne and environmental pathogen responsible for both sporadic cases and outbreaks of food poisoning, which can lead to serious sequelae, such as haemolytic uraemic syndrome. The structural subunit of E. coli O157 : H7 flagella is flagellin, which is both the antigenic determinant of the H7 serotype, an important factor in colonization, and an immunomodulatory protein that has been determined to be a major pro-inflammatory component through the instigation of host cell signalling pathways. Flagellin has highly conserved N- and C-terminal regions that are recognized by the host cell pattern recognition receptor Toll-like receptor (TLR) 5. Activation of this receptor triggers cell signalling cascades, which are known to activate host cell kinases and transcription factors that respond with the production of inflammatory mediators such as the chemokine interleukin-8 (IL-8), although the exact components of this pathway are not yet fully characterized. We demonstrate that E. coli O157 : H7-derived flagellin induces rapid phosphorylation of the epidermal growth factor receptor (EGFR), as an early event in intestinal epithelial cell signalling, and that this is required for the release of the pro-inflammatory cytokine IL-8.
Application of suppressive subtractive hybridization to the identification of genetic differences between two Lactococcus garvieae strains showing distinct differences in virulence for rainbow trout and mouse
Authors: Reimundo Pilar , Rivas Amable J. , Osorio Carlos R. , Méndez Jéssica , Pérez-Pascual David , Navais Roberto , Gómez Esther , Sotelo Miguel , Lemos Manuel L. , Guijarro José A.
Published: May 2011

Lactococcus garvieae is the causative microbial agent of lactococcosis, an important and damaging fish disease in aquaculture. This bacterium has also been isolated from vegetables, milk, cheese, meat and sausages, from cow and buffalo as a mastitis agent, and even from humans, as an opportunistic infectious agent. In this work pathogenicity experiments were performed in rainbow trout and mouse models with strains isolated from human (L. garvieae HF) and rainbow trout (L. garvieae UNIUDO74; henceforth referred to as 074). The mean LD50 value in rainbow trout obtained for strain 074 was 2.1×102±84 per fish. High doses of the bacteria caused specific signs of disease as well as histological alterations in mice. In contrast, strain HF did not prove to be pathogenic either for rainbow trout or for mice. Based on these virulence differences, two suppressive subtractive hybridizations were carried out to identify unique genetic sequences present in L. garvieae HF (SSHI) and L. garvieae 074 (SSHII). Differential dot-blot screening of the subtracted libraries allowed the identification of 26 and 13 putative ORFs specific for L. garvieae HF and L. garvieae 074, respectively. Additionally, a PCR-based screening of 12 of the 26 HF-specific putative ORFs and the 13 074-specific ones was conducted to identify their presence/absence in 25 L. garvieae strains isolated from different origins and geographical areas. This study demonstrates the existence of genetic heterogeneity within L. garvieae isolates and provides a more complete picture of the genetic background of this bacterium.
Rice ABI5-Like1 Regulates Abscisic Acid and Auxin Responses by Affecting the Expression of ABRE-Containing Genes
Authors: Yang Xi , Yang Ya-Nan , Xue Liang-Jiao , Zou Mei-Juan , Liu Jian-Ying , Chen Fan , Xue Hong-Wei
Published: May 2011

Abscisic acid (ABA) regulates plant development and is crucial for plant responses to biotic and abiotic stresses. Studies have identified the key components of ABA signaling in Arabidopsis (Arabidopsis thaliana), some of which regulate ABA responses by the transcriptional regulation of downstream genes. Here, we report the functional identification of rice (Oryza sativa) ABI5-Like1 (ABL1), which is a basic region/leucine zipper motif transcription factor. ABL1 is expressed in various tissues and is induced by the hormones ABA and indole-3-acetic acid and stress conditions including salinity, drought, and osmotic pressure. The ABL1 deficiency mutant, abl1, shows suppressed ABA responses, and ABL1 expression in the Arabidopsis abi5 mutant rescued the ABA sensitivity. The ABL1 protein is localized to the nucleus and can directly bind ABA-responsive elements (ABREs; G-box) in vitro. A gene expression analysis by DNA chip hybridization confirms that a large proportion of down-regulated genes of abl1 are involved in stress responses, consistent with the transcriptional activating effects of ABL1. Further studies indicate that ABL1 regulates the plant stress responses by regulating a series of ABRE-containing WRKY family genes. In addition, the abl1 mutant is hypersensitive to exogenous indole-3-acetic acid, and some ABRE-containing genes related to auxin metabolism or signaling are altered under ABL1 deficiency, suggesting that ABL1 modulates ABA and auxin responses by directly regulating the ABRE-containing genes.
Lipase Activity in Insect Oral Secretions Mediates Defense Responses in Arabidopsis
Authors: Schäfer Martin , Fischer Christine , Meldau Stefan , Seebald Eileen , Oelmüller Ralf , Baldwin Ian T.
Published: May 2011

How plants perceive herbivory is not yet well understood. We investigated early responses of the model plant Arabidopsis (Arabidopsis thaliana) to attack from the generalist grasshopper herbivore, Schistocerca gregaria (Caelifera). When compared with wounding alone, S. gregaria attack and the application of grasshopper oral secretions (GS) to puncture wounds elicited a rapid accumulation of various oxylipins, including 13-hydroperoxy octadecatrienoic acid, 12-oxo-phytodienoic acid (OPDA), jasmonic acid, and jasmonic acid-isoleucine. Additionally, GS increased cytosolic calcium levels, mitogen-activated protein kinase (MPK3 and MPK6) activity, and ethylene emission but not the accumulation of hydrogen peroxide. Although GS contain caeliferin A16:0, a putative elicitor of caeliferan herbivores, treatment with pure, synthetic caeliferin A16:0 did not induce any of the observed responses. With mutant plants, we demonstrate that the observed changes in oxylipin levels are independent of MPK3 and MPK6 activity but that MPK6 is important for the GS-induced ethylene release. Biochemical and pharmacological analyses revealed that the lipase activity of GS plays a central role in the GS-induced accumulation of oxylipins, especially OPDA, which could be fully mimicked by treating puncture wounds only with a lipase from Rhizopus arrhizus. GS elicitation increased the levels of OPDA-responsive transcripts. Because the oral secretions of most insects used to study herbivory-induced responses in Arabidopsis rapidly elicit similar accumulations of OPDA, we suggest that lipids containing OPDA (arabidopsides) play an important role in the activation of herbivory-induced responses.
Vacuolar Ca2+/H+ Transport Activity Is Required for Systemic Phosphate Homeostasis Involving Shoot-to-Root Signaling in Arabidopsis
Authors: Liu Tzu-Yin , Aung Kyaw , Tseng Ching-Ying , Chang Tzu-Yun , Chen Ying-Shin , Chiou Tzyy-Jen
Published: May 2011

Calcium ions (Ca2+) and Ca2+-related proteins mediate a wide array of downstream processes involved in plant responses to abiotic stresses. In Arabidopsis (Arabidopsis thaliana), disruption of the vacuolar Ca2+/H+ transporters CAX1 and CAX3 causes notable alterations in the shoot ionome, including phosphate (Pi) content. In this study, we showed that the cax1/cax3 double mutant displays an elevated Pi level in shoots as a result of increased Pi uptake in a miR399/PHO2-independent signaling pathway. Microarray analysis of the cax1/cax3 mutant suggests the regulatory function of CAX1 and CAX3 in suppressing the expression of a subset of shoot Pi starvation-responsive genes, including genes encoding the PHT1;4 Pi transporter and two SPX domain-containing proteins, SPX1 and SPX3. Moreover, although the expression of several PHT1 genes and PHT1;1/2/3 proteins is not up-regulated in the root of cax1/cax3, results from reciprocal grafting experiments indicate that the cax1/cax3 scion is responsible for high Pi accumulation in grafted plants and that the pht1;1 rootstock is sufficient to moderately repress such Pi accumulation. Based on these findings, we propose that CAX1 and CAX3 mediate a shoot-derived signal that modulates the activity of the root Pi transporter system, likely in part via posttranslational regulation of PHT1;1 Pi transporters.
Cell Wall Damage-Induced Lignin Biosynthesis Is Regulated by a Reactive Oxygen Species- and Jasmonic Acid-Dependent Process in Arabidopsis
Authors: Denness Lucinda , McKenna Joseph Francis , Segonzac Cecile , Wormit Alexandra , Madhou Priya , Bennett Mark , Mansfield John , Zipfel Cyril , Hamann Thorsten
Published: May 2011

The plant cell wall is a dynamic and complex structure whose functional integrity is constantly being monitored and maintained during development and interactions with the environment. In response to cell wall damage (CWD), putatively compensatory responses, such as lignin production, are initiated. In this context, lignin deposition could reinforce the cell wall to maintain functional integrity. Lignin is important for the plant’s response to environmental stress, for reinforcement during secondary cell wall formation, and for long-distance water transport. Here, we identify two stages and several components of a genetic network that regulate CWD-induced lignin production in Arabidopsis (Arabidopsis thaliana). During the early stage, calcium and diphenyleneiodonium-sensitive reactive oxygen species (ROS) production are required to induce a secondary ROS burst and jasmonic acid (JA) accumulation. During the second stage, ROS derived from the NADPH oxidase RESPIRATORY BURST OXIDASE HOMOLOG D and JA-isoleucine generated by JASMONIC ACID RESISTANT1, form a negative feedback loop that can repress each other’s production. This feedback loop in turn seems to influence lignin accumulation. Our results characterize a genetic network enabling plants to regulate lignin biosynthesis in response to CWD through dynamic interactions between JA and ROS.
Nonphosphorylating Glyceraldehyde-3-Phosphate Dehydrogenase Is Phosphorylated in Wheat Endosperm at Serine-404 by an SNF1-Related Protein Kinase Allosterically Inhibited by Ribose-5-Phosphate
Authors: Piattoni Claudia Vanesa , Bustos Diego Martín , Guerrero Sergio Adrián , Iglesias Alberto Álvaro
Published: May 2011

Nonphosphorylating glyceraldehyde-3-phosphate dehydrogenase (np-Ga3PDHase) is a cytosolic unconventional glycolytic enzyme of plant cells regulated by phosphorylation in heterotrophic tissues. After interaction with 14-3-3 proteins, the phosphorylated enzyme becomes less active and more sensitive to regulation by adenylates and inorganic pyrophosphate. Here, we acknowledge that in wheat (Triticum aestivum), np-Ga3PDHase is specifically phosphorylated by the SnRK (SNF1-related) protein kinase family. Interestingly, only the kinase present in heterotrophic tissues (endosperm and shoots, but not in leaves) was found active. The specific SnRK partially purified from endosperm exhibited a requirement for Mg2+ or Mn2+ (being Ca2+ independent), having a molecular mass of approximately 200 kD. The kinase also phosphorylated standard peptides SAMS, AMARA, and SP46, as well as endogenous sucrose synthase, results suggesting that it could be a member of the SnRK1 subfamily. Concurrently, the partially purified wheat SnRK was recognized by antibodies raised against a peptide conserved between SnRK1s from sorghum (Sorghum bicolor) and maize (Zea mays) developing seeds. The wheat kinase was allosterically inhibited by ribose-5-phosphate and, to a lesser extent, by fructose-1,6-bisphosphate and 3-phosphoglycerate, while glucose-6-phosphate (the main effector of spinach [Spinacia oleracea] leaves, SnRK1) and trehalose-6-phosphate produced little or no effect. Results support a distinctive allosteric regulation of SnRK1 present in photosynthetic or heterotrophic plant tissues. After in silico analysis, we constructed two np-Ga3PDHase mutants, S404A and S447A, identifying serine-404 as the target of phosphorylation. Results suggest that both np-Ga3PDHase and the specific kinase could be under control, critically affecting the metabolic scenario involving carbohydrates and reducing power partition and storage in heterotrophic plant cells.
Background subtraction for fluorescence EXAFS data of a very dilute dopantZinZ + 1 host
Authors: Medling Scott , Bridges Frank
Published: May 2011

When conducting EXAFS at the CuK-edge for ZnS:Cu with very low Cu concentration (<0.04% Cu), a large background was present that increased with energy. This background arises from a Zn X-ray Raman peak, which moves through the Cu fluorescence window, plus the tail of the Zn fluorescence peak. This large background distorts the EXAFS and must be removed separately before reducing the data. A simple means to remove this background is described.
Nicotine dependence, abuse and craving: dimensionality in an Israeli sample
Authors: Shmulewitz Dvora , Keyes Katherine M. , Wall Melanie M. , Aharonovich Efrat , Aivadyan Christina , Greenstein Eliana , Spivak Baruch , Weizman Abraham , Frisch Amos , Grant Bridget F. , Hasin Deborah
Published: May 2011

Aims  Evidence‐based changes planned for Diagnostic and Statistical Manual 5th edition (DSM‐5) substance use disorders (SUDs) include combining dependence and three of the abuse criteria into one disorder and adding a criterion indicating craving. Because DSM‐IV did not include a category for nicotine abuse, little empirical support is available for aligning the nicotine use disorder criteria with the DSM‐5 criteria for other SUDs.

Design  Latent variable analyses, bootstrap tests and likelihood ratio tests were used to explore the unidimensionality, psychometric properties and information of the nicotine criteria.

Setting and participants  A sample of household residents selected from the Israeli population register yielded 727 life‐time cigarette smokers.

Measurements  DSM‐IV nicotine dependence criteria and proposed abuse and craving criteria, assessed with a structured interview.

Findings  Three abuse criteria (hazardous use, social/interpersonal problems and neglect roles) were prevalent among smokers, formed a unidimensional latent trait with nicotine dependence criteria, were intermixed with dependence criteria across the severity spectrum and significantly increased the diagnostic information over the dependence‐only model. A craving criterion was shown to fit well with the other criteria.

Conclusion  Similar to findings from research on other substances, nicotine dependence, abuse and craving criteria appear to derive from a common underlying dimension. The results support alignment of nicotine criteria with those for alcohol and drug use disorders in Diagnostic and Statistical Manual 5th edition.
The social norms of birth cohorts and adolescent marijuana use in the United States, 1976–2007
Authors: Keyes Katherine M. , Schulenberg John E. , O'Malley Patrick M. , Johnston Lloyd D. , Bachman Jerald G. , Li Guohua , Hasin Deborah
Published: May 2011

Aims Studies of the relationship between social norms and marijuana use have generally focused on individual attitudes, leaving the influence of larger societal‐level attitudes unknown. The present study investigated societal‐level disapproval of marijuana use defined by birth cohort or by time‐period.

Design Combined analysis of nationally representative annual surveys of secondary school students in the United States conducted from 1976 to 2007 as part of the Monitoring the Future study.

Setting In‐school surveys completed by adolescents in the United States.

Participants A total of 986 003 adolescents in grades 8, 10 and 12.

Measurements Main predictors included the percentage of students who disapproved of marijuana in each birth cohort and time‐period. Multi‐level models with individuals clustered in time‐periods of observation and birth cohorts were modeled, with past‐year marijuana use as the outcome.

Findings Results indicated a significant and strong effect of birth cohort disapproval of marijuana use in predicting individual risk of marijuana use, after controlling for individual‐level disapproval, perceived norms towards marijuana and other characteristics. Compared to birth cohorts in which most (87–90.9%) adolescents disapproved of marijuana use, odds of marijuana use were 3.53 times higher in cohorts where fewer than half (42–46.9%) disapproved (99% confidence interval: 2.75, 4.53).

Conclusions Individuals in birth cohorts that are more disapproving of marijuana use are less likely to use, independent of their personal attitudes towards marijuana use. Social norms and attitudes regarding marijuana use cluster in birth cohorts, and this clustering has a direct effect on marijuana use even after controlling for individual attitudes and perceptions of norms.
Proteolysis, protein oxidation and protease activity in dry‐cured Xuanwei ham during the salting stages
Authors: Wang Zhenyu , Xu Yansheng , Zhang Jihong , Li Xiang , Lin Zusong , Ma Changwei
Published: May 2011

Twenty‐four experimental dry‐cured Xuanwei hams were salted using a standard method for 90 days. The proteolysis, protein oxidation and protease activities in biceps femoris (BF) and semimembranoesus (SM) muscles of dry‐cured Xuanwei ham were investigated during the salting phase. At the end of salting, the salt content increased to 35.2 g kg−1 muscle in BF and 54.2 g kg−1 muscle in SM. During the salting stage, salt soluble proteins were degraded mainly into water soluble proteins that were further broken down to peptides with molecular weights mostly greater than 1 kDa. Although large amounts of smaller peptides and free amino acids were generated, especially when the hams were aged. The carbonyl contents were increased but lower than 1.57 nmol mg−1 proteins in muscles during the salting stage. The cathepsin B, dipeptidyl peptidase I (DPP I), alanyl (AAP), arginyl (RAP) and leucyl (LAP) aminopeptidase all remained active while salt content strongly inhibited cathepsin L and DPP IV in the first 90 days. The results suggested that the salting process promoted the hydrolysis of proteins, and increased the muscle protein oxidation at a slower rate.
Understanding dietary decision‐making in patients attending a secondary prevention clinic following myocardial infarction
Authors: Doyle Barbara , Fitzsimons Donna , McKeown Pascal , McAloon Toni
Published: May 2011

Aims and objectives.  This study aimed to explore the issues that influence the dietary choices made by patients attending a secondary prevention clinic following a myocardial infarction.

Background.  Secondary prevention clinics play an important role in promoting dietary advice, yet evidence suggests that many individuals are neither implementing nor maintaining the lifestyle changes recommended. Research largely focuses on compliance to lifestyle changes in general, and only a small number of quantitative studies address the issues surrounding adherence to dietary advice.

Design.  Phenomenology was selected as the most appropriate approach for this qualitative study, enabling patients’ lived experiences of dietary decision‐making to be explored.

Method.  A purposive sample of nine participants was selected from a cardiac secondary prevention clinic. Semi‐structured interviews were taped, transcribed and analysed using an interpretative approach.

Results.  Data analysis produced six central themes contributing to patients’ decision‐making. Fear, determination and self‐control were enabling factors and poor recall of information, a need for additional support and a lack of will power were disabling factors. Findings suggest that patient motivation and ability to make sustainable dietary change can decline as disabling factors reduce determination and self‐control, and initial fear of their heart condition subsides.

Conclusion.  In this study, patients’ motivation regarding dietary decision‐making changed over time and was strongly influenced by a fear of future heart problems.

Relevance to clinical practice.  Health care professionals need to understand the temporal nature of decision‐making postmyocardial infarction and adopt a wide repertoire of responsive strategies that support patients to follow a healthy diet in the longer term.
Sortase independent and dependent systems for acquisition of haem and haemoglobin in Listeria monocytogenes
Authors: Xiao Qiaobin , Jiang Xiaoxu , Moore Kyle J. , Shao Yi , Pi Hualiang , Dubail Iharilalao , Charbit Alain , Newton Salete M. , Klebba Phillip E.
Published: May 2011

We studied three Fur‐regulated systems of Listeria monocytogenes: the srtB region, that encodes sortase‐anchored proteins and a putative ABC transporter, and the fhu and hup operons, that produce putative ABC transporters for ferric hydroxamates and haemin (Hn)/haemoglobin (Hb) respectively. Deletion of lmo2185 in the srtB region reduced listerial [59Fe]‐Hn transport, and purified Lmo2185 bound [59Fe]‐Hn (KD = 12 nM), leading to its designation as a Hn/Hb binding protein (hbp2). Purified Hbp2 also acted as a haemophore, capturing and supplying Hn from the environment. Nevertheless, Hbp2 only functioned in [59Fe]‐Hn transport at external concentrations less than 50 nM: at higher Hn levels its uptake occurred with equivalent affinity and rate without Hbp2. Similarly, deletion of sortase A had no effect on ferric siderophore or Hn/Hb transport at any concentration, and the srtA‐independence of listerial Hn/Hb uptake distinguished it from comparable systems of Staphylococcus aureus. In the cytoplasmic membrane, the Hup transporter was specific for Hn: its lipoprotein (HupD) only showed high affinity for the iron porphyrin (KD = 26 nM). Conversely, the FhuD lipoprotein encoded by the fhu operon had broad specificity: it bound both ferric siderophores and Hn, with the highest affinity for ferrioxamine B (KD = 123 nM). Deletions of Hup permease components hupD, hupG or hupDGC reduced Hn/Hb uptake, and complementation of ΔhupC and ΔhupG by chromosomal integration of hupC+ and hupG+ alleles on pPL2 restored growth promotion by Hn/Hb. However, ΔhupDGC did not completely eliminate [59Fe]‐Hn transport, implying the existence of another cytoplasmic membrane Hn transporter. The overall KM of Hn uptake by wild‐type strain EGD‐e was 1 nM, and it occurred at similar rates (Vmax = 23 pmol 109 cells−1 min−1) to those of ferric siderophore transporters. In the ΔhupDGC strain uptake occurred at a threefold lower rate (Vmax = 7 pmol 109 cells−1 min−1). The results show that at low (< 50 nM) levels of Hn, SrtB‐dependent peptidoglycan‐anchored proteins (e.g. Hbp2) bind the porphyrin, and HupDGC or another transporter completes its uptake into the cytoplasm. However, at higher concentrations Hn uptake is SrtB‐independent: peptidoglycan‐anchored binding proteins are dispensable because HupDGC directly absorbs and internalizes Hn. Finally, ΔhupDGC increased the LD50 of L. monocytogenes 100‐fold in the mouse infection model, reiterating the importance of this system in listerial virulence.
Quantitative trait loci analysis reveals a correlation between the ratio of sucrose/raffinose family oligosaccharides and seed vigour in Medicago truncatula
Authors: VANDECASTEELE CÉLINE , TEULAT‐MERAH BÉATRICE , MORÈRE‐LE PAVEN MARIE‐CHRISTINE , LEPRINCE OLIVIER , LY VU BENOIT , VIAU LAURE , LEDROIT LYDIE , PELLETIER SANDRA , PAYET NICOLE , SATOUR PASCALE , LEBRAS CAMILLE , GALLARDO KARINE , HUGUET THIERRY , LIMAMI ANIS M. , PROSPERI JEAN‐MARIE , BUITINK JULIA
Published: May 2011

Seed vigour is important for successful establishment and high yield, especially under suboptimal environmental conditions. In legumes, raffinose oligosaccharide family (RFO) sugars have been proposed as an easily available energy reserve for seedling establishment. In this study, we investigated whether the composition or amount of soluble sugars (sucrose and RFO) is part of the genetic determinants of seed vigour of Medicago truncatula using two recombinant inbred line (RIL) populations. Quantitative trait loci (QTL) mapping for germination rate, hypocotyl and radicle growth under water deficit and nutritional stress, seed weight and soluble sugar content was performed using RIL populations LR1 and LR4. Seven of the 12 chromosomal regions containing QTL for germination rate or post‐germinative radicle growth under optimal or stress conditions co‐located with Suc/RFO QTL. A significant negative correlation was also found between seed vigour traits and Suc/RFO. In addition, one QTL that explained 80% of the variation in the ratio stachyose/verbascose co‐located with a stachyose synthase gene whose expression profile in the parental lines could explain the variation in oligosaccharide composition. The correlation and co‐location of Suc/RFO ratio with germination and radicle growth QTL suggest that an increased Suc/RFO ratio in seeds of M. truncatula might negatively affect seed vigour.
Comparative physiology and transcriptional networks underlying the heat shock response in Populus trichocarpa, Arabidopsis thaliana and Glycine max
Authors: WESTON DAVID J. , KARVE ABHIJIT A. , GUNTER LEE E. , JAWDY SARA S. , YANG XIAOHAN , ALLEN SARA M. , WULLSCHLEGER STAN D.
Published: May 2011

The heat shock response continues to be layered with additional complexity as interactions and crosstalk among heat shock proteins (HSPs), the reactive oxygen network and hormonal signalling are discovered. However, comparative analyses exploring variation in each of these processes among species remain relatively unexplored. In controlled environment experiments, photosynthetic response curves were conducted from 22 to 42 °C and indicated that temperature optimum of light‐saturated photosynthesis was greater for Glycine max relative to Arabidopsis thaliana or Populus trichocarpa. Transcript profiles were taken at defined states along the temperature response curves, and inferred pathway analysis revealed species‐specific variation in the abiotic stress and the minor carbohydrate raffinose/galactinol pathways. A weighted gene co‐expression network approach was used to group individual genes into network modules linking biochemical measures of the antioxidant system to leaf‐level photosynthesis among P. trichocarpa, G. max and A. thaliana. Network‐enabled results revealed an expansion in the G. max HSP17 protein family and divergence in the regulation of the antioxidant and heat shock modules relative to P. trichocarpa and A. thaliana. These results indicate that although the heat shock response is highly conserved, there is considerable species‐specific variation in its regulation.
Revealing complexity and specificity in the activation of lipase‐mediated oxylipin biosynthesis: a specific role of the Nicotiana attenuata GLA1 lipase in the activation of jasmonic acid biosynthesis in leaves and roots
Authors: BONAVENTURE GUSTAVO , SCHUCK STEFAN , BALDWIN IAN T.
Published: May 2011

The activation of enzymatic oxylipin biosynthesis upon wounding, herbivory and pathogen attack depends on the biochemical activation of lipases that make polyunsaturated fatty acids (PUFAs) available to lipoxygenases (LOXs). The identity and number of the lipases involved in this process remain controversial and they probably differ among plant species. Analysis of transgenic Nicotiana attenuata plants (ir‐gla1) stably reduced in the expression of the NaGLA1 gene showed that this plastidial glycerolipase is a major supplier of trienoic fatty acids for jasmonic acid (JA) biosynthesis in leaves and roots after wounding and simulated herbivory, but not during infection with the oomycete Phytophthora parasitica (var. nicotianae). NaGLA1 was not essential for the developmental control of JA biosynthesis in flowers and for the biosynthesis of C6 volatiles by the hydroperoxide lyase (HPL) pathway; however, it affected the metabolism of divinyl ethers (DVEs) early during infection with P. parasitica (var. nicotianae) and the accumulation of NaDES1 and NaLOX1 mRNAs. Profiling of lysolipids by LC–MS/MS was consistent with a rapid activation of NaGLA1 and indicated that this lipase utilizes different lipid classes as substrates. The results revealed the complexity and specificity of the regulation of lipase‐mediated oxylipin biosynthesis, highlighting the existence of pathway‐ and stimulus‐specific lipases.
Oxidation–reduction signalling components in regulatory pathways of state transitions and photosystem stoichiometry adjustment in chloroplasts
Authors: PUTHIYAVEETIL SUJITH , IBRAHIM ISKANDER M. , ALLEN JOHN F.
Published: May 2011

State transitions and photosystem stoichiometry adjustment are two oxidation–reduction (redox)‐regulated acclimatory responses in photosynthesis. State transitions are short‐term adaptations that, in chloroplasts, involve reversible post‐translational modification by phosphorylation of light‐harvesting complex II (LHC II). Photosystem stoichiometry adjustments are long‐term responses involving transcriptional regulation of reaction centre genes. Both responses are initiated by changes in light quality and are regulated by the redox state of plastoquinone (PQ). The LHC II kinase involved in the state 2 transition is a serine/threonine kinase known as STT7 in Chlamydomonas, and as STN7 in Arabidopsis. The phospho‐LHC II phosphatase that produces the state 1 transition is a PP2C‐type protein phosphatase currently termed both TAP38 and PPH1. In plants and algae, photosystem stoichiometry adjustment is governed by a modified two‐component sensor kinase of cyanobacterial origin – chloroplast sensor kinase (CSK). CSK is a sensor of the PQ redox state. Chloroplast sigma factor 1 (SIG1) and plastid transcription kinase (PTK) are the functional partners of CSK in chloroplast gene regulation. We suggest a signalling pathway for photosystem stoichiometry adjustment. The signalling pathways of state transitions and photosystem stoichiometry adjustments are proposed to be distinct, with the two pathways sensing PQ redox state independently of each other.
Estimation of canopy average mesophyll conductance using δ13C of phloem contents
Authors: UBIERNA NEREA , MARSHALL JOHN D.
Published: May 2011

Conductance to CO2 inside leaves, known as mesophyll conductance (gm), imposes large limitations on photosynthesis. Because gm is difficult to quantify, it is often neglected in calculations of 13C photosynthetic discrimination. The ‘soluble sugar method’ estimates gm via differences between observed photosynthetic discrimination, calculated from the δ13C of soluble sugars, and discrimination when gm is infinite. We expand upon this approach and calculate a photosynthesis‐weighted average for canopy mesophyll conductance (cgm) using δ13C of stem phloem contents. We measured gas exchange at three canopy positions and collected stem phloem contents in mature trees of three conifer species (Pseudotsuga menziesii, Thuja plicata and Larix occidentalis). We generated species‐specific and seasonally variable estimates of cgm. We found that cgm was significantly different among species (0.41, 0.22 and 0.09 mol m−2 s−1 for Larix, Pseudotsuga and Thuja, respectively), but was similar throughout the season. Ignoring respiratory and photorespiratory fractionations (cΔef) resulted in ≈30% underestimation of cgm in Larix and Pseudotsuga, but was innocuous in Thuja. Substantial errors (∼1–4‰) in photosynthetic discrimination calculations were introduced by neglecting cgm and cΔef. Our method is easy to apply and cost‐effective, captures species variation and would have captured seasonal variation had it existed. The method provides an average canopy value, which makes it suitable for parameterization of canopy‐scale models of photosynthesis, even in tall trees.
PHOSPHATIDYLSERINE SYNTHASE1 is required for microspore development in Arabidopsis thaliana
Authors: Yamaoka Yasuyo , Yu Yanbo , Mizoi Junya , Fujiki Yuki , Saito Kyoko , Nishijima Masahiro , Lee Youngsook , Nishida Ikuo
Published: May 2011

Phosphatidylserine (PS) has many important biological roles, but little is known about its role in plants, partly because of its low abundance. We show here that PS is enriched in Arabidopsis floral tissues and that genetic disruption of PS biosynthesis decreased heterozygote fertility due to inhibition of pollen maturation. At1g15110, designated PSS1, encodes a base‐exchange‐type PS synthase. Escherichia coli cells expressing PSS1 accumulated PS in the presence of l‐serine at 23°C. Promoter‐GUS assays showed PSS1 expression in developing anther pollen and tapetum. A few seeds with pss1‐1 and pss1‐2 knockout alleles escaped embryonic lethality but developed into sterile dwarf mutant plants. These plants contained no PS, verifying that PSS1 is essential for PS biosynthesis. Reciprocal crossing revealed reduced pss1 transmission via male gametophytes, predicting a rate of 61.6%pss1‐1 pollen defects in PSS1/pss1‐1 plants. Alexander’s staining of inseparable qrt1‐1 PSS1/pss1‐1 quartets revealed a rate of 42% having three or four dead pollen grains, suggesting sporophytic pss1‐1 cell death effects. Analysis with the nuclear stain 4′,6‐diamidino‐2‐phenylindole (DAPI) showed that all tetrads from PSS1/pss1‐1 anthers retain their nuclei, whereas unicellular microspores were sometimes anucleate. Transgenic Arabidopsis expressing a GFP‐LactC2 construct that binds PS revealed vesicular staining in tetrads and bicellular microspores and nuclear membrane staining in unicellular microspores. Hence, distribution and/or transport of PS across membranes were dynamically regulated in pollen microspores. However, among unicellular microspores from PSS1/pss1‐2 GFP‐LactC2 plants, all anucleate microspores showed little GFP‐LactC2 fluorescence, suggesting that pss1‐2 microspores are more sensitive to sporophytic defects or show partial gametophytic defects.
Dopaminergic genes modulate response inhibition in alcohol abusing adults
Authors: Filbey Francesca M. , Claus Eric D. , Morgan Marilee , Forester Glen R. , Hutchison Kent
Published: May 2011

Compulsion in alcohol use disorders (AUD) has been attributed to impairment in response inhibition. Because genes that regulate dopamine (DA) have been implicated not only for risk for AUD but also for impulsivity based on behavioral studies, we set out to examine the underlying neural mechanisms associated with these effects. We collected functional magnetic resonance imaging images on 53 heavy drinking but otherwise healthy adults while performing the Go/NoGo task. We predicted that genetic variants previously reported in the literature to be associated with substance abuse, specifically the DRD2 rs1799732 and DRD4 VNTR, will modulate neural processes underlying response inhibition. Our results showed differential neural response for the DRD4 VNTR during successful inhibition in the inferior frontal gyrus (IFG) (cluster‐corrected P < 0.05, z = 1.9). Similarly, DRD2 rs1799732 groups were significantly different in the precuneus and cingulate gyrus during successful response inhibition (cluster‐corrected P < 0.05, z = 1.9). These findings provide further evidence for the role of DAergic genes in modulating neural response in areas that underlie response inhibition and self‐monitoring processes. Variants within these genes appear to influence processes related to impulsive behavior, which may increase one's risk for alcohol abuse and dependence.
HLA‐DQB1*06:41 shown by sequence‐based typing may be associated with DRB1*13:02
Authors: Witter K. , Keller E. , Kutsch M. , Albert T. , Dick A.
Published: May 2011

In this report we present DQB1*06:41, a novel allele probably associated with DRB1*13:02.
Composition and use of puppy milk replacers in German Shepherd puppies in the Netherlands
Authors: Corbee R. J. , Tryfonidou M. A. , Beckers I. P. , Hazewinkel H. A. W.
Published: May 2011

Enostosis or eosinophilic panosteitis is a common disease in young growing large‐breed dogs, such as the German Shepherd, and the risk of developing the disease by 3–4 months of age is increased by a high calcium intake. The aim of the study was to investigate whether German Shepherd puppies raised on milk replacers receive more calcium and/or vitamin D than their requirements in the pre‐weaning period and thus are at increased risk of developing skeletal diseases. To this end, we surveyed German Shepherd breeders in the Netherlands about the use of puppy milk replacers (PMR). The metabolizable energy, calcium, phosphorus and vitamin D content of the eight most used PMR were compared with that of bitch milk, as reported in the literature. The protein and fat content of most PMR were somewhat lower (range 24.4–33.2 g per 100 g on dmb and 18.3–37.5 g per 100 g on dmb respectively) compared with bitch milk (31.9 and 40.2 g on dmb respectively). The vitamin D content of one of the PMR samples was sevenfold the level recommended by the NRC (Nutrient Requirements of Dogs and Cats, National Academy Press, 2006) and threefold the average level of bitch milk. The clinical relevance of this high amount is questionable, as bitch milk contains mainly 25‐hydroxy‐vitamin D [3843 μg (96.1 IU) per 100 g on dmb] and only limited amounts of vitamin D [524 μg (13.3 IU) per 100 g on dmb], as was determined in this study. Dutch German Shepherd breeders tended to overfeed their puppies. We calculated that misguided use of PMR can increase the risk of excessive calcium, phosphorus and possibly vitamin D intake during a vulnerable period, potentially giving rise to bone and cartilage problems later in life.
First report of the benthic dinoflagellate, Gambierdiscus belizeanus (Gonyaulacales: Dinophyceae) for the east coast of Sabah, Malaysian Borneo
Authors: Leaw Chui‐Pin , Lim Po‐Teen , Tan Toh‐Hii , Tuan‐Halim Tuan Nurhariani , Cheng Kok‐Wah , Ng Boon‐Koon , Usup Gires
Published: May 2011

Species of the genus Gambierdiscus Adachi & Fukuyo, in particular G. toxicus Adachi & Fukuyo are known producers of neurotoxins associated with ciguatera fish poisoning (CFP). In this study live samples were collected from seaweed beds of the east coast of Sabah, Malaysian Borneo and a strain of Gambierdiscus was isolated and cultured. Examination of the thecal fine morphology was undertaken using light, epifluorescence, and scanning electron microscopy. Observed morphological features and their associated morphometric information enabled identification to Gambierdiscus belizeanus Faust. This represents the first report for the occurrence of G. belizeanus in the Asia Pacific region.