bluuebunny/crossref_metadata_2025 huggingface dataset:
Iodine nutritional status of children on the island of Tanna, Republic of Vanuatu
Authors: Li Mu , McKelleher Natalie , Moses Theto , Mark John , Byth Karen , Ma Gary , Eastman Creswell J
Published: January 2009

Objective

To evaluate the iodine nutritional status of children living on the island of Tanna, Republic of Vanuatu.

Design

Cross-sectional study. Urine and household salt samples were collected for iodine measurement. Thyroid volumes were measured by ultrasound. A food consumption frequency survey was carried out, particularly in relation to salt, iodine-rich foods and foods that containing thiocyanate, a potentially goitrogenic substance. Urinary thiocyanate levels were also measured.

Setting

Island rural communities in Tanna, Vanuatu.

Subjects

One hundred and fifty-three schoolchildren between 8 and 10 years of age from four locations on the island participated.

Results

The median urinary iodine excretion (UIE) among the children was 49mg/l, indicating moderate iodine deficiency. This was corroborated by 27% of boys and 33% of girls having thyroid glands greater than the international standard for their age, and 36% of boys and 45% of girls having thyroid glands greater than the international standard for their body surface area based on ultrasonography. There was a highly statistically significant inverse correlation between thyroid volume and UIE for boys and girls (r= −0·444,P= 0·001 andr= −0·319,P= 0·005, respectively). There was no correlation between thiocyanate and UIE or thyroid volume. Only 34% of children reported to consume fish (tinned or fresh) on a weekly basis.

Conclusions

Against the common perception, the study has demonstrated that the children on the island of Tanna were in a state of moderate iodine deficiency. More data need to be collected from other Pacific Island countries in order to provide evidence for formulating public policy in prevention and control of iodine deficiency disorders in these nations.
Die Lebenssituation demenziell erkrankter türkischer Migranten/-innen und ihrer Angehörigen
Authors: Piechotta Gudrun , Matter Christa
Published: January 2009

In den 60er und 70er Jahren sind Tausende von so genannten Gastarbeiterinnen und Gastarbeiter angeworben worden. Heute sind diese Menschen im Rentenalter – und mit zunehmendem Alter steigt ihr Risiko, an einer Demenz zu erkranken. Da repräsentative Daten fehlen, kann nur vermutet werden, wie viele von ihnen im Einwanderungsland Bundesrepublik Deutschland erkrankt sind. Auch auf der qualitativen bzw. subjektiven Ebene sind Fragen bis heute nicht angemessen zu beantworten: Wie nehmen die immigrierten Menschen – und ihre Angehörigen – eine solche Erkrankung wahr? Wie gehen sie mit den krankheitsbedingten Symptomen um? Wie und wer begleitet und umsorgt sie? Wie gehen die Angehörigen mit der Situation um? Und ein dritter Fragenkomplex, inkl. praxisbezogener Konsequenzen, bedarf dringend der Aufmerksamkeit: Mit welchen Barrieren sind (demenziell erkrankte) Migrantinnen und Migranten im Altenhilfe- bzw. Pflegeversicherungssystem konfrontiert? Welche kultursensiblen Wege müssen (aus)gebaut werden? Die ungewisse Datenlage, die o. g. beispielhaft aufgeführten Fragen und der Umstand, dass die Beratungssprechstunden der Alzheimer-Gesellschaft Berlin e. V. kaum von Menschen mit Migrationshintergrund aufgesucht werden, hat zu einem qualitativen Forschungsprojekt an der Alice Salomon Hochschule – in Kooperation mit der Alzheimer-Gesellschaft Berlin e. V. – geführt. Ziel war, am Beispiel der türkischen Migrantengruppe in Berlin, eine explorative Studie durchzuführen, die verschiedenste Blickwinkel bündelt und konkrete Anregungen für einen kultursensiblen Umgang mit demenziell erkrankten Migrantinnen und Migranten gibt sowie für die Beratung und Unterstützung ihrer Angehörigen.
Ältere Migrantinnen und Migranten
Authors: Mayr Isolde , Baumann Urs
Published: January 2009

Die nach dem Krieg zugewanderten ArbeitsmigrantInnen rücken in höhere Altersklassen vor, ihre Lebenssituation ist ein wenig erforschtes Thema. Die vorliegende Studie bringt einen Beitrag zu älteren MigrantInnen, indem deren Zugehörigkeitsgefühle, Verbundenheit mit dem Herkunftsland, Aspekte des Kontaktnetzes, Heimwehgefühle und die Lebenszufriedenheit untersucht werden. Dazu wurden 40 Migrantinnen und Migranten im Alter zwischen 52 und 74 Jahren aus dem ehemaligen Jugoslawien, die seit mindestens 15 Jahren in Österreich leben, interviewt. Als Ergebnisse können sowohl differenzierte Zugehörigkeits- als auch Fremdheitsgefühle festgestellt werden. Eine besondere Bedeutung kommt den transnationalen Beziehungsnetzen zu, jedoch planen nur wenige eine Rückkehr in die alte Heimat. Als Zukunftsoption wird überwiegend das Pendeln zwischen beiden Ländern gewählt, die Lebenszufriedenheit dieser Personen ist höher. Zugehörigkeitsgefühle, die sich nur auf die alte Heimat beziehen, sind mit stärkerem Heimweh verbunden, insbesondere bei ständigem Aufenthalt der wichtigsten Kontaktpersonen im Herkunftsland.
Intergenerative Integrationsprojekte
Authors: Gaderer Elisabeth , Baumann Urs
Published: January 2009

Aufgrund der Annahme eines bestehenden Generationenkonflikts zwischen Jung und Alt werden international und zunehmend auch national intergenerative Initiativen, die in Anlehnung an die Kontakthypothese, die Generationensolidarität zwischen den Generationen fördern sollen, diskutiert. Die vorliegende Arbeit analysiert die Einstellung – erhoben mittels Interview – von SeniorInnen in Seniorenheimen (N = 92; M = 82.7 Jahre) zu Intergenerativen Integrationsprojekten, welche inhaltlich durch regelmäßige, organisierte Aktivitäten zwischen älteren Personen und Kindern bzw. Jugendlichen, die in keinem verwandtschaftlichem Verhältnis stehen, gekennzeichnet sind. Insbesondere ging es um die Einstellung zu durchführbaren Aktivitäten, möglichen positiven und negativen Auswirkungen, Frequenz, Dauer und erwünschten interagierenden Kinderaltersgruppen. Zudem wurden personenbezogene Merkmale der SeniorenheimbewohnerInnen, die eine Befürwortung und Teilnahme an einem derartigen Projekte fördern, untersucht. Die Ergebnisse zeigen, dass die SeniorenheimbewohnerInnen für sich selbst nur geringe Vorteile und Nachteile aus Intergenerativen Integrationsprojekten ziehen. Gründe für die gering eingestuften positivem Auswirkungen und die geringe Befürwortung von Intergenerativen Integrationsprojekten wurde in der vorliegenden Arbeit in Zusammenhang mit dem Konzept der Entwicklungsaufgabe im hohen Alter diskutiert.
Subjektive Beurteilungen und Wahrnehmungen von Pflegenden und Gepflegten in der Partnerpflege
Authors: Karrasch Ralph-Michael , Reichert Monika
Published: January 2009

Höhere Grade der körperlichen, insbesondere jedoch der psychischen Belastung des Pflegenden sowie bestimmte Persönlichkeitseigenschaften und Verhaltensweisen der Beteiligten wie hohe psychische Erregbarkeit, Ungeduld und Launenhaftigkeit erhöhen die Auftretenswahrscheinlichkeit von Gewalt. Die subjektive Wahrnehmung der Pflegesituation, sowie von Auslösern auftretender Gewalt sowie subjektive Beurteilungen des körperlichen/psychischen Befindens und damit auch des Leistungsvermögens beider Partner beeinflussen die Gewaltentstehung und lassen Defizite hinsichtlich der Fähigkeit erkennen, sich in den anderen hineinversetzen zu können. Gerade das Erkennen eigener Anteile an der Entstehung auftretender Dissonanzen bzw. problematischer Verhaltensweisen schien vor allem den Pflegenden kaum möglich, was einer suffizienten Bewältigung von Gewalt entgegenstand. Die Ergebnisse der Studie machen deutlich, dass im Bemühen, Überforderungen im Rahmen der Pflege besser verhindern oder meistern zu können, neben der Vermittlung von Bewältigungsstrategien und Maßnahmen zur Stressreduktion auch die Kommunikation zwischen beiden Partnern gefördert werden muss, um Gewalt induzierende Missverständnisse und Fehlbeurteilungen verhindern zu können. Hierzu sollten neben einer vermehrten Bereitstellung von psychosozialen Beratungsangeboten insbesondere psychotherapeutische Verfahren, welche insbesondere eine Stärkung des dyadischen Copings anstreben, genutzt werden.
Aktivierung mit Musik
Authors: Böhler Gertrude , Jenull Brigitte
Published: January 2009

Ziel der vorliegenden Arbeit war den Interventionsansatz «Aktivierung mit Musik» im Setting Pflegeheim umzusetzen und zu überprüfen, ob Pflegeheimbewohner/-innen zu einer regelmäßigen Teilnahme zu motivieren und stabilisierende Auswirkungen auf ihren körperlichen und kognitiven Gesundheitsstatus zu erzielen sind (kognitive Gesundheit: MMSE, Konzentration: AKT, Selbstständigkeit: Barthel-Index, Selbsteinschätzung der Beschwerden: NSL). Die Teilnehmer/-innen (N = 16) absolvierten zwölf Gruppensitzungen, deren kognitive und körperlichen Übungseinheiten auf die Gruppeninteressen abgestimmt waren. Die einzelnen Übungen wurden von Musik begleitet. Alle Pflegeheimbewohner/-innen nahmen regelmäßig am Interventionsprogramm teil. Über den gesamten Untersuchungszeitraum konnte eine Stabilität in den erhobenen Parametern erreicht werden.
Untersuchung zur Validität der deutschsprachigen Version der Dementia Mood Assessment Scale (DMAS) von Sunderland
Authors: Gutzmann Hans , Richert Annette , Mayer Daniela , Schmidt Karl-Heinz
Published: January 2009

Hintergrund: Demenzen und Depressionen sind die häufigsten psychiatrischen Störungen im Alter. Häufig treten sie als diagnostisch differenzierbare Komorbidität auf. Die Konsequenzen des Erkennens einer sekundären Depression sind angesichts der unterschiedlichen Beeinflussbarkeit durch eine medikamentöse oder nichtmedikamentöse Behandlung besonders bedeutsam. Übliche Depressionsskalen bergen die Gefahr, dass der Untersucher keine verlässliche Aussage darüber treffen kann, was die Skala bei Demenzkranken misst. Sunderland, Altermann et al. (1988) entwickelten angesichts dieser Problematik die Dementia Mood Assessment Scale (DMAS), die gezielt die kognitiven Merkmale einer Demenz ausblendet, auch wenn die Stimmungslage sehr wohl die kognitive Leistung beeinträchtigen kann. Methodik und Ergebnisse: Es wurden die ersten 17 Merkmale der DMAS bei 50 ambulanten und stationären Demenzkranken (mittleres Alter 74.1 Jahre) untersucht. Bei einer Faktorenanalyse ergaben sich drei inhaltlich gut voneinander abgrenzbare Faktoren, durch die sich 72.4 % der Varianz aufklären ließen: Faktor 1: Agitiertheit/Klagsamkeit; Faktor 2: Depressive Gestimmtheit; Faktor 3: Apathie. Je nach Texthalbierungsmethode ergab sich ein Reliabilitätskoeffizient für die Gesamtskala von r tt = 0.96. Die Übereinstimmungsvalidität der DMAS mit der Montgomery Asberg Depression Rating Scale (MADRS) ist nicht nur mit den einzelnen Faktoren, sondern auch mit der DMAS-Gesamtskala sehr hoch (r = 0.94) und belegt, dass die DMAS sowohl hinsichtlich des Gesamtwertes als auch auf der Skalenebene das Merkmal Schwere der Depression quantitativ gut abbildet. Es ergab sich ein mäßiger (r = –0.39), aber statistisch bedeutsamer, korrelativer Zusammenhang zwischen Ausprägungsgrad der Depression und Schweregrad der mittels MMSE erfassten kognitiven Beeinträchtigung. Ein bedeutsamer Zusammenhang mit dem Geschlecht der Untersuchten fand sich dagegen ebenso wenig, wie mit dem Lebensalter. Bewertung: Die DMAS soll helfen, die Gestimmtheit eines Demenzkranken zu beurteilen und das Ausmaß der depressiven Verstimmung zu quantifizieren.
Transpolar voltage and polar cap flux during the substorm cycle and steady convection events
Authors: Lockwood Mike , Hairston Marc , Finch Ivan , Rouillard Alexis
Published: January 2009

Transpolar voltages observed during traversals of the polar cap by the Defense Meteorological Satellite Program (DMSP) F‐13 spacecraft during 2001 are analyzed using the expanding‐contracting polar cap model of ionospheric convection. Each of the 10,216 passes is classified by its substorm phase or as a steady convection event (SCE) by inspection of the AE indices. For all phases, we detect a contribution to the transpolar voltage by reconnection in both the dayside magnetopause and in the cross‐tail current sheet. Detection of the IMF influence is 97% certain during quiet intervals and >99% certain during substorm/SCE growth phases but falls to 75% in substorm expansion phases: It is only 27% during SCEs. Detection of the influence of the nightside voltage is only 19% certain during growth phases, rising during expansion phases to a peak of 96% in recovery phases: During SCEs, it is >99%. The voltage during SCEs is dominated by the nightside, not the dayside, reconnection. On average, substorm expansion phases halt the growth phase rise in polar cap flux rather than reversing it. The main destruction of the excess open flux takes place during the 6‐ to 10‐hour interval after the recovery phase (as seen in AE) and at a rate which is relatively independent of polar cap flux because the NENL has by then retreated to the far tail. The best estimate of the voltage associated with viscous‐like transfer of closed field lines into the tail is around 10 kV.
Rainfall estimation by rain gauge‐radar combination: A concurrent multiplicative‐additive approach
Authors: García‐Pintado Javier , Barberá Gonzalo G. , Erena Manuel , Castillo Victor M.
Published: January 2009

A procedure (concurrent multiplicative‐additive objective analysis scheme [CMA‐OAS]) is proposed for operational rainfall estimation using rain gauges and radar data. On the basis of a concurrent multiplicative‐additive (CMA) decomposition of the spatially nonuniform radar bias, within‐storm variability of rainfall and fractional coverage of rainfall are taken into account. Thus both spatially nonuniform radar bias, given that rainfall is detected, and bias in radar detection of rainfall are handled. The interpolation procedure of CMA‐OAS is built on Barnes' objective analysis scheme (OAS), whose purpose is to estimate a filtered spatial field of the variable of interest through a successive correction of residuals resulting from a Gaussian kernel smoother applied on spatial samples. The CMA‐OAS, first, poses an optimization problem at each gauge‐radar support point to obtain both a local multiplicative‐additive radar bias decomposition and a regionalization parameter. Second, local biases and regionalization parameters are integrated into an OAS to estimate the multisensor rainfall at the ground level. The procedure is suited to relatively sparse rain gauge networks. To show the procedure, six storms are analyzed at hourly steps over 10,663 km2. Results generally indicated an improved quality with respect to other methods evaluated: a standard mean‐field bias adjustment, a spatially variable adjustment with multiplicative factors, and ordinary cokriging.
Genetic Obesity Affects Neural Ketone Body Utilization in the Rat Brain
Authors: Narishima Ryota , Yamasaki Masahiro , Hasegawa Shinya , Fukui Tetsuya
Published: January 2009

Obesity causes various physiological disorders between the central nervous system and peripheral tissues. Ketone bodies have a neuro‐protective role and are strongly affected by obesity‐related metabolic disorders. To clarify the effects of obesity on ketone body utilization in brain, we examined the mRNA localization of acetoacetyl‐CoA synthetase (AACS), which activates ketone bodies for the synthesis of fatty acid and cholesterol, in various brain regions of Zucker fatty rats by in situ hybridization. The AACS mRNA level was increased in the paraventricular thalamic nucleus (PVT) but not affected in the cerebrum and hippocampus in Zucker fatty rats. In contrast, the AACS mRNA level was reduced in the arcuate hypothalamic nucleus (Arc) and ventromedial hypothalamic nucleus (VMH) in the hypothalamus. Succinyl‐CoA:3‐oxoacid CoA‐transferase (SCOT) mRNA level was decreased only in the PVT but not affected in the Arc and VMH. These data raise the possibility that AACS is regulated by the leptin signaling pathway in the hypothalamus but not in the PVT. As AACS was expressed in neural‐like cells, ketone bodies are assumed to be utilized for the synthesis of lipidic substances and to cause metabolic disorders in the nervous system.
Demystifying the Poggendorff: A Start
Authors: Parks Theodore E
Published: January 2009

As is well known, little or no illusory misalignment occurs in a reduced Poggendorff pattern which consists of only the two acute angles, a failure which has been a problem for various proposed explanations of the misalignment seen in the complete classic pattern. Happily, however, that failure (as well, more important, as the power of the classic pattern) can be explained by a theory which encompasses both pictorial height-in-scene and illusory rotation-of-the-diagonals as contributing factors.
Factors Influencing Manual Discrimination of Orientations in 5-Month-Old Infants
Authors: Kerzerho Stéphanie , Gentaz Edouard , Streri Arlette
Published: January 2009

Factors affecting manual discrimination of spatial orientations and orientation preferences in 5-month-old infants have been investigated by using a familiarisation/reaction to novelty procedure. In the first experiment we explored whether the ‘vertical preference’ observed by Gentaz and Streri (2004 Journal of Cognitive Neuroscience16 1–7) and Kerzerho et al (2005 NeuroReport16 1833–1837) is an intrinsic preference or whether it is due to familiarisation. In the second experiment we examined whether the magnitude of angular deviation to the vertical influences the direction of preference. Results showed that when both gravitational vertical and body axes were aligned, the intrinsic ‘vertical preference’ exists when the angular difference between the two orientations was 10°. When the angular deviation from the vertical was greater than 10°, the novel orientation was preferred. This modification of orientation preference in the manual discrimination of orientation by 5-month-old infants is discussed in relation to the magnitude of the angular deviation to the gravitational vertical and the spatial reference cues available in each condition.
Look who's Talking: Visual Detection of Speech from Whole-Body Biological Motion Cues during Emotive Interpersonal Conversation
Authors: Rose David , Clarke Tanya J
Published: January 2009

Biological motion stimuli contain a great deal of information about the person and action depicted. Here, we extend the known range by showing that viewers can see which member of a pair of conversing actors is talking. Moreover, the ability varies with the emotional content of the conversation. The implications for social cognitive neuroscience are discussed.
Effect of liveweight gain of pregnant 15-month-old Angus heifers on the milk intake of their first calves and the liveweight of their first and second calves
Authors: Hickson R. E. , Lopez-Villalobos N. , Kenyon P. R. , Morris S. T.
Published: January 2009

Nutritional methods of manipulating birthweight of calves would be useful to beef cattle farmers as a tool for managing dystocia, particularly in 2-year-old heifers. This experiment examined the impact of liveweight gain during pregnancy on birthweight, liveweight to weaning, body dimensions and milk intake of the calves, as well as subsequent liveweight and maternal performance of the heifers. Treatments were high (1.22 ± 0.12 kg/day; H) or moderate (0.56 ± 0.11 kg/day; M) liveweight gain for 10 days before conception, and moderate liveweight gain (0.54 ± 0.30 kg/day; M) or liveweight loss (–0.11 ± 0.30 kg/day; L) for the first trimester (93 days) of pregnancy. HL heifers delivered calves that were lighter absolutely and relative to postpartum liveweight of the heifers than the HM, MM or ML heifers. The 8–15% reduction in birthweight could have a substantial impact on incidence of dystocia, but mechanisms for the reduction were unclear. Liveweight gain treatments had no effect on body dimensions or milk intake of the calves. MM and HM calves were heavier during the rearing period than ML calves. There was no effect of treatment on days to calving or inter-calving interval between first and second calves. Conception rate at the third joining period was not different among treatments. The liveweight gain treatments applied achieved a reduction in birthweight and generally had only minor effects on the subsequent performance of the heifers.
Structure of the human RECQ1 helicase reveals a putative strand-separation pin
Authors: Pike Ashley C. W. , Shrestha Binesh , Popuri Venkateswarlu , Burgess-Brown Nicola , Muzzolini Laura , Costantini Silvia , Vindigni Alessandro , Gileadi Opher
Published: January 2009

RecQ-like helicases, which include 5 members in the human genome, are important in maintaining genome integrity. We present a crystal structure of a truncated form of the human RECQ1 protein with Mg-ADP. The truncated protein is active in DNA fork unwinding but lacks other activities of the full-length enzyme: disruption of Holliday junctions and DNA strand annealing. The structure of human RECQ1 resembles that ofEscherichia coliRecQ, with some important differences. All structural domains are conserved, including the 2 RecA-like domains and the RecQ-specific zinc-binding and winged-helix (WH) domains. However, the WH domain is positioned at a different orientation from that of theE. colienzyme. We identify a prominent β-hairpin of the WH domain as essential for DNA strand separation, which may be analogous to DNA strand-separation features of other DNA helicases. This hairpin is significantly shorter in theE. colienzyme and is not required for its helicase activity, suggesting that there are significant differences between the modes of action of RecQ family members.
Differential requirements for clathrin in receptor-mediated endocytosis and maintenance of synaptic vesicle pools
Authors: Sato Ken , Ernstrom Glen G. , Watanabe Shigeki , Weimer Robby M. , Chen Chih-Hsiung , Sato Miyuki , Siddiqui Ayesha , Jorgensen Erik M. , Grant Barth D.
Published: January 2009

Clathrin is a coat protein involved in vesicle budding from several membrane-bound compartments within the cell. Here we present an analysis of a temperature-sensitive (ts) mutant of clathrin heavy chain (CHC) in a multicellular animal. As expectedCaenorhabditis elegans chc-1(b1025ts)mutant animals are defective in receptor-mediated endocytosis and arrest development soon after being shifted to the restrictive temperature. Steady-state clathrin levels in these mutants are reduced by more than 95% at all temperatures. Hub interactions and membrane associations are lost at the restrictive temperature.chc-1(b1025ts) animals become paralyzed within minutes of exposure to the restrictive temperature because of a defect in the nervous system. Surprisingly synaptic vesicle number is not reduced inchc-1(b1025ts) animals. Consistent with the normal number of vesicles, postsynaptic miniature currents occur at normal frequencies. Taken together, these results indicate that a high level of CHC activity is required for receptor-mediated endocytosis in nonneuronal cells but is largely dispensable for maintenance of synaptic vesicle pools.
Adjuvanticity of a synthetic cord factor analogue for subunit Mycobacterium tuberculosis vaccination requires FcRγ–Syk–Card9–dependent innate immune activation
Authors: Werninghaus Kerstin , Babiak Anna , Groß Olaf , Hölscher Christoph , Dietrich Harald , Agger Else Marie , Mages Jörg , Mocsai Attila , Schoenen Hanne , Finger Katrin , Nimmerjahn Falk , Brown Gordon D. , Kirschning Carsten , Heit Antje , Andersen Peter , Wagner Hermann , Ruland Jürgen , Lang Roland
Published: January 2009

Novel vaccination strategies against Mycobacterium tuberculosis (MTB) are urgently needed. The use of recombinant MTB antigens as subunit vaccines is a promising approach, but requires adjuvants that activate antigen-presenting cells (APCs) for elicitation of protective immunity. The mycobacterial cord factor Trehalose-6,6-dimycolate (TDM) and its synthetic analogue Trehalose-6,6-dibehenate (TDB) are effective adjuvants in combination with MTB subunit vaccine candidates in mice. However, it is unknown which signaling pathways they engage in APCs and how these pathways are coupled to the adaptive immune response. Here, we demonstrate that these glycolipids activate macrophages and dendritic cells (DCs) via Syk–Card9–Bcl10–Malt1 signaling to induce a specific innate activation program distinct from the response to Toll-like receptor (TLR) ligands. APC activation by TDB and TDM was independent of the C-type lectin receptor Dectin-1, but required the immunoreceptor tyrosine-based activation motif–bearing adaptor protein Fc receptor γ chain (FcRγ). In vivo, TDB and TDM adjuvant activity induced robust combined T helper (Th)-1 and Th-17 T cell responses to a MTB subunit vaccine and partial protection against MTB challenge in a Card9-dependent manner. These data provide a molecular basis for the immunostimulatory activity of TDB and TDM and identify the Syk–Card9 pathway as a rational target for vaccine development against tuberculosis.
Jeremy Farrar: When disaster strikes
Authors: Maxmen Amy
Published: January 2009

Jeremy Farrar had not intended to be at the forefront of avian influenza research. But as the director of the Oxford University Clinical Research Unit in Ho Chi Minh City, the bird flu outbreak found him.
IslandViewer: an integrated interface for computational identification and visualization of genomic islands
Authors: Langille Morgan G. I. , Brinkman Fiona S. L.
Published: January 2009

Summary: Genomic islands (clusters of genes of probable horizontal origin; GIs) play a critical role in medically important adaptations of bacteria. Recently, several computational methods have been developed to predict GIs that utilize either sequence composition bias or comparative genomics approaches. IslandViewer is a web accessible application that provides the first user-friendly interface for obtaining precomputed GI predictions, or predictions from user-inputted sequence, using the most accurate methods for genomic island prediction: IslandPick, IslandPath-DIMOB and SIGI-HMM. The graphical interface allows easy viewing and downloading of island data in multiple formats, at both the chromosome and gene level, for method-specific, or overlapping, GI predictions.

Availability: The IslandViewer web service is available at http://www.pathogenomics.sfu.ca/islandviewer and the source code is freely available under the GNU GPL license.

Contact:  brinkman@sfu.ca
Jalview Version 2—a multiple sequence alignment editor and analysis workbench
Authors: Waterhouse Andrew M. , Procter James B. , Martin David M. A. , Clamp Michèle , Barton Geoffrey J.
Published: January 2009

Summary: Jalview Version 2 is a system for interactive WYSIWYG editing, analysis and annotation of multiple sequence alignments. Core features include keyboard and mouse-based editing, multiple views and alignment overviews, and linked structure display with Jmol. Jalview 2 is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server.

Availability: The Jalview 2 Desktop application and JalviewLite applet are made freely available under the GPL, and can be downloaded from www.jalview.org

Contact:  g.j.barton@dundee.ac.uk
CPSP-web-tools: a server for 3D lattice protein studies
Authors: Mann Martin , Smith Cameron , Rabbath Mohamad , Edwards Marlien , Will Sebastian , Backofen Rolf
Published: January 2009

Summary: Studies on proteins are often restricted to highly simplified models to face the immense computational complexity of the associated problems. Constraint-based protein structure prediction (CPSP) tools is a package of very fast algorithms for ab initio optimal structure prediction and related problems in 3D HP-models [cubic and face centered cubic (FCC)]. Here, we present CPSP-web-tools, an interactive online interface of these programs for their immediate use. They include the first method for the direct prediction of optimal energies and structures in 3D HP side-chain models. This newest extension of the CPSP approach is described here for the first time.

Availability and Implementation: Free access at http://cpsp.informatik.uni-freiburg.de

Contact:  cpsp@informatik.uni-freiburg.de; cpsp@informatik.uni-freiburg.de
Suppression of inflammation in rat autoimmune myocarditis by S100A8/A9 through modulation of the proinflammatory cytokine network
Authors: Otsuka Kaoru , Terasaki Fumio , Ikemoto Masaki , Fujita Shuichi , Tsukada Bin , Katashima Takashi , Kanzaki Yumiko , Sohmiya Koichi , Kono Tatsuji , Toko Haruhiro , Fujita Masatoshi , Kitaura Yasushi
Published: January 2009

Aims

S100A8/A9 is expressed in activated monocytes/macrophages and assumed to be heavily involved in the pathogenesis of acute inflammation. Although several studies have asserted that S100A8/A9 has a proinflammatory function, the exact biological function of S100A8/A9 is yet to be described. We examined the anti‐inflammatory effects of S100A8/A9 on experimental autoimmune myocarditis (EAM) in rats.

Methods and results

Experimental autoimmune myocarditis was induced in Lewis rats by immunization with porcine cardiac myosin. The recombinant (R‐) S100A8/A9 was injected intraperitoneally into EAM rats. R‐S100A8/A9 attenuated the severity of myocarditis, as evidenced by echocardiographic and histological findings. In addition, we found that not only the mRNA expression of proinflammatory cytokines [interleukin (IL)‐1β, IL‐6, and tumour necrosis factor (TNF)‐α] in the myocardium, but also their serum concentrations were suppressed in EAM rats treated with R‐S100A8/A9. Nuclear factor‐kappa B expression in inflammatory cells was also suppressed in the treated rats. To elucidate the mechanistic function of S100A8/A9 on proinflammatory cytokines in vivo, we used an ELISA on the supernatant of homogenized heart tissue treated with R‐S100A8/A9. The findings revealed high‐affinity binding of R‐S100A8/A9 with IL‐1β, IL‐6, and TNF‐α in the myocardium, suggesting the trapping of proinflammatory cytokines by R‐S100A8/A9.

Conclusion

S100A8/A9 attenuates EAM through modulation of the proinflammatory cytokine network.
The advantage of explicitly incorporating predation mortality into age-structured stock assessment models: an application for Atlantic mackerel
Authors: Moustahfid H. , Link J. S. , Overholtz W. J. , Tyrrell M. C.
Published: January 2009

Moustahfid, H., Link, J. S., Overholtz, W. J., and Tyrrell, M. C. 2009. The advantage of explicitly incorporating predation mortality into age-structured stock assessment models: an application for Atlantic mackerel. – ICES Journal of Marine Science, 66: 445–454. An age-structured assessment programme (ASAP) that explicitly incorporates predation mortality was applied to Atlantic mackerel (Scomber scombrus) in the Northwest Atlantic. Predatory removals were modelled in the same manner as fishing mortality, with a comparable set of time-series, to produce estimates of predation mortality at age and for each year. Results from the analysis showed that incorporating predation into a mackerel stock assessment model notably altered model outputs. When excluding explicitly modelled rates of predation, the model underestimated the magnitude and uncertainty in spawning-stock biomass (SSB) and recruitment. Further, the rates of predation mortality varied across time and were higher for younger fish. Predation mortality was higher than fishing mortality for fish aged 1 year, approximately equal for 2-year-olds, and lower for older fish (3 years and older). Biological reference points for Atlantic mackerel differed considerably when predation mortality was included. For example, SSBMSY was more than twice as high in the model where predation was incorporated than in the fisheries-only model. Although there are several caveats to the predation model outputs, chief of which is that the estimates are conservative because some mackerel predators were excluded, the results demonstrate the feasibility of executing such an approach with an extant tool. The approach presented here ultimately has the advantage of detecting, and upon detection parsing out, the impact of predators relative to fisheries and has the potential to provide useful information to those interested in small pelagic fish and their associated fisheries.
A simple genetic identification method for Northeast Atlantic smoothhound sharks (Mustelus spp.)
Authors: Farrell Edward D. , Clarke Maurice W. , Mariani Stefano
Published: January 2009

Farrell, E. D., Clarke, M. W., and Mariani, S. 2009. A simple genetic identification method for Northeast Atlantic smoothhound sharks (Mustelus spp.). – ICES Journal of Marine Science, 66: 561–565. Considerable ambiguity exists in the identification of the commercially valuable smoothhound sharks (Mustelus spp.) in the Northeast (NE) Atlantic. The lack of a clear and accurate method of identification prevents the collation of reliable species-specific landings and survey data for these fish and hinders the accurate delineation of the distribution ranges of species and stock boundaries, making it impossible to apply sound species-specific conservation and management strategies. This paper reports on the development of a multiplex PCR reaction that utilizes a set of mtDNA primers for the identification of Mustelus asterias, Mustelus mustelus, and Galeorhinus galeus. The high throughput method allows for the rapid and cost-effective identification of large numbers of samples; its application to 431 fish collected between 2006 and 2008 also raises important questions regarding the biogeography of the genus Mustelus in the NE Atlantic.
Seasonal and interannual variability of primary and export production in the South China Sea: a three-dimensional physical–biogeochemical model study
Authors: Liu Guimei , Chai Fei
Published: January 2009

Liu, G., and Chai, F. 2009. Seasonal and interannual variability of primary and export production in the South China Sea: a three-dimensional physical–biogeochemical model study. – ICES Journal of Marine Science, 66: 420–431. To investigate the seasonal and interannual variations in biological productivity in the South China Sea (SCS), a Pacific basin-wide physical–biogeochemical model has been developed and used to estimate the biological productivity and export flux in the SCS. The Pacific circulation model, based on the Regional Ocean Model Systems (ROMS), is forced with daily air–sea fluxes derived from the NCEP (National Centers for Environmental Prediction) reanalysis between 1990 and 2004. The biogeochemical processes are simulated with a carbon, Si(OH)4, and nitrogen ecosystem (CoSiNE) model consisting of silicate, nitrate, ammonium, two phytoplankton groups (small phytoplankton and large phytoplankton), two zooplankton grazers (small micrograzers and large mesozooplankton), and two detritus pools. The ROMS–CoSiNE model favourably reproduces many of the observed features, such as Chl a, nutrients, and primary production (PP) in the SCS. The modelled depth-integrated PP over the euphotic zone (0–125 m) varies seasonally, with the highest value of 386 mg C m−2 d−1 during winter and the lowest value of 156 mg C m−2 d−1 during early summer. The annual mean value is 196 mg C m−2 d−1. The model-integrated annual mean new production (uptake of nitrate), in carbon units, is 64.4 mg C m−2 d−1, which yields an f-ratio of 0.33 for the entire SCS. The modelled export ratio (e-ratio: the ratio of export to PP) is 0.24 for the basin-wide SCS. The year-to-year variation of biological productivity in the SCS is weaker than the seasonal variation. The large phytoplankton group tends to dominate over the smaller phytoplankton group, and likely plays an important role in determining the interannual variability of primary and new production.
Lack of spatial genetic variation in the edible crab (Cancer pagurus) in the Kattegat–Skagerrak area
Authors: Ungfors Anette , McKeown Niall J. , Shaw Paul W. , André Carl
Published: January 2009

Ungfors, A., McKeown, N. J., Shaw, P. W., and André, C. 2009. Lack of spatial genetic variation in the edible crab (Cancer pagurus) in the Kattegat–Skagerrak area. – ICES Journal of Marine Science, 66: 462–469. The stock structure of the edible crab (Cancer pagurus L.) in the Kattegat and Skagerrak was investigated using eight microsatellite DNA loci. Replicate samples, collected 4–6 years apart, were derived from the Kattegat (Grove Bank, 57°N) and the Skagerrak (Lunneviken, 59°N), plus a geographical outgroup sample from the Norwegian Sea (Midsund, 62°N). Genetic differentiation among samples, estimated as global FST = 0.002, was significant (p = 0.03) when the statistical test was based on allele frequencies, but not when based on genotype frequencies. Moreover, all single- and multilocus pairwise tests between samples were non-significant. An analysis of molecular variance, AMOVA, did not reveal significant differentiation between spatial (Kattegat vs. Skagerrak) or temporal (2001/2002 vs. 2006/2007) groups of samples. Power analysis suggested that the loci and sample sizes employed conferred a power of >90% of detecting even low (true FST = 0.002) levels of population structure. Low spatial and temporal genetic structure might be explained by either or both of (i) high levels of contemporary gene flow in the area attributable to adult migration or larval dispersal or both factors taken together, and (ii) patterns of historical gene flow persisting among recently founded large populations.
Induced Postharvest Yellowing in Southern U.S. Rice Cultivars
Authors: Belefant‐Miller Helen
Published: January 2009

Rice can yellow during storage if moisture levels and temperatures are allowed to increase. This postharvest yellowed (PHY), or stackburn, rice is reduced in value but no study has investigated the inherent potential within rice germplasm for limiting PHY. To screen a large number of cultivars for propensity to PHY, a laboratory method for PHY using a small amount of rice was used. Ninety‐eight popular southern U.S. rice cultivars were yellowed under laboratory conditions. Additional samples of the low‐yellowing and high‐yellowing cultivars were retested after two and three years of storage as rough rice using higher amounts and larger containers. All cultivars showed greater color change with the higher amounts of rice and when yellowed as milled rather than as rough rice. Length of time of storage and storage temperature did not affect the degree of PHY. The low‐ and high‐yellowing groups remained distinguishable but the overall high level of coloring in southern U.S. rice cultivars indicates that a more diverse germplasm should be investigated to increase the likelihood of identifying low‐PHY cultivars.
Autophagy Is Enhanced and Floral Development Is Impaired in AtHVA22d RNA Interference Arabidopsis
Authors: Chen Ching-Nen Nathan , Chen Hau-Ren , Yeh Su-Ying , Vittore Gina , Ho Tuan-Hua David
Published: January 2009

Autophagy is an intracellular process in which a portion of cytoplasm is transported into vacuoles for recycling. Physiological roles of autophagy in plants include recycling nutrients during senescence, sustaining life during starvation, and the formation of central digestive vacuoles. The regulation of autophagy and the formation of autophagosomes, spherical double membrane structures containing cytoplasm moving toward vacuoles, are poorly understood. HVA22 is a gene originally cloned from barley (Hordeum vulgare), which is highly induced by abscisic acid and environmental stress. Homologs of HVA22 include Yop1 in yeast, TB2/DP1 in human, and AtHVA22a to -e in Arabidopsis (Arabidopsis thaliana). Reverse genetics followed by a cell biology approach were employed to study the function of HVA22 homologs. The AtHVA22d RNA interference (RNAi) Arabidopsis plants produced small siliques with reduced seed yield. This phenotype cosegregated with the RNAi transgene. Causes of the reduced seed yield include short filaments, defective carpels, and dysfunctional pollen grains. Enhanced autophagy was observed in the filament cells. The number of autophagosomes in root tips of RNAi plants was also increased dramatically. The yop1 deletion mutant of Saccharomyces cerevisiae was used to verify our hypothesis that HVA22 homologs are suppressors of autophagy. Autophagy activity of this mutant during nitrogen starvation increased in 5 min and reached a plateau after 2 h, with about 80% of cells showing autophagy, while the wild-type cells exhibited low levels of autophagy following 8 h of nitrogen starvation. We conclude that HVA22 homologs function as suppressors of autophagy in both plants and yeast. Potential mechanisms of this suppression and the roles of abscisic acid-induced HVA22 expression in vegetative and reproductive tissues are discussed.
Biotic and Abiotic Stimulation of Root Epidermal Cells Reveals Common and Specific Responses to Arbuscular Mycorrhizal Fungi
Authors: Genre Andrea , Ortu Giuseppe , Bertoldo Chiara , Martino Elena , Bonfante Paola
Published: January 2009

During arbuscular mycorrhizal (AM) colonization, a focal accumulation of organelles occurs in root epidermal cells, prior to fungal penetration, beneath adhering hyphopodia. This is followed by the appearance of the prepenetration apparatus (PPA), a transcellular column of cytoplasm connected to the nucleus and rich in cytoskeleton and secretory endomembranes. This apparatus appears to be responsible for the construction of an apoplastic compartment that confines the fungus within the cell lumen. To identify AM-specific elements within the PPA response, we challenged root cultures of Medicago truncatula, expressing a green fluorescent protein tag for the endoplasmic reticulum, with an AM symbiont, a necrotrophic pathogen, a hemibiotrophic pathogen, a noncompatible endomycorrhizal fungus, or abiotic physical stimuli. Parallel experiments were made on a M. truncatula nonsymbiotic mutant (doesn't make infections, dmi3-1). The results have highlighted a correlation between physical stimulation of the cell surface and nuclear repositioning. Cytoplasmic aggregation was only induced by contact with compatible fungi, whereas PPA appearance was specifically triggered by the AM fungus. The dmi3-1 mutant did not develop cytoplasmic aggregation or PPA and underwent cell death upon physical stimulation. The up-regulation of an expansin-like gene, already identified as an early marker of AM fungal contact, was triggered in wild-type roots by all the fungi tested. Such observations identify responses that are specific to mycorrhizal interactions and extend the role of the DMI3 protein, a calcium/calmodulin-dependent kinase, from symbiotic to pathogenic interactions.
Chloroplast NADPH-Thioredoxin Reductase Interacts with Photoperiodic Development in Arabidopsis
Authors: Lepistö Anna , Kangasjärvi Saijaliisa , Luomala Eeva-Maria , Brader Günter , Sipari Nina , Keränen Mika , Keinänen Markku , Rintamäki Eevi
Published: January 2009

Chloroplast NADPH-thioredoxin reductase (NTRC) belongs to the thioredoxin systems that control crucial metabolic and regulatory pathways in plants. Here, by characterization of T-DNA insertion lines of NTRC gene, we uncover a novel connection between chloroplast thiol redox regulation and the control of photoperiodic growth in Arabidopsis (Arabidopsis thaliana). Transcript and metabolite profiling revealed severe developmental and metabolic defects in ntrc plants grown under a short 8-h light period. Besides reduced chlorophyll and anthocyanin contents, ntrc plants showed alterations in the levels of amino acids and auxin. Furthermore, a low carbon assimilation rate of ntrc leaves was associated with enhanced transpiration and photorespiration. All of these characteristics of ntrc were less severe when plants were grown under a long 16-h photoperiod. Transcript profiling revealed that the mutant phenotypes of ntrc were accompanied by differential expression of genes involved in stomatal development, chlorophyll biosynthesis, chloroplast biogenesis, and circadian clock-linked light perception systems in ntrc plants. We propose that NTRC regulates several key processes, including chlorophyll biosynthesis and the shikimate pathway, in chloroplasts. In the absence of NTRC, imbalanced metabolic activities presumably modulate the chloroplast retrograde signals, leading to altered expression of nuclear genes and, ultimately, to the formation of the pleiotrophic phenotypes in ntrc mutant plants.
Substrates Related to Chromatin and to RNA-Dependent Processes Are Modified by Arabidopsis SUMO Isoforms That Differ in a Conserved Residue with Influence on Desumoylation
Authors: Budhiraja Ruchika , Hermkes Rebecca , Müller Stefan , Schmidt Jürgen , Colby Thomas , Panigrahi Kishore , Coupland George , Bachmair Andreas
Published: January 2009

The higher plant Arabidopsis (Arabidopsis thaliana) has eight genes potentially coding for small ubiquitin-related modifier (SUMO) proteins. However, two well-expressed isoforms differ from fungal and animal consensus in a conserved glutamine (Gln) residue situated four residues from the carboxyl terminus. We tested deviations in this position in the background of SUMO1, the isoform with the highest expression level, and found that changes do not prevent conjugation to substrate proteins in vivo. Replacement of this conserved Gln by alanine resulted in a protein that was less readily removed from a substrate by SUMO protease EARLY IN SHORT DAYS4 in an in vitro reaction and apparently led to higher levels of SUMO conjugates when expressed in vivo. We used the SUMO1 variant with the Gln-to-alanine substitution, as well as SUMO3 and SUMO5 (which carry methionine and leucine, respectively, at this position), to enrich in vivo substrates. Identification of the most abundant proteins contained in these fractions indicated that they are involved in DNA-related, or in RNA-dependent, processes, such as regulation of chromatin structure, splicing, or translation. The majority of the identified bona fide substrates contain predicted sumoylation sites. A subset of the proteins was expressed in Escherichia coli and could be sumoylated in vitro.
Multiple Repeats of a Promoter Segment Causes Transcription Factor Autoregulation in Red Apples
Authors: Espley Richard V. , Brendolise Cyril , Chagné David , Kutty-Amma Sumathi , Green Sol , Volz Richard , Putterill Jo , Schouten Henk J. , Gardiner Susan E. , Hellens Roger P. , Allan Andrew C.
Published: January 2009

Mutations in the genes encoding for either the biosynthetic or transcriptional regulation of the anthocyanin pathway have been linked to color phenotypes. Generally, this is a loss of function resulting in a reduction or a change in the distribution of anthocyanin. Here, we describe a rearrangement in the upstream regulatory region of the gene encoding an apple (Malus × domestica) anthocyanin-regulating transcription factor, MYB10. We show that this modification is responsible for increasing the level of anthocyanin throughout the plant to produce a striking phenotype that includes red foliage and red fruit flesh. This rearrangement is a series of multiple repeats, forming a minisatellite-like structure that comprises five direct tandem repeats of a 23-bp sequence. This MYB10 rearrangement is present in all the red foliage apple varieties and species tested but in none of the white fleshed varieties. Transient assays demonstrated that the 23-bp sequence motif is a target of the MYB10 protein itself, and the number of repeat units correlates with an increase in transactivation by MYB10 protein. We show that the repeat motif is capable of binding MYB10 protein in electrophoretic mobility shift assays. Taken together, these results indicate that an allelic rearrangement in the promoter of MYB10 has generated an autoregulatory locus, and this autoregulation is sufficient to account for the increase in MYB10 transcript levels and subsequent ectopic accumulation of anthocyanins throughout the plant.