bluuebunny/crossref_metadata_2025 huggingface dataset:
Left ventricular function and geometry in fetuses with severe tricuspid regurgitation
Authors: Ishii T. , Tworetzky W. , Harrild D. M. , Marcus E. N. , McElhinney D. B.
Published: October 2011

Objective

Neonatal congenital tricuspid valve (TV) dysplasia and/or displacement (Ebstein's malformation) with severe tricuspid regurgitation (TR) is a challenging condition in which outcomes are frequently poor. Little is known about left ventricular (LV) function during the perinatal period in patients with congenital TV disease. The objective of this study was to evaluate LV function in fetuses with congenital TV anomalies associated with significant TR.

Methods

Serial fetal echocardiograms in 16 fetuses with congenital TV dysplasia and/or displacement (five neonatal survivors and 11 fetal or neonatal deaths) were reviewed. LV stroke volume, LV end‐diastolic volume (LVEDV), LV end‐diastolic dimension (LVIDd), the LV eccentricity index, thoracic and cardiac areas and the cardiothoracic area ratio (CTAR), the right atrium area index, and LV longitudinal strains were compared according to gestational age and clinical outcome.

Results

The gestational age‐adjusted LVEDV (Z‐score) was lower in late gestation (−1.2 ± 1.2 at last examination ≥ 28 weeks) than earlier in gestation (0.3 ± 1.5 at last examination < 28 weeks) and LV output was lower than reported late‐gestation normal values. LV short‐axis dimension correlated with LV volume and CTAR. LV mid‐septal strain was lower than the normal average of fetal mid‐septal strain and correlated with the LV eccentricity index. Among these parameters, only the LV eccentricity index differed between survivors and non‐survivors.

Conclusion

LV function and anatomy are abnormal in fetuses with severe congenital TV anomalies and may be important contributors to outcome. Copyright © 2012 ISUOG. Published by John Wiley & Sons, Ltd.
COMMEMORATING HEROES IN WINDHOEK AND EENHANA: MEMORY, CULTURE AND NATIONALISM IN NAMIBIA, 1990–2010
Authors: Becker Heike
Published: October 2011

In post-colonial Namibia public memory of the liberation war prioritizes the armed struggle from exile. This master narrative of national liberation, having become the new nation's foundation myth, legitimizes the power of the post-colonial SWAPO elite as the sole, heroic liberators from apartheid and colonialism. It has not remained uncontested, however. The article develops the complex transfigurations of liberation war memory, culture and nationalism in post-colonial Namibia around a discussion of two memory sites. The National Heroes’ Acre near Windhoek, inaugurated in 2002, appears as the cast-in-stone nationalist master narrative, aimed at homogenizing the multi-faceted agencies during the liberation war, whereas the Heroes’ Memorial Shrine at Eenhana, constructed in 2007, expressly recognizes the heterogeneity of war-time experiences. The Eenhana site further gives visual expression to recent Namibian unity-in-diversity discourses, which have followed, and partly been running alongside, a period of ideational emphasis on nation building, based on a national culture supposedly forged through the nation's joint struggle against oppression and colonialism. I argue that the social processes of remembering and forgetting political resistance, on the one hand, and those of cultural reinvention in the new nation on the other, are entangled, and that both registers of imagining the Namibian nation have shifted since the country's independence in 1990.
Cascade cell lyses and DNA extraction for identification of genes and microorganisms in kefir grains
Authors: Kowalczyk Magdalena , Kolakowski Piotr , Radziwill-Bienkowska Joanna M , Szmytkowska Agnieszka , Bardowski Jacek
Published: October 2011

Kefir is a dairy product popular in many countries in Central Europe, especially in Poland and other countries of Eastern and Northern Europe. This type of fermented milk is produced by a complex population of symbiotic bacteria and yeasts. In this work, conditions for DNA extraction, involving disruption of kefir grains and a cascade of cell lysis treatments, were established. Extraction procedure of total microbial DNA was carried out directly from fresh kefir grains. Using different lysis stringency conditions, five DNA pools were obtained. Genetic diversity of DNA pools were validated by RAPD analysis, which showed differences in patterns of amplified DNA fragments, indicating diverse microbial composition of all the analysed samples. These DNA pools were used for construction of genomic DNA libraries for sequencing. As much as 50% of the analysed nucleotide sequences showed homology to sequences from bacteria belonging to theLactobacillusgenus. Several sequences were similar to sequences from bacteria representingLactococcus, Oenococcus, Pediococcus, StreptococcusandLeuconostocspecies. Among homologues of yeast proteins were those fromCandida albicans, Candida glabrata, Kluyveromyces lactisandSaccharomyces cerevisiae. In addition, several sequences were found to be homologous to sequences from bacteriophages.
Insight into the structure of compound words among speakers of Chinese and English
Authors: ZHANG JIE , ANDERSON RICHARD C. , WANG QIUYING , PACKARD JEROME , WU XINCHUN , TANG SHAN , KE XIAOLING
Published: October 2011

Knowledge of compound word structures in Chinese and English was investigated, comparing 435 Chinese and 258 Americans, including second, fourth, and sixth graders, and college undergraduates. As anticipated, the results revealed that Chinese speakers performed better on a word structure analogy task than their English-speaking counterparts. Also, as anticipated, speakers of both languages performed better on noun + noun and verb + particle compounds, which are more productive in their respective languages than noun + verb and verb + noun compounds, which are less productive. Both Chinese and English speakers performed significantly better on novel compounds than on familiar compounds, most likely because familiar compounds are lexicalized and do not invite decomposition into constituents.
Syllabic patterns in the early vocalizations of Quichua children
Authors: GILDERSLEEVE-NEUMANN CHRISTINA E. , DAVIS BARBARA L. , MACNEILAGE PETER F.
Published: October 2011

To understand the interactions between production patterns common to children regardless of language environment and the early appearance of production effects based on perceptual learning from the ambient language requires the study of languages with diverse phonological properties. Few studies have evaluated early phonological acquisition patterns of children in non-Indo-European language environments. In the current study, across- and within-syllable consonant–vowel co-occurrence patterns in babbling were analyzed for a 6-month period for seven Ecuadorean Quichua learning children who were between 9 and 17 months of age at study onset. Their babbling utterances were compared to the babbling of six English-learning children between 9 and 22 months of age. Child patterns for both languages were compared with Quichua and English ambient language patterns. Babbling output was highly similar for the child groups: Quichua and English children's babbling demonstrated similar predicted within-syllable (coronal-front vowel, labial-central vowel, dorsal-back vowel) patterns, and across-syllable manner variegation patterns for consonants. These patterns were observed at significantly greater rates in the child groups than in the respective adult language input patterns, suggesting production system influences common to children across languages rather than ambient language perceptual learning effects during these children's babbling period.
Processing words and Short Message Service shortcuts in sentential contexts: An eye movement study
Authors: GANUSHCHAK LESYA Y. , KROTT ANDREA , FRISSON STEVEN , MEYER ANTJE S.
Published: October 2011

The present study investigated whether Short Message Service shortcuts are more difficult to process in sentence context than the spelled-out word equivalent and, if so, how any additional processing difficulty arises. Twenty-four student participants read 37 Short Message Service shortcuts and word equivalents embedded in semantically plausible and implausible contexts (e.g., He left/drank u/you a note) while their eye movements were recorded. There were effects of plausibility and spelling on early measures of processing difficulty (first fixation durations, gaze durations, skipping, and first-pass regression rates for the targets), but there were no interactions of plausibility and spelling. Late measures of processing difficulty (second run gaze duration and total fixation duration) were only affected by plausibility but not by spelling. These results suggest that shortcuts are harder to recognize, but that, once recognized, they are integrated into the sentence context as easily as ordinary words.
Die Psychotherapie Drogenabhängiger in Substitutionsbehandlung
Authors: Specka Michael , Scherbaum Norbert
Published: October 2011

Fragestellung: Angesichts des hohen Ausmaßes an komorbiden psychischen Störungen bei Opiatabhängigen in Substitutionsbehandlung ist eine begleitende psychiatrisch-psychotherapeutische Behandlung in der Regel notwendig. Es ist allerdings zu fragen, ob entsprechende Strategien bei dieser speziellen Patientengruppe auch evaluiert wurden. Methodik: Literaturübersicht mit Fokus auf psychotherapeutische Interventionen mit dem Ziel der Linderung komorbider substanzbezogener Störungen. Ergebnisse: In randomisierten kontrollierten Prüfungen konnte die Wirksamkeit insbesondere einer kognitiven Verhaltenstherapie wie auch des Contingency Management zur Reduktion des Suchtmittelkonsums bei Substitutionspatienten belegt werden. Im Fokus der zumeist US-amerikanischen Untersuchungen stehen kokainbezogene Störungen. Schlussfolgerungen: Eine begleitende Psychotherapie bei Substitutionspatienten ist wirksam. Hindernisse für die Implementierung in der klinischen Versorgung sind mutmaßlich mangelnde Kenntnis der Datenlage bei einem verbreiteten therapeutischen Nihilismus in der Behandlung Drogenabhängiger, aber auch begrenzte finanzielle und personelle Ressourcen für eine begleitende Psychotherapie.
Psychotherapie bei Abhängigkeits- erkrankungen und Posttraumatischer Belastungsstörung
Authors: Schäfer Ingo , Schulze Claudia , Stubenvoll Martina
Published: October 2011

Fragestellung: Die Posttraumatische Belastungsstörung (PTBS) gehört mit einer Punktprävalenz von 15 – 41 % zu den häufigsten komorbiden Störungen bei Personen mit Abhängigkeitserkrankungen. Erst in den letzten Jahren wurde verstärkt damit begonnen, traumatherapeutische Interventionen an diese Patientengruppe zu adaptieren. Die vorliegende Arbeit soll einen Überblick über den aktuellen Stand dieser Entwicklung geben, mit einem Schwerpunkt auf empirisch überprüften Therapieverfahren. Ergebnisse: Im klinischen Alltag werden alle Interventionen, die sich im Rahmen der Traumatherapie bewährt haben, auch bei Suchtkranken erfolgreich eingesetzt. Dabei steht inzwischen fest, dass Ansätze aus beiden Bereichen von Beginn der Therapie an miteinander kombiniert werden sollten. Die existierenden randomisierten kontrollierten Studien beziehen sich sämtlich auf ein stabilisierendes Therapieprogramm („Sicherheit finden“), dessen Effektivität inzwischen als belegt gelten kann. Schlussfolgerungen: Insgesamt hat sich die Behandlung Suchtkranker mit komorbider PTBS in den letzten Jahren stark entwickelt. Allerdings liegen zur Trauma-Exposition bei dieser Patientengruppe bislang kaum systematischen Befunde vor. Weitere Evaluationsstudien sollten folgen, um das gesamte Spektrum traumaspezifischer Interventionen bei Suchtkranken angemessen bewerten zu können.
Probability density function of steady state concentration in two‐dimensional heterogeneous porous media
Authors: Cirpka Olaf A. , de Barros Felipe P. J. , Chiogna Gabriele , Nowak Wolfgang
Published: October 2011

Spatial variability of hydraulic aquifer parameters causes meandering, squeezing, stretching, and enhanced mixing of steady state plumes in concentrated hot‐spots of mixing. Because the exact spatial distribution of hydraulic parameters is uncertain, the spatial distribution of enhanced mixing rates is also uncertain. We discuss how relevant the resulting uncertainty of mixing rates is for predicting concentrations. We develop analytical solutions for the full statistical distribution of steady state concentration in two‐dimensional, statistically uniform domains with log‐hydraulic conductivity following an isotropic exponential model. In particular, we analyze concentration statistics at the fringes of wide plumes, conceptually represented by a solute introduced over half the width of the domain. Our framework explicitly accounts for uncertainty of streamline meandering and uncertainty of effective transverse mixing (defined at the Darcy scale). We make use of existing low‐order closed‐form expressions that lead to analytical expressions for the statistical distribution of local concentration values. Along the expected position of the plume fringe, the concentration distribution strongly clusters at its extreme values. This behavior extends over travel distances of up to tens of integral scales for the parameters tested in our study. In this regime, the uncertainty of effective transverse mixing is substantial enough to have noticeable effects on the concentration probability density function. At significantly larger travel distances, intermediate concentration values become most likely, and uncertainty of effective transverse mixing becomes negligible. A comparison to numerical Monte Carlo simulations of flow and solute transport show excellent agreement with the theoretically derived expressions.
A common structural blueprint for plant UDP-sugar-producing pyrophosphorylases
Authors: Kleczkowski Leszek A. , Geisler Matt , Fitzek Elisabeth , Wilczynska Malgorzata
Published: October 2011

Plant pyrophosphorylases that are capable of producing UDP-sugars, key precursors for glycosylation reactions, include UDP-glucose pyrophosphorylases (A- and B-type), UDP-sugar pyrophosphorylase and UDP-N-acetylglucosamine pyrophosphorylase. Although not sharing significant homology at the amino acid sequence level, the proteins share a common structural blueprint. Their structures are characterized by the presence of the Rossmann fold in the central (catalytic) domain linked to enzyme-specific N-terminal and C-terminal domains, which may play regulatory functions. Molecular mobility between these domains plays an important role in substrate binding and catalysis. Evolutionary relationships and the role of (de)oligomerization as a regulatory mechanism are discussed.
Ectopic expression of Hmgn2 antagonizes mouse erythroid differentiation in vitro
Authors: Kulkeaw Kasem , Inoue Tomoko , Mizuochi Chiyo , Horio Yuka , Ishihama Yasushi , Sugiyama Daisuke
Published: October 2011

Hmgn2 (high mobility group nucleosomal 2), a ubiquitous nucleosome‐binding protein that unfolds chromatin fibres and enhances DNA replication, reportedly regulates differentiation of epithelial and mesenchymal cells. To investigate how Hmgn2 regulates HC (haemopoietic cell) differentiation, we quantified Hmgn2 expression in HCs of mouse FL (fetal liver) during erythroid differentiation. Hmgn2 expression levels were >10‐fold higher in immature erythroid progenitors than in mature erythroid cells, suggesting that Hmgn2 antagonizes erythroid differentiation. To address this issue, Hmgn2 were transfected into both Friend erythroleukaemia cells and FL HCs. There was a 3.3‐fold decrease in relatively mature c‐Kit+/CD71+ erythroid cells, a 2.9‐fold increase in immature c‐Kit+/CD71− erythroid cells in transfected Friend cells, a 1.1‐fold decrease in relatively mature CD71+/Ter119+ erythroid cells, and a 1.7‐fold increase in relatively immature c‐Kit+/CD71+ erythroid cells in FL HCs accompanied by down‐regulation of genes encoding the erythroid transcription factors, Gata1 and Klf1. Two days after Hmgn2 transfection of Friend erythroleukaemia cells, the number of S‐phase cells increased, whereas the number of cells in G1 decreased, while that of mitotic cells remained unchanged. We conclude that ectopic expression of Hmgn2 antagonizes mouse erythroid differentiation in vitro, which may be due to enhancement of DNA replication and/or blocking entry of mitosis at S‐phase.
Human spermatozoa vitrified in the absence of permeable cryoprotectants: birth of two healthy babies
Authors: Isachenko Vladimir , Isachenko Evgenia , Petrunkina Anna M. , Sanchez Raul
Published: October 2011

Herein, we report the birth of two healthy babies to a woman following intracytoplasmic sperm injection (ICSI) using motile spermatozoa vitrified without permeable cryoprotectants. Spermatozoa (in a case of oligoasthenoteratozoospermia) were cooled in cut standard straws in human tubal fluid supplemented with 0.5% human serum albumin and 0.25 M sucrose. Sperm motility, capacitation-like changes, acrosome reaction and mitochondrial membrane potential (MMP) were compared in fresh and vitrified spermatozoa. Eight mature (MII) oocytes were microinjected with the vitrified–warmed motile spermatozoa. Although the motility of vitrified–warmed spermatozoa was markedly lower than that of fresh spermatozoa (60% v. 90%, respectively), there were no immediate visible differences in the percentages of capacitated and acrosome-reacted vitrified and fresh spermatozoa (10% v. 8% and 5% v. 8%, respectively). However, the MMP in vitrified spermatozoa was apparently adversely affected in the ejaculate used for ICSI compared with fresh spermatozoa (63% v. 96% spermatozoa with high MMP). Eighteen hours later, six oocytes showed signs of normal fertilisation. Two-pronuclear oocytes were cultured in vitro for 24 h and two four-blastomere embryos were transferred. Two healthy girls were born at term. Our findings suggest that permeable cryoprotectant-free vitrification can be applied successfully for some procedures in assisted reproduction, in particular in ICSI with motile vitrified spermatozoa, to achieve normal pregnancy and birth.
A role for c-Myc in regulating anti-mycobacterial responses
Authors: Yim Howard C. H. , Li James C. B. , Pong John C. H. , Lau Allan S. Y.
Published: October 2011

c-Myc (Myc) is a well known transcription factor that regulates many essential cellular processes; however, its role in modulating immunity is not known. Here, we showed different species of mycobacteria can induce Myc expression via ERK1/2 and JNK activation. Unexpectedly, the induced Myc is localized in the cytoplasm but not in the nucleus. This induced Myc expression is associated with the induction of TNF-α and IL-6 and with the suppression of intracellular mycobacterial growth. To delineate the underlying mechanisms, we demonstrated that Myc enhances IRAK1 degradation, leading to specific activations of ERK1/2 and p38 MAPK but not Akt, and reduces IκBα protein recovery upon degradation. Hence, our findings may provide insights into a potential role for Myc in regulating the antimicrobial responses.
Evidence of magnetic isotope effects during thermochemical sulfate reduction
Authors: Oduro Harry , Harms Brian , Sintim Herman O. , Kaufman Alan J. , Cody George , Farquhar James
Published: October 2011

Thermochemical sulfate reduction experiments with simple amino acid and dilute concentrations of sulfate reveal significant degrees of mass-independent sulfur isotope fractionation. Enrichments of up to 13‰ for
33
S are attributed to a magnetic isotope effect (MIE) associated with the formation of thiol-disulfide, ion-radical pairs. Observed
36
S depletions in products are explained here by classical (mass-dependent) isotope effects and mixing processes. The experimental data contrasts strongly with multiple sulfur isotope trends in Archean samples, which exhibit significant
36
S anomalies. These results support an origin other than thermochemical sulfate reduction for the mass-independent signals observed for early Earth samples.
𝐴-hypergeometric systems that come from geometry
Authors: Adolphson Alan , Sperber Steven
Published: October 2011

In recent work, Beukers characterizedA{A}-hypergeometric systems having a full set of algebraic solutions. He accomplished this by (1) determining whichA{A}-hypergeometric systems have a full set of polynomial solutions moduloppfor almost all primesppand (2) showing that these systems come from geometry. He then applied a fundamental theorem of N. Katz, which says that such systems have a full set of algebraic solutions. In this paper we establish some connections between nonresonantAA-hypergeometric systems and de Rham-type complexes, which leads to a determination of whichAA-hypergeometric systems come from geometry. We do not use the fact that the system is irreducible or find integral formulas for its solutions.
Splice variant–specific cellular function of the formin INF2 in maintenance of Golgi architecture
Authors: Ramabhadran Vinay , Korobova Farida , Rahme Gilbert J. , Higgs Henry N.
Published: October 2011

INF2 is a unique formin that can both polymerize and depolymerize actin filaments. Mutations in INF2 cause the kidney disease focal and segmental glomerulosclerosis. INF2 can be expressed as two C-terminal splice variants: CAAX and non-CAAX. The CAAX isoform contains a C-terminal prenyl group and is tightly bound to endoplasmic reticulum (ER). The localization pattern and cellular function of the non-CAAX isoform have not been studied. Here we find that the two isoforms are expressed in a cell type–dependent manner, with CAAX predominant in 3T3 fibroblasts and non-CAAX predominant in U2OS, HeLa, and Jurkat cells. Although INF2-CAAX is ER localized in an actin-independent manner, INF2–non-CAAX localizes in an actin-dependent meshwork pattern distinct from ER. INF2–non-CAAX is loosely attached to this meshwork, being extracted by brief digitonin treatment. Suppression of INF2–non-CAAX causes fragmentation of the Golgi apparatus. This effect is counteracted by treatment with the actin monomer–sequestering drug latrunculin B. We also find discrete patches of actin filaments in the peri-Golgi region, and these patches are reduced upon INF2 suppression. Our results suggest that the non-CAAX isoform of INF2 serves a distinct cellular function from that of the CAAX isoform.
Managing Political Risk in Global Business: Beiersdorf 1914–1990
Authors: Jones Geoffrey , Lubinski Christina
Published: October 2011

This article is concerned with business strategies of political risk management during the twentieth century. It focuses especially on Beiersdorf, a pharmaceutical and skin care company in Germany. During World War I, the expropriation of its brands and trademarks revealed its vulnerability to political risk. Following the advent of the Nazi regime in 1933, the largely Jewish owned and managed company faced a uniquely challenging combination of home and host country political risk. This article reviews the company's responses to these adverse circumstances, challenging the prevailing literature that interprets so-called “cloaking” activities as one element of businesses' cooperation with the Nazis. We also depart from the previous literature in assessing the outcomes of the company's strategies after 1945 and examine the challenges and costs faced by the company in recovering the ownership of its brands. While the management of distance became much easier over the course of the twentieth century because of communications improvements, this article shows that the management of governments and political risk grew sharply.
Diffusible Signal Factor-Mediated Quorum Sensing Plays a Central Role in Coordinating Gene Expression of Xanthomonas citri subsp. citri
Authors: Guo Yinping , Zhang Yanping , Li Jian-Liang , Wang Nian
Published: October 2011

Diffusible signal factor (DSF) family signal-mediated quorum sensing (QS) has been identified in many gram-negative bacteria. This QS pathway of Xanthomonas spp. consists of three major QS components: RpfF, RpfC, and RpfG. The rpfF gene encodes a putative enoyl-CoA hydratase that catalyzes the synthesis of the signal molecule. RpfC and RpfG serve as a two-component system for the perception and transduction of the extracellular DSF family signals. In order to further characterize the QS regulatory network in Xanthomonas citri subsp. citri, we investigated the RpfF, RpfC, and RpfG regulons by using transcriptome analyses. Comparison of the transcriptomes of the QS mutants (rpfF, rpfC, and rpfG) with that of the wild-type strain revealed a core group of genes controlled by all three QS components, suggesting that the RpfC-RpfG two-component system is a major and conserved signal perception and transduction system for DSF family signal-mediated QS in X. citri subsp. citri. The unique genes controlled by RpfF alone indicate the complexity of the QS pathway and the involvement of additional sensory mechanisms in X. citri subsp. citri. The unique genes controlled by RpfC and RpfG, respectively, support the possibility that RpfC and RpfG play broader roles in gene regulation other than transduction of DSF signals.
Effect of PrP genotype and route of inoculation on the ability of discriminatory Western blot to distinguish scrapie from sheep bovine spongiform encephalopathy
Authors: Migliore Sergio , Esposito Elena , Pirisinu Laura , Marcon Stefano , Di Bari Michele , D’Agostino Claudia , Chiappini Barbara , Conte Michela , Sezzi Erminia , De Grossi Luigi , Agrimi Umberto , Vaccari Gabriele , Nonno Romolo
Published: October 2011

Procedures for discriminating scrapie from bovine spongiform encephalopathy (BSE) in sheep are relevant to ascertain whether BSE has entered the sheep population. This study was aimed at investigating whether the suitability of an official EU discriminative method is affected by the sheep PrP genotype and route of infection.
New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes
Authors: Parker Brian J. , Moltke Ida , Roth Adam , Washietl Stefan , Wen Jiayu , Kellis Manolis , Breaker Ronald , Pedersen Jakob Skou
Published: October 2011

Regulatory RNA structures are often members of families with multiple paralogous instances across the genome. Family members share functional and structural properties, which allow them to be studied as a whole, facilitating both bioinformatic and experimental characterization. We have developed a comparative method, EvoFam, for genome-wide identification of families of regulatory RNA structures, based on primary sequence and secondary structure similarity. We apply EvoFam to a 41-way genomic vertebrate alignment. Genome-wide, we identify 220 human, high-confidence families outside protein-coding regions comprising 725 individual structures, including 48 families with known structural RNA elements. Known families identified include both noncoding RNAs, e.g., miRNAs and the recently identified MALAT1/MEN β lincRNA family; and cis-regulatory structures, e.g., iron-responsive elements. We also identify tens of new families supported by strong evolutionary evidence and other statistical evidence, such as GO term enrichments. For some of these, detailed analysis has led to the formulation of specific functional hypotheses. Examples include two hypothesized auto-regulatory feedback mechanisms: one involving six long hairpins in the 3′-UTR of MAT2A, a key metabolic gene that produces the primary human methyl donor S-adenosylmethionine; the other involving a tRNA-like structure in the intron of the tRNA maturation gene POP1. We experimentally validate the predicted MAT2A structures. Finally, we identify potential new regulatory networks, including large families of short hairpins enriched in immunity-related genes, e.g., TNF, FOS, and CTLA4, which include known transcript destabilizing elements. Our findings exemplify the diversity of post-transcriptional regulation and provide a resource for further characterization of new regulatory mechanisms and families of noncoding RNAs.
Evidence of abundant stop codon readthrough in Drosophila and other metazoa
Authors: Jungreis Irwin , Lin Michael F. , Spokony Rebecca , Chan Clara S. , Negre Nicolas , Victorsen Alec , White Kevin P. , Kellis Manolis
Published: October 2011

While translational stop codon readthrough is often used by viral genomes, it has been observed for only a handful of eukaryotic genes. We previously used comparative genomics evidence to recognize protein-coding regions in 12 species of Drosophila and showed that for 149 genes, the open reading frame following the stop codon has a protein-coding conservation signature, hinting that stop codon readthrough might be common in Drosophila. We return to this observation armed with deep RNA sequence data from the modENCODE project, an improved higher-resolution comparative genomics metric for detecting protein-coding regions, comparative sequence information from additional species, and directed experimental evidence. We report an expanded set of 283 readthrough candidates, including 16 double-readthrough candidates; these were manually curated to rule out alternatives such as A-to-I editing, alternative splicing, dicistronic translation, and selenocysteine incorporation. We report experimental evidence of translation using GFP tagging and mass spectrometry for several readthrough regions. We find that the set of readthrough candidates differs from other genes in length, composition, conservation, stop codon context, and in some cases, conserved stem–loops, providing clues about readthrough regulation and potential mechanisms. Lastly, we expand our studies beyond Drosophila and find evidence of abundant readthrough in several other insect species and one crustacean, and several readthrough candidates in nematode and human, suggesting that functionally important translational stop codon readthrough is significantly more prevalent in Metazoa than previously recognized.
Scaling of lunge‐feeding performance in rorqual whales: mass‐specific energy expenditure increases with body size and progressively limits diving capacity
Authors: Goldbogen Jeremy A. , Calambokidis John , Croll Donald A. , McKenna Megan F. , Oleson Erin , Potvin Jean , Pyenson Nicholas D. , Schorr Greg , Shadwick Robert E. , Tershy Bernie R.
Published: October 2011

1. Diving capacity generally increases with body size both within and among taxanomic groups because of the differential scaling between body oxygen stores and metabolic rate.

2. Despite being some of the largest animals of all time, rorqual whales exhibit very short dive times relative to other large divers because of the high energetic costs incurred during lunge feeding. This mode of filter feeding requires high drag for the engulfment of large volumes of prey‐laden water, and the magnitude of both drag and engulfment volume is largely determined by the size and shape of the skull.

3. The positive allometry of rorqual skulls increases mass‐specific engulfment capacity in larger whales, but the energetic requirements of feeding are also predicted to increase and thus further limit diving capacity.

4. To test the hypothesis that the energetic cost of a lunge is disproportionately higher in larger rorquals, we compared diving and lunge‐feeding performance among three different‐sized species (blue, fin and humpback whales) foraging on krill.

5. Our hydrodynamic analyses indicate that the mass‐specific energy expenditure will increase with body size if rorquals lunge at length‐specific speeds (in body lengths per second) that are independent of body size, a condition that is supported by tag data.

6. Although the absolute time required to filter each volume of water increased with body size, maximum dive duration and depth were not significantly different among species. As a consequence, the maximum number of lunges executed per dive decreased with body size.

7. These data suggest that, unlike all other true divers, adult rorqual species do not exhibit a positive relationship between body size and diving capacity. Larger rorquals forfeit diving capacity for greater engulfment capacity, a trade‐off that favours the efficient exploitation of patchily dense prey aggregations. Such a trade‐off may underlie different foraging strategies associated with resource partitioning, life history and ecological niche.
Wood density explains architectural differentiation across 145 co‐occurring tropical tree species
Authors: Iida Yoshiko , Poorter Lourens , Sterck Frank J. , Kassim Abd R. , Kubo Takuya , Potts Matthew D. , Kohyama Takashi S.
Published: October 2011

1.Because of its mechanical properties, wood density may affect the way that trees expand their stem and crown to exploit favourable light conditions in a mechanically stable way. From engineering theory and wood density properties, it is predicted that in terms of biomass investment, low‐density wood is more efficient for vertical stem expansion, while high‐density wood is more efficient for horizontal branch expansion. So far, these predictions have rarely been tested by empirical studies.

2.We tested these predictions for 145 co‐occurring tree species in a Malaysian tropical rainforest. For each species, we selected trees across a broad size range and measured architectural dimensions (stem diameter, height of the lowest foliage and crown width). We used a hierarchical Bayesian model to estimate species‐specific allometric relationships between architectural dimensions including estimated stem biomass. Then, we examined correlations between species wood density and estimated architectural variables at standardized heights.

3.When species were compared at standardized tree heights, wood density correlated negatively with stem diameter and positively with stem biomass at most reference heights. This indicates that species with low wood density produce thicker stems but at lower biomass costs. Wood density correlated positively with crown width and negatively with height of the lowest foliage, which indicates that high wood density species have wider and deeper crowns than low wood density species. These relationships were maintained at most reference heights. However, the relationship with crown width was nonsignificant above 18 m height. This may reflect large plastic response of lateral crown expansion to a local condition.

4. Wood density explains the trade‐off between effective vertical stem expansion and horizontal crown expansion across co‐occurring tropical tree species. Such mechanical constraints characterize the difference in tree architecture between low wood density species that show an efficient height expansion to attain better light conditions in the exposed canopy and high wood density species that show an efficient horizontal crown expansion to enhance current light interception and persistence in the shaded forest understorey. Our study thus suggests that the mechanical constraints set by wood density contribute to the co‐existence of species differing in architecture and light capture strategy.
Sleep structure and feeding pattern changes induced by the liver’s thermal status in the rat
Authors: EL HAJJAJI FATIM‐ZOHRA , PELLETIER AMANDINE , DELANAUD STÉPHANE , LIBERT JEAN‐PIERRE , BACH VÉRONIQUE , LOOS NATHALIE
Published: October 2011

Given the liver’s importance in controlling metabolic homeostasis in mammals, we sought to establish (i) whether the thermal status of this organ was involved in the link between sleep, thermoregulation and food intake and (ii) how the hypothalamic structures affect the functional interactions between processes involved in regulation of the body’s energy balance. In 10 freely moving rats, the liver was heated artificially to and maintained at set‐point temperatures of 39.5, 40.0 and 40.5 °C for 4 h. Each animal’s feeding activity, cortical temperature and brown adipose tissue (TBAT) temperature were measured continuously. Sleep organization and wakefulness were scored from electroencephalograms. Each animal served as its own control. Heating the liver induced a decrease in food intake and TBAT, corresponding to the development of a hypometabolic hypothermic status. The total amounts of wakefulness and rapid eye movement sleep fell, whereas the total amount of slow wave sleep increased accordingly. Our findings show that the liver is involved significantly in the body’s thermodynamic equilibrium. The organ’s thermal status can induce well‐coordinated behavioural and autonomic adaptive responses involved in the control of food intake and in the maintenance of body homeothermia. Our study provides indirect evidence of the existence of hepatic thermosensors afferent to feeding and sleeping hypothalamic integrating centres that can be stimulated by physiological increases in liver temperature.
A multi‐repeat adhesin of the phytopathogen, Pectobacterium atrosepticum, is secreted by a Type I pathway and is subject to complex regulation involving a non‐canonical diguanylate cyclase
Authors: Pérez‐Mendoza Daniel , Coulthurst Sarah J. , Humphris Sonia , Campbell Emma , Welch Martin , Toth Ian K. , Salmond George P. C.
Published: October 2011

Cyclic diguanylate (c‐di‐GMP) is a second messenger controlling many important bacterial processes. The phytopathogen Pectobacterium atrosepticum SCRI1043 (Pba1043) possesses a Type I secretion system (T1SS) essential for the secretion of a proteinaceous multi‐repeat adhesin (MRP) required for binding to the host plant. The genes encoding the MRP and the T1SS are tightly linked to genes encoding several putative c‐di‐GMP regulatory components. We show that c‐di‐GMP regulates secreted MRP levels in Pba1043 through the action of two genes encoding predicted diguanylate cyclase (DGC) and phosphodiesterase proteins (ECA3270 and ECA3271). Phenotypic analyses and quantification of c‐di‐GMP levels demonstrated that ECA3270 and ECA3271 regulate secreted MRP levels by increasing and decreasing, respectively, the intracellular levels of c‐di‐GMP. Moreover, ECA3270 represents the first active DGC reported to have an alternative active‐site motif from the ‘canonical’ GG[D/E]EF. ECA3270 has an A‐site motif of SGDEF and analysis of single amino acid replacements demonstrated that the first position of this motif can tolerate functional substitution. Serine in position one of the A‐site is also observed in many other DGCs. Finally, another T1SS‐linked regulator (ECA3265) also plays an important role in regulating secreted MRP, with an altered localization of MRP observed in an ECA3265 mutant background. Mutants defective in these three T1SS‐linked regulators exhibit a reduction in root binding and virulence, confirming that this complex, finely tuned regulation system is crucial in the interaction with host plants.
Disruption and complementation of the selenocysteine biosynthesis pathway reveals a hierarchy of selenoprotein gene expression in the archaeon Methanococcus maripaludis
Authors: Stock Tilmann , Selzer Mirjam , Connery Sarah , Seyhan Deniz , Resch Armin , Rother Michael
Published: October 2011

Proteins containing selenocysteine are found in members of all three domains of life, Bacteria, Eukarya and Archaea. A dedicated tRNA (tRNAsec) serves as a scaffold for selenocysteine synthesis. However, sequence and secondary structures differ in tRNAsec from the different domains. An Escherichia coli strain lacking the gene for tRNAsec could only be complemented with the homologue from Methanococcus maripaludis when a single base in the anticodon loop was exchanged demonstrating that this base is a crucial determinant for archaeal tRNAsec to function in E. coli. Complementation in trans of M. maripaludis JJ mutants lacking tRNAsec, O‐phosphoseryl‐tRNAsec kinase or O‐phosphoseryl‐tRNAsec:selenocysteine synthase with the corresponding genes from M. maripaludis S2 restored the mutant's ability to synthesize selenoproteins. However, only partial restoration of the wild‐type selenoproteome was observed as only selenocysteine‐containing formate dehydrogenase was synthesized. Quantification of transcripts showed that disrupting the pathway of selenocysteine synthesis leads to downregulation of selenoprotein gene expression, concomitant with upregulation of a selenium‐independent backup system, which is not re‐adjusted upon complementation. This transcriptional arrest was independent of selenophosphate but depended on the ‘history’ of the mutants and was inheritable, which suggests that a stable genetic switch may cause the resulting hierarchy of selenoproteins synthesized.
Crh, the paralogue of the phosphocarrier protein HPr, controls the methylglyoxal bypass of glycolysis in Bacillus subtilis
Authors: Landmann Jens J. , Busse Ricarda A. , Latz Jan‐Hendrik , Singh Kalpana D. , Stülke Jörg , Görke Boris
Published: October 2011

The histidine protein HPr has a key role in regulation of carbohydrate utilization in low‐GC Gram‐positive bacteria. Bacilli possess the paralogue Crh. Like HPr, Crh becomes phosphorylated by kinase HPrK/P in response to high fructose‐1,6‐bisphosphate concentrations. However, Crh can only partially substitute for the regulatory functions of HPr leaving its role mysterious. Using protein co‐purification, we identified enzyme methylglyoxal synthase MgsA as interaction partner of Crh in Bacillus subtilis. MgsA converts dihydroxyacetone‐phosphate to methylglyoxal and thereby initiates a glycolytic bypass that prevents the deleterious accumulation of phospho‐sugars under carbon overflow conditions. However, methylgyloxal is toxic and its production requires control. We show here that exclusively the non‐phosphorylated form of Crh interacts with MgsA in vivo and inhibits MgsA activity in vitro. Accordingly, Crh inhibits methylglyoxal formation in vivo under nutritional famine conditions that favour a low HPr kinase activity. Thus, Crh senses the metabolic state of the cell, as reflected by its phosphorylation state, and accordingly controls flux through the harmful methylglyoxal pathway. Interestingly, HPr is unable to bind and regulate MgsA, making this a bona fide function of Crh. Four residues that differ in the interaction surfaces of HPr and Crh may account for this difference.
Species diversity, phylogeny and genetic variability of begomovirus populations infecting leguminous weeds in northeastern Brazil
Authors: Silva S. J. C. , Castillo‐Urquiza G. P. , Hora‐Júnior B. T. , Assunção I. P. , Lima G. S. A. , Pio‐Ribeiro G. , Mizubuti E. S. G. , Zerbini F. M.
Published: October 2011

A survey of begomoviruses infecting leguminous weeds (family Fabaceae) was carried out in four states of northeastern Brazil. A total of 26 full‐length begomovirus components (19 DNA‐A and seven DNA‐B, with three pairs of cognate A and B components) were amplified using rolling‐circle amplification, then cloned and sequenced. Sequence analysis indicated the presence of six species, four of them novel. In phylogenetic analysis five of the viruses clustered with other Brazilian begomoviruses, but one of them (Euphorbia yellow mosaic virus, EuYMV) clustered with viruses from other countries in Central and South America. Evidence of recombination was found among isolates of Macroptilium yellow spot virus (MaYSV). The MaYSV population had a high degree of genetic variability. Macroptilium lathyroides was revealed as a common host for several of these viruses, and could act as a mixing vessel from which recombinant viruses could emerge. The results indicate that leguminous weeds are reservoirs of several begomoviruses in Brazil, and could play a significant role in begomovirus epidemics, both as inoculum sources and as sources of emerging novel viruses.
Activated Monocytes Prime Naïve T Cells Against Autologous Cancer: Vigorous Cancer DestructionIn VitroandIn Vivo
Authors: Laumbacher B. , Gu S. , Wank R.
Published: October 2011

It has not been considered so far that antigen‐presenting cells (APC) may phagocytose immunogenic material from autologous cancer cells. Assuming the presence of cancer‐immunogenic material in APC, we developed a novel autologous priming method that does not require tumour cells or identified peptides. Cancer‐immunogenic information came from CD14+monocytes. When stimulated with CD3‐activated T cells, monocytes primed CD3+CD4+and CD3+CD8+resting/naïve T cells to become powerful effector cells within 24 h. During priming, depletion of CD14+monocytes but not CD1a+CD83+dendritic cells prevented T cell priming. During cancer cell destruction, dendritic cells, but not monocytes, enhanced cancer cell lysis. The cascade‐primed (CAPRI) immune cell quartet comprising monocytes, dendritic cells, CD4+T and CD8+T cells induced a significant decrease in the number of suppressive CD25highFoxP3+CD4+T cells. CAPRI cells induced a marked upregulation of MHC class I and class II expression in cancer cells, which is crucial for autoimmune‐like lysis. We showin vivoevidence of the CAPRI cell concept in nude mice. In humans, we present circumstantial clinical evidence showing the efficacy of CAPRI cells in an adjuvant treatment attempt for breast cancer patients with metastasis (N = 42). Compared to patients at the Munich Tumor Center (no CAPRI treatmentN = 428), almost double the expected number of patients survived 5 years (P = 1.36 × 10−14). The CAPRI method is a safe procedure without negative side effects. High numbers of cancer‐specific CAPRI cells can be obtained within a week against different cancer types for efficient adoptive cell therapy.
Optimization of a Staphylococcus aureus adhesion assay for equine corneocytes
Authors: Griffeth Gregory C. , Callori Nancy , Rankin Shelley C. , Boston Raymond C. , Morris Daniel O.
Published: October 2011

Meticillin‐resistant Staphylococcus aureus (MRSA) causes serious skin and soft‐tissue infections of humans and animals. Multiple strains of MRSA have been characterized, and one in particular, designated as strain USA 500, causes infections predominantly of horses and the people who work with them. The purpose of this study was to optimize an assay which could subsequently be used to compare the relative avidity of different S. aureus strains for equine corneocytes. Corneocytes were collected from the perineal skin of 10 healthy horses onto adhesive discs. The discs were then incubated at 37 °C with an S. aureus field strain at each of three concentrations [107, 108 and 109 colony forming units (CFU)/mL] and for each of three incubation periods (45, 90 and 180 min). After standardized rinsing and staining procedures, discs were examined at ×1,000 magnification and areas containing confluent corneocytes photographed. The percentage of surface area occupied by adherent bacteria was analysed using image processing and analysis software. Significant colour space image processing was required to distinguish bacteria from the ubiquitous melanin granules present within equine corneocytes. Objective and subjective methods were used to determine optimal conditions for specific adherence without introducing confounding factors. A bacterial concentration of 108 CFU/mL incubated with corneocytes for 45 min produced maximal bacterial adhesion with the least amount of interbacterial clumping. Future studies should utilize these conditions for optimal assay performance.