CRONOS: the cross-reference navigation server

Summary: Cross-mapping of gene and protein identifiers betweendifferent databases is a tedious and time-consuming task. Toovercome this, we developed CRONOS, a cross-reference serverthat contains entries from five mammalian organisms presentedby major gene and protein information resources. Sequence similarityanalysis of the mapped entries shows that the cross-referencesare highly accurate. In total, up to 18 different identifiertypes can be used for identification of cross-references. Thequality of the mapping could be improved substantially by exclusionof ambiguous gene and protein names which were manually validated.Organism-specific lists of ambiguous terms, which are valuablefor a variety of bioinformatics applications like text miningare available for download. Availability: CRONOS is freely available to non-commercial usersat http://mips.gsf.de/genre/proj/cronos/index.html, web servicesare available at http://mips.gsf.de/CronosWSService/CronosWS?wsdl. Contact: brigitte.waegele{at}helmholtz-muenchen.de Supplementary information: Supplementary data are availableat Bioinformatics online. The online Supplementary Materialcontains all figures and tables referenced by this article. Associate Editor: Martin Bishop     

Effects of light or dark phase testing on behavioural and cognitive performance in DBA mice

Behavioural experiments in mice are often carried out during the resting phase of these nocturnal animals. Ignoring the fact that mice are more active during the dark period, results from resting-phase testing has also been used to characterize these animals. Since the influence of the light/dark cycle on testing is likely to be a relevant factor for the analysis of behavioural results, the aim of this study was to evaluate the effects of the relative time of the day as well as light conditions during testing on behavioural and cognitive performance in inbred mice. Na?ve DBA/2N (DBA) mice were tested in the modified hole board (mHB) either during the dark phase under red light or during the light phase under white light. Different behavioural dimensions and cognitive functions were evaluated in parallel. Depending on the testing conditions, the results showed significant differences in behavioural activity, with DBA mice being less inhibited during dark phase. The same experimental group made fewer memory errors in a visuo-spatial task and showed a faster habituation compared with the group tested during the dark phase. From the results we conclude that testing during the light phase induces a pronounced behavioural inhibition as well as a cognitive disruption in DBA mice, which should be taken into account when cognitively testing these animals.     

New insights into the respiration and metabolic physiology of Lystrosaurus

Laaß, M., Hampe, O., Schudack, M., Hoff, C., Kardjilov, N. and Hilger A. (2010). New insights into the respiration and metabolic physiology of Lystrosaurus. —Acta Zoologica (Stockholm) 92 : 363–371. The first examination by neutron tomography of a skull of Lystrosaurus declivis (Therapsida, Anomodontia) from the Lower Triassic of South Africa showed complexly constructed cartilaginous maxilloturbinals in the nasal cavity. They were situated directly in the respiratory air flow and fill out most of the ventral part of the nasal chamber. Because maxilloturbinals in extant mammals and birds serve as a countercurrent exchange system for thermoregulation and humidification, their presence in the anomodont Lystrosaurus suggests strongly that Lystrosaurus was already endothermic. The endothermic metabolism allowed Lystrosaurus to tolerate high ambient temperature fluctuations. The complexly constructed maxilloturbinals could have reduced respiratory water loss because of higher ventilation rates in drought conditions in the Karoo basin.     

Reverse engineering of protein secretion by uncoupling of cell cycle phases from growth

The demand for recombinant proteins both for biopharmaceutical and technical applications is rapidly growing, and therefore the need to establish highly productive expression systems is steadily increasing. Yeasts, such as Pichia pastoris, are among the widely used production platforms with a strong emphasis on secreted proteins. Protein secretion is a limiting factor of productivity. There is strong evidence that secretion is coupled to specific growth rate (µ) in yeast, being higher at higher µ. For maximum productivity and product titer, high specific secretion rates at low µ would be desired. At high secretion rates cultures contain a large fraction of cells in the G2 and M phases of cell cycle. Consequently, the cell design target of a high fraction of cells in G2 + M phase was achieved by constitutive overexpression of the cyclin gene CLB2. Together with predictive process modeling this reverse engineered production strain improved the space time yield (STY) of an antibody Fab fragment by 18% and the product titer by 53%. This concept was verified with another secreted protein, human trypsinogen. Biotechnol. Bioeng. 2011;108: 2403–2412. © 2011 Wiley Periodicals, Inc.     

Resistance to <Emphasis Type="Italic">Soil-borne cereal mosaic virus</Emphasis> in durum wheat is controlled by a major QTL on chromosome arm 2BS and minor loci

Soil-borne cereal mosaic (SBCM) is a viral disease, which seriously affects hexaploid as well as tetraploid wheat crops in Europe. In durum wheat (Triticum durum Desf.), the elite germplasm is characterized by a wide range of responses to SBCMV, from susceptibility to almost complete resistance. In this study, the genetic analysis of SBCMV resistance was carried out using a population of 181 durum wheat recombinant inbred lines (RILs) obtained from Meridiano (resistant) × Claudio (moderately susceptible), which were profiled with SSR and DArT markers. The RILs were characterized for SBCMV response in the field under severe and uniform SBCMV infection during 2007 and 2008. A wide range of disease reactions (as estimated by symptom severity and DAS-ELISA) was observed. A large portion of the variability for SBCMV response was explained by a major QTL (QSbm.ubo-2BS) located in the distal telomeric region of chromosome 2BS near the marker triplet Xbarc35–Xwmc661–Xgwm210, with R ² values ranging from 51.6 to 91.6%. The favorable allele was contributed by Meridiano. Several QTLs with minor effects on SBCMV response were also detected. Consistently with the observed transgressive segregation, the resistance alleles at minor QTLs were contributed by both parents. The presence and effects of QSbm.ubo-2BS were validated through association mapping in a panel of 111 elite durum wheat accessions.     

Interaction of a Blumeria graminis f. sp. hordei effector candidate with a barley ARF‐GAP suggests that host vesicle trafficking is a fungal pathogenicity target

Filamentous phytopathogens, such as fungi and oomycetes, secrete effector proteins to establish successful interactions with their plant hosts. In contrast with oomycetes, little is known about effector functions in true fungi. We used a bioinformatics pipeline to identify Blumeria effector candidates (BECs) from the obligate biotrophic barley powdery mildew pathogen, Blumeria graminis f. sp. hordei (Bgh). BEC1–BEC5 are expressed at different time points during barley infection. BEC1, BEC2 and BEC4 have orthologues in the Arabidopsis thaliana‐infecting powdery mildew fungus Golovinomyces orontii. Arabidopsis lines stably expressing the G. orontii BEC2 orthologue, GoEC2, are more susceptible to infection with the non‐adapted fungus Erysiphe pisi, suggesting that GoEC2 contributes to powdery mildew virulence. For BEC3 and BEC4, we identified thiopurine methyltransferase, a ubiquitin‐conjugating enzyme, and an ADP ribosylation factor‐GTPase‐activating protein (ARF‐GAP) as potential host targets. Arabidopsis knockout lines of the respective HvARF‐GAP orthologue (AtAGD5) allowed higher entry levels of E. pisi, but exhibited elevated resistance to the oomycete Hyaloperonospora arabidopsidis. We hypothesize that ARF‐GAP proteins are conserved targets of powdery and downy mildew effectors, and we speculate that BEC4 might interfere with defence‐associated host vesicle trafficking.     

Prevalence of Abdominal Obesity in Spanish Children and Adolescents. Do We Need Waist Circumference Measurements in Pediatric Practice?

Background

Evidence indicates that central adiposity has increased to a higher degree than general adiposity in children and adolescents in recent decades. However, waist circumference is not a routine measurement in clinical practice.

Objective

This study aimed to determine the prevalence of abdominal obesity based on waist circumferences (WC) and waist to height ratio (WHtR) in Spanish children and adolescents aged 6 to 17 years. Further, the prevalence of abdominal obesity (AO) among normal and overweight individuals was analyzed.

Design

Data were obtained from a study conducted from 1998 to 2000 in a representative national sample of 1521 children and adolescents aged 6 to 17 years (50.0% female) in Spain. WC and WHtR measurements were obtained in addition to BMI. AO was defined as WHtR ≥0.50 (WHtR-AO), sex and age specific WC≥90^th percentile (WC-AO1), and sex and age specific WC cut-off values associated with high trunk fat measured by by dual-energy X-ray absorptiometry (WC-AO2).

Results

IOTF- based overweight and obsity prevalence was 21.5% and 6.6% in children and 17.4% and 5.2% in adolescents, respectively. Abdominal obesity (AO) was defined as WHtR≥0.50 (WHtR-AO), sex- and age-specific WC≥90th percentile (WC-AO1), and sex- and age-specific WC cut-off values associated with high trunk fat measured by dual-energy X-ray absorptiometry (WC-AO2). The respective prevalence of WHtR-AO, WC-AO1, and WC-AO2 was 21.3% (24.6% boys; 17.9% girls), 9.4% (9.1% boys; 9.7% girls), and 26.8% (30.6% boys;22.9% girls) in children and 14.3% (20.0% boys; 8.7% girls), 9.6% (9.8% boys; 9.5% girls), and 21.1% (28.8% boys; 13.7% girls) in adolescents.

Conclusion

The prevalence of AO in Spanish children and adolescents is of concern. The high proportion of AO observed in young patients who are normal weight or overweight indicates a need to include waist circumference measurements in routine clinical practice.