Introducing “best single template” models as reference baseline for the Continuous Automated Model Evaluation (CAMEO)

Critical blind assessment of structure prediction techniques is crucial for the scientific community to establish the state of the art, identify bottlenecks, and guide future developments. In Critical Assessment of Techniques in Structure Prediction (CASP), human experts assess the performance of participating methods in relation to the difficulty of the prediction task in a biennial experiment on approximately 100 targets. Yet, the development of automated computational modeling methods requires more frequent evaluation cycles and larger sets of data. The “Continuous Automated Model EvaluatiOn (CAMEO)” platform complements CASP by conducting fully automated blind prediction evaluations based on the weekly pre-release of sequences of those structures, which are going to be published in the next release of the Protein Data Bank (PDB). Each week, CAMEO publishes benchmarking results for predictions corresponding to a set of about 20 targets collected during a 4-day prediction window. CAMEO benchmarking data are generated consistently for all methods at the same point in time, enabling developers to cross-validate their method's performance, and referring to their results in publications. Many successful participants of CASP have used CAMEO—either by directly benchmarking their methods within the system or by comparing their own performance to CAMEO reference data. CAMEO offers a variety of scores reflecting different aspects of structure modeling, for example, binding site accuracy, homo-oligomer interface quality, or accuracy of local model confidence estimates. By introducing the "bestSingleTemplate" method based on structure superpositions as a reference for the accuracy of 3D modeling predictions, CAMEO facilitates objective comparison of techniques and fosters the development of advanced methods.     

The complex barnacle perfume: identification of waterborne pheromone homologues in Balanus improvisus and their differential expression during settlement

A key question in barnacle biology is the nature of cues that induce gregarious settlement. One of the characterised cues is the waterborne settlement pheromone (WSP). This study aimed to identify WSP homologues in Balanus improvisus and to investigate their expression during settlement. Six WSP homologues were identified, all containing an N-terminal signal peptide, a conserved core region, and a variable C-terminus comprising several -GR- and -HDDH- motifs. The B. improvisus WSP homologues were expressed in all settlement stages but showed different expression patterns. The homologue most similar to the B. amphitrite WSP was the most abundant and was constantly expressed during settlement. In contrast, several of the other WSP homologues showed the greatest expression in the juvenile stage. The presence of several WSP homologues suggests the existence of a pheromone mix, where con-specificity might be determined by a combination of sequence characteristics and the concentration of the individual components.     

Stromalin Constrains Memory Acquisition by Developmentally Limiting Synaptic Vesicle Pool Size

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Secreting oviduct epithelial cells of Coturnix coturnix japonica (QOEC) and changes to their proteome after nonviral transfection

The quail oviduct (Coturnix c. japonica) is a natural candidate avian bioreactor, while the secretive quail oviduct epithelial cells (QOECs) are potential in vitro producers of recombinant proteins and vaccines. In view of the need for highly performing and transformable cell lines, QOEC may potentially act as an alternative bioreactor platform to the existing ones, for example, to the Chinese hamster ovary. The aim of this work was to characterize QOECs and their response to nucleofection with a nonviral plasmid DNA carrying the human interferon-α 2a gene (hIFNλ2a), in vitro. Primary QOEC cultures from laying quails (10-15 weeks old) were characterized by their proliferation rate, doubling time, and multilineage differentiation. Electroporation to cell nuclei (nucleofection) was used to deliver nonviral plasmid DNA containing a reporter GFP and hIFN under the ovalbumin promoter. The posttransfection analysis included polymerase chain reaction, Western blot analysis, and liquid chromatography coupled to tandem mass spectrometry. QOEC showed a typical epithelial characteristic in a primary 2D monolayer culture system and retained secretive potential up to the first passage. QOEC showed differentiation into osteoblastic lineage after stimulation. The nucleofection mean efficiency was low (2.3%). Differences of up to 10% in the proteomic profiles between nontransfected and transfected QOEC were found, the most important of these were related to the absence of keratins and cell-adhesion proteins in the transfected QOEC. Concluding, with the practical information provided here, QOEC have the potential to serve as an avian secreting cellular platform. QOEC may be further transformed to cell lineage to meet the requirement for a stable, electrocompetent, and transfectable model. The first proteomic comparison of QOEC delivered in this study showed, in the majority, a stable proteome of the nontransfected vs transfected QOEC.     

Improvement of almond production using Bombus terrestris (Hymenoptera: Apidae) in Mediterranean conditions

Almond trees are one of the most important crops in the Balearic Islands. The pollination of almonds is limited to the activity of insects, and cross‐pollination is necessary for fruit development. Currently, honey bees and wild bee populations are declining considerably due to multiple causes, such as the use of pesticides, diseases and habitat loss. An alternative to increase the almond production is the use of commercial pollinators. In this long‐term (3 years) study, the effect of the introduction of Bombus terrestris colonies on almond production was evaluated in two orchards. Two experimental designs were carried out to study the best management of this pollinator. For 2 years, all bumble bee colonies were placed in the middle of the plot and during the last year, the bumble bee colonies were distributed homogenously in the plot. Fruit set and the foraging behaviour of bumble bees during the blossoming period was determined, and the effect of different environmental variables on the visitation rate of bumble bees was assessed by means of a generalized linear mixed model (GLMM). Moreover, for the first time, the spatial distribution of fruit set was evaluated. Our results show that fruit set was significantly higher in the fields where B. terrestris had been introduced than in the control plots. This increased production resulted in a positive economic balance for the farmer. Moreover, bumble bees showed to prefer trees in a southwest orientation that were close to their colony. The activity of bumble bees showed to be significantly influenced by wind speed (the higher the speed the more flowers are visited by B. terrestris) and time after flowering (visitation rate decreased with days after flowering). In order to improve its management and obtain the highest possible almond production, it is important to understand the activity and behaviour of this pollinator.     

Modelling time‐varying low‐temperature‐induced mortality rates for pupae of Tuta absoluta (Gelechiidae,Lepidoptera)

In a series of laboratory experiments, acclimated pupae of Tuta absoluta were exposed to various constant low temperatures in order to estimate their maximum survival times (Kaplan–Meier, Lt_99.99). A Weibull function was fitted to the data points, describing maximum survival time as a function of temperature. In another experiment at ?6°C, the progress of mortality increasing with exposure time was identified. These values were fitted by a sigmoidal function converging asymptotically to 100% mortality for very long exposure times. Analysing mortality data from the maximum survival experiment by a generalized linear model showed a significant common slope parameter (p < .001) that reveals parallelism of the survival curves at each temperature if a log time axis is used. These curves appear stretched (time scaled) if plotted with a nonlogarithmic time axis. By combining these mathematical relations, it was possible to calculate a species‐specific ‘mortality surface’ which exhibits mortalities, depending on temperature and duration of exposure. In order to accumulate hourly mortalities for courses of varying temperatures, an algorithm was developed which yields mortality values from that surface taking into account the attained mortality level. In validation experiments, recorded mortalities were compared against modelled mortalities. Prediction of mortality was partially supported by the model, but pupae experiencing intensely fluctuating temperatures showed decreased mortality, probably caused by rapid cold hardening during exposure. Despite this observation, mortality data converged to distinct levels very close to 100% depending on the intensity of temperature fluctuations that were characteristic for different types of experiments. The highest mortality limit occurred at intensely fluctuating temperatures in laboratory experiments. This constituted a benchmark that was not reached under various field conditions. Thus, it was possible to identify temperature limits for the extinction of field populations of Tuta absoluta pupae.     

Haemolymph ecdysteroids in the solitary and gregarious larvae of Schistocerca gregaria

In the penultimate and last instar larvae of Schistocerca gregaria, 20-hydroxyecdysone (20E) makes up 74–84% of detected ecdysteroids in the females, and 63–74% in the males. Remaining ecdysteroids include ecdysone, a compound with HPLC and TLC retention times of makisterone A, and highly polar metabolites. Except for the last instar females, the contents of ecdysone and the unknown compound are higher in the solitary phase, while that of polar metabolites is higher in the gregarious phase. The phases also differ in that the molt-inducing ecdysteroid peaks last longer in the gregarious than in the solitary larvae. Peak concentrations reach 3.0–4.0 μg 20E equiv./ml in penultimate female instar, 2.5–3.0 μg/ml in penultimate male instar, and 1.5–2.0 μg/ml in the last larval instar of both sexes. © 1996 Wiley-Liss, Inc.