ALBERT

Description: We report the current status of the FlyBase annotated gene set for Drosophila melanogaster and highlight improvements based on high-throughput data. The FlyBase annotated gene set consists entirely of manually annotated gene models, with the exception of some classes of small non-coding RNAs. All gene models have been reviewed using evidence from high-throughput datasets, primarily from the modENCODE project. These datasets include RNA-Seq coverage data, RNA-Seq junction data, transcription start site profiles, and translation stop-codon read-through predictions. New annotation guidelines were developed to take into account the use of the high-throughput data. We describe how this flood of new data was incorporated into thousands of new and revised annotations. FlyBase has adopted a philosophy of excluding low-confidence and low-frequency data from gene model annotations; we also do not attempt to represent all possible permutations for complex and modularly organized genes. This has allowed us to produce a high-confidence, manageable gene annotation dataset that is available at FlyBase ( http://flybase.org ). Interesting aspects of new annotations include new genes (coding, non-coding, and antisense), many genes with alternative transcripts with very long 3' UTRs (up to 15–18 kb), and a stunning mismatch in the number of male-specific genes (approximately 13% of all annotated gene models) vs. female-specific genes (less than 1%). The number of identified pseudogenes and mutations in the sequenced strain also increased significantly. We discuss remaining challenges, for instance, identification of functional small polypeptides and detection of alternative translation starts.

Description: In the context of the FlyBase annotated gene models in Drosophila melanogaster , we describe the many exceptional cases we have curated from the literature or identified in the course of FlyBase analysis. These range from atypical but common examples such as dicistronic and polycistronic transcripts, noncanonical splices, trans -spliced transcripts, noncanonical translation starts, and stop-codon readthroughs, to single exceptional cases such as ribosomal frameshifting and HAC1-type intron processing. In FlyBase, exceptional genes and transcripts are flagged with Sequence Ontology terms and/or standardized comments. Because some of the rule-benders create problems for handlers of high-throughput data, we discuss plans for flagging these cases in bulk data downloads.

Description: One dimensional atmospheric boundary layer (ABL) model coupled with detailed atmospheric chemistry and aerosol dynamical model, the model SOSAA, was used to predict the ABL and detailed aerosol population (characterized by the number size distribution) time evolution. The model was applied over a period of ten days in May 2013 for a pine forest site in southern Finland. The period was characterized by frequent new particle formation events and simultaneous intensive aerosol transformation. Throughout this study we refer to nucleation, condensational growth and coagulation as aerosol dynamical processes, i.e. the processes that govern the particle size distribution evolution. The aim of the study was to analyze and quantify the role of aerosol and ABL dynamics in vertical transport of aerosols. It was of particular interest to what extent the fluxes above canopy deviate due to above mentioned processes from the particle dry deposition on the canopy foliage. The model simulations revealed that the particle concentration change due to aerosol dynamics can frequently exceed the effect of particle deposition even an order of magnitude or more. The impact is however strongly dependent on particle size and time. In spite of the fact that the time scale of turbulent transfer inside canopy is much smaller than the time scales of aerosol dynamics and dry deposition, letting to assume well mixed properties of air, the fluxes at the canopy top frequently deviate from deposition inside forest. This is due to transformation of aerosol concentration throughout the ABL and resulting complicated pattern of vertical transport. Therefore we argue that the comparison of time scales of aerosol dynamics and deposition defined for the processes below the flux measurement level do not unambiguously describe the importance of aerosol dynamics for vertical transport within canopy. We conclude that under dynamical conditions the micrometeorological particle flux measurements such as performed by the eddy covariance technique do not generally represent the dry deposition. The deviation can be systematic for certain size ranges so that the conclusion applies also to time averaged particle fluxes.