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BackgroundTools for high throughput sequencing and de novo assembly make the analysis of transcriptomes (i.e. the suite of genes expressed in a tissue) feasible for almost any organism. Yet a challenge for biologists is that it can be difficult to assign identities to gene sequences, especially from non-model organisms. Phylogenetic analyses are one useful method for assigning identities to these sequences, but such methods tend to be time-consuming because of the need to re-calculate trees for every gene of interest and each time a new data set is analyzed. In response, we employed existing tools for phylogenetic analysis to produce a computationally efficient, tree-based approach for annotating transcriptomes or new genomes that we term Phylogenetically-Informed Annotation (PIA), which places uncharacterized genes into pre-calculated phylogenies of gene families.ResultsWe generated maximum likelihood trees for 109 genes from a Light Interaction Toolkit (LIT), a collection of genes that underlie the function or development of light-interacting structures in metazoans. To do so, we searched protein sequences predicted from 29 fully-sequenced genomes and built trees using tools for phylogenetic analysis in the Osiris package of Galaxy (an open-source workflow management system). Next, to rapidly annotate transcriptomes from organisms that lack sequenced genomes, we repurposed a maximum likelihood-based Evolutionary Placement Algorithm (implemented in RAxML) to place sequences of potential LIT genes on to our pre-calculated gene trees. Finally, we implemented PIA in Galaxy and used it to search for LIT genes in 28 newly-sequenced transcriptomes from the light-interacting tissues of a range of cephalopod mollusks, arthropods, and cubozoan cnidarians. Our new trees for LIT genes are available on the Bitbucket public repository ( http://bitbucket.org/osiris_phylogenetics/pia/ ) and we demonstrate PIA on a publicly-accessible web server ( http://galaxy-dev.cnsi.ucsb.edu/pia/ ).ConclusionsOur new trees for LIT genes will be a valuable resource for researchers studying the evolution of eyes or other light-interacting structures. We also introduce PIA, a high throughput method for using phylogenetic relationships to identify LIT genes in transcriptomes from non-model organisms. With simple modifications, our methods may be used to search for different sets of genes or to annotate data sets from taxa outside of Metazoa.

Abstract Background The phyla Cnidaria, Placozoa, Ctenophora, and Porifera emerged before the split of proto- and deuterostome animals, about 600 million years ago. These early metazoans are interesting, because they can give us important information on the evolution of various tissues and organs, such as eyes and the nervous system. Generally, cnidarians have simple nervous systems, which use neuropeptides for their neurotransmission, but some cnidarian medusae belonging to the class Cubozoa (box jellyfishes) have advanced image-forming eyes, probably associated with a complex innervation. Here, we describe a new transcriptome database from the cubomedusa Tripedalia cystophora. Results Based on the combined use of the Illumina and PacBio sequencing technologies, we produced a highly contiguous transcriptome database from T. cystophora. We then developed a software program to discover neuropeptide preprohormones in this database. This script enabled us to annotate seven novel T. cystophora neuropeptide preprohormone cDNAs: One coding for 19 copies of a peptide with the structure pQWLRGRFamide; one coding for six copies of a different RFamide peptide; one coding for six copies of pQPPGVWamide; one coding for eight different neuropeptide copies with the C-terminal LWamide sequence; one coding for thirteen copies of a peptide with the RPRAamide C-terminus; one coding for four copies of a peptide with the C-terminal GRYamide sequence; and one coding for seven copies of a cyclic peptide, of which the most frequent one has the sequence CTGQMCWFRamide. We could also identify orthologs of these seven preprohormones in the cubozoans Alatina alata, Carybdea xaymacana, Chironex fleckeri, and Chiropsalmus quadrumanus. Furthermore, using TBLASTN screening, we could annotate four bursicon-like glycoprotein hormone subunits, five opsins, and 52 other family-A G protein-coupled receptors (GPCRs), which also included two leucine-rich repeats containing G protein-coupled receptors (LGRs) in T. cystophora. The two LGRs are potential receptors for the glycoprotein hormones, while the other GPCRs are candidate receptors for the above-mentioned neuropeptides. Conclusions By combining Illumina and PacBio sequencing technologies, we have produced a new high-quality de novo transcriptome assembly from T. cystophora that should be a valuable resource for identifying the neuronal components that are involved in vision and other behaviors in cubomedusae.

Background: Frailty is characterized by loss of biological reserves and is associated with an increased risk of adverse health outcomes. Frailty can be operationalized using a Frailty Index (FI) based on the accumulation of health deficits; items under health evaluation in the well-established Comprehensive Geriatric Assessment (CGA) have been used to generate an FI-CGA. Traditionally, constructing the FI-CGA has relied on paper-based recording and manual data processing. As this can be time-consuming and error-prone, it limits widespread uptake of this proven type of frailty assessment. Here, we report the development of an electronic tool, the eFI-CGA, for use on personal computers by frontline healthcare providers, to collect CGA data and automate FI-CFA calculation. The ultimate goal is to support early identification and management of frailty at points-of-care, and make uptake in Electronic Medical Records (EMR) feasible and transparent.Methods: An electronic CGA (eCGA) form was implemented to operate on Microsoft's WinForms platform and coded using C# programming language. Users complete the eCGA form, from which items under the CGA evaluation are automatically retrieved and processed to output an eFI-CGA score. A user-friendly interface and secured data saving methods were implemented. The software was debugged and tested using systematically designed simulation data, addressing different logic, syntax, and application errors, and then tested with clinical assessment. The user manual and manual scoring were used as ground truth to compare eFI-CGA input and automated eFI score calculations. Frontline health-provider user feedback was incorporated to improve the end-user experience.Results: The Standalone eFI-CGA software tool was developed and optimized for use on personal computers. The user interface adapted the design of paper-based CGA form to facilitate familiarity for clinical users. Compared to known scores, the software tool generated eFI-CGA scores with 100% accuracy to four decimal places. The eFI-CGA allowed secure data storage and retrieval of multiple types, including user input, completed eCGA form, coded items, and calculated eFI-CGA scores. It also permitted recording of actions requiring clinical follow-up, facilitating care planning. Application bugs were identified and resolved at various stages of the implementation, resulting in efficient system performance.Discussion: Accurate, robust, and reliable computerized frailty assessments are needed to promote effective frailty assessment and management, as a key tool in health care systems facing up to frailty. Our research has enabled the delivery of the standalone eFI-CGA software technology to empower effective frailty assessment and management by various healthcare providers at points-of-care, facilitating integrated care of older adults.

Abstract Background Opsins are G protein-coupled receptors used for both visual and non-visual photoreception, and these proteins evolutionarily date back to the base of the bilaterians. In the current sequencing age, phylogenomic analysis has proven to be a powerful tool, facilitating the increase in knowledge about diversity within the opsin subclasses and, so far, at least nine types of opsins have been identified. Within echinoderms, opsins have been studied in Echinoidea and Ophiuroidea, which do not possess proper image forming eyes, but rather widely dispersed dermal photoreceptors. However, most species of Asteroidea, the starfish, possess true eyes and studying them will shed light on the diversity of opsin usage within echinoderms and help resolve the evolutionary history of opsins. Results Using high-throughput RNA sequencing, we have sequenced and analyzed the transcriptomes of different Acanthaster planci tissue samples: eyes, radial nerve, tube feet and a mixture of tissues from other organs. At least ten opsins were identified, and eight of them were found significantly differentially expressed in both eyes and radial nerve, with R-opsin being the most highly expressed in the eye. Conclusion This study provides new important insight into the involvement of opsins in visual and nonvisual photoreception. Of relevance, we found the first indication of an r-opsin photopigment expressed in a well-developed visual eye in a deuterostome animal. Additionally, we provided tissue specific A. planci transcriptomes that will aid in future Evo Devo studies.

In 2016, a Pennsylvania Library Association Leadership Academy group, with the guidance of their mentors, was assigned to develop a podcast program featuring outstanding Pennsylvania librarians. The group of geographically dispersed librarians, representing different types of libraries, worked together to overcome their limited knowledge of podcasting. In the first few months after receiving the assignment, the team developed a method for identifying interviewees, employed freely available technology to record, edit, and host the podcast, and promoted the final podcast product, PaLAunchPod on February 1, 2017. With 6 full episodes (including a two-part episode) completed, the original podcast team entrusted its work to a new group of Leadership Academy program librarians.

Nitaret is one of the stable components of nitrogen in the nature. Nitrate compounds are highly soluble and can easily imported to the surface and groundwaters and finally lead to be polluted of them. Denitrification is one of permanent removal methods of nitrate from terrestrial and aquatic ecosystems. In this study, denitrification process and nitrate removal rate changes with time in a column experimental study was evaluated on two types of denitrification beds, first type was a mixture of bagasse and soil (30 % of the volume of bagasse and 70 % of the volume of soil) and second type was only soil without bagasse. All experiments were performed under saturation conditions (anaerobic conditions). The influent nitrate concentraion to the all beds was considered an average of 45 mg/l. With sampling of inflow and outflow of the columns, nitrate removal changes were assessed over a period of three months. The maximum percentage of nitrate removal in columns with mixture of soil and bagasse were occurred in the end of the experiment (94%) and in columns without the bagasse were ocured in the first of the experiment (89%).The results showed that sugar cane bagasse as a carbonic source can be very useful in the design of carbonic filters and denitrification walls for nitrate favorable removal of inlet concentrated solutions. Overall, the results confirm that the denitrification process is one of the main mechanisms of biological nitrate removal from anaerobic enviroments.

As a corallivore, the crown-of-thorns starfish (COTS; Acanthaster species complex), has significant impacts on coral mortality and community structure on tropical reefs throughout its Indo-Pacific range. COTS form aggregations which systematically move through and across reefs causing significant loss in hard coral cover. Previous work has shown that their behaviours on the reef are influenced by rheotaxis, olfaction and vision, with vision guiding adult animals to their coral habitat at short distances. As the compound eye of starfish grows throughout life the visual capacity of juvenile eyes is putatively less than for adult animals. Here we show this to be the case. Juvenile eyes have approximately the same visual field as adult eyes but significantly lower spatial resolution. They display negative phototaxis, as observed in adults, but we found no direct proof for the use of spatial resolution in this behaviour. Our results show that juveniles are able to use their eyes to locate their habitat: the coral reef. However, their putatively lower spatial resolution would make this visual task more difficult than for the adults. This article has an associated First Person interview with the first author of the paper.