ICAT: a novel algorithm to robustly identify cell states following perturbations in single cell transcriptomes

IOS-1656752 - National Science FoundationFirst author draf

Metabolic variability in seafloor brines revealed by carbon and sulphur dynamics

Brine fluids that upwell from deep, hot reservoirs below the sea bed supply the sea floor with energy-rich substrates and nutrients that are used by diverse microbial ecosystems. Contemporary hypersaline environments formed by brine seeps may provide insights into the metabolism and distribution of microorganisms on the early Earth or on extraterrestrial bodies. Here we use geochemical and genetic analyses to characterize microbial community composition and metabolism in two seafloor brines in the Gulf of Mexico: an active mud volcano and a quiescent brine pool. Both brine environments are anoxic and hypersaline. However, rates of sulphate reduction and acetate production are much higher in the brine pool, whereas the mud volcano supports much higher rates of methane production. We find no evidence of anaerobic oxidation of methane, despite high methane fluxes at both sites. We conclude that the contrasting microbial community compositions and metabolisms are linked to differences in dissolved-organic-matter input from the deep subsurface and different fluid advection rates between the two sites. DOI: 10.1038/NGEO47

Examples of sequence conservation analyses capture a subset of mouse long non-coding RNAs sharing homology with fish conserved genomic elements

Background: Long non-coding RNAs (lncRNA) are a major class of non-coding RNAs. They are involved in diverse intra-cellular mechanisms like molecular scaffolding, splicing and DNA methylation. Through these mechanisms they are reported to play a role in cellular differentiation and development. They show an enriched expression in the brain where they are implicated in maintaining cellular identity, homeostasis, stress responses and plasticity. Low sequence conservation and lack of functional annotations make it difficult to identify homologs of mammalian lncRNAs in other vertebrates. A computational evaluation of the lncRNAs through systematic conservation analyses of both sequences as well as their genomic architecture is required.Results: Our results show that a subset of mouse candidate lncRNAs could be distinguished from random sequences based on their alignment with zebrafish phastCons elements. Using ROC analyses we were able to define a measure to select significantly conserved lncRNAs. Indeed, starting from ~2,800 mouse lncRNAs we could predict that between 4 and 11% present conserved sequence fragments in fish genomes. Gene ontology (GO) enrichment analyses of protein coding genes, proximal to the region of conservation, in both organisms highlighted similar GO classes like regulation of transcription and central nervous system development. The proximal coding genes in both the species show enrichment of their expression in brain. In summary, we show that interesting genomic regions in zebrafish could be marked based on their sequence homology to a mouse lncRNA, overlap with ESTs and proximity to genes involved in nervous system development.Conclusions: Conservation at the sequence level can identify a subset of putative lncRNA orthologs. The similar protein-coding neighborhood and transcriptional information about the conserved candidates provide support to the hypothesis that they share functional homology. The pipeline herein presented represents a proof of principle showing that a portion between 4 and 11% of lncRNAs retains region of conservation between mammals and fishes. We believe this study will result useful as a reference to analyze the conservation of lncRNAs in newly sequenced genomes and transcriptomes. \uc2\ua9 2013 Basu et al.; licensee BioMed Central Ltd

Role of nucleus accumbens core but not shell in incubation of methamphetamine craving after voluntary abstinence

We recently introduced an animal model to study incubation of drug craving after prolonged voluntary abstinence, mimicking the human condition of relapse after successful contingency management treatment. Here we studied the role of the nucleus accumbens (NAc) in this model. We trained rats to self-administer a palatable solution (sucrose+maltodextrin 1%, 6 h/day, 6 days) and methamphetamine (6 h/day, 12 days). We then evaluated relapse to methamphetamine seeking after 1 and 15 days of voluntary abstinence, achieved via a discrete choice procedure between the palatable solution and methamphetamine (14 days). We used RNAscope in-situ hybridization to quantify the co-labeling of the neuronal activity marker Fos, and dopamine Drd1- and Drd2-expressing medium spiny neurons (MSNs) in NAc core and shell during the incubation tests. Next, we determined the effect of pharmacological inactivation of NAc core and shell by either GABAA and GABAB agonists (muscimol+baclofen, 50+50 ng/side), Drd1-Drd2 antagonist (flupenthixol, 10 µg/side) or the selective Drd1 or Drd2 antagonists (SCH39166 1.0 µg/side or raclopride 1.0 µg/side) during the relapse tests. Incubated methamphetamine seeking after voluntary abstinence was associated with a selective increase of Fos expression in the NAc core, but not shell, and Fos was co-labeled with both Drd1- and Drd2-MSNs. NAc core, but not shell, injections of muscimol+baclofen, flupenthixol, SCH39166, and raclopride reduced methamphetamine seeking after 15 days of abstinence. Together, our results suggest that dopamine transmission through Drd1 and Drd2 in NAc core is critical to the incubation of methamphetamine craving after voluntary abstinence

Long Lamai community ICT4D E‐commerce system modelling: an agent oriented role‐based approach

This paper presents the post‐mortem report upon completion of the Long Lamai e‐commerce development project. Some weaknesses with regards to the current software modelling approach are identified and an alternative role‐based approach is proposed. We argue that the existing software modelling technique is not suitable for modelling, making it difficult to establish a good contract between stakeholders causing delays in the project delivery. The role‐based approach is able to explicitly highlight the responsibilities among stakeholders, while also forming the contract agreement among them leading towards sustainable ICT4D

Eventdisplay: An Analysis and Reconstruction Package for Ground-based Gamma-ray Astronomy

Eventdisplay is a reconstruction and analysis pipeline for data of Imaging Atmospheric Cherenkov Telescopes (IACT). It has been primarily developed for VERITAS and CTA analysis. Code, analysis files and scripts can be find in the Eventdisplay GitHub Organisation . Docker images are available from the Eventdisplay container registry . This release includes: prod6 analysis improvements bug fixes in cut classes used for DL2 export simplified smallest diff calculation for disp method improved documentation and FAIRness In case Eventdisplay is used in a research project, please cite the following publication: Maier, G.; Holder, J., Eventdisplay: An Analysis and Reconstruction Package for Ground-based Gamma-ray Astronomy, 35th International Cosmic Ray Conference. 10-20 July, 2017. Bexco, Busan, Korea, Proceedings of Science, Vol. 301. Online at [ https://pos.sissa.it/cgi-bin/reader/conf.cgi?confid=301 ], id.747 arXiv:1708.04048 What's Changed Prod6 analysis - patch release by @GernotMaier in https://github.com/Eventdisplay/Eventdisplay/pull/135 Bug fix in setting cut_classes for background events by @GernotMaier in https://github.com/Eventdisplay/Eventdisplay/pull/136 Create fair-software.yml by @GernotMaier in https://github.com/Eventdisplay/Eventdisplay/pull/138 Improved documentation and testing of faireness. by @GernotMaier in https://github.com/Eventdisplay/Eventdisplay/pull/139 Simplify smallest diff calculation for dispBDT reconstruction by @GernotMaier in https://github.com/Eventdisplay/Eventdisplay/pull/137 Min number of events for angular resolution by @GernotMaier in https://github.com/Eventdisplay/Eventdisplay/pull/140 Full Changelog : https://github.com/Eventdisplay/Eventdisplay/compare/v5.8.0...v5.9.