SignificanceOur study exploits time—the relatively unexplored fourth dimension of gene regulatory networks (GRNs)—to learn the temporal transcriptional logic underlying dynamic nitrogen (N) signaling in plants. We introduce several conceptual innovations to the analysis of time-series data in the area of predictive GRNs. Our resulting network now provides the “transcriptional logic” for transcription factor perturbations aimed at improving N-use efficiency, an important issue for global food production in marginal soils and for sustainable agriculture. More broadly, the combination of the time-based approaches we develop and deploy can be applied to uncover the temporal “transcriptional logic” for any response system in biology, agriculture, or medicine.

The relative importance of regulation at the mRNA versus protein level is subject to ongoing debate. To address this question in a dynamic system, we mapped proteomic and transcriptomic changes in mammalian cells responding to stress induced by dithiothreitol over 30 h. Specifically, we estimated the kinetic parameters for the synthesis and degradation of RNA and proteins, and deconvoluted the response patterns into common and unique to each regulatory level using a new statistical tool. Overall, the two regulatory levels were equally important, but differed in their impact on molecule concentrations. Both mRNA and protein changes peaked between two and eight hours, but mRNA expression fold changes were much smaller than those of the proteins. mRNA concentrations shifted in a transient, pulse‐like pattern and returned to values close to pre‐treatment levels by the end of the experiment. In contrast, protein concentrations switched only once and established a new steady state, consistent with the dominant role of protein regulation during misfolding stress. Finally, we generated hypotheses on specific regulatory modes for some genes.

doi: bioRxiv preprint first posted online Nov. 26, 2015; 2 Standfirst textUsing a new statistical tool to analyze time-series protein and matching mRNA concentration data, this study deconvoluted the contributions of mRNA and protein level regulation in the response of mammalian cells to stress of the endoplasmatic reticulum.-We quantified protein and mRNA concentrations for 3,235 genes across two replicates and time points, with a high-confidence dataset of 1,237 genes/mRNAs.-We use a new statistical tool to quantify the contribution of regulatory processes, and we find that mRNA and protein level regulation play similarly important roles.-mRNA and protein level regulation have different dynamics: mRNA concentrations spike in their change and return to pre-perturbation levels, while protein concentrations switch in their behavior and reach a new steady-state.-We generated hypotheses on modes of regulation for several groups of genes.All rights reserved. No reuse allowed without permission.(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.Thecopyright holder for this preprint . http://dx.doi.org/10.1101/032797 doi: bioRxiv preprint first posted online Nov. 26, 2015; 3 AbstractThe relative importance of regulation at the mRNA versus protein level is subject to ongoing debate. To address this question in a dynamic system, we mapped the proteomics and transcriptomics changes in mammalian cells responding to stress induced by dithiothreitol over 30 hours. Specifically, we estimated the kinetic parameters for synthesis and degradation of RNA and proteins, and deconvoluted response patterns common and unique to each regulatory level using a new statistical tool. Overall, both regulatory levels were equally important, but differed in their impact on molecule concentrations. Both mRNA and protein changes peaked between two and eight hours, but mRNA expression fold changes were much smaller than those of the proteins. Further, mRNA concentrations were regulated in a transient, spike-like pattern and returned to values close to pre-treatment levels by the end of the experiment. In contrast, protein concentrations switched only once and established a new steady state, consistent with the dominant role of protein regulation during misfolding stress. Finally, we generated hypotheses on specific regulatory modes for example groups of genes. Words: 173 (of 175 max)All rights reserved. No reuse allowed without permission.(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint . http://dx

Microbial eukaryotes (protists) are important components of terrestrial and aquatic environments, as well as animal and human microbiomes. Their relationships with metazoa range from mutualistic to parasitic and zoonotic (i.e., transmissible between humans and animals). Despite their ecological importance, our knowledge of protists in urban environments lags behind that of bacteria, largely due to a lack of experimentally validated high-throughput protocols that produce accurate estimates of protist diversity while minimizing non-protist DNA representation. We optimized protocols for detecting zoonotic protists in raw sewage samples, with a focus on trichomonad taxa. First, we investigated the utility of two commonly used variable regions of the 18S rRNA marker gene, V4 and V9, by amplifying and Sanger sequencing 23 different eukaryotic species, including 16 protist species such as Cryptosporidium parvum, Giardia intestinalis, Toxoplasma gondii, and species of trichomonad. Next, we optimized wet-lab methods for sample processing and Illumina sequencing of both regions from raw sewage collected from a private apartment building in New York City. Our results show that both regions are effective at identifying several zoonotic protists that may be present in sewage. A combination of small extractions (1 mL volumes) performed on the same day as sample collection, and the incorporation of a vertebrate blocking primer, is ideal to detect protist taxa of interest and combat the effects of metazoan DNA. We expect that the robust, standardized methods presented in our workflow will be applicable to investigations of protists in other environmental samples, and will help facilitate large-scale investigations of protistan diversity.Electronic supplementary materialThe online version of this article (doi:10.1007/s00248-017-0996-9) contains supplementary material, which is available to authorized users.

multienzyme extraction protocol that we developed, called Polyzyme or MetaPolyZyme. Presently, the XMP is characterizing sample sites around the world with the intent of discovering new species, genes, and gene clusters. Once a project site is complete, the resulting data will be publically available. Sites include Lake Hillier in Western Australia, the "Door to Hell" crater in Turkmenistan, deep ocean brine lakes of the Gulf of Mexico, deep ocean sediments from Greenland, permafrost tunnels in Alaska, ancient microbial biofilms from Antarctica, Blue Lagoon Iceland, Ethiopian toxic hot springs, and the acidic hypersaline ponds in Western Australia.