12-h clock regulation of genetic information flow by XBP1s

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Pan, Y., Ballance, H., Meng, H., Gonzalez, N., Kim, S., Abdurehman, L., York, B., Chen, X., Schnytzer, Y., Levy, O., Dacso, C. C., McClung, C. A., O'Malley, B. W., Liu, S., & Zhu, B. 12-h clock regulation of genetic information flow by XBP1s. Plos Biology, 18(1), (2020): e3000580, doi:10.1371/journal.pbio.3000580.Our group recently characterized a cell-autonomous mammalian 12-h clock independent from the circadian clock, but its function and mechanism of regulation remain poorly understood. Here, we show that in mouse liver, transcriptional regulation significantly contributes to the establishment of 12-h rhythms of mRNA expression in a manner dependent on Spliced Form of X-box Binding Protein 1 (XBP1s). Mechanistically, the motif stringency of XBP1s promoter binding sites dictates XBP1s’s ability to drive 12-h rhythms of nascent mRNA transcription at dawn and dusk, which are enriched for basal transcription regulation, mRNA processing and export, ribosome biogenesis, translation initiation, and protein processing/sorting in the Endoplasmic Reticulum (ER)-Golgi in a temporal order consistent with the progressive molecular processing sequence described by the central dogma information flow (CEDIF). We further identified GA-binding proteins (GABPs) as putative novel transcriptional regulators driving 12-h rhythms of gene expression with more diverse phases. These 12-h rhythms of gene expression are cell autonomous and evolutionarily conserved in marine animals possessing a circatidal clock. Our results demonstrate an evolutionarily conserved, intricate network of transcriptional control of the mammalian 12-h clock that mediates diverse biological pathways. We speculate that the 12-h clock is coopted to accommodate elevated gene expression and processing in mammals at the two rush hours, with the particular genes processed at each rush hour regulated by the circadian and/or tissue-specific pathways.This study was supported by the American Diabetes Association junior faculty development award 1-18-JDF-025 to B.Z., by funding from National Institute of Health HD07879 and 1P01DK113954 to B.W.O, by funding from National Science Foundation award 1703170 to C.C.D. and B.Z., and by funding from Brockman Foundation to C.C.D and B.W.O. This work was further supported by the UPMC Genome Center with funding from UPMC’s Immunotherapy and Transplant Center. This research was supported in part by the University of Pittsburgh Center for Research Computing through the resources provided. Research reported in this publication was further supported by the National Institute of Diabetes And Digestive And Kidney Diseases of the National Institutes of Health under award number P30DK120531 to Pittsburgh Liver Research Center, in which both S.L. and B.Z. are members. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Proteomic analysis of rat serum revealed the effects of chronic sleep deprivation on metabolic, cardiovascular and nervous system

Sleep is an essential and fundamental physiological process that plays crucial roles in the balance of psychological and physical health. Sleep disorder may lead to adverse health outcomes. The effects of sleep deprivation were extensively studied, but its mechanism is still not fully understood. The present study aimed to identify the alterations of serum proteins associated with chronic sleep deprivation, and to seek for potential biomarkers of sleep disorder mediated diseases. A label-free quantitative proteomics technology was used to survey the global changes of serum proteins between normal rats and chronic sleep deprivation rats. A total of 309 proteins were detected in the serum samples and among them, 117 proteins showed more than 1.8-folds abundance alterations between the two groups. Functional enrichment and network analyses of the differential proteins revealed a close relationship between chronic sleep deprivation and several biological processes including energy metabolism, cardiovascular function and nervous function. And four proteins including pyruvate kinase M1, clusterin, kininogen1 and profilin-1were identified as potential biomarkers for chronic sleep deprivation. The four candidates were validated via parallel reaction monitoring (PRM) based targeted proteomics. In addition, protein expression alteration of the four proteins was confirmed in myocardium and brain of rat model. In summary, the comprehensive proteomic study revealed the biological impacts of chronic sleep deprivation and discovered several potential biomarkers. This study provides further insight into the pathological and molecular mechanisms underlying sleep disorders at protein level

Continuous Manufacturing of Cocrystals Using Solid State Shear Milling Technology

yesSolid state shear milling (S3M) is reported as a scalable, continuous, polymer-assisted cocrystallization technique. A specially designed milling pan was employed to provide high levels of applied shear, and the addition of a polymeric processing aid enabled generation of high stress fields. Carbamazepine–salicylic acid cocrystals were produced with 5–25 wt % of poly(ethylene oxide) (PEO). A systematic study was carried out to understand the effect of process variables on properties and performance of the cocrystals. S3M offers an important new route for continuous manufacturing of pharmaceutical cocrystals

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Circadian regulation and phytohormone responses of cytochrome P450 monooxygenase genes in Arabidopsis

Plant growth and development are regulated by both hormone and circadian signaling pathways. The growing number of signaling molecules whose syntheses are circadian-regulated (e.g. jasmonic acid, auxin) and the time-of-day-specific transcripts of cytochrome P450 monooxygenases (P450s) involved in their syntheses and catabolisms suggest an interactions between hormone signaling network and circadian signaling network. The first phase of my research profiled a total of 98 P450 genes in Arabidopsis thaliana as circadian-regulated at a transcriptional level under varying photoperiod and thermocycle conditions, and demonstrated that P450s involved in phenylpropanoid, carotenoid, oxylipin, glucosinolate and brassinosteroid biosynthese pathways are circadian-regulated. The next phase of my research investigated the circadian rhythms of P450 genes under different phytohormone treatments including methyl jasmonate (MeJ), salicylic acid (SA), abscisic acid (ABA) and indole-3-acetic acid (IAA). My analysis of transcript profiles of seedlings treated with individual hormones indicated the responses of many P450 genes to these hormone treatments are gated by circadian clock. And different hormone inductions also provided feedback to the circadian clock of P450 gene expressions by affecting their phase, amplitude, period and precision. In silico cis-element analyses of co-regulated promoters in different pathways identified that many known elements including Evening Element, CCA1 Binding Site and G-Box variant elements, as well as some novel elements including JA1 and TRP1 were over-represented and likely to be important in circadian regulation and/or hormone induction. The third phase of my research focused on the bHLH transcription factor MYC2, which plays a critical role in JA signaling and its crosstalk with many other stresses. Analysis of myc2 knockout plants confirmed that MYC2 positively regulated the JA pathway and negatively regulated the IG pathway, and that the MeJ responses of JA signaling genes were only moderately reduced in the mutant seedlings. The work suggests that there are transcription factors other than MYC2 playing a major role in regulating the responses to MeJ. Three closely related genes MYC3, MYC4 and MYC5 were found to bind to the same DNA binding sites as MYC2, which might play different roles, in concert with MYC2 in the integration of JA-signaling to control both circadian and hormone response processes

Identification of the proteome complement of hypopharyngeal glands from two strains of honeybees (Apis mellifera)

We investigated the protein complement of the hypopharyngeal gland (HG) of winter worker bees from a strain of Apis mellifera artificially selected for increased royal jelly yield and A. m. carnica winter worker bees. Proteins were partially identified using two-dimensional gel electrophoresis (2-DE). MALDI-TOF MS and protein engine identification tools that were utilized for the honeybee genome. Most identified proteins in the two bees strains were assigned to major royal jelly (RJ) proteins (MRJPs). Marked differences were found in the heterogeneity of the MRJPs, in particular MRJP3. Two of the proteins, $\alpha$-glucosidase and glucose oxidase, were related to carbohydrate metabolism and energy. For the first time in the HG of honeybees, two proteins, peroxiredoxin and thioredoxin peroxidase, which are related to antioxidation functions, and actin 5C, a major cytoskeletal actin protein which may supply enough actin for normal function of cells, have been identified. Results suggest that the HGs serve a storage function in winter and that during the winter period the HG of high RJ producing bees store more proteins than those of Carnica bees

Improved carrier phase shift modulation and voltage equalization control strategy in modular multilevel converter

In order to solve the problem of traditional carrier phase-shift modulation with multiple ratios or PI controllers and cumbersome tuning parameters, this paper uses improved carrier phase-shift modulation. The total turn-on number of sub-modules each bridge arm is determined by comparing the sinusoidal modulated wave with the triangular carrier, and then the control signal is generated according to the capacitance voltage sorting result and the bridge arm current polarity. However, this modulation method uses a sorting method that causes the insulated gate bipolar transistor (IGBT) have an excessively high switching frequency. Therefore, a sorting trigger condition that can effectively reduce the switching frequency is used. The method determines whether to reorder based on the error between the voltage average and the actual value. For the circulation problem, the double-frequency negative sequence component is extracted by rotating coordinate transformation, and it is suppressed by PI control. A 21-level MMC model was built in MATLAB/simulink to analyze the sub-module capacitor voltage fluctuation, output current, voltage distortion rate and bridge arm circulation. It is verified that the modulation method can combine the sorting algorithm and circulation suppression method at the same time, and has better voltage equalization and circulation suppression effects

Identification of the proteome complement of high royal jelly producing bees (Apis mellifera) during worker larval development

To investigate the composition and function of the proteome during larval development of worker bees from a strain of Apis mellifera L. artificially selected for increased royal jelly yield, proteins were partially identified by two-dimensional gel electrophoresis, mass spectrometry and protein engine identification tools that were applied to the honeybee genome. Out of 48 high abundance proteins selected for MS fingerprinting, 22 could be identified as representing annotated genes of the honey bee. These including 9 nutrient related proteins, 6 proteins associated with carbohydrate metabolism and energy production, 3 heat shock proteins, 4 other proteins related to the metabolism of amino acids, fatty acid metabolism, larval growth and cell cycle, respectively