Evidence for a major role of antisense RNAs in cyanobacterial gene regulation

Information on the numbers and functions of naturally occurring antisense RNAs (asRNAs) in eubacteria has thus far remained incomplete. Here, we screened the model cyanobacterium Synechocystis sp. PCC 6803 for asRNAs using four different methods. In the final data set, the number of known noncoding RNAs rose from 6 earlier identified to 60 and of asRNAs from 1 to 73 (28 were verified using at least three methods). Among these, there are many asRNAs to housekeeping, regulatory or metabolic genes, as well as to genes encoding electron transport proteins. Transferring cultures to high light, carbon-limited conditions or darkness influenced the expression levels of several asRNAs, suggesting their functional relevance. Examples include the asRNA to rpl1, which accumulates in a light-dependent manner and may be required for processing the L11 r-operon and the SyR7 noncoding RNA, which is antisense to the murF 5′ UTR, possibly modulating murein biosynthesis. Extrapolated to the whole genome, ∼10% of all genes in Synechocystis are influenced by asRNAs. Thus, chromosomally encoded asRNAs may have an important function in eubacterial regulatory networks

Elements of the heterocyst-specific transcriptome unraveled by co-expression analysis in Nostoc sp. PCC 7120 [Dataset]

Supplementary data file 1 “genomeplot_WT_hetR_-N_chromosome.pdf”. Overview (chromosome) combining log2-normalized expression values (left y axis) from the microarray analysis of cultures of wild type and hetR strain subjected to nitrogen deprivation for 0-6-12-24 hours as indicated by coloured lines, with the reads numbers from the RNA-Seq dataset in (Mitschke, J., Vioque, A., Haas, F., Hess, W.R., and Muro-Pastor, A.M. (2011). Dynamics of transcriptional start site selection during nitrogen stress-induced cell differentiation in Anabaena sp. PCC7120. Proc. Natl. Acad. Sci. USA 108, 20130-20135) (right y axis). Supplementary data file 2 “genomeplot_WT_hetR_-N_plasmids.pdf”. Overview (six plasmids combined) combining log2-normalized expression values (left y axis) from the microarray analysis of cultures of wild type and hetR strain subjected to nitrogen deprivation for 0-6-12-24 hours as indicated by coloured lines, with the reads numbers from the RNA-Seq dataset in (Mitschke, J., Vioque, A., Haas, F., Hess, W.R., and Muro-Pastor, A.M. (2011). Dynamics of transcriptional start site selection during nitrogen stress-induced cell differentiation in Anabaena sp. PCC7120. Proc. Natl. Acad. Sci. USA 108, 20130-20135) (right y axis). Supplementary data file 3 “genomeplot_WT_+N_-N_chromosome.pdf”. Overview (chromosome) combining log2-normalized expression values (left y axis) from the microarray analysis of cultures of wild type at 0 and 8 h after nitrogen depletion and at 0 and 8 h after NH4 addition as indicated by coloured lines, with the reads numbers from the RNA-Seq dataset in (Mitschke, J., Vioque, A., Haas, F., Hess, W.R., and Muro-Pastor, A.M. (2011). Dynamics of transcriptional start site selection during nitrogen stress-induced cell differentiation in Anabaena sp. PCC7120. Proc. Natl. Acad. Sci. USA 108, 20130-20135) (right y axis). Supplementary data file 4 “genomeplot_WT_+N_-N_plasmids.pdf”. Overview (six plasmids combined) combining log2-normalized expression values (left y axis) from the microarray analysis of cultures of wild type at 0 and 8 h after nitrogen depletion and at 0 and 8 h after NH4 addition as indicated by coloured lines, with the reads numbers from the RNA-Seq dataset in (Mitschke, J., Vioque, A., Haas, F., Hess, W.R., and Muro-Pastor, A.M. (2011). Dynamics of transcriptional start site selection during nitrogen stress-induced cell differentiation in Anabaena sp. PCC7120. Proc. Natl. Acad. Sci. USA 108, 20130-20135) (right y axis). Supplementary data file 5 “Co-expression network”. Cytoscape (www.cytoscape.org) file corresponding to the co-expression network constructed.Peer reviewe

Finding Auxetic Frameworks in Periodic Tessellations

It appears that most models for micro-structured materials with auxetic deformations were found by clever intuition, possibly combined with optimization tools, rather than by systematic searches of existing structure archives. Here we review our recent approach of finding micro-structured materials with auxetic mechanisms within the vast repositories of planar tessellations. This approach has produced two previously unknown auxetic mechanisms, which have Poisson's ratio νss = -1 when realized as a skeletal structure of stiff incompressible struts pivoting freely at common vertices. One of these, baptized Triangle-Square Wheels, has been produced as a linear-elastic cellular structure from Ti-6Al-4V alloy by selective electron beam melting. Its linear-elastic properties were measured by tensile experiments and yield an effective Poisson's ratio νLE ≈ -0.75, also in agreement with finite element modeling. The similarity between the Poisson's ratios νSS of the skeletal structure and νLE of the linear-elastic cellular structure emphasizes the fundamental role of geometry for deformation behavior, regardless of the mechanical details of the system. The approach of exploiting structure archives as candidate geometries for auxetic materials also applies to spatial networks and tessellations and can aid the quest for inherently three-dimensional auxetic mechanisms

Murine Oncostatin M Has Opposing Effects on the Proliferation of OP9 Bone Marrow Stromal Cells and NIH/3T3 Fibroblasts Signaling through the OSMR

The IL-6 family cytokine Oncostatin M (OSM) is involved in cell development, growth, hematopoiesis, inflammation, and cancer. Intriguingly, OSM has proliferative and antiproliferative effects depending on the target cell. The molecular mechanisms underlying these opposing effects are not fully understood. Previously, we found OSM upregulation in different myeloproliferative syndromes. However, OSM receptor (OSMR) expression was detected on stromal cells but not the malignant cells themselves. In the present study, we, therefore, investigated the effect of murine OSM (mOSM) on proliferation in stromal and fibroblast cell lines. We found that mOSM impairs the proliferation of bone marrow (BM) stromal cells, whereas fibroblasts responded to mOSM with increased proliferation. When we set out to reveal the mechanisms underlying these opposing effects, we detected increased expression of the OSM receptors OSMR and LIFR in stromal cells. Interestingly, Osmr knockdown and Lifr overexpression attenuated the OSM-mediated effect on proliferation in both cell lines indicating that mOSM affected the proliferation signaling mainly through the OSMR. Furthermore, mOSM induced activation of the JAK-STAT, PI3K-AKT, and MAPK-ERK pathways in OP9 and NIH/3T3 cells with differences in total protein levels between the two cell lines. Our findings offer new insights into the regulation of proliferation by mOSM