Additional file 1: of Systems-epigenomics inference of transcription factor activity implicates aryl-hydrocarbon-receptor inactivation as a key event in lung cancer development

Additional file containing all Additional file 1: Figures S1–S10 and Table S2. (PDF 1142 kb

Putative global minima for hydrated sulfite ions with 1-20 water molecules. from Isomers and energy landscapes of micro-hydrated sulfite and chlorate clusters

Putative GM structures and energies in kcal/mol for sulfite ions with 1-20 water molecules in XYZ format

Low energy minima in the chlorate + 8H2O landscape from Isomers and energy landscapes of micro-hydrated sulfite and chlorate clusters

Structures and energies in kcal/mol for pictured low energy minima in the landscape for chlorate ions with 8 water molecules in XYZ format

Reliable Tracking In-Solution Protein Unfolding via Ultrafast Thermal Unfolding/Ion Mobility-Mass Spectrometry

Sequential unfolding of monomeric proteins is important for the global understanding of local conformational elements (e.g., secondary structures and domain connections) within those protein assemblies. Ion mobility-mass spectrometry (IM-MS) is an emerging and promising technique for probing gradual protein structural perturbations in the gas phase. However, it is still challenging to track sequential unfolding in the solution phase. Here, we extended IM-MS to track in-solution sequential unfolding of monomeric proteins having single and/or multidomains. The present method combines ultrafast local heating effect (LHE)-driven sequential unfolding with IM-MS identification. Protein sequential unfolding in solution is demonstrated by the rapid and controllable IM-MS data switch between native and gradually unfolded states. Our results show that LHE induces gradual protein conformational transitions associated with biological functions, where IM-MS tracks the sequential unfolding of monomeric proteins

MOESM2 of Tissue-independent and tissue-specific patterns of DNA methylation alteration in cancer

Additional file 2. Pdf document containing all Supplementary Figures S1–11, as well as Supplementary Table S2

Quantitative RT-PCR Gene Evaluation and RNA Interference in the Brown Marmorated Stink Bug

<div><p>The brown marmorated stink bug (<i>Halyomorpha halys</i>) has emerged as one of the most important invasive insect pests in the United States. Functional genomics in <i>H</i>. <i>halys</i> remains unexplored as molecular resources in this insect have recently been developed. To facilitate functional genomics research, we evaluated ten common insect housekeeping genes (<i>RPS26</i>, <i>EF1A</i>, <i>FAU</i>, <i>UBE4A</i>, <i>ARL2</i>, <i>ARP8</i>, <i>GUS</i>, <i>TBP</i>, <i>TIF6</i> and <i>RPL9</i>) for their stability across various treatments in <i>H</i>. <i>halys</i>. Our treatments included two biotic factors (tissues and developmental stages) and two stress treatments (RNAi injection and starvation). Reference gene stability was determined using three software algorithms (geNorm, NormFinder, BestKeeper) and a web-based tool (RefFinder). The qRT-PCR results indicated <i>ARP8</i> and <i>UBE4A</i> exhibit the most stable expression across tissues and developmental stages, <i>ARL2</i> and <i>FAU</i> for dsRNA treatment and <i>TBP</i> and <i>UBE4A</i> for starvation treatment. Following the dsRNA treatment, all genes except <i>GUS</i> showed relatively stable expression. To demonstrate the utility of validated reference genes in accurate gene expression analysis and to explore gene silencing in <i>H</i>. <i>halys</i>, we performed RNAi by administering dsRNA of target gene (catalase) through microinjection. A successful RNAi response with over 90% reduction in expression of target gene was observed.</p></div

RefFinder ranking of eight candidate reference genes for for qRT-PCR studies in brown marmorated stink bug.

<p>RefFinder ranking of eight candidate reference genes for for qRT-PCR studies in brown marmorated stink bug.</p

Comparisons of RNAi related genes among <i>D. melanogaster</i> and <i>G. nigrifrons</i>.

<p>Comparisons of RNAi related genes among <i>D. melanogaster</i> and <i>G. nigrifrons</i>.</p

Assembly, Morphology, Diffusivity, and Indentation of Hydrogel-Supported Lipid Bilayers

Recognizing the limitations of solid-supported lipid bilayers to reproduce the behavior of cell membranes, including bendability, transmembrane protein inclusion, and virus entry, this study describes a novel biomimetic system for cell membranes with the potential to overcome these and other limitations. The developed strategy utilizes a hydrogel with tunable mechanical behavior that resembles those of living cells as the soft support for the phospholipid bilayer, while a polyelectrolyte multilayer film serves as an intermediate layer to facilitate the self-assembly of the lipid bilayer on the soft cushion. Quartz crystal microbalance studies show that, upon coming into contact with the polyelectrolyte film, vesicles fuse and rupture to yield a robust lipid bilayer. Fluorescence recovery after photobleaching confirms the formation of a membrane, while atomic force microscopy shows a low adhesion between the indenting probe and the bilayer. More importantly, in comparison to the solid-supported lipid bilayer, the response of this biomimetic system to nanoindentation demonstrates its increased mechanical stability and bendability when assembled on a soft cushion. Hence, the developed hydrogel-supported lipid bilayers can mimic biomechanical properties of cell membranes, which will enable scientists to study and to understand biophysicochemical interactions between cell membranes and extracellular entities

Invertebrate comparative genomics.

<p>The number of significant ortholog matches (E-value <10⁻¹⁰) as well as the number of unique invertebrate transcripts for all eight pair-wise invertebrate comparisons with <i>Graminella nigrifrons.</i> These invertebrates are <i>Acyrthosiphon pisum</i> (pea aphid, order Hemiptera), <i>Apis mellifera</i> (honey bee, order Hymenoptera), <i>Nasonia vitripennis</i> (parasitic wasp, order Hymenoptera), <i>Tribolium castaneum</i> (red flour beetle, order Coleoptera), <i>Anopheles gambiae</i> (malaria mosquito, order Diptera), <i>Drosophila. melanogaster</i> (fruit fly, order Diptera), and <i>Caenorhabditis elegans</i> (soil nematode, order Rhabditida).</p