Individual MicroRNAs (miRNAs) Display Distinct mRNA Targeting Rules

MicroRNAs (miRNAs) guide Argonaute (AGO)-containing microribonucleoprotein (miRNP) complexes to target mRNAs.It has been assumed that miRNAs behave similarly to each other with regard to mRNA target recognition. The usual assumptions, which are based on prior studies, are that miRNAs target preferentially sequences in the 3\u27UTR of mRNAs,guided by the 5\u27 seed portion of the miRNAs. Here we isolated AGO- and miRNA-containing miRNPs from human H4 tumor cells by co-immunoprecipitation (co-IP) with anti-AGO antibody. Cells were transfected with miR-107, miR-124,miR-128, miR-320, or a negative control miRNA. Co-IPed RNAs were subjected to downstream high-density Affymetrix Human Gene 1.0 ST microarray analyses using an assay we validated previously-a RIP-Chip experimental design. RIP-Chip data provided a list of mRNAs recruited into the AGO-miRNP in correlation to each miRNA. These experimentally identified miRNA targets were analyzed for complementary six nucleotide seed sequences within the transfected miRNAs. We found that miR-124 targets tended to have sequences in the 3\u27UTR that would be recognized by the 5\u27 seed of miR-124, as described in previous studies. By contrast, miR-107 targets tended to have \u27seed\u27 sequences in the mRNA open reading frame, but not the 3\u27 UTR. Further, mRNA targets of miR-128 and miR-320 are less enriched for 6-mer seed sequences in comparison to miR-107 and miR-124. In sum, our data support the importance of the 5\u27 seed in determining binding characteristics for some miRNAs; however, the binding rules are complex, and individual miRNAs can have distinct sequence determinants that lead to mRNA targeting

Mid Infrared Properties of Low Metallicity Blue Compact Dwarf Galaxies From Spitzer/IRS

We present a {\em Spitzer}-based mid-infrared study of a large sample of Blue Compact Dwarf galaxies (BCD) using the Infrared Spectrograph (IRS), including the first mid-IR spectrum of IZw18, the archetype for the BCD class and among the most metal poor galaxies known. We show the spectra of Polycyclic Aromatic Hydrocarbon (PAH) emission in low-metallicity environment. We find that the equivalent widths (EW) of PAHs at 6.2, 7.7, 8.6 and 11.2 $\mu$m are generally weaker in BCDs than in typical starburst galaxies and that the fine structure line ratio, [NeIII]/[NeII], has a weak anti-correlation with the PAH EW. A much stronger anti-correlation is shown between the PAH EW and the product of the [NeIII]/[NeII] ratio and the UV luminosity density divided by the metallicity. We conclude that PAH EW in metal-poor high-excitation environments is determined by a combination of PAH formation and destruction effects.Comment: 41 pages, 14 figure

Modulation of synaptic function by VAC14, a protein that regulates the phosphoinositides PI(3,5)P 2 and PI(5)P

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/102191/1/embj2012200.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/102191/2/embj2012200-sup-0001.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/102191/3/embj2012200-reviewer_comments.pd

Probing the excitation of extreme starbursts: high-resolution mid-infrared spectroscopy of blue compact dwarfs

We present an analysis of the mid-infrared emission lines for a sample of 12 low-metallicity blue compact dwarf (BCD) galaxies based on high-resolution observations obtained with Infrared Spectrograph on board the Spitzer Space Telescope. We compare our sample with a local sample of typical starburst galaxies and active galactic nuclei (AGNs) to study the ionization field of starbursts over a broad range of physical parameters and examine its difference from the one produced by the AGN. The high-ionization line [O IV]25.89 μm is detected in most of the BCDs, starbursts, and AGNs in our sample. We propose a diagnostic diagram of the line ratios [O IV]25.89 μm/[S III]33.48 μm as a function of [Ne III]15.56 μm/[Ne II]12.81 μm which can be useful in identifying the principal excitation mechanism in a galaxy. Galaxies in this diagram split naturally into two branches. Classic AGNs as well as starburst galaxies with an AGN component populate the upper branch, with stronger AGNs displaying higher [Ne III]/[Ne II] ratios. BCDs and pure starbursts are located in the lower branch. We find that overall the placement of galaxies on this diagram correlates well with their corresponding locations in the log([N II]/Hα) versus log([O III]/Hβ) diagnostic diagram, which has been widely used in the optical. The two diagrams provide consistent classifications of the excitation mechanism in a galaxy. On the other hand, the diagram of [Ne III]15.56 μm/[Ne II]12.81 μm versus [S IV]10.51 μm/[S III]18.71 μm is not as efficient in separating AGNs from BCDs and pure starbursts. Our analysis demonstrates that BCDs in general do display higher [Ne III]/[Ne II] and [S IV]/[S III] line ratios than starbursts, with some reaching values even higher than those found at the centers of AGNs.Despite their hard radiation field though, no [Ne V]14.32μmemission has been detected in the BCDs of our sample

Exposed CendR Domain in Homing Peptide Yields Skin-Targeted Therapeutic in Epidermolysis Bullosa

Systemic skin-selective therapeutics would be a major advancement in the treatment of diseases affecting the entire skin, such as recessive dystrophic epidermolysis bullosa (RDEB), which is caused by mutations in the COL7A1 gene and manifests in transforming growth factor-beta (TGF-beta)-driven fibrosis and malignant transformation. Homing peptides containing a C-terminal R/KXXR/K motif (C-end rule [CendR] sequence) activate an extravasation and tissue penetration pathway for tumor-specific drug delivery. We have previously described a homing peptide CRKDKC (CRK) that contains a cryptic CendR motif and homes to angiogenic blood vessels in wounds and tumors, but it cannot penetrate cells or tissues. In this study, we demonstrate that removal of the cysteine from CRK to expose the CendR sequence confers the peptide novel ability to home to normal skin. Fusion of the truncated CRK (tCRK) peptide to the C terminus of an extracellular matrix protein de-corin (DCN), a natural TGF-beta inhibitor, resulted in a skin-homing therapeutic molecule (DCN-tCRK). Systemic DCN-tCRK administration in RDEB mice led to inhibition of TGF-beta signaling in the skin and significant improvement in the survival of RDEB mice. These results suggest that DCN-tCRK has the potential to be utilized as a novel therapeutic compound for the treatment of dermatological diseases such as RDEB.Peer reviewe

A Spitzer high resolution mid-infrared spectral atlas of starburst galaxies

We present an atlas of Spitzer/IRS high resolution (R~600) 10-37um spectra for 24 well known starburst galaxies. The spectra are dominated by fine-structure lines, molecular hydrogen lines, and emission bands of polycyclic aromatic hydrocarbons. Six out of the eight objects with a known AGN component show emission of the high excitation [NeV] line. This line is also seen in one other object (NGC4194) with, a priori, no known AGN component. In addition to strong polycyclic aromatic hydrocarbon emission features in this wavelength range (11.3, 12.7, 16.4um), the spectra reveal other weak hydrocarbon features at 10.6, 13.5, 14.2um, and a previously unreported emission feature at 10.75um. An unidentified absorption feature at 13.7um is detected in many of the starbursts. We use the fine-structure lines to derive the abundance of neon and sulfur for 14 objects where the HI 7-6 line is detected. We further use the molecular hydrogen lines to sample the properties of the warm molecular gas. Several basic diagrams characterizing the properties of the sample are also shown. We have combined the spectra of all the pure starburst objects to create a high S/N template, which is available to the community.Comment: 25 pages (emulate apj), 6 tables, 14 figures, Accepted for publication in ApJ

Experimental Therapy of Ovarian Cancer with Synthetic Makaluvamine Analog: In Vitro and In Vivo Anticancer Activity and Molecular Mechanisms of Action

The present study was designed to determine the biological effects of novel marine alkaloid analog 7-(4-fluorobenzylamino)-1,3,4,8-tetrahydropyrrolo[4,3,2-de]quinolin-8(1H)-one (FBA-TPQ) on human ovarian cancer cells for its anti-tumor potential and the underlying mechanisms as a novel chemotherapeutic agent. Human ovarian cancer cells (A2780 and OVCAR-3), and Immortalized non-tumorigenic human Ovarian Surface Epithelial cells (IOSE-144), were exposed to FBA-TPQ for initial cytotoxicity evaluation (via MTS assay kit, Promega). The detailed in-vitro (cell level) and in-vivo (animal model) studies on the antitumor effects and possible underlying mechanisms of action of the compounds were then performed. FBA-TPQ exerted potent cytotoxicity against human ovarian cancer A2780 and OVCAR-3 cells as an effective inhibitor of cell growth and proliferation, while exerting lesser effects on non-tumorigenic IOSE-144 cells. Further study in the more sensitive OVCAR-3 cell line showed that it could potently induce cell apoptosis (Annexin V-FITC assay), G2/M cell cycle arrest (PI staining analysis) and also dose-dependently inhibit OVCAR-3 xenograft tumors' growth on female athymic nude mice (BALB/c, nu/nu). Mechanistic studies (both in vitro and in vivo) revealed that FBA-TPQ might exert its activity through Reactive Oxygen Species (ROS)-associated activation of the death receptor, p53-MDM2, and PI3K-Akt pathways in OVCAR-3 cells, which is in accordance with in vitro microarray (Human genome microarrays, Agilent) data analysis (GEO accession number: GSE25317). In conclusion, FBA-TPQ exhibits significant anticancer activity against ovarian cancer cells, with minimal toxicity to non-tumorigenic human IOSE-144 cells, indicating that it may be a potential therapeutic agent for ovarian cancer

Longitudinal residual strain and stress-strain relationship in rat small intestine

BACKGROUND: To obtain a more detailed description of the stress-free state of the intestinal wall, longitudinal residual strain measurements are needed. Furthermore, data on longitudinal stress-strain relations in visceral organs are scarce. The present study aims to investigate the longitudinal residual strain and the longitudinal stress-strain relationship in the rat small intestine. METHODS: The longitudinal zero-stress state was obtained by cutting tissue strips parallel to the longitudinal axis of the intestine. The longitudinal residual stress was characterized by a bending angle (unit: degrees per unit length and positive when bending outwards). Residual strain was computed from the change in dimensions between the zero-stress state and the no-load state. Longitudinal stresses and strains were computed from stretch experiments in the distal ileum at luminal pressures ranging from 0–4 cmH(2)O. RESULTS: Large morphometric variations were found between the duodenum and ileum with the largest wall thickness and wall area in the duodenum and the largest inner circumference and luminal area in the distal ileum (p < 0.001). The bending angle did not differ between the duodenum and ileum (p > 0.5). The longitudinal residual strain was tensile at the serosal surface and compressive at the mucosal surface. Hence, the neutral axis was approximately in the mid-wall. The longitudinal residual strain and the bending angle was not uniform around the intestinal circumference and had the highest values on the mesenteric sides (p < 0.001). The stress-strain curves fitted well to the mono-exponential function with determination coefficients above 0.96. The α constant increased with the pressure, indicating the intestinal wall became stiffer in longitudinal direction when pressurized. CONCLUSION: Large longitudinal residual strains reside in the small intestine and showed circumferential variation. This indicates that the tissue is not uniform and cannot be treated as a homogenous material. The longitudinal stiffness of the intestinal wall increased with luminal pressure. Longitudinal residual strains must be taken into account in studies of gastrointestinal biomechanical properties

WISE Discovery of Low Metallicity Blue Compact Dwarf Galaxies

We report two new low metallicity blue compact dwarf galaxies (BCDs), WISEP J080103.93+264053.9 (hereafter W0801+26) and WISEP J170233.53+180306.4 (hereafter W1702+18), discovered using the Wide-field Infrared Survey Explorer (WISE). We identified these two BCDs from their extremely red colors at mid-infrared wavelengths, and obtained follow-up optical spectroscopy using the Low Resolution Imaging Spectrometer on Keck I. The mid-infrared properties of these two sources are similar to the well studied, extremely low metallicity galaxy SBS 0335-052E. We determine metallicities of 12 + log(O/H) = 7.75 and 7.63 for W0801+26 and W1702+18, respectively, placing them amongst a very small group of very metal deficient galaxies (Z 300 Angstrom Hbeta equivalent widths, similar to SBS 0335-052E, imply the existence of young (< 5 Myr) star forming regions. We measure star formation rates of 2.6 and 10.9 Msun/yr for W0801+26 and W1702+18, respectively. These BCDs, showing recent star formation activity in extremely low metallicity environments, provide new laboratories for studying star formation in extreme conditions and are low-redshift analogs of the first generation of galaxies to form in the universe. Using the all-sky WISE survey, we discuss a new method to identify similar star forming, low metallicity BCDs.Comment: Accepted for publication in ApJ