Genome-wide analysis to predict protein sequence variations that change phosphorylation sites or their corresponding kinases

We define phosphovariants as genetic variations that change phosphorylation sites or their interacting kinases. Considering the essential role of phosphorylation in protein functions, it is highly likely that phosphovariants change protein functions and may constitute a proportion of the mechanisms by which genetic variations cause individual differences or diseases. We categorized phosphovariants into three subtypes and developed a system that predicts them. Our method can be used to screen important polymorphisms and help to identify the mechanisms of genetic diseases

Digital Workflow for Retrofitting a Surveyed Crown Using a Removable Partial Denture as an Antagonist

Digital workflow expedites the procedure of retrofitting a surveyed crown against an existing removable partial denture (RPD). This article describes a simple and straightforward technique of digital workflow where an existing RPD is scanned as an antagonist to design the rest seat, guide plane, and height of contour of a surveyed crown.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/156192/2/jopr13187_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156192/1/jopr13187.pd

Physical properties and biological effects of mineral trioxide aggregate mixed with methylcellulose and calcium chloride

Objectives: Methylcellulose (MC) is a chemical compound derived from cellulose. MTA mixed with MC reduces setting time and increases plasticity. This study assessed the influence of MC as an anti-washout ingredient and CaCl2 as a setting time accelerator on the physical and biological properties of MTA. Material and Methods: Test materials were divided into 3 groups; Group 1(control): distilled water; Group 2: 1% MC/CaCl2; Group 3: 2% MC/CaCl2. Compressive strength, pH, flowability and cell viability were tested. The gene expression of bone sialoprotein (BSP) was detected by RT-PCR and real­ time PCR. The expression of alkaline phosphatase (ALP) and mineralization behavior were evaluated using an ALP staining and an alizarin red staining. Results: Compressive strength, pH, and cell viability of MTA mixed with MC/CaCl2 were not significantly different compared to the control group. The flowability of MTA with MC/CaCI2 has decreased significantly when compared to the control (

Human Umbilical Cord Blood-Derived Mesenchymal Stem Cell Therapy Promotes Functional Recovery of Contused Rat Spinal Cord through Enhancement of Endogenous Cell Proliferation and Oligogenesis

Numerous studies have shown the benefits of mesenchymal stem cells (MSCs) on the repair of spinal cord injury (SCI) model and on behavioral improvement, but the underlying mechanisms remain unclear. In this study, to investigate possible mechanisms by which MSCs contribute to the alleviation of neurologic deficits, we examined the potential effect of human umbilical cord blood-derived MSCs (hUCB-MSCs) on the endogenous cell proliferation and oligogenesis after SCI. SCI was injured by contusion using a weight-drop impactor and hUCB-MSCs were transplanted into the boundary zone of the injured site. Animals received a daily injection of bromodeoxyuridine (BrdU) for 7 days after treatment to identity newly synthesized cells of ependymal and periependymal cells that immunohistochemically resembled stem/progenitor cells was evident. Behavior analysis revealed that locomotor functions of hUCB-MSCs group were restored significantly and the cavity volume was smaller in the MSCs-transplanted rats compared to the control group. In MSCs-transplanted group, TUNEL-positive cells were decreased and BrdU-positive cells were significantly increased rats compared with control group. In addition, more of BrdU-positive cells expressed neural stem/progenitor cell nestin and oligo-lineage cell such as NG2, CNPase, MBP and glial fibrillary acidic protein typical of astrocytes in the MSC-transplanted rats. Thus, endogenous cell proliferation and oligogenesis contribute to MSC-promoted functional recovery following SCI

Isolation and Expression Profile of the Ca2+-Activated Chloride Channel-like Membrane Protein 6 Gene in Xenopus laevis

To clone the first anion channel from Xenopus laevis (X. laevis), we isolated a calcium-activated chloride channel (CLCA)-like membrane protein 6 gene (CMP6) in X. laevis. As a first step in gene isolation, an expressed sequence tags database was screened to find the partial cDNA fragment. A putative partial cDNA sequence was obtained by comparison with rat CLCAs identified in our laboratory. First stranded cDNA was synthesized by reverse transcription polymerase-chain reaction (RT-PCR) using a specific primer designed for the target cDNA. Repeating the 5' and 3' rapid amplification of cDNA ends, full-length cDNA was constructed from the cDNA pool. The full-length CMP6 cDNA completed via 5'- and 3'-RACE was 2,940 bp long and had an open reading frame (ORF) of 940 amino acids. The predicted 940 polypeptides have four major transmembrane domains and showed about 50% identity with that of rat brain CLCAs in our previously published data. Semi-quantification analysis revealed that CMP6 was most abundantly expressed in small intestine, colon and liver. However, all tissues except small intestine, colon and liver had undetectable levels. This result became more credible after we did real-time PCR quantification for the target gene. In view of all CLCA studies focused on human or murine channels, this finding suggests a hypothetical protein as an ion channel, an X. laevis CLCA

Crystal structure of hyperthermophilic esterase EstE1 and the relationship between its dimerization and thermostability properties

<p>Abstract</p> <p>Background</p> <p>EstE1 is a hyperthermophilic esterase belonging to the hormone-sensitive lipase family and was originally isolated by functional screening of a metagenomic library constructed from a thermal environmental sample. Dimers and oligomers may have been evolutionally selected in thermophiles because intersubunit interactions can confer thermostability on the proteins. The molecular mechanisms of thermostabilization of this extremely thermostable esterase are not well understood due to the lack of structural information.</p> <p>Results</p> <p>Here we report for the first time the 2.1-Å resolution crystal structure of EstE1. The three-dimensional structure of EstE1 exhibits a classic α/β hydrolase fold with a central parallel-stranded beta sheet surrounded by alpha helices on both sides. The residues Ser154, Asp251, and His281 form the catalytic triad motif commonly found in other α/β hydrolases. EstE1 exists as a dimer that is formed by hydrophobic interactions and salt bridges. Circular dichroism spectroscopy and heat inactivation kinetic analysis of EstE1 mutants, which were generated by structure-based site-directed mutagenesis of amino acid residues participating in EstE1 dimerization, revealed that hydrophobic interactions through Val274 and Phe276 on the β8 strand of each monomer play a major role in the dimerization of EstE1. In contrast, the intermolecular salt bridges contribute less significantly to the dimerization and thermostability of EstE1.</p> <p>Conclusion</p> <p>Our results suggest that intermolecular hydrophobic interactions are essential for the hyperthermostability of EstE1. The molecular mechanism that allows EstE1 to endure high temperature will provide guideline for rational design of a thermostable esterase/lipase using the lipolytic enzymes showing structural similarity to EstE1.</p

The Ship Detection Using Airborne and In-situ Measurements Based on Hyperspectral Remote Sensing

International audienceMaritime accidents around the Korean Peninsula are increasing, and the ship detection research using remote sensing data is consequently becoming increasingly important. This study presented a new ship detection algorithm using hyperspectral images that provide the spectral information of several hundred channels in the ship detection field, which depends on high resolution optical imagery. We applied a spectral matching algorithm between the reflection spectrum of the ship deck obtained from two field observations and the ship and seawater spectrum of the hyperspectral sensor of an airborne visible/infrared imaging spectrometer. A total of five detection algorithms were used, namely spectral distance similarity (SDS), spectral correlation similarity (SCS), spectral similarity value (SSV), spectral angle mapper (SAM), and spectral information divergence (SID). SDS showed an error in the detection of seawater inside the ship, and SAM showed a clear classification result with a difference between ship and seawater of approximately 1.8 times. Additionally, the present study classified the vessels included in hyperspectral images by presenting the adaptive thresholds of each technique. As a result, SAM and SID showed superior ship detection abilities compared to those of other detection algorithms

A New Method for Investigation of the Hair Shaft: Hard X-Ray Microscopy with a 90-nm Spatial Resolution

Various methods have been used to investigate the hair shaft. In the ultrastructural hair field, scanning and transmission electron microscopies are widely used investigative methods, but they have some technical limitations. Recently, X-ray microscopes with sub-micron spatial resolution have emerged as useful instruments because they offer a unique opportunity to observe the interior of an undamaged sample in greater detail. In this report, we examined damaged hair shaft tips using hard X-ray microscopy with a 90 nm spatial resolution. The results of this study suggest that hard X-ray microscopy is an alternative investigative method for hair morphology studies