MOD(i) : a powerful and convenient web server for identifying multiple post-translational peptide modifications from tandem mass spectra

MOD(i) () is a powerful and convenient web service that facilitates the interpretation of tandem mass spectra for identifying post-translational modifications (PTMs) in a peptide. It is powerful in that it can interpret a tandem mass spectrum even when hundreds of modification types are considered and the number of potential PTMs in a peptide is large, in contrast to most of the methods currently available for spectra interpretation that limit the number of PTM sites and types being used for PTM analysis. For example, using MOD(i), one can consider for analysis both the entire PTM list published on the unimod webpage () and user-defined PTMs simultaneously, and one can also identify multiple PTM sites in a spectrum. MOD(i) is convenient in that it can take various input file formats such as .mzXML, .dta, .pkl and .mgf files, and it is equipped with a graphical tool called MassPective developed to display MOD(i)'s output in a user-friendly manner and helps users understand MOD(i)'s output quickly. In addition, one can perform manual de novo sequencing using MassPective

Angiographic and Clinical Result of Endovascular Treatment in Paraclinoid Aneurysms

PurposeThe purpose of this study was to analyze the results of an immediate and mid-term angiographic and clinical follow-up of endovascular treatment for paraclinoid aneurysms.Materials and MethodsFrom January 2002 to December 2012, a total of 113 consecutive patients (mean age: 56.2 years) with 116 paraclinoid saccular aneurysms (ruptured or unruptured) were treated with endovascular coiling procedures. Clinical and angiographic outcomes were retrospectively evaluated.ResultsNinety-three patients (82.3%) were female. The mean size of the aneurysm was 5.5 mm, and 101 aneurysms (87.1%) had a wide neck. Immediate catheter angiography showed complete occlusion in 40 aneurysms (34.5%), remnant sac in 51 (43.9%), and remnant neck in 25 (21.6%). Follow-up angiographic studies were performed on 80 aneurysms (69%) at a mean period of 20.4 months. Compared with immediate angiographic results, follow-up angiograms showed no change in 38 aneurysms, improvement in 37 (Fig. 2), and recanalization in 5. There were 6 procedure-related complications (5.2%), with permanent morbidity in one patient.ConclusionOut study suggests that properly selected patients with paraclinoid aneurysms can be successfully treated by endovascular means

Muscle differentiation induced up-regulation of calcium-related gene expression in quail myoblasts

Objective In the poultry industry, the most important economic traits are meat quality and carcass yield. Thus, many studies were conducted to investigate the regulatory pathways during muscle differentiation. To gain insight of muscle differentiation mechanism during growth period, we identified and validated calcium-related genes which were highly expressed during muscle differentiation through mRNA sequencing analysis. Methods We conducted next-generation-sequencing (NGS) analysis of mRNA from undifferentiated QM7 cells and differentiated QM7 cells (day 1 to day 3 of differentiation periods). Subsequently, we obtained calcium related genes related to muscle differentiation process and examined the expression patterns by quantitative reverse-transcription polymerase chain reaction (qRT-PCR). Results Through RNA sequencing analysis, we found that the transcription levels of six genes (troponin C1, slow skeletal and cardiac type [TNNC1], myosin light chain 1 [MYL1], MYL3, phospholamban [PLN], caveolin 3 [CAV3], and calsequestrin 2 [CASQ2]) particularly related to calcium regulation were gradually increased according to days of myotube differentiation. Subsequently, we validated the expression patterns of calcium-related genes in quail myoblasts. These results indicated that TNNC1, MYL1, MYL3, PLN, CAV3, CASQ2 responded to differentiation and growth performance in quail muscle. Conclusion These results indicated that calcium regulation might play a critical role in muscle differentiation. Thus, these findings suggest that further studies would be warranted to investigate the role of calcium ion in muscle differentiation and could provide a useful biomarker for muscle differentiation and growth

Retroperitoneal Giant Liposarcoma

Retroperitoneal liposarcoma is an infrequent, locally aggressive malignancy. We report two cases of huge retroperitoneal liposarcomas. The presence of a palpable abdominal mass was a common symptom of the two patients. Preoperative imaging study showed huge retroperitoneal tumors. Both patients underwent complete surgical resections, and a negative microscopic margin was achieved in both cases. The histopathologic diagnosis was a well-differentiated retroperitoneal liposarcoma. Neither of the two patients developed a recurring tumor during the 1.5 years of follow-up

Cell Labeling and Tracking Method without Distorted Signals by Phagocytosis of Macrophages

Cell labeling and tracking are important processes in understanding biologic mechanisms and the therapeutic effect of inoculated cells in vivo. Numerous attempts have been made to label and track inoculated cells in vivo; however, these methods have limitations as a result of their biological effects, including secondary phagocytosis of macrophages and genetic modification. Here, we investigated a new cell labeling and tracking strategy based on metabolic glycoengineering and bioorthogonal click chemistry. We first treated cells with tetra-acetylated N-azidoacetyl-D-mannosamine to generate unnatural sialic acids with azide groups on the surface of the target cells. The azide-labeled cells were then transplanted to mouse liver, and dibenzyl cyclooctyne-conjugated Cy5 (DBCO-Cy5) was intravenously injected into mice to chemically bind with the azide groups on the surface of the target cells in vivo for target cell visualization. Unnatural sialic acids with azide groups could be artificially induced on the surface of target cells by glycoengineering. We then tracked the azide groups on the surface of the cells by DBCO-Cy5 in vivo using bioorthogonal click chemistry. Importantly, labeling efficacy was enhanced and false signals by phagocytosis of macrophages were reduced. This strategy will be highly useful for cell labeling and tracking

<i>gzK</i>-colour-selected star-forming galaxies in the <i>AKARI</i> NEP-Deep Field

We study the clustering property and physical parameters of gzK-colour-selected star-forming galaxies (sgzKs) based on the Canada–France–Hawaii Telescope surveys over 0.55 deg2 in the AKARI North Ecliptic Pole-Deep Field. Two-point correlation functions for two magnitude-limited cases, Ks &amp;lt; 21.1 (N = 234) and Ks &amp;lt; 21.5 (N = 428), are estimated using a single power-law function with the fixed slope of 0.8. The bias factors of sgzKs with Ks &amp;lt; 21.1 and 21.5 are 5.79 ± 1.07 and 4.00 ± 0.67, respectively, representing that sgzKs with z ∼ 1.7 reside in dark matter haloes more massive than $10^{13} ~\rm M_{\odot }$. We find that haloes hosting sgzKs with Ks &amp;lt; 21.5 evolve into haloes that host local massive galaxies with ∼6 L*. This suggests that sgzKs with Ks &amp;lt; 21.5 are likely to be predecessors of local massive galaxies. The evolutionary track of bias factor for host haloes of the bright sgzKs is similar to that of the bright passive extremely red objects, implying a possible connection between the two populations of galaxies. From the spectral energy distribution fitting, we estimate physical parameters and active galactic nucleus (AGN) contribution for 75 mid-infrared (MIR)-detected sgzKs with Ks &amp;lt; 21.5. The median values of stellar mass and star formation rate are 9.5 × 1010$\rm M_{\odot }$ and 162 $\rm M_{\odot }$ yr−1, respectively. MIR-detected sgzKs have a variety of AGN contributions ranging from 0 to 80 per cent. The number ratio of sgzKs with larger AGN contribution than 10 per cent is 30 per cent