21.神経芽細胞腫肝転移例の1年生存(第589回千葉医学会例会・第2回千葉大学小児外科教室例会)

Additional file 2: Table S1. A list of phosphoPSMs identified by MASCOT and SEQUEST

Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes

© 2017 Wong et al.; Published by Cold Spring Harbor Laboratory Press. Complementing genome sequence with deep transcriptome and proteome data could enable more accurate assembly and annotation of newly sequenced genomes. Here, we provide a proof-of-concept of an integrated approach for analysis of the genome and proteome of Anopheles stephensi, which is one of the most important vectors of the malaria parasite. To achieve broad coverage of genes, we carried out transcriptome sequencing and deep proteome profiling of multiple anatomically distinct sites. Based on transcriptomic data alone, we identified and corrected 535 events of incomplete genome assembly involving 1196 scaffolds and 868 protein-coding gene models. This proteogenomic approach enabled us to add 365 genes that were missed during genome annotation and identify 917 gene correction events through discovery of 151 novel exons, 297 protein extensions, 231 exon extensions, 192 novel protein start sites, 19 novel translational frames, 28 events of joining of exons, and 76 events of joining of adjacent genes as a single gene. Incorporation of proteomic evidence allowed us to change the designation of more than 87 predicted noncoding RNAs to conventional mRNAs coded by protein-coding genes. Importantly, extension of the newly corrected genome assemblies and gene models to 15 other newly assembled Anopheline genomes led to the discovery of a large number of apparent discrepancies in assembly and annotation of these genomes. Our data provide a framework for how future genome sequencing efforts should incorporate transcriptomic and proteomic analysis in combination with simultaneous manual curation to achieve near complete assembly and accurate annotation of genomes

Skull metastasis of follicular thyroid carcinoma: a rare case report

Abstract: Follicular thyroid carcinoma is a malignant epithelial tumor arising in both eutopic thyroid gland and/or heterotopic thyroid tissue. Follicular cancer accounts for 5-15% of all thyroid cancers in iodine sufficient areas i.e. is the second commonest form of differentiated thyroid malignancy. It spreads via haematogenous routes. So it spreads to lungs and bones. In thyroid cancer only 2.5 % cases shows skull metastases. Here, presenting a 61 year old female with a swelling in the skull left frontotemporal region for 4 years duration with proptosis. She also had thyroid swelling of 20 years duration which is asymptomatic. Cytological confirmation was done to diagnose follicular carcinoma with skull bone metastasis. After total thyroidectomy external beam radiotherapy was given to skull metastases in view of threatened vision. Radioiodine therapy was given afterwards

Delineation of safe groundwater aquifers in a Fluoride contaminated region: Walwa Taluka, Maharashtra

Groundwater aquifer contamination has leads health problems in village areas of Maharashtra, India. In this study, groundwater analysis was carried out for different groundwater parameters along with fluoride to delineate the high and low contaminated fluoride region in the Walwa taluka, Maharashtra. A distinct contaminated regions for high and low F‒ contaminated regions were identified in the collected post monsoon groundwater samples (n = 144). In total 98% samples are unsuitable for consumption. Hydro-geochemistry of the region showed highest anion concentration for bicarbonate (1880 mg/L), whereas highest cation concentration for calcium was measured as 118 mg/L. It is main cause for alkaline groundwater condition in this region. The 2D ordinary kriging results are well corborated with the obtained hydrogeochemistry results. The low F‒ concentration region was found near the Krishna River, whereas high concentration regions were found near the agricultural and high land region. The primary hydrogeochemistry of the region suggests that the geogenic source of F‒ minerals in the region. The practice of fertiliser, herbicides and pesticides on agricultural field suggests that these are the secondary source for groundwater F‒ contamination. The applied numerical groundwater modelling software, provided technically viable and effective decision making-tool for identification of safe region in the study area

Meningioma of Foramen Magnum Causing Drop Attacks

A 52-year-old female presented with frequent episodes of falls without loss of consciousness. These episodes lasted for brief period followed by full neurological recovery. Magnetic resonance imaging (MRI) of the brain showed foramen magnum meningioma encasing left vertebral artery. The patient had dramatic improvement after excision of the tumor

Characterization of human pineal gland proteome

We employed a high-resolution mass spectrometry-based approach to characterize the proteome of the human pineal gland.</p

Giant exchange bias in antiferromagnetic Pr2CoFe0.5Mn0.5O6: a structural and magnetic properties study

Antiferromagnetic (AFM) materials with a colossal exchange bias (EB) effect find applications as high-density spintronic devices. We report structural (geometrical and electronic) and magnetic studies in the polycrystalline Pr2CoFe0.5Mn0.5O6 double perovskite system. The observed lack of training effect suggests the existence of robust EB. In addition, the detailed magnetic studies and Raman studies unravel the Griffith-like phase along with the spin-phonon coupling in the present system. The x-ray photoemission spectroscopy (XPS) analysis supports more than one valence state of B-site elements, which is accountable for the competition between ferromagnetic (FM) and AFM interactions in addition to the anti-site disorder in the system. The neutron measurement confirms the G-type AFM spin arrangement, accredited by the DFT calculation. The magnetic studies have correlated with the electronic structure, neutron study, and theoretical first principle calculations

Comprehensive Proteomics Analysis of Glycosomes from Leishmania donovani

Leishmania donovani is a kinetoplastid protozoan that causes a severe and fatal disease kala-azar, or visceral leishmaniasis. L. donovani infects human host after the phlebotomine sandfly takes a blood meal and resides within the phagolysosome of infected macrophages. Previous studies on host–parasite interactions have not focused on Leishmania organelles and the role that they play in the survival of this parasite within macrophages. Leishmania possess glycosomes that are unique and specialized subcellular microbody organelles. Glycosomes are known to harbor most peroxisomal enzymes and, in addition, they also possess nine glycolytic enzymes. In the present study, we have carried out proteomic profiling using high resolution mass spectrometry of a sucrose density gradient-enriched glycosomal fraction isolated from L. donovani promastigotes. This study resulted in the identification of 4022 unique peptides, leading to the identification of 1355 unique proteins from a preparation enriched in L. donovani glycosomes. Based on protein annotation, 566 (41.8%) were identified as hypothetical proteins with no known function. A majority of the identified proteins are involved in metabolic processes such as carbohydrate, lipid, and nucleic acid metabolism. Our present proteomic analysis is the most comprehensive study to date to map the proteome of L. donovani glycosomes

Moving from unsequenced to sequenced genome:Reanalysis of the proteome of Leishmania donovani

The kinetoplastid protozoan parasite, Leishmania donovani, is the causative agent of kala azar or visceral leishmaniasis. Kala azar is a severe form of leishmaniasis that is fatal in the majority of untreated cases. Studies on proteomic analysis of L. donovani thus far have been carried out using homology-based identification based on related Leishmania species (L. infantum, L. major and L. braziliensis) whose genomes have been sequenced. Recently, the genome of L. donovani was fully sequenced and the data became publicly available. We took advantage of the availability of its genomic sequence to carry out a more accurate proteogenomic analysis of L. donovani proteome using our previously generated dataset. This resulted in identification of 17,504 unique peptides upon database-dependent search against the annotated proteins in L. donovani. These peptides were assigned to 3999 unique proteins in L. donovani. 2296 proteins were identified in both the life stages of L. donovani, while 613 and 1090 proteins were identified only from amastigote and promastigote stages, respectively. The proteomic data was also searched against six-frame translated L. donovani genome, which led to 255 genome search-specific peptides (GSSPs) resulting in identification of 20 novel genes and correction of 40 existing gene models in L. donovani. BIOLOGICAL SIGNIFICANCE: Leishmania donovani genome sequencing was recently completed, which permitted us to use a proteogenomic approach to map its proteome and to carry out annotation of it genome. This resulted in mapping of 50% (3999 proteins) of L. donovani proteome. Our study identified 20 novel genes previously not predicted from the L. donovani genome in addition to correcting annotations of 40 existing gene models. The identified proteins may help in better understanding of stage-specific protein expression profiles in L. donovani and to identify novel stage-specific drug targets in L. donovani which could be used in the treatment of leishmaniasis

Downregulation of S100 calcium binding protein A9 in esophageal squamous cell carcinoma

The development of esophageal squamous cell carcinoma (ESCC) is poorly understood and the major regulatory molecules involved in the process of tumorigenesis have not yet been identified. We had previously employed a quantitative proteomic approach to identify differentially expressed proteins in ESCC tumors. A total of 238 differentially expressed proteins were identified in that study including S100 calcium binding protein A9 (S100A9) as one of the major downregulated proteins. In the present study, we carried out immunohistochemical validation of S100A9 in a large cohort of ESCC patients to determine the expression and subcellular localization of S100A9 in tumors and adjacent normal esophageal epithelia. Downregulation of S100A9 was observed in 67% (n=192) of 288 different ESCC tumors, with the most dramatic downregulation observed in the poorly differentiated tumors (99/111). Expression of S100A9 was restricted to the prickle and functional layers of normal esophageal mucosa and localized predominantly in the cytoplasm and nucleus whereas virtually no expression was observed in the tumor and stromal cells. This suggests the important role that S100A9 plays in maintaining the differentiated state of epithelium and suggests that its downregulation may be associated with increased susceptibility to tumor formation