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https://www.readbyqxmd.com/read/28915902/development-and-clinical-application-of-radiomics-in-lung-cancer
#1
REVIEW
Bojiang Chen, Rui Zhang, Yuncui Gan, Lan Yang, Weimin Li
Since the discovery of X-rays at the end of the 19(th) century, medical imageology has progressed for 100 years, and medical imaging has become an important auxiliary tool for clinical diagnosis. With the launch of the human genome project (HGP) and the development of various high-throughput detection techniques, disease exploration in the post-genome era has extended beyond investigations of structural changes to in-depth analyses of molecular abnormalities in tissues, organs and cells, on the basis of gene expression and epigenetics...
September 15, 2017: Radiation Oncology
https://www.readbyqxmd.com/read/28904337/toxoplasma-modulates-signature-pathways-of-human-epilepsy-neurodegeneration-cancer
#2
Huân M Ngô, Ying Zhou, Hernan Lorenzi, Kai Wang, Taek-Kyun Kim, Yong Zhou, Kamal El Bissati, Ernest Mui, Laura Fraczek, Seesandra V Rajagopala, Craig W Roberts, Fiona L Henriquez, Alexandre Montpetit, Jenefer M Blackwell, Sarra E Jamieson, Kelsey Wheeler, Ian J Begeman, Carlos Naranjo-Galvis, Ney Alliey-Rodriguez, Roderick G Davis, Liliana Soroceanu, Charles Cobbs, Dennis A Steindler, Kenneth Boyer, A Gwendolyn Noble, Charles N Swisher, Peter T Heydemann, Peter Rabiah, Shawn Withers, Patricia Soteropoulos, Leroy Hood, Rima McLeod
One third of humans are infected lifelong with the brain-dwelling, protozoan parasite, Toxoplasma gondii. Approximately fifteen million of these have congenital toxoplasmosis. Although neurobehavioral disease is associated with seropositivity, causality is unproven. To better understand what this parasite does to human brains, we performed a comprehensive systems analysis of the infected brain: We identified susceptibility genes for congenital toxoplasmosis in our cohort of infected humans and found these genes are expressed in human brain...
September 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28901826/nuclear-networking
#3
Wei Xie, Brian Burke
Nuclear lamins are intermediate filament proteins that represent important structural components of metazoan nuclear envelopes (NEs). By combining proteomics and superresolution microscopy, we recently reported that both A- and B-type nuclear lamins form spatially distinct filament networks at the nuclear periphery of mouse fibroblasts. In particular, A-type lamins exhibit differential association with nuclear pore complexes (NPCs). Our studies reveal that the nuclear lamina network in mammalian somatic cells is less ordered and more complex than that of amphibian oocytes, the only other system in which the lamina has been visualized at high resolution...
July 4, 2017: Nucleus
https://www.readbyqxmd.com/read/28900183/a-brain-derived-neurotrophic-factor-mimetic-is-sufficient-to-restore-cone-photoreceptor-visual-function-in-an-inherited-blindness-model
#4
Conor Daly, Lisa Shine, Theresa Heffernan, Sudhakar Deeti, Alison L Reynolds, John J O'Connor, Eugène T Dillon, David J Duffy, Walter Kolch, Gerard Cagney, Breandán N Kennedy
Controversially, histone deacetylase inhibitors (HDACi) are in clinical trial for the treatment of inherited retinal degeneration. Utilizing the zebrafish dye (ucd6) model, we determined if treatment with HDACi can rescue cone photoreceptor-mediated visual function. dye exhibit defective visual behaviour and retinal morphology including ciliary marginal zone (CMZ) cell death and decreased photoreceptor outer segment (OS) length, as well as gross morphological defects including hypopigmentation and pericardial oedema...
September 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28892625/platinum-binds-proteins-in-the-endoplasmic-reticulum-of-s-cerevisiae-and-induces-er-stress
#5
Rachael M Cunningham, Victoria J DeRose
Pt(II)-based anticancer drugs are widely used in the treatment of a variety of cancers, but their clinical efficacy is hindered by undesirable side effects and resistance. While much research has focused on Pt(II) drug interactions with DNA, there is increasing interest in proteins as alternative targets and contributors to cytotoxic and resistance mechanisms. Here we describe a chemical proteomic method for isolation and identification of cellular protein targets of platinum compounds using Pt(II) reagents that have been modified for participation in the 1,3 dipolar cycloaddition "click" reaction...
September 11, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28887014/osiris9a-is-a-major-component-of-silk-fiber-in-lepidopteran-insects
#6
Chun Liu, Wenbo Hu, Tingcai Cheng, Zhangchuan Peng, Kazuei Mita, Qingyou Xia
In a previous high-throughput proteomics study, it was found that the silkworm cocoon contains hundreds of complex proteins, many of which have unknown functions, in addition to fibroins, sericins, and some protease inhibitors. Osiris was one of the proteins with no known function. In this study, we identified the Osiris gene family members and constructed a phylogenetic tree based on the sequences from different species. Our results indicate that the Osiris9 gene subfamily contains six members; it is specifically expressed in lepidopteran insects and has evolved by gene duplication...
September 5, 2017: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28867899/homology-modeling-and-protein-interaction-map-of-chrna7-neurogenesis-protein
#7
Ruchi Yadav, Deepshikha Deepshikha, Prachi Srivastava
CHRNA7 is a neurodevelopmental protein involved in differentiation and neurogenesis, which is also named as nicotinic acetylcholine receptors, cholinergic receptor, nicotinic, alpha 7 (neuronal). The protein encoded by this gene forms a homo-oligomeric channel. It is a major component of brain nicotinic receptors displays that are blocked by and sensitive to alpha-bungarotoxin. Studies reports involvement of CHRNA7 protein in different neurological diseases. Non-availability of 3-dimensional (3D) structure leads the study toward structure 3D prediction along with its interaction analysis...
July 2017: Annals of Neurosciences
https://www.readbyqxmd.com/read/28837811/fast-quantitative-and-variant-enabled-mapping-of-peptides-to-genomes
#8
Christoph N Schlaffner, Georg J Pirklbauer, Andreas Bender, Jyoti S Choudhary
Current tools for visualization and integration of proteomics with other omics datasets are inadequate for large-scale studies and capture only basic sequence identity information. Furthermore, the frequent reformatting of annotations for reference genomes required by these tools is known to be highly error prone. We developed PoGo for mapping peptides identified through mass spectrometry to overcome these limitations. PoGo reduced runtime and memory usage by 85% and 20%, respectively, and exhibited overall superior performance over other tools on benchmarking with large-scale human tissue and cancer phosphoproteome datasets comprising ∼3 million peptides...
August 23, 2017: Cell Systems
https://www.readbyqxmd.com/read/28837603/proteomic-analysis-of-protein-phosphatase-z1-from-candida-albicans
#9
Bernadett Márkus, Krisztina Szabó, Walter P Pfliegler, Katalin Petrényi, Enikő Boros, István Pócsi, József Tőzsér, Éva Csősz, Viktor Dombrádi
Protein phosphatase Z is a "novel type" fungus specific serine/threonine protein phosphatase. Previously our research group identified the CaPPZ1 gene in the opportunistic pathogen Candida albicans and reported that the gene deletion had several important physiological consequences. In order to reveal the protein targets and the associated mechanisms behind the functions of the phosphatase a proteomic method was adopted for the comparison of the cappz1 deletion mutant and the genetically matching QMY23 control strain...
2017: PloS One
https://www.readbyqxmd.com/read/28829774/a-large-scale-plasmodium-vivax-saimiri-boliviensis-trophozoite-schizont-transition-proteome
#10
D C Anderson, Stacey A Lapp, John W Barnwell, Mary R Galinski
Plasmodium vivax is a complex protozoan parasite with over 6,500 genes and stage-specific differential expression. Much of the unique biology of this pathogen remains unknown, including how it modifies and restructures the host reticulocyte. Using a recently published P. vivax reference genome, we report the proteome from two biological replicates of infected Saimiri boliviensis host reticulocytes undergoing transition from the late trophozoite to early schizont stages. Using five database search engines, we identified a total of 2000 P...
2017: PloS One
https://www.readbyqxmd.com/read/28826210/the-experiment-data-depot-a-web-based-software-tool-for-biological-experimental-data-storage-sharing-and-visualization
#11
William Morrell, Garrett Birkel, Mark Forrer, Teresa Lopez, Tyler Backman, Michael Dussault, Christopher J Petzold, Edward E K Baidoo, Zak Costello, David Ando, Jorge Alonso Gutierrez, Kevin George, Aindrila Mukhopadhyay, Ian Vaino, Jay D Keasling, Paul D Adams, Nathan J Hillson, Hector Garcia Martin
Although recent advances in synthetic biology allow us to produce biological designs more efficiently than ever, our ability to predict the end result of these designs is still nascent. Predictive models require large amounts of high-quality data to be parametrized and tested, which are not generally available. Here, we present the Experiment Data Depot (EDD), an online tool designed as a repository of standardized experimental data and metadata. EDD provides a convenient way to upload a variety of data types, visualize these data, and export them in a standardized fashion for use with predictive algorithms...
August 21, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28822794/lipidomics-informatics-for-life-science
#12
D Schwudke, A Shevchenko, N Hoffmann, R Ahrends
Lipidomics encompasses analytical approaches that aim to identify and quantify the complete set of lipids, defined as lipidome in a given cell, tissue or organism as well as their interactions with other molecules. The majority of lipidomics workflows is based on mass spectrometry and has been proven as a powerful tool in system biology in concert with other Omics disciplines. Unfortunately, bioinformatics infrastructures for this relatively young discipline are limited only to some specialists. Search engines, quantification algorithms, visualization tools and databases developed by the 'Lipidomics Informatics for Life-Science' (LIFS) partners will be restructured and standardized to provide broad access to these specialized bioinformatics pipelines...
August 16, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28808136/eplant-visualizing-and-exploring-multiple-levels-of-data-for-hypothesis-generation-in-plant-biology
#13
Jamie Waese, Jim Fan, Asher Pasha, Hans Yu, Geoffrey Fucile, Ruian Shi, Matthew Cumming, Lawrence Kelley, Michael Sternberg, Vivek Krishnakumar, Erik Ferlanti, Jason Miller, Chris Town, Wolfgang Stuerzlinger, Nicholas J Provart
A big challenge in current systems biology research arises when different types of data must be accessed from separate sources and visualized using separate tools. The high cognitive load required to navigate such a workflow is detrimental to hypothesis generation. Accordingly, there is a need for a robust research platform that incorporates all data, and provides integrated search, analysis, and visualization features through a single portal. Here, we present ePlant (http://bar.utoronto.ca/eplant), a visual analytic tool for exploring multiple levels of Arabidopsis data through a zoomable user interface...
August 14, 2017: Plant Cell
https://www.readbyqxmd.com/read/28807817/assessment-of-glutathione-glutathione-disulphide-ratio-and-s-glutathionylated-proteins-in-human-blood-solid-tissues-and-cultured-cells
#14
REVIEW
Daniela Giustarini, Graziano Colombo, Maria Lisa Garavaglia, Emanuela Astori, Nicola Marcello Portinaro, Francesco Reggiani, Salvatore Badalamenti, Anna Maria Aloisi, Annalisa Santucci, Ranieri Rossi, Aldo Milzani, Isabella Dalle-Donne
Glutathione (GSH) is the major non-protein thiol in humans and other mammals, which is present in millimolar concentrations within cells, but at much lower concentrations in the blood plasma. GSH and GSH-related enzymes act both to prevent oxidative damage and to detoxify electrophiles. Under oxidative stress, two GSH molecules become linked by a disulphide bridge to form glutathione disulphide (GSSG). Therefore, assessment of the GSH/GSSG ratio may provide an estimation of cellular redox metabolism. Current evidence resulting from studies in human blood, solid tissues, and cultured cells suggests that GSH also plays a prominent role in protein redox regulation via S -glutathionylation, i...
August 12, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/28755236/date-fruit-proteomics-during-development-and-ripening-stages
#15
Claudius Marondedze
Gel-based comparative proteomics approach is a valuable technique for studying the changes in abundance of proteins in any given system. The combination of this technique with mass spectrometry has provided immense insight into protein dynamics during fruit development and ripening. This chapter describes, informatively, the procedures for carrying out comparative proteomics analysis of date palm (Phoenix dactylifera L.) fruits at different developmental stages using a combination of two-dimensional gel electrophoresis (2-DE) and mass spectrometry...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28754825/fluorescent-imaging-of-protein-myristoylation-during-cellular-differentiation-and-development
#16
Andrew J Witten, Karin F K Ejendal, Lindsey M Gengelbach, Meghan A Traore, Xu Wang, David M Umulis, Sarah Calve, Tamara L Kinzer-Ursem
Protein post-translational modifications (PTMs) serve to give proteins new cellular functions and can influence spatial localization and enzymatic activity; greatly enriching the complexity of the proteome. Lipidation is a PTM that regulates protein stability, function and subcellular localization. To complement advances in proteomic identification of lipidated proteins, we have developed methods to image the spatial distribution of proteins that have been co- and post-translationally modified via the addition of myristic acid to the N-terminus...
July 28, 2017: Journal of Lipid Research
https://www.readbyqxmd.com/read/28747503/identification-of-vaccinia-virus-replisome-and-transcriptome-proteins-by-ipond-coupled-with-mass-spectrometry
#17
Tatiana G Senkevich, George Katsafanas, Andrea Weisberg, Lisa R Olano, Bernard Moss
Poxviruses replicate within the cytoplasm and encode proteins for DNA and mRNA synthesis. To investigate poxvirus replication and transcription from a new perspective, we incorporated 5-ethynyl-2' -deoxyuridine (EdU) into nascent DNA in cells infected with vaccinia virus (VACV). The EdU-labeled DNA was conjugated to fluor- or biotin-azide and visualized by confocal, super resolution and transmission electron microscopy. Nuclear labeling decreased dramatically after infection, accompanied by intense labeling of cytoplasmic foci...
July 26, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28735397/global-proteomic-profiling-and-identification-of-stress-responsive-proteins-using-two-dimensional-gel-electrophoresis
#18
Pragya Barua, Dipak Gayen, Nilesh Vikram Lande, Subhra Chakraborty, Niranjan Chakraborty
Global proteome profiling is a direct representation of the protein set in an organism, organ, tissues, or an organelle. One of the main objectives of proteomic analysis is the comparison and relative quantitation of proteins under a defined set of conditions. Two-dimensional gel electrophoresis (2-DE) has gained prominence over the last 4 decades for successfully aiding differential proteomics, providing visual confirmation of changes in protein abundance, which otherwise cannot be predicted from genome analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28732463/common-and-phylogenetically-widespread-coding-for-peptides-by-bacterial-small-rnas
#19
Robin C Friedman, Stefan Kalkhof, Olivia Doppelt-Azeroual, Stephan A Mueller, Martina Chovancová, Martin von Bergen, Benno Schwikowski
BACKGROUND: While eukaryotic noncoding RNAs have recently received intense scrutiny, it is becoming clear that bacterial transcription is at least as pervasive. Bacterial small RNAs and antisense RNAs (sRNAs) are often assumed to be noncoding, due to their lack of long open reading frames (ORFs). However, there are numerous examples of sRNAs encoding for small proteins, whether or not they also have a regulatory role at the RNA level. METHODS: Here, we apply flexible machine learning techniques based on sequence features and comparative genomics to quantify the prevalence of sRNA ORFs under natural selection to maintain protein-coding function in 14 phylogenetically diverse bacteria...
July 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28729539/comparative-proteomic-analysis-of-human-embryonic-stem-cell-derived-and-primary-human-retinal-pigment-epithelium
#20
Heidi Hongisto, Antti Jylhä, Janika Nättinen, Jochen Rieck, Tanja Ilmarinen, Zoltán Veréb, Ulla Aapola, Roger Beuerman, Goran Petrovski, Hannu Uusitalo, Heli Skottman
Human embryonic stem cell-derived retinal pigment epithelial cells (hESC-RPE) provide an unlimited cell source for retinal cell replacement therapies. Clinical trials using hESC-RPE to treat diseases such as age-related macular degeneration (AMD) are currently underway. Human ESC-RPE cells have been thoroughly characterized at the gene level but their protein expression profile has not been studied at larger scale. In this study, proteomic analysis was used to compare hESC-RPE cells differentiated from two independent hESC lines, to primary human RPE (hRPE) using Isobaric tags for relative quantitation (iTRAQ)...
July 20, 2017: Scientific Reports
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