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https://www.readbyqxmd.com/read/28430886/intrinsic-protein-disorder-reduces-small-scale-gene-duplicability
#1
Sanghita Banerjee, Felix Feyertag, David Alvarez-Ponce
Whereas the rate of gene duplication is relatively high, only certain duplications survive the filter of natural selection and can contribute to genome evolution. However, the reasons why certain genes can be retained after duplication whereas others cannot remain largely unknown. Many proteins contain intrinsically disordered regions (IDRs), whose structures fluctuate between alternative conformational states. Due to their high flexibility, IDRs often enable protein-protein interactions and are the target of post-translational modifications...
April 19, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28430854/dynamic-modeling-and-network-approaches-for-omics-time-course-data-overview-of-computational-approaches-and-applications
#2
Yulan Liang, Arpad Kelemen
Inferring networks and dynamics of genes, proteins, cells and other biological entities from high-throughput biological omics data is a central and challenging issue in computational and systems biology. This is essential for understanding the complexity of human health, disease susceptibility and pathogenesis for Predictive, Preventive, Personalized and Participatory (P4) system and precision medicine. The delineation of the possible interactions of all genes/proteins in a genome/proteome is a task for which conventional experimental techniques are ill suited...
April 18, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28430122/a-comprehensive-diverse-omics-approach-to-better-understanding-the-molecular-pathomechanisms-of-down-syndrome
#3
REVIEW
Keiichi Ishihara, Satoshi Akiba
Diverse '-omics' technologies permit the comprehensive quantitative profiling of a variety of biological molecules. Comparative '-omics' analyses, such as transcriptomics and proteomics, are powerful and useful tools for unraveling the molecular pathomechanisms of various diseases. As enhanced oxidative stress has been demonstrated in humans and mice with Down syndrome (DS), a redox proteomic analysis is useful for understanding how enhanced oxidative stress aggravates the state of individuals with oxidative stress-related disorders...
April 21, 2017: Brain Sciences
https://www.readbyqxmd.com/read/28429743/novel-sumo-protease-senp7s-regulates-%C3%AE-catenin-signaling-and-mammary-epithelial-cell-transformation
#4
Samaneh Karami, Feng-Ming Lin, Santosh Kumar, Shaymaa Bahnassy, Hariprasad Thangavel, Maram Quttina, Yue Li, Jing Ren, Tasneem Bawa-Khalfe
SUMO post-translational modification of proteins or SUMOylation ensures normal cell function. Disruption of SUMO dynamics prompts various pathophysiological conditions, including cancer. The burden of deSUMOylating the large SUMO-proteome rests on 6 full-length mammalian SUMO-proteases or SENP. While multiple SENP isoforms exist, the function of these isoforms remains undefined. We now delineate the biological role of a novel SENP7 isoform SENP7S in mammary epithelial cells. SENP7S is the predominant SENP transcript in human mammary epithelia but is significantly reduced in precancerous ductal carcinoma in situ and all breast cancer subtypes...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28429085/the-role-of-rna-alternative-splicing-in-regulating-cancer-metabolism
#5
REVIEW
Itamar Kozlovski, Zahava Siegfried, Adi Amar-Schwartz, Rotem Karni
Tumor cells alter their metabolism by a wide array of mechanisms to promote growth and proliferation. Dysregulated expression and/or somatic mutations of key components of the glycolytic pathway/TCA cycle as well as other metabolic pathways allow tumor cells to improve their ability to survive harsh conditions such as hypoxia and the presence of reactive oxygen species, as well as the ability to obtain nutrients to increase lipids, protein, and nucleic acids biogenesis. Approximately 95% of the human protein encoding genes undergo alternative splicing (AS), a regulated process of gene expression that greatly diversifies the proteome by creating multiple proteins from a single gene...
April 20, 2017: Human Genetics
https://www.readbyqxmd.com/read/28428613/differential-regulation-of-pkd-isoforms-in-oxidative-stress-conditions-through-phosphorylation-of-a-conserved-tyr-in-the-p-1-loop
#6
Mathias Cobbaut, Rita Derua, Heike Döppler, Hua Jane Lou, Sandy Vandoninck, Peter Storz, Benjamin E Turk, Thomas Seufferlein, Etienne Waelkens, Veerle Janssens, Johan Van Lint
Protein kinases are essential molecules in life and their crucial function requires tight regulation. Many kinases are regulated via phosphorylation within their activation loop. This loop is embedded in the activation segment, which additionally contains the Mg(2+) binding loop and a P + 1 loop that is important in substrate binding. In this report, we identify Abl-mediated phosphorylation of a highly conserved Tyr residue in the P + 1 loop of protein kinase D2 (PKD2) during oxidative stress. Remarkably, we observed that the three human PKD isoforms display very different degrees of P + 1 loop Tyr phosphorylation and we identify one of the molecular determinants for this divergence...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28428241/heralds-of-parallel-ms-data-independent-acquisition-surpassing-sequential-identification-of-data-dependent-acquisition-in-proteomics
#7
Roland Bruderer, Oliver Martin Bernhardt, Tejas Gandhi, Yue Xuan, Julia Sondermann, Manuela Schmidt, David Gomez-Varela, Lukas Reiter
Comprehensive, reproducible and precise analysis of large sample cohorts is one of the key objectives of quantitative proteomics. Here, we present an implementation of data-independent acquisition using its parallel acquisition nature that surpasses the serial limitation of data-dependent acquisition on a quadrupole ultra-high field Orbitrap mass spectrometer. In deep single shot data-independent acquisition, we quantified over 7,500 proteins of human cell lines and 9,000 proteins of mouse tissues, with fewer than 2...
April 20, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28427537/metabolomics-nutrition-and-potential-biomarkers-of-food-quality-intake-and-health-status
#8
Jean-Louis Sébédio
Diet, dietary patterns, and other environmental factors such as exposure to toxins are playing an important role in the prevention/development of many diseases, like obesity, type 2 diabetes, and consequently on the health status of individuals. A major challenge nowadays is to identify novel biomarkers to detect as early as possible metabolic dysfunction and to predict evolution of health status in order to refine nutritional advices to specific population groups. Omics technologies such as genomics, transcriptomics, proteomics, and metabolomics coupled with statistical and bioinformatics tools have already shown great potential in this research field even if so far only few biomarkers have been validated...
2017: Advances in Food and Nutrition Research
https://www.readbyqxmd.com/read/28427148/in-depth-proteomic-profiling-of-left-ventricular-tissues-in-human-end-stage-dilated-cardiomyopathy
#9
Shanshan Liu, Yan Xia, Xiaohui Liu, Yi Wang, Zhangwei Chen, Juanjuan Xie, Juying Qian, Huali Shen, Pengyuan Yang
Dilated cardiomyopathy (DCM) is caused by reduced left ventricular (LV) myocardial function, which is one of the most common causes of heart failure (HF). We performed iTRAQ-coupled 2D-LC-MS/MS to profile the cardiac proteome of LV tissues from healthy controls and patients with end-stage DCM. We identified 4263 proteins, of which 125 were differentially expressed in DCM tissues compared to LV controls. The majority of these were membrane proteins related to cellular junctions and neuronal metabolism. In addition, these proteins were involved in membrane organization, mitochondrial organization, translation, protein transport, and cell death process...
February 25, 2017: Oncotarget
https://www.readbyqxmd.com/read/28426766/activated-entomopathogenic-nematode-infective-juveniles-release-lethal-venom-proteins
#10
Dihong Lu, Marissa Macchietto, Dennis Chang, Mirayana M Barros, James Baldwin, Ali Mortazavi, Adler R Dillman
Entomopathogenic nematodes (EPNs) are unique parasites due to their symbiosis with entomopathogenic bacteria and their ability to kill insect hosts quickly after infection. It is widely believed that EPNs rely on their bacterial partners for killing hosts. Here we disproved this theory by demonstrating that the in vitro activated infective juveniles (IJs) of Steinernema carpocapsae (a well-studied EPN species) release venom proteins that are lethal to several insects including Drosophila melanogaster. We confirmed that the in vitro activation is a good approximation of the in vivo process by comparing the transcriptomes of individual in vitro and in vivo activated IJs...
April 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28426554/barking-up-the-right-tree-advancing-our-understanding-and-treatment-of-lymphoma-with-a-spontaneous-canine-model
#11
Dania Villarnovo, Angela L McCleary-Wheeler, Kristy L Richards
PURPOSE OF REVIEW: Spontaneous lymphoma in pet dogs is increasingly recognized as an ideal model for studying the disease in humans and for developing new targeted therapeutics for patients. Increasing interest by funding agencies, the private sector, and multidisciplinary academic collaborations between different disciplines and sectors now enables large knowledge gaps to be addressed and provides additional proof-of-concept examples to showcase the significance of the canine model. RECENT FINDINGS: The current review addresses the rationale for a canine lymphoma model including the valuable role it can play in drug development, serving as a link between mouse xenograft models and human clinical trials and the infrastructure that is now in place to facilitate these studies...
April 19, 2017: Current Opinion in Hematology
https://www.readbyqxmd.com/read/28426283/identification-of-the-proteome-complement-of-humantlk1-reveals-it-binds-and-phosphorylates-nek1-regulating-its-activity
#12
Vibha Singh, Zachary M Connelly, Xinggui Shen, Arrigo De Benedetti
The Tousled Like kinases (TLKs) are involved in numerous cellular functions, including the DNA Damage Response (DDR), but only a handful of substrates have been identified thus far. Through a novel proteomic screen, we have now identified 165 human proteins interacting with TLK1, and we have focused this work on NEK1 because of its known role in the DDR, upstream of ATR and Chk1. TLK1 and NEK1 were found to interact by coIP, and their binding is strengthened following exposure of cells to H2O2. Following incubation with doxorubicin, TLK1 and NEK1 relocalize with nuclear repair foci along with γH2AX...
April 20, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28424990/proteomic-analysis-of-the-hippocampus-in-mouse-models-of-trigeminal-neuralgia-and-inescapable-shock-induced-depression
#13
Qing-Huan Guo, Qing-He Tong, Ning Lu, Hong Cao, Liu Yang, Yu-Qiu Zhang
To investigate the behavioral and biomolecular similarity between neuralgia and depression, a trigeminal neuralgia (TN) mouse model was established by constriction of the infraorbital nerve (CION) to mimic clinical trigeminal neuropathic pain. A mouse learned helplessness (LH) model was developed to investigate inescapable foot-shock-induced psychiatric disorders like depression in humans. Mass spectrometry was used to assess changes in the biomolecules and signaling pathways in the hippocampus from TN or LH mice...
April 19, 2017: Neuroscience Bulletin
https://www.readbyqxmd.com/read/28424693/human-melanoma-derived-extracellular-vesicles-regulate-dendritic-cell-maturation
#14
Rachel L G Maus, James W Jakub, Wendy K Nevala, Trace A Christensen, Klara Noble-Orcutt, Zohar Sachs, Tina J Hieken, Svetomir N Markovic
Evolution of melanoma from a primary tumor to widespread metastasis is crucially dependent on lymphatic spread. The mechanisms regulating the initial step in metastatic dissemination via regional lymph nodes remain largely unknown; however, evidence supporting the establishment of a pre-metastatic niche is evolving. We have previously described a dysfunctional immune profile including reduced expression of dendritic cell (DC) maturation markers in the first node draining from the primary tumor, the sentinel lymph node (SLN)...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28424404/upregulation-of-minichromosome-maintenance-complex-component-3-during-epithelial-to-mesenchymal-transition-in-human-prostate-cancer
#15
Paul A Stewart, Zahraa I Khamis, Haiyen E Zhau, Peng Duan, Quanlin Li, Leland W K Chung, Qing-Xiang Amy Sang
Metastasis is often associated with epithelial-to-mesenchymal transition (EMT). To understand the molecular mechanisms of this process, we conducted proteomic analysis of androgen-repressed cancer of the prostate (ARCaP), an experimental model of metastatic human prostate cancer. The protein signatures of epithelial (ARCaPE) and mesenchymal (ARCaPM) cells were consistent with their phenotypes. Importantly, the expression of mini-chromosome maintenance 3 (MCM3) protein, a crucial subunit of DNA helicase, was significantly higher in ARCaPM cells than that of ARCaPE cells...
April 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/28424047/deciphering-mechanisms-underlying-the-genetic-variation-of-general-production-and-liver-quality-traits-in-the-overfed-mule-duck-by-pqtl-analyses
#16
Yoannah François, Alain Vignal, Caroline Molette, Nathalie Marty-Gasset, Stéphane Davail, Laurence Liaubet, Christel Marie-Etancelin
BACKGROUND: The aim of this study was to analyse the mechanisms that underlie phenotypic quantitative trait loci (QTL) in overfed mule ducks by identifying co-localized proteomic QTL (pQTL). The QTL design consisted of three families of common ducks that were progeny-tested by using 294 male mule ducks. This population of common ducks was genotyped using a genetic map that included 334 genetic markers located across 28 APL chromosomes (APL for Anas platyrhynchos). Mule ducks were phenotyped for 49 traits related to growth, metabolism, overfeeding ability and meat and fatty liver quality, and 326 soluble fatty liver proteins were quantified...
April 19, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28423718/itraq-based-quantitative-proteomic-analysis-of-yamanaka-factors-reprogrammed-breast-cancer-cells
#17
Kun Wang, Zhiyan Shan, Lian Duan, Tiantian Gong, Feng Liu, Yue Zhang, Zhendong Wang, Jingling Shen, Lei Lei
Cancer cells had been developed to be reprogrammed into embryonic stem like cells by induced pluripotent stem cells (iPSCs) technology, however, the tumor differentiation/dedifferentiation mechanisms had not yet been analyzed on a genome-wide scale. Here, we inserted the four stem cell transcription factor genes OCT4, SOX2, C-MYC and KLF4 into MCF cells (MCFs), represented a female breast cancer cell type, and obtained iPSCs (Mcfips) in about 3 weeks. By using the LC MS/MS iTRAQ technology, we analyzed the proteomic changes between MCFs and Mcfips...
March 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423569/accurate-prediction-of-protein-protein-interactions-by-integrating-potential-evolutionary-information-embedded-in-pssm-profile-and-discriminative-vector-machine-classifier
#18
Zheng-Wei Li, Zhu-Hong You, Xing Chen, Li-Ping Li, De-Shuang Huang, Gui-Ying Yan, Ru Nie, Yu-An Huang
Identification of protein-protein interactions (PPIs) is of critical importance for deciphering the underlying mechanisms of almost all biological processes of cell and providing great insight into the study of human disease. Although much effort has been devoted to identifying PPIs from various organisms, existing high-throughput biological techniques are time-consuming, expensive, and have high false positive and negative results. Thus it is highly urgent to develop in silico methods to predict PPIs efficiently and accurately in this post genomic era...
April 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28421530/time-of-day-dependent-neuronal-injury-after-ischemic-stroke-implication-of-circadian-clock-transcriptional-factor-bmal1-and-survival-kinase-akt
#19
Mustafa Caglar Beker, Berrak Caglayan, Esra Yalcin, Ahmet Burak Caglayan, Seyma Turkseven, Busra Gurel, Taha Kelestemur, Elif Sertel, Zafer Sahin, Selim Kutlu, Ulkan Kilic, Ahmet Tarik Baykal, Ertugrul Kilic
Occurrence of stroke cases displays a time-of-day variation in human. However, the mechanism linking circadian rhythm to the internal response mechanisms against pathophysiological events after ischemic stroke remained largely unknown. To this end, temporal changes in the susceptibility to ischemia/reperfusion (I/R) injury were investigated in mice in which the ischemic stroke induced at four different Zeitgeber time points with 6-h intervals (ZT0, ZT6, ZT12, and ZT18). Besides infarct volume and brain swelling, neuronal survival, apoptosis, ischemia, and circadian rhythm related proteins were examined using immunohistochemistry, Western blot, planar surface immune assay, and liquid chromatography-mass spectrometry tools...
April 18, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28421279/sporulation-how-to-survive-on-planet-earth-and-beyond
#20
REVIEW
Mingwei Huang, Christina M Hull
Sporulation is a strategy widely utilized by a wide variety of organisms to adapt to changes in their individual environmental niches and survive in time and/or space until they encounter conditions acceptable for vegetative growth. The spores produced by bacteria have been the subjects of extensive studies, and several systems such as Bacillus subtilis have provided ample opportunities to understand the molecular basis of spore biogenesis and germination. In contrast, the spores of other microbes, such as fungi, are relatively poorly understood...
April 18, 2017: Current Genetics
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