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https://www.readbyqxmd.com/read/29786161/evidence-for-horizontal-gene-transfer-and-separation-of-effector-recognition-from-effector-function-revealed-by-analysis-of-effector-genes-shared-between-cape-gooseberry-and-tomato-infecting-formae-speciales-of-fusarium-oxysporum
#1
Jaime Simbaqueba, Ann-Maree Catanzariti, Carolina González, David A Jones
RNAseq reads from cape-gooseberry plants (Physalis peruviana) infected with Fusarium oxysporum f. sp. physali (Foph) were mapped against the lineage-specific transcriptome of Fusarium oxysporum f. sp. lycopersici (Fol) to look for putative effector genes. Homologues of Fol SIX1 (designated SIX1a and SIX1b), SIX7, SIX10, SIX12, SIX15 and Ave1 were identified. The near identity of the Foph and Fol SIX7, SIX10 and SIX12 genes and their intergenic regions suggest that this gene cluster may have undergone recent lateral transfer...
May 22, 2018: Molecular Plant Pathology
https://www.readbyqxmd.com/read/29783994/large-scale-transcriptomic-analysis-reveals-that-pridopidine-reverses-aberrant-gene-expression-and-activates-neuroprotective-pathways-in-the-yac128-hd-mouse
#2
Rebecca Kusko, Jennifer Dreymann, Jermaine Ross, Yoonjeong Cha, Renan Escalante-Chong, Marta Garcia-Miralles, Liang Juin Tan, Michael E Burczynski, Ben Zeskind, Daphna Laifenfeld, Mahmoud Pouladi, Michal Geva, Iris Grossman, Michael R Hayden
BACKGROUND: Huntington Disease (HD) is an incurable autosomal dominant neurodegenerative disorder driven by an expansion repeat giving rise to the mutant huntingtin protein (mHtt), which is known to disrupt a multitude of transcriptional pathways. Pridopidine, a small molecule in development for treatment of HD, has been shown to improve motor symptoms in HD patients. In HD animal models, pridopidine exerts neuroprotective effects and improves behavioral and motor functions. Pridopidine binds primarily to the sigma-1 receptor, (IC50 ~ 100 nM), which mediates its neuroprotective properties, such as rescue of spine density and aberrant calcium signaling in HD neuronal cultures...
May 21, 2018: Molecular Neurodegeneration
https://www.readbyqxmd.com/read/29779018/common-and-unique-transcriptional-responses-to-dietary-restriction-and-loss-of-insulin-receptor-substrate-1-irs1-in-mice
#3
Melissa M Page, Eugene F Schuster, Manikhandan Mudaliar, Pawel Herzyk, Dominic J Withers, Colin Selman
Dietary restriction (DR) is the most widely studied non-genetic intervention capable of extending lifespan across multiple taxa. Modulation of genes, primarily within the insulin/insulin-like growth factor signalling (IIS) and the mechanistic target of rapamycin (mTOR) signalling pathways also act to extend lifespan in model organisms. For example, mice lacking insulin receptor substrate-1 (IRS1) are long-lived and protected against several age-associated pathologies. However, it remains unclear how these particular interventions act mechanistically to produce their beneficial effects...
May 20, 2018: Aging
https://www.readbyqxmd.com/read/29777630/microrna-493-is-a-prognostic-factor-in-triple-negative-breast-cancer
#4
Ling Yao, Yirong Liu, Zhigang Cao, Junjing Li, Yanni Huang, Xin Hu, Zhiming Shao
Breast cancer is one of the most common malignant diseases in women, in which triple-negative breast cancer (TNBC) exhibits higher aggressiveness and recurrence rates, while there are no effective targets or tailored treatments for patients with this subtype. Thus, finding effective prognostic markers for TNBC might help clinicians in their ability to care for their patients. We used tissue microarrays (TMAs) to detect miR-493 expression in breast cancer samples. A miRCURY LNATM detection probe specific for miR-493 was used in in situ hybridization assays...
May 19, 2018: Cancer Science
https://www.readbyqxmd.com/read/29774023/ferritin-h-deficiency-in-myeloid-compartments-dysregulates-host-energy-metabolism-and-increases-susceptibility-to-mycobacterium-tuberculosis-infection
#5
Vineel P Reddy, Krishna C Chinta, Vikram Saini, Joel N Glasgow, Travis D Hull, Amie Traylor, Fernanda Rey-Stolle, Miguel P Soares, Rajhmun Madansein, Md Aejazur Rahman, Coral Barbas, Kievershen Nargan, Threnesan Naidoo, Pratistadevi K Ramdial, James F George, Anupam Agarwal, Adrie J C Steyn
Iron is an essential factor for the growth and virulence of Mycobacterium tuberculosis ( Mtb) . However, little is known about the mechanisms by which the host controls iron availability during infection. Since ferritin heavy chain (FtH) is a major intracellular source of reserve iron in the host, we hypothesized that the lack of FtH would cause dysregulated iron homeostasis to exacerbate TB disease. Therefore, we used knockout mice lacking FtH in myeloid-derived cell populations to study Mtb disease progression...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29773831/dnajc17-is-localized-in-nuclear-speckles-and-interacts-with-splicing-machinery-components
#6
A Pascarella, G Ferrandino, S C Credendino, C Moccia, F D'Angelo, B Miranda, C D'Ambrosio, P Bielli, O Spadaro, M Ceccarelli, A Scaloni, C Sette, M De Felice, G De Vita, E Amendola
DNAJC17 is a heat shock protein (HSP40) family member, identified in mouse as susceptibility gene for congenital hypothyroidism. DNAJC17 knockout mouse embryos die prior to implantation. In humans, germline homozygous mutations in DNAJC17 have been found in syndromic retinal dystrophy patients, while heterozygous mutations represent candidate pathogenic events for myeloproliferative disorders. Despite widespread expression and involvement in human diseases, DNAJC17 function is still poorly understood. Herein, we have investigated its function through high-throughput transcriptomic and proteomic approaches...
May 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29770330/the-prediction-of-drug-disease-correlation-based-on-gene-expression-data
#7
Hui Cui, Menghuan Zhang, Qingmin Yang, Xiangyi Li, Michael Liebman, Ying Yu, Lu Xie
The explosive growth of high-throughput experimental methods and resulting data yields both opportunity and challenge for selecting the correct drug to treat both a specific patient and their individual disease. Ideally, it would be useful and efficient if computational approaches could be applied to help achieve optimal drug-patient-disease matching but current efforts have met with limited success. Current approaches have primarily utilized the measureable effect of a specific drug on target tissue or cell lines to identify the potential biological effect of such treatment...
2018: BioMed Research International
https://www.readbyqxmd.com/read/29768440/transcriptome-analysis-reveals-a-stress-response-of-shewanella-oneidensis-deprived-of-background-levels-of-ionizing-radiation
#8
Hugo Castillo, Xiaoping Li, Faye Schilkey, Geoffrey B Smith
Natural ionizing background radiation has exerted a constant pressure on organisms since the first forms of life appeared on Earth, so that cells have developed molecular mechanisms to avoid or repair damages caused directly by radiation or indirectly by radiation-induced reactive oxygen species (ROS). In the present study, we investigated the transcriptional effect of depriving Shewanella oneidensis cultures of background levels of radiation by growing the cells in a mine 655 m underground, thus reducing the dose rate from 72...
2018: PloS One
https://www.readbyqxmd.com/read/29767749/association-of-brca2-k3326-with-small-cell-lung-cancer-and-squamous-cell-cancer-of-the-skin
#9
Thorunn Rafnar, Gudbjorg R Sigurjonsdottir, Simon N Stacey, Gisli Halldorsson, Patrick Sulem, Luba M Pardo, Hannes Helgason, Stefan T Sigurdsson, Thorkell Gudjonsson, Laufey Tryggvadottir, Gudridur H Olafsdottir, Jon G Jonasson, Kristin Alexiusdottir, Asgeir Sigurdsson, Julius Gudmundsson, Jona Saemundsdottir, Jon K Sigurdsson, Hrefna Johannsdottir, Andre Uitterlinden, Sita H Vermeulen, Tessel E Galesloot, Dawn C Allain, Martin Lacko, Bardur Sigurgeirsson, Kristin Thorisdottir, Oskar T Johannsson, Fridbjorn Sigurdsson, Gunnar B Ragnarsson, Helgi Isaksson, Hronn Hardardottir, Tomas Gudbjartsson, Daniel F Gudbjartsson, Gisli Masson, Lambertus A M L Kiemeney, Amanda Ewart Toland, Tamar Nijsten, Wilbert H M Peters, Jon H Olafsson, Steinn Jonsson, Unnur Thorsteinsdottir, Gudmar Thorleifsson, Kari Stefansson
Background: Most pathogenic mutations in the BRCA2 gene carry a high risk of hereditary breast and ovarian cancer (HBOC). However, a stop-gain mutation, K3326* (rs11571833), confers risk of lung cancer and cancers of the upper-aero-digestive tract but only a modest risk of breast or ovarian cancer. The Icelandic population provides an opportunity for comprehensive characterization of the cancer risk profiles of K3326* and HBOC mutations because a single mutation, BRCA2 999del5, is responsible for almost all BRCA2-related HBOC in the population...
May 14, 2018: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/29765384/the-hydrophobin-like-omssp1-may-be-an-effector-in-the-ericoid-mycorrhizal-symbiosis
#10
Salvatore Casarrubia, Stefania Daghino, Annegret Kohler, Emmanuelle Morin, Hassine-Radhouane Khouja, Yohann Daguerre, Claire Veneault-Fourrey, Francis M Martin, Silvia Perotto, Elena Martino
Mutualistic and pathogenic plant-colonizing fungi use effector molecules to manipulate the host cell metabolism to allow plant tissue invasion. Some small secreted proteins (SSPs) have been identified as fungal effectors in both ectomycorrhizal and arbuscular mycorrhizal fungi, but it is currently unknown whether SSPs also play a role as effectors in other mycorrhizal associations. Ericoid mycorrhiza is a specific endomycorrhizal type that involves symbiotic fungi mostly belonging to the Leotiomycetes (Ascomycetes) and plants in the family Ericaceae...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29761495/changes-in-gene-expression-during-germination-reveal-pea-genotypes-with-either-quiescence-or-escape-mechanisms-of-waterlogging-tolerance
#11
Md Shahin Uz Zaman, Al Imran Malik, William Erskine, Parwinder Kaur
Waterlogging causes germination failure in pea (Pisum sativum L.). Three genotypes (BM-3, NL-2 and Kaspa) contrasting in ability to germinate in waterlogged soil were exposed to different durations of waterlogging. Whole genome RNAseq was employed to capture differentially expressing genes. The ability to germinate in waterlogged soil was associated with testa colour and testa membrane integrity as confirmed by electrical conductivity measurements. Genotypes Kaspa and NL-2 displayed different mechanisms of tolerance...
May 14, 2018: Plant, Cell & Environment
https://www.readbyqxmd.com/read/29761469/hymenoptera-genome-database-using-hymenopteramine-to-enhance-genomic-studies-of-hymenopteran-insects
#12
Christine G Elsik, Aditi Tayal, Deepak R Unni, Gregory W Burns, Darren E Hagen
The Hymenoptera Genome Database (HGD; http://hymenopteragenome.org ) is a genome informatics resource for insects of the order Hymenoptera, which includes bees, ants and wasps. HGD provides genome browsers with manual annotation tools (JBrowse/Apollo), BLAST, bulk data download, and a data mining warehouse (HymenopteraMine). This chapter focuses on the use of HymenopteraMine to create annotation data sets that can be exported for use in downstream analyses. HymenopteraMine leverages the InterMine platform to combine genome assemblies and official gene sets with data from OrthoDB, RefSeq, FlyBase, Gene Ontology, UniProt, InterPro, KEGG, Reactome, dbSNP, PubMed, and BioGrid, as well as precomputed gene expression information based on publicly available RNAseq...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29759639/uniparental-disomy-unveils-a-novel-recessive-mutation-in-pomt2
#13
Brianna N Brun, Tobias Willer, Benjamin W Darbro, Hernan D Gonorazky, Sergey Naumenko, James J Dowling, Kevin P Campbell, Steven A Moore, Katherine D Mathews
Mutations in POMT2 are most commonly associated with Walker-Warburg syndrome and Muscle-Eye-Brain disease, but can also cause limb girdle muscular dystrophy (LGMD2N). We report a case of LGMD due to a novel mutation in POMT2 unmasked by uniparental isodisomy. The patient experienced proximal muscle weakness from three years of age with minimal progression. She developed progressive contractures and underwent unilateral Achilles tenotomy. By age 11, she had borderline low left ventricular ejection fraction and mild restrictive lung disease...
April 10, 2018: Neuromuscular Disorders: NMD
https://www.readbyqxmd.com/read/29759078/transcriptome-analysis-of-alcohol-treated-microglia-reveals-downregulation-of-beta-amyloid-phagocytosis
#14
Sergey Kalinin, Marta González-Prieto, Hannah Scheiblich, Lucia Lisi, Handojo Kusumo, Michael T Heneka, Jose L M Madrigal, Subhash C Pandey, Douglas L Feinstein
BACKGROUND: Microglial activation contributes to the neuropathology associated with chronic alcohol exposure and withdrawal, including the expression of inflammatory and anti-inflammatory genes. In the current study, we examined the transcriptome of primary rat microglial cells following incubation with alcohol alone, or alcohol together with a robust inflammatory stimulus. METHODS: Primary microglia were prepared from mixed rat glial cultures. Cells were incubated with 75 mM ethanol alone or with proinflammatory cytokines ("TII": IL1β, IFNγ, and TNFα)...
May 14, 2018: Journal of Neuroinflammation
https://www.readbyqxmd.com/read/29758193/inhibition-of-pancreatic-cancer-panc1-cell-migration-by-omeprazole-is-dependent-on-aryl-hydrocarbon-receptor-activation-of-jnk
#15
Un-Ho Jin, Keshav Karki, Sang-Bae Kim, Stephen Safe
Several aryl hydrocarbon receptor (AhR)-active pharmaceuticals were screened as inhibitors of pancreatic cancer cell invasion and identified two compounds, omeprazole, that inhibited invasion. Inhibition of highly invasive Panc1 cell invasion by omeprazole involves an AhR-dependent non-genomic pathway, and omeprazole-mediated inhibition of Panc1 cell invasion was dependent on Jun-N-terminal kinase (JNK) and mitogen-activated kinase kinase 7 (MKK7). The failure of omeprazole to induce nuclear translocation of the AhR was not due to overexpression of cytosolic AhR partner proteins Hsp90 or XAP2, and results of DNA sequencing show that the AhR expressed in Panc1 cells was not mutated...
May 11, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29754406/targeting-twist1-through-loss-of-function-inhibits-tumorigenicity-of-human-glioblastoma
#16
Andrei M Mikheev, Svetlana A Mikheeva, Liza J Severs, Cory C Funk, Lei Huang, José L McFaline-Figueroa, Jeanette Schwensen, Cole Trapnell, Nathan D Price, Stephen Wong, Robert C Rostomily
Twist1 (TW) is a bHLH transcription factor (TF) and master regulator of the epithelial to mesenchymal transition (EMT). In vitro, TW promotes mesenchymal change, invasion and self-renewal in glioblastoma (GBM) cells. However the potential therapeutic relevance of TW has not been established through loss of function studies in human GBM cell xenograft models. The effects of TW loss of function (gene editing and knock down) on inhibition of tumorigenicity of U87MG and GBM4 glioma stem cells were tested in orthotopic xenograft models and conditional knockdown in established flank xenograft tumors...
May 13, 2018: Molecular Oncology
https://www.readbyqxmd.com/read/29746548/anti-angiogenic-vegfaxxxb-transcripts-are-not-expressed-in-the-medio-basal-hypothalamus-of-the-seasonal-sheep
#17
Didier Lomet, Benoît Piégu, Shona H Wood, Hugues Dardente
This study investigated Vegfa expression in the pars tuberalis (PT) of the pituitary and medio-basal hypothalamus (MBH) of sheep, across seasons and reproductive states. It has recently been proposed that season impacts alternative splicing of Vegfa mRNA in the PT, which shifts the balance between angiogenic VEGFAxxx and anti-angiogenic VEGFAxxxb isoforms (with xxx the number of amino acids of the mature VEGFA proteins) to modulate seasonal breeding. Here, we used various RT-PCR methodologies and analysis of RNAseq datasets to investigate seasonal variation in expression and splicing of the ovine Vegfa gene...
2018: PloS One
https://www.readbyqxmd.com/read/29742977/the-thyroid-hormone-receptors-regulate-the-expression-of-micrornas-with-key-roles-in-skin-homeostasis
#18
Lidia Ruiz-Llorente, Constanza Contreras-Jurado, Mónica Martínez-Fernández, Jesus Maria Paramio, Ana Aranda
BACKGROUND: MicroRNAs (miRNAs) play a unique role in posttranscriptional regulation of gene expression and control different aspects of skin development, homeostasis and disease. Although it is generally accepted that thyroid hormones signaling is important in skin pathophysiology, the role of their nuclear receptors (TRs) in cutaneous miRNA expression has yet to be explored. METHODS: We have used RNAseq to compare the skin miRnome of wild-type mice and genetically modified mice lacking both TRα1 and TRβ, the main thyroid hormone binding isoforms...
May 10, 2018: Thyroid: Official Journal of the American Thyroid Association
https://www.readbyqxmd.com/read/29741611/crispr-cas9-editing-in-human-pluripotent-stem-cell-cardiomyocytes-highlights-arrhythmias-hypocontractility-and-energy-depletion-as-potential-therapeutic-targets-for-hypertrophic-cardiomyopathy
#19
Diogo Mosqueira, Ingra Mannhardt, Jamie R Bhagwan, Katarzyna Lis-Slimak, Puspita Katili, Elizabeth Scott, Mustafa Hassan, Maksymilian Prondzynski, Stephen C Harmer, Andrew Tinker, James G W Smith, Lucie Carrier, Philip M Williams, Daniel Gaffney, Thomas Eschenhagen, Arne Hansen, Chris Denning
Aims: Sarcomeric gene mutations frequently underlie hypertrophic cardiomyopathy (HCM), a prevalent and complex condition leading to left ventricle thickening and heart dysfunction. We evaluated isogenic genome-edited human pluripotent stem cell-cardiomyocytes (hPSC-CM) for their validity to model, and add clarity to, HCM. Methods and results: CRISPR/Cas9 editing produced 11 variants of the HCM-causing mutation c.C9123T-MYH7 [(p.R453C-β-myosin heavy chain (MHC)] in 3 independent hPSC lines...
May 8, 2018: European Heart Journal
https://www.readbyqxmd.com/read/29740845/hop-family-plays-a-major-role-in-long-term-acquired-thermotolerance-in-arabidopsis
#20
Nuria Fernández-Bautista, Lourdes Fernández-Calvino, Alfonso Muñoz, René Toribio, Hans P Mock, M Mar Castellano
HOP is a family of cytosolic cochaperones whose molecular role in thermotolerance is quite unknown in eukaryotes and unexplored in plants. In this article, we describe that the three members of the AtHOP family display a different induction pattern under heat, being HOP3 highly regulated during the challenge and the attenuation period. Despite HOP3 is the most heat-regulated member, the analysis of the hop1 hop2 hop3 triple mutant demonstrates that the three HOP proteins act redundantly to promote long term acquired thermotolerance in Arabidopsis...
May 8, 2018: Plant, Cell & Environment
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