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https://www.readbyqxmd.com/read/27931186/transcriptome-profiling-reveals-differential-gene-expression-of-detoxification-enzymes-in-a-hemimetabolous-tobacco-pest-after-feeding-on-jasmonate-silenced-nicotiana-attenuata-plants
#1
Cristina M Crava, Christoph Brütting, Ian T Baldwin
BACKGROUND: The evolutionary arms race between plants and insects has driven the co-evolution of sophisticated defense mechanisms used by plants to deter herbivores and equally sophisticated strategies that enable phytophagous insects to rapidly detoxify the plant's defense metabolites. In this study, we identify the genetic determinants that enable the mirid, Tupiocoris notatus, to feed on its well-defended host plant, Nicotiana attenuata, an outstanding model for plant-insect interaction studies...
December 8, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27931035/diabetic-phenotype-in-the-small-intestine-of-zucker-diabetic-fatty-rats
#2
Henning Hvid, Stina Rikke Jensen, Brent M Witgen, Christian Fledelius, Jesper Damgaard, Charles Pyke, Thomas Bovbjerg Rasmussen
BACKGROUND/AIMS: In contrast to streptozotocin (STZ)-induced rodent models of diabetes, there are no thorough characterizations of the intestinal phenotype and the underlying changes in the global gene-expression of genetic models of diabetes, such as the Zucker diabetic fatty (ZDF) rat. The aim of the present study was to characterize the intestine in the ZDF rat. METHODS: The intestine of ZDF rats and lean controls was examined macroscopically and histologically, and ribonucleic acid sequencing (RNAseq) was performed in samples of jejunal mucosa...
December 9, 2016: Digestion
https://www.readbyqxmd.com/read/27913251/unmapped-reads-from-cattle-rnaseq-data-a-source-for-missing-and-misassembled-sequences-in-the-reference-assemblies-and-for-detection-of-pathogens-in-the-host
#3
Tahir Usman, Frieder Hadlich, Wiebke Demasius, Rosemarie Weikard, Christa Kühn
Usually, reads from transcriptome sequencing data unmapped to the target species reference genome are disregarded. A recent RNAseq project on the new fatal disease Bovine Neonatal Pancytopenia had indicated an unexplained immune response signature to a double stranded RNA virus. To unravel its background, contigs were de novo assembled from unmapped RNAseq reads and aligned against the bovine genome assemblies and multispecies NCBI databases. Lack of genuine virus sequence contigs rejected the hypothesis of a live virus being causal for the unexplained immune response...
November 29, 2016: Genomics
https://www.readbyqxmd.com/read/27911273/robust-detection-of-immune-transcripts-in-ffpe-samples-using-targeted-rna-sequencing
#4
Benjamin E Paluch, Sean T Glenn, Jeffrey M Conroy, Antonios Papanicolau-Sengos, Wiam Bshara, Angela R Omilian, Elizabeth Brese, Mary Nesline, Blake Burgher, Jonathan Andreas, Kunle Odunsi, Kevin Eng, Ji He, Maochun Qin, Mark Gardner, Lorenzo Galluzzi, Carl D Morrison
Current criteria for identifying cancer patients suitable for immunotherapy with immune checkpoint blockers (ICBs) are subjective and prone to misinterpretation, as they mainly rely on the visual assessment of CD274 (best known as PD-L1) expression levels by immunohistochemistry (IHC). To address this issue, we developed a RNA sequencing (RNAseq)-based approach that specifically measures the abundance of immune transcripts in formalin-fixed paraffin embedded (FFPE) specimens. Besides exhibiting superior sensitivity as compared to whole transcriptome RNAseq, our assay requires little starting material, implying that it is compatible with RNA degradation normally caused by formalin...
November 29, 2016: Oncotarget
https://www.readbyqxmd.com/read/27907106/brain-transcriptional-profiles-of-male-alternative-reproductive-tactics-and-females-in-bluegill-sunfish
#5
Charlyn G Partridge, Matthew D MacManes, Rosemary Knapp, Bryan D Neff
Bluegill sunfish (Lepomis macrochirus) are one of the classic systems for studying male alternative reproductive tactics (ARTs) in teleost fishes. In this species, there are two distinct life histories: parental and cuckolder, encompassing three reproductive tactics, parental, satellite, and sneaker. The parental life history is fixed, whereas individuals who enter the cuckolder life history transition from sneaker to satellite tactic as they grow. For this study, we used RNAseq to characterize the brain transcriptome of the three male tactics and females during spawning to identify gene ontology (GO) categories and potential candidate genes associated with each tactic...
2016: PloS One
https://www.readbyqxmd.com/read/27896376/reducing-the-bottleneck-in-discovery-of-novel-antibiotics
#6
Marcus B Jones, William C Nierman, Yue Shan, Bryan C Frank, Amy Spoering, Losee Ling, Aaron Peoples, Ashley Zullo, Kim Lewis, Karen E Nelson
Most antibiotics were discovered by screening soil actinomycetes, but the efficiency of the discovery platform collapsed in the 1960s. By now, more than 3000 antibiotics have been described and most of the current discovery effort is focused on the rediscovery of known compounds, making the approach impractical. The last marketed broad-spectrum antibiotics discovered were daptomycin, linezolid, and fidaxomicin. The current state of the art in the development of new anti-infectives is a non-existent pipeline in the absence of a discovery platform...
November 28, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27895224/nkd-transcription-factors-are-central-regulators-of-maize-endosperm-development
#7
Bryan C Gontarek, Anjanasree K Neelakandan, Hao Wu, Philip W Becraft
NAKED ENDOSPERM1 (NKD1) and NKD2 are duplicate INDETERMINATE DOMAIN (IDD) transcription factors important for maize (Zea mays) endosperm development. RNAseq analysis of the nkd1 nkd2 mutant endosperm revealed that NKD1 and NKD2 influence 6.4% of the transcriptome in developing aleurone and 6.7% in starchy endosperm. Processes regulated by NKD1 and NKD2 include gene expression, epigenetic functions, cell growth and division, hormone pathways and resource reserve deposition. The NKD1 and NKD2 proteins bind a consensus DNA sequence of TTGTCGT with slightly different properties...
November 28, 2016: Plant Cell
https://www.readbyqxmd.com/read/27892518/brain-microbiota-disruption-within-inflammatory-demyelinating-lesions-in-multiple-sclerosis
#8
W G Branton, J Q Lu, M G Surette, R A Holt, J Lind, J D Laman, C Power
Microbial communities reside in healthy tissues but are often disrupted during disease. Bacterial genomes and proteins are detected in brains from humans, nonhuman primates, rodents and other species in the absence of neurological disease. We investigated the composition and abundance of microbiota in frozen and fixed autopsied brain samples from patients with multiple sclerosis (MS) and age- and sex-matched nonMS patients as controls, using neuropathological, molecular and bioinformatics tools. 16s rRNA sequencing revealed Proteobacteria to be the dominant phylum with restricted diversity in cerebral white matter (WM) from MS compared to nonMS patients...
November 28, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27884156/targeted-myocardial-gene-expression-in-failing-hearts-by-rna-sequencing
#9
Kajari Dhar, Alexandra M Moulton, Eric Rome, Fang Qiu, Jeff Kittrell, Eugenia Raichlin, Ronald Zolty, John Y Um, Michael J Moulton, Hesham Basma, Daniel R Anderson, James D Eudy, Brian D Lowes
BACKGROUND: Myocardial recovery with left ventricular assist device (LVAD) therapy is highly variable and difficult to predict. Next generation ribonucleic acid (RNA) sequencing is an innovative, rapid, and quantitative approach to gene expression profiling in small amounts of tissue. Our primary goal was to identify baseline transcriptional profiles in non-ischemic cardiomyopathies that predict myocardial recovery in response to LVAD therapy. We also sought to verify transcriptional differences between failing and non-failing human hearts...
November 25, 2016: Journal of Translational Medicine
https://www.readbyqxmd.com/read/27872161/identification-of-urinary-exosomal-non-coding-rnas-as-novel-biomarkers-in-chronic-kidney-disease
#10
Rimpi Khurana, Glory Ranches, Simon Schafferer, Melanie Lukasser, Michael Rudnicki, Gert Mayer, Alexander Hüttenhofer
In chronic kidney disease (CKD), the decline in glomerular filtration rate is associated with increased morbidity and mortality and thus poses a major challenge for healthcare systems. While the contribution of tissue-derived miRNAs and mRNAs to CKD progression has extensively been studied, little is known about the role of urinary exosomes and their association with CKD. Exosomes are small, membrane-derived endocytic vesicles that contribute to cell-to-cell communication and are present in various body fluids, such as blood or urine...
November 21, 2016: RNA
https://www.readbyqxmd.com/read/27869336/use-of-the-synergist-piperonyl-butoxide-can-slow-the-development-of-alpha-cypermethrin-resistance-in-the-whitefly-bemisia-tabaci
#11
C T Zimmer, M Panini, K S Singh, E L Randall, L M Field, E Roditakis, E Mazzoni, C Bass
The development of insecticide resistance in insect pests of crops is a growing threat to sustainable food production, and strategies that slow the development of resistance are therefore urgently required. The insecticide synergist piperonyl butoxide (PBO) inhibits certain insect detoxification systems and so may delay the evolution of metabolic resistance. In the current study we characterized resistance development in the silverleaf whitefly, Bemisia tabaci, after selection with either a neonicotinoid (thiacloprid) or pyrethroid (alpha-cypermethrin) insecticide alone or in combination with PBO...
November 21, 2016: Insect Molecular Biology
https://www.readbyqxmd.com/read/27864379/foxn4-promotes-gene-expression-required-for-multiple-motile-cilia-formation
#12
Evan P Campell, Ian K Quigley, Chris Kintner
Multiciliated cell (MCC) differentiation involves extensive organelle biogenesis required to extend hundreds of motile cilia. Key transcriptional regulators have been identified that drive gene expression required for organelle biogenesis during MCC differentiation, which are activated by, and act downstream, of two related, small coiled-coil proteins, Multicilin and Gemc1. Here we identify foxn4 as a new downstream target of Multicilin required for MCC differentiation in the Xenopus skin. When Foxn4 activity is inhibited in Xenopus embryos, MCCs show transient ciliogenesis defects similar to those observed in mutants in Foxj1, a known key regulator of genes required for motile ciliation...
November 18, 2016: Development
https://www.readbyqxmd.com/read/27863452/mutation-in-non-coding-rna-rnu12-causes-early-onset-cerebellar-ataxia
#13
Mahmoud Fawzi Elsaid, Nader Chalhoub, Tawfeg Ben-Omran, Pankaj Kumar, Hussein Kamel, Khalid Ibrahim, Yasmin Mohamoud, Eman Al-Dous, Iman Al-Azwani, Joel A Malek, Karsten Suhre, M Elizabeth Ross, Alice Abdel Aleem
OBJECTIVE: Exome sequences account for only 2% of the genome and may overlook mutations causing disease. To obtain a more complete view, whole genome sequencing (WGS) was analyzed in a large consanguineous family in which members displayed autosomal recessively inherited cerebellar ataxia manifesting before two years of age. METHODS: WGS from blood derived gDNA was used for homozygosity mapping and a rare variant search. RNA from isolated blood leukocytes was used for quantitative PCR, RNA sequencing and comparison of the transcriptomes of affected and unaffected family members...
November 18, 2016: Annals of Neurology
https://www.readbyqxmd.com/read/27863424/novel-metastatic-models-of-esophageal-adenocarcinoma-derived-from-flo-1-cells-highlight-the-importance-of-e-cadherin-in-cancer-metastasis
#14
David S Liu, Sanne J M Hoefnagel, Oliver M Fisher, Kausilia K Krishnadath, Karen G Montgomery, Rita A Busuttil, Andrew J Colebatch, Matthew Read, Cuong P Duong, Wayne A Phillips, Nicholas J Clemons
There is currently a paucity of preclinical models available to study the metastatic process in esophageal cancer. Here we report FLO-1, and its isogenic derivative FLO-1LM, as two spontaneously metastatic cell line models of human esophageal adenocarcinoma. We show that FLO-1 has undergone epithelial-mesenchymal transition and metastasizes following subcutaneous injection in mice. FLO-1LM, derived from a FLO-1 liver metastasis, has markedly enhanced proliferative, clonogenic, anti-apoptotic, invasive, immune-tolerant and metastatic potential...
November 16, 2016: Oncotarget
https://www.readbyqxmd.com/read/27856567/transcriptional-and-translational-regulation-by-rna-thermometers-riboswitches-and-the-srna-dsra-in-escherichia-coli-o157-h7-sakai-under-combined-cold-and-osmotic-stress-adaptation
#15
Sarah Maria Hücker, Svenja Simon, Siegfried Scherer, Klaus Neuhaus
The enteric pathogen Escherichia coli O157:H7 Sakai (EHEC) is able to grow at lower temperatures compared to commensal E. coli Growth at environmental conditions displays complex challenges different to those in a host. EHEC was grown at 37°C (control) and at 14°C with 4% NaCl, a combination of cold and osmotic stress as present in the food chain. Comparison of RNAseq and RIBOseq data provided a snap shot of ongoing transcription and translation, differentiating transcriptional and post-transcriptional gene regulation, respectively...
November 16, 2016: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/27856275/rnaseq-profiling-of-primary-microglia-and-astrocyte-cultures-in-near-term-ovine-fetus-a-glial-in-vivo-in-vitro-multi-hit-paradigm-in-large-mammalian-brain
#16
M Cortes, M Cao, H L Liu, P Burns, C Moore, G Fecteau, A Desrochers, L B Barreiro, J P Antel, M G Frasch
BACKGROUND: The chronically instrumented fetal sheep is a widely used animal model to study fetal brain development in health and disease, but no methods exist yet to interrogate dedicated brain cell populations to identify their molecular and genomic phenotype. For example, the molecular mechanisms whereby microglia or astrocytes contribute to inflammation in the brain remain incompletely understood. NEW METHOD: Here we present a protocol to derive primary pure microglial or astrocyte cultures from near-term fetal sheep brain, after the animals have been chronically instrumented and studied in vivo...
November 14, 2016: Journal of Neuroscience Methods
https://www.readbyqxmd.com/read/27855558/diagnostic-evaluation-of-rna-sequencing-for-the-detection-of-genetic-abnormalities-associated-with-ph-like-acute-lymphoblastic-leukemia-all
#17
Kai Lee Yap, Larissa V Furtado, Kazuma Kiyotani, Emily Curran, Wendy Stock, Jennifer L McNeer, Sabah Kadri, Jeremy P Segal, Yusuke Nakamura, Michelle M Le Beau, Sandeep Gurbuxani, Gordana Raca
Philadelphia (Ph)-like acute lymphoblastic leukemia (ALL) is a molecular subtype of high-risk B-cell ALL characterized by formation of abnormal gene fusions involving tyrosine kinase (TK) and cytokine receptor genes and activation of TK signaling. Because of the diversity of associated genetic changes, the detection of Ph-like ALL cases currently requires multiple cytogenetic and molecular assays; thus, our goal was to develop a consolidated workflow for detecting genetic abnormalities in Ph-like ALL. We found that total and targeted RNA sequencing (RNAseq)-based approach allowed the detection of abnormal fusion transcripts (EBF1-PDGFRB, P2RY8-CRLF2, RCSD1-ABL1, and RCSD1-ABL2)...
November 17, 2016: Leukemia & Lymphoma
https://www.readbyqxmd.com/read/27855160/transcription-factors-encoded-on-core-and-accessory-chromosomes-of-fusarium-oxysporum-induce-expression-of-effector-genes
#18
H Charlotte van der Does, Like Fokkens, Ally Yang, Sarah M Schmidt, Léon Langereis, Joanna M Lukasiewicz, Timothy R Hughes, Martijn Rep
Proteins secreted by pathogens during host colonization largely determine the outcome of pathogen-host interactions and are commonly called 'effectors'. In fungal plant pathogens, coordinated transcriptional up-regulation of effector genes is a key feature of pathogenesis and effectors are often encoded in genomic regions with distinct repeat content, histone code and rate of evolution. In the tomato pathogen Fusarium oxysporum f. sp. lycopersici (Fol), effector genes reside on one of four accessory chromosomes, known as the 'pathogenicity' chromosome, which can be exchanged between strains through horizontal transfer...
November 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27852308/systems-analysis-identifies-mir-29b-regulation-of-invasiveness-in-melanoma
#19
Miles C Andrews, Joseph Cursons, Daniel G Hurley, Matthew Anaka, Jonathan S Cebon, Andreas Behren, Edmund J Crampin
BACKGROUND: In many cancers, microRNAs (miRs) contribute to metastatic progression by modulating phenotypic reprogramming processes such as epithelial-mesenchymal plasticity. This can be driven by miRs targeting multiple mRNA transcripts, inducing regulated changes across large sets of genes. The miR-target databases TargetScan and DIANA-microT predict putative relationships by examining sequence complementarity between miRs and mRNAs. However, it remains a challenge to identify which miR-mRNA interactions are active at endogenous expression levels, and of biological consequence...
November 16, 2016: Molecular Cancer
https://www.readbyqxmd.com/read/27849178/modulation-of-pertussis-and-adenylate-cyclase-toxins-by-sigma-factor-rpoe-in-bordetella-pertussis
#20
Mariette Barbier, Dylan Boehm, Emel Sen-Kiliç, Claire Bonnin, Theo Pinheiro, Casey Hoffman, Mary Gray, Erik Hewlett, F Heath Damron
Bordetella pertussis is a human pathogen that can infect the respiratory tract and cause the disease known as whooping cough. B. pertussis uses pertussis toxin (PT) and adenylate cyclase toxin (ACT) to kill and modulate host cells to allow the pathogen to survive and persist. B. pertussis encodes many uncharacterized transcription factors and very little is known about their functions. RpoE is a sigma factor which in other bacteria, responds to oxidative, heat, and other environmental stresses. RseA is a negative regulator of RpoE that sequesters the sigma factor to regulate gene expression based on conditions...
November 14, 2016: Infection and Immunity
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