Comparative transcriptome analysis of field- and chamber-grown samples of Colobanthus quitensis (Kunth) Bartl, an Antarctic flowering plant.
AuthorsCho SM, Lee H, Jo H, Lee H, Kang Y, Park H, Lee J
JournalSci Rep
PubMed ID30038328
'Colobanthus quitensis is one of the two vascular plants inhabiting the Antarctic. In natural habitats, it grows in the form of a cushion or mats, commonly observed in high latitudes or alpine vegetation. Although this species has been investigated over many years to study its geographical distribution and physiological adaptations ... More
Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples.
AuthorsPaskey AC, Frey KG, Schroth G, Gross S, Hamilton T, Bishop-Lilly KA
JournalBMC Genomics
PubMed ID30808306
'Sequencing-based detection and characterization of viruses in complex samples can suffer from lack of sensitivity due to a variety of factors including, but not limited to, low titer, small genome size, and contribution of host or environmental nucleic acids. Hybridization-based target enrichment is one potential method for increasing the sensitivity ... More
Transcriptomic study of Herpes simplex virus type-1 using full-length sequencing techniques.
AuthorsBoldogkoi Z, Szucs A, Balázs Z, Sharon D, Snyder M, Tombácz D
JournalSci Data
PubMed ID30480662
Herpes simplex virus type-1 (HSV-1) is a human pathogenic member of the Alphaherpesvirinae subfamily of herpesviruses. The HSV-1 genome is a large double-stranded DNA specifying about 85 protein coding genes. The latest surveys have demonstrated that the HSV-1 transcriptome is much more complex than it had been thought before. Here, ... More
Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments.
AuthorsTian L, Dong X, Freytag S, Lê Cao KA, Su S, JalalAbadi A, Amann-Zalcenstein D, Weber TS, Seidi A, Jabbari JS, Naik SH, Ritchie ME
JournalNat Methods
PubMed ID31133762
Single cell RNA-sequencing (scRNA-seq) technology has undergone rapid development in recent years, leading to an explosion in the number of tailored data analysis methods. However, the current lack of gold-standard benchmark datasets makes it difficult for researchers to systematically compare the performance of the many methods available. Here, we generated ... More
A Designed Small Molecule Inhibitor of a Non-Coding RNA Sensitizes HER2 Negative Cancers to Herceptin.
AuthorsCostales MG, Hoch DG, Abegg D, Childs-Disney JL, Velagapudi SP, Adibekian A, Disney MD
JournalJ Am Chem Soc
PubMed ID30726072
A small molecule (1) with overlapping affinity for two microRNA (miRNA) precursors was used to inform design of a dimeric compound (2) selective for one of the miRNAs. In particular, 2 selectively targets the microRNA(miR)-515 hairpin precursor to inhibit production of miR-515 that represses sphingosine kinase 1 (SK1), a key ... More
Naringenin Promotes Thermogenic Gene Expression in Human White Adipose Tissue.
AuthorsRebello CJ, Greenway FL, Lau FH, Lin Y, Stephens JM, Johnson WD, Coulter AA
JournalObesity (Silver Spring)
PubMed ID30506905
Naringenin, a citrus flavonoid, prevents diet-induced weight gain and improves glucose and lipid metabolism in rodents. There is evidence that naringenin activates brown fat and increases energy expenditure in mice, but little is known about its effects in humans. The goal of this study was to examine the effects of ... More
Tumor suppressor MCPH1 regulates gene expression profiles related to malignant conversion and chromosomal assembly.
AuthorsTervasmäki A, Mantere T, Eshraghi L, Laurila N, Tuppurainen H, Ronkainen VP, Koivuluoma S, Devarajan R, Peltoketo H, Pylkäs K
JournalInt J Cancer
PubMed ID30809794
Strong inherited predisposition to breast cancer is estimated to cause about 5-10% of all breast cancer cases. As the known susceptibility genes, such as BRCA1 and BRCA2, explain only a fraction of this, additional predisposing genes and related biological mechanisms are actively being searched for. We have recently identified a ... More
Identification and characterization of a core set of ROS wave-associated transcripts involved in the systemic acquired acclimation response of Arabidopsis to excess light.
AuthorsZandalinas SI, Sengupta S, Burks D, Azad RK, Mittler R
JournalPlant J
PubMed ID30556340
Systemic acquired acclimation (SAA) plays a key role in optimizing growth and preventing damage associated with fluctuating or abrupt changes in the plant environment. To be effective, SAA has to occur at a rapid rate and depend on rapid signaling pathways that transmit signals from affected tissues to all parts ... More
miR-155 harnesses Phf19 to potentiate cancer immunotherapy through epigenetic reprogramming of CD8
AuthorsJi Y, Fioravanti J, Zhu W, Wang H, Wu T, Hu J, Lacey NE, Gautam S, Le Gall JB, Yang X, Hocker JD, Escobar TM, He S, Dell'Orso S, Hawk NV, Kapoor V, Telford WG, Di Croce L, Muljo SA, Zhang Y, Sartorelli V, Gattinoni L
JournalNat Commun
PubMed ID31089138
T cell senescence and exhaustion are major barriers to successful cancer immunotherapy. Here we show that miR-155 increases CD8
The innate immune sensor Toll-like receptor 2 controls the senescence-associated secretory phenotype.
AuthorsHari P, Millar FR, Tarrats N, Birch J, Quintanilla A, Rink CJ, Fernández-Duran I, Muir M, Finch AJ, Brunton VG, Passos JF, Morton JP, Boulter L, Acosta JC
JournalSci Adv
PubMed ID31183403
Cellular senescence is a stress response program characterized by a robust cell cycle arrest and the induction of a proinflammatory senescence-associated secretory phenotype (SASP) that is triggered through an unknown mechanism. Here, we show that, during oncogene-induced senescence (OIS), the Toll-like receptor 2 (TLR2) and its partner TLR10 are key ... More
RNA base-pairing complexity in living cells visualized by correlated chemical probing.
AuthorsMustoe AM, Lama NN, Irving PS, Olson SW, Weeks KM
JournalProc Natl Acad Sci U S A
PubMed ID31744869
RNA structure and dynamics are critical to biological function. However, strategies for determining RNA structure in vivo are limited, with established chemical probing and newer duplex detection methods each having deficiencies. Here we convert the common reagent dimethyl sulfate into a useful probe of all 4 RNA nucleotides. Building on ... More
Circulating RNA Transcriptome of Pregnant Women with TSH Just Above the Trimester-Specific Reference and its Correlation with the Hypertensive Phenotype.
AuthorsHirata AHL, Rocha LAJ, da Silva VA, de Almeida RJ, Bacigalupo LDS, Varela P, Martins L, Pesquero JB, Dellê H, Camacho CP
JournalSci Rep
PubMed ID32296081
During gestation, a woman's body undergoes physiological changes that alter thyroid function. Pregnant women with hypothyroidism may exhibit gestational complications, including hypertension and preeclampsia. We investigated differentially expressed genes (DEGs) in circulating RNAs from pregnant women with TSH levels just above the normal range to determine the impact of a ... More