BackgroundRNA-seq and small RNA-seq are powerful, quantitative tools to study gene regulation and function. Common high-throughput sequencing methods rely on polymerase chain reaction (PCR) to expand the starting material, but not every molecule amplifies equally, causing some to be overrepresented. Unique molecular identifiers (UMIs) can be used to distinguish undesirable PCR duplicates derived from a single molecule and identical but biologically meaningful reads from different molecules.ResultsWe have incorporated UMIs into RNA-seq and small RNA-seq protocols and developed tools to analyze the resulting data. Our UMIs contain stretches of random nucleotides whose lengths sufficiently capture diverse molecule species in both RNA-seq and small RNA-seq libraries generated from mouse testis. Our approach yields high-quality data while allowing unique tagging of all molecules in high-depth libraries.ConclusionsUsing simulated and real datasets, we demonstrate that our methods increase the reproducibility of RNA-seq and small RNA-seq data. Notably, we find that the amount of starting material and sequencing depth, but not the number of PCR cycles, determine PCR duplicate frequency. Finally, we show that computational removal of PCR duplicates based only on their mapping coordinates introduces substantial bias into data analysis.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4933-1) contains supplementary material, which is available to authorized users.

1,8-Dihydroxy-2-naphthaldehyde (DHNA), having doubly intramolecular hydrogen bonds, was strategically designed and synthesized in an aim to probe a long-standing fundamental issue regarding synchronous versus asynchronous double-proton transfer in the excited state. In cyclohexane, DHNA shows the lowest lying S0 →S1 (π-π*) absorption at ∼400 nm. Upon excitation, two large Stokes shifted emission bands maximized at 520 and 650 nm are resolved, which are ascribed to the tautomer emission resulting from the first and second proton-transfer products, denoted by TA* and TB*, respectively. The first proton transfer (DHNA* → TA*) is ultrafast (< system response of 150 fs), whereas the second proton transfer is reversible, for which the rates of forward (TA* → TB*) and backward (TA* ← TB*) proton transfer were determined to be (1.7 ps)(-1) and (3.6 ps)(-1), respectively. The fast equilibrium leads to identical population lifetimes of ∼54 ps for both TA* and TB* tautomers. Similar excited-state double-proton transfer takes place for DHNA in a single crystal, resulting in TA* (560 nm) and TB* (650 nm) dual-tautomer emission. A comprehensive 2D plot of reaction potential energy surface further proves that the sequential two-step proton motion is along the minimum energetic pathway firmly supporting the experimental results. Using DHNA as a paradigm, we thus demonstrate unambiguously a stepwise, proton-relay type of intramolecular double-proton transfer reaction in the excited state, which should gain fundamental understanding of the multiple proton transfer reactions.

A series of new amino (NH)-type intramolecular hydrogen-bonding (H-bonding) compounds have been strategically designed and synthesized. These molecules comprise a 2-(imidazo[1,2-a]pyridin-2-yl)aniline moiety, in which one of the amino hydrogens was replaced with substituents of different electronic properties. This, together with the versatile capability for modifying the parent moiety, makes feasible comprehensive spectroscopy and dynamics studies of excited-state intramolecular proton transfer (ESIPT) as a function of N-H acidity. Different from other (NH)-type ESIPT systems where the ESIPT rate and exergonicity increase with an increase in the N-H acidity and hence the H-bonding strength, the results reveal an irregular relationship among ESIPT dynamics, thermodynamics and H-bond strength. This discrepancy may be rationalized by the localized zwitterionic nature of 2-(imidazo[1,2-a]pyridin-2-yl)aniline in the proton-transfer tautomer form, which is different from the π-delocalized tautomer form in other (NH)-type ESIPT systems.

Mushroom-forming fungi in the order Agaricales represent an independent origin of bioluminescence in the tree of life; yet the diversity, evolutionary history, and timing of the origin of fungal luciferases remain elusive. We sequenced the genomes and transcriptomes of five bonnet mushroom species (Mycena spp.), a diverse lineage comprising the majority of bioluminescent fungi. Two species with haploid genome assemblies ∼150 Mb are among the largest in Agaricales, and we found that a variety of repeats between Mycena species were differentially mediated by DNA methylation. We show that bioluminescence evolved in the last common ancestor of mycenoid and the marasmioid clade of Agaricales and was maintained through at least 160 million years of evolution. Analyses of synteny across genomes of bioluminescent species resolved how the luciferase cluster was derived by duplication and translocation, frequently rearranged and lost in most Mycena species, but conserved in the Armillaria lineage. Luciferase cluster members were coexpressed across developmental stages, with the highest expression in fruiting body caps and stipes, suggesting fruiting-related adaptive functions. Our results contribute to understanding a de novo origin of bioluminescence and the corresponding gene cluster in a diverse group of enigmatic fungal species.

Sesame lignans have antioxidative and anti-inflammatory properties. We focused on the effects of the lignans sesamin and sesamol on the expression of endothelial-leukocyte adhesion molecules in tumor necrosis factor-alpha (TNF-alpha)-treated human aortic endothelial cells (HAECs). When HAECs were pretreated with sesamin (10 or 100 microM), the TNF-alpha-induced expression of intercellular cell adhesion molecule-1 (ICAM-1) was significantly reduced (35 or 70% decrease, respectively) by Western blotting. Sesamol was less effective at inhibiting ICAM-1 expression (30% decrease at 100 microM). Sesamin and sesamol reduced the marked TNF-alpha-induced increase in human antigen R (HuR) translocation and the interaction between HuR and the 3'UTR of ICAM-1 mRNA. Both significantly reduced the binding of monocytes to TNF-alpha-stimulated HAECs. Sesamin significantly attenuated TNF-alpha-induced ICAM-1 expression and cell adhesion by downregulation of extracellular signal-regulated kinase 1/2 and p38. Furthermore, in vivo, sesamin attenuated intimal thickening and ICAM-1 expression seen in aortas of apolipoprotein-E-deficient mice. Taken together, these data suggest that sesamin inhibits TNF-alpha-induced extracellular signal-regulated kinase/p38 phosphorylation, nuclear translocation of NF-kappaB p65, cytoplasmic translocalization of HuR and thereby suppresses ICAM-1 expression, resulting in reduced adhesion of leukocytes. These results also suggest that sesamin may prevent the development of atherosclerosis and inflammatory responses.

Both FS- and MK-assisted LASIK reduced CS and TBUT and increased corneal staining and OSDI scores. However, TBUT was significantly higher in the FS group than in the MK group after operation.

The long noncoding RNA, Growth arrest-specific 5 (GAS5) plays a crucial role in the development of oral cancer. However, potential genetic variants in GAS5 that affect the susceptibility and progression of oral cancer have rarely been explored. In this study, two loci of GAS5 single nucleotide polymorphisms (SNPs) (rs145204276 and rs55829688) were genotyped by using the TaqMan allelic discrimination in 1125 oral cancer patients and 1195 non-oral-cancer individuals. After statistical analyses, the distribution of both the GAS5 SNP rs145204276 and GAS5 SNP rs55829688 frequencies were similar between the study and control groups. However, the patients with GAS5 SNP rs145204276 variants (Ins/Del or Del/Del) showed a higher tendency of moderate to poor cell differentiation of oral cancer (OR: 1.454, 95% CI: 1.041–2.031, p = 0.028). Moreover, the GAS5 SNP rs145204276 variants (Ins/Del or Del/Del) in the non-alcohol-drinking population were associated with significantly advanced tumor stage (OR: 1.500, 95% CI: 1.081–2.081, p = 0.015) and larger tumor size (OR: 1.494, 95% CI: 1.076–2.074, p = 0.016). Furthermore, individuals with the GAS5 SNP rs145204276 variant were associated with a higher expression of GAS5 in the GTEx database (p = 0.002), and the higher GAS5 level was associated with poor cell differentiation, advanced tumor stage and larger tumor size in head and neck squamous cell carcinoma from the TCGA database (all p < 0.05). In conclusion, the GAS5 SNP rs145204276 variant is related to poor-differentiation cell status in oral cancer. Besides, the presence of the GAS5 SNP rs145204276 variant is associated with a worse tumor stage and tumor size in oral cancer patients without alcohol drinking.

Background Neutrophil gelatinase-associated lipocalin (NGAL), a promising renal biomarker, can exists as a monomer, a dimer and/or in a NGAL/matrix metalloproteinase-9 (MMP-9) complex form when associated with different urinary diseases in humans and dogs. In this study, the presence of the various different molecular forms of NGAL in cat urine (uNGAL) was examined and whether these forms are correlated with different urinary diseases was explored. Results One hundred and fifty-nine urine samples from cats with various different diseases, including acute kidney injury (AKI, 22 cats), chronic kidney disease (CKD, 55 cats), pyuria (44 cats) and other non-renal and non-pyuria diseases (non-RP, 26 cats), as well as healthy animals (12 cats), were collected. The molecular forms of and concentrations of urinary NGAL in these cats were analyzed, and their uNGAL-to-creatinine ratio (UNCR) were determined. The cats with AKI had the highest UNCR (median: 2.92 × 10 − 6 ), which was followed by pyuria (median: 1.43 × 10 − 6 ) and CKD (median: 0.56 × 10 − 6 ); all of the above were significantly higher than the healthy controls (median: 0.17 × 10 − 6 ) ( p < 0.05). Three different NGAL molecular forms as well as the MMP-9 monomer were able to be detected in the cat urine samples. Moreover, the cases where urine NGAL monomer were present also had significantly higher levels of BUN (median: 18.9 vs 9.6 mmol/L) and creatinine (327.1 vs 168 umol/L). The presence of dimeric NGAL was found to be associated with urinary tract infections. Most cats in the present study (126/159, 79.2%) and more than half of healthy cats (7/12, 58.3%) had detectable NGAL/MMP-9 complex present in their urine. Conclusions The monomeric and dimeric molecular forms of uNGAL suggest upper and lower urinary tract origins of disease, respectively, whereas the presence of the uNGAL/MMP-9 complex is able to be detected in most cats, including seemingly healthy ones.