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The Reverse Transcription Signature of N-\u3csub\u3e1\u3c/sub\u3e-Methyladenosine in RNA-Seq is Sequence Dependent

The combination of Reverse Transcription (RT) and high-throughput sequencing has emerged as a powerful combination to detect modified nucleotides in RNA via analysis of either abortive RT-products or of the incorporation of mismatched dNTPs into cDNA. Here we simultaneously analyze both parameters in detail with respect to the occurrence of N-1-methyladenosine (m1A) in the template RNA. This naturally occurring modification is associated with structural effects, but it is also known as a mediator of antibiotic resistance in ribosomal RNA. In structural probing experiments with dimethylsulfate, m1A is routinely detected by RT-arrest. A specifically developed RNA-Seq protocol was tailored to the simultaneous analysis of RT-arrest and misincorporation patterns. By application to a variety of native and synthetic RNA preparations, we found a characteristic signature of m1A, which, in addition to an arrest rate, features misincorporation as a significant component. Detailed analysis suggests that the signature depends on RNA structure and on the nature of the nucleotide 3’ of m1A in the template RNA, meaning it is sequence dependent. The RT-signature ofm1Awas used for inspection and confirmation of suspected modification sites and resulted in the identification of hitherto unknown m1A residues in trypanosomal tRNA

Nontargeted screening using gas chromatography– atmospheric pressure ionization mass spectrometry: Recent trends and emerging potential

Gas chromatography–high-resolution mass spectrometry (GC–HRMS) is a powerful non-targeted screening technique that promises to accelerate the identification of environmental pollu-tants. Currently, most GC–HRMS instruments are equipped with electron ionization (EI), but atmospheric pressure ionization (API) ion sources have attracted renewed interest because: (i) colli-sional cooling at atmospheric pressure minimizes fragmentation, resulting in an increased yield of molecular ions for elemental composition determination and improved detection limits; (ii) a wide range of sophisticated tandem (ion mobility) mass spectrometers can be easily adapted for opera-tion with GC–API; and (iii) the conditions of an atmospheric pressure ion source can promote structure diagnostic ion–molecule reactions that are otherwise difficult to perform using conventional GC–MS instrumentation. This literature review addresses the merits of GC–API for nontargeted screening while summarizing recent applications using various GC–API techniques. One perceived drawback of GC–API is the paucity of spectral libraries that can be used to guide structure elucida-tion. Herein, novel data acquisition, deconvolution and spectral prediction tools will be reviewed. With continued development, it is anticipated that API may eventually supplant EI as the de facto GC–MS ion source used to identify unknowns

A matched study of surgically treated stage IB adenosquamous carcinoma and adenocarcinoma of the uterine cervix

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72055/1/j.1525-1438.1993.03040245.x.pd

Foot and ankle surgery in Australia: a descriptive analysis of the Medicare Benefits Schedule database, 1997–2006

This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

The Isl1/Ldb1 complex orchestrates heart-specific chromatin organization and transcriptional regulation

Cardiac stem/progenitor cells hold great potential for regenerative therapies however the mechanisms regulating their expansion and differentiation remain insufficiently defined. Here we show that the multi-adaptor protein Ldb1 is a central regulator of cardiac progenitor cell differentiation and second heart field (SHF) development. Mechanistically, we demonstrate that Ldb1 binds to the key regulator of SHF progenitors Isl1 and protects it from proteasomal degradation. Furthermore, the Isl1/Ldb1 complex promotes long-range promoter-enhancer interactions at the loci of the core cardiac transcription factors Mef2c and Hand2. Chromosome conformation capture followed by sequencing identified surprisingly specific, Ldb1-mediated interactions of the Isl1/Ldb1 responsive Mef2c anterior heart field enhancer with genes which play key roles in cardiac progenitor cell function and cardiovascular development. Importantly, the expression of these genes was downregulated upon Ldb1 depletion and Isl1/Ldb1 haplodeficiency. In conclusion, the Isl1/Ldb1 complex orchestrates a network for heart-specific transcriptional regulation and coordination in three-dimensional space during cardiogenesis