Transcriptome Analysis of the Model Protozoan, Tetrahymena thermophila, Using Deep RNA Sequencing

Background: The ciliated protozoan Tetrahymena thermophila is a well-studied single-celled eukaryote model organism for cellular and molecular biology. However, the lack of extensive T. thermophila cDNA libraries or a large expressed sequence tag (EST) database limited the quality of the original genome annotation. Methodology/Principal Findings: This RNA-seq study describes the first deep sequencing analysis of the T. thermophila transcriptome during the three major stages of the life cycle: growth, starvation and conjugation. Uniquely mapped reads covered more than 96 % of the 24,725 predicted gene models in the somatic genome. More than 1,000 new transcribed regions were identified. The great dynamic range of RNA-seq allowed detection of a nearly six order-of-magnitude range of measurable gene expression orchestrated by this cell. RNA-seq also allowed the first prediction of transcript untranslated regions (UTRs) and an updated (larger) size estimate of the T. thermophila transcriptome: 57 Mb, or about 55 % of the somatic genome. Our study identified nearly 1,500 alternative splicing (AS) events distributed over 5.2 % of T. thermophila genes. This percentage represents a two order-of-magnitude increase over previous EST-based estimates in Tetrahymena. Evidence of stage-specific regulation of alternative splicing was also obtained. Finally, our study allowed us to completely confirm about 26.8 % of the genes originally predicted by the gene finder, to correct coding sequence boundaries an

3D MRI Analysis of the Lower Legs of Treated Idiopathic Congenital Talipes Equinovarus (Clubfoot)

Peer reviewedPublisher PD

Cities of consumption: the impact of corporate practices on the health of urban populations

http://deepblue.lib.umich.edu/bitstream/2027.42/61247/1/Freudenberg N, Galea S Cities of consumption the impact of corporate practices on the health of urban populations.pd

Targeting DNA repair

Genomic instability is a characteristic of most human cancers and plays critical roles in both cancer development and progression. There are various forms of genomic instability arising from many different pathways, such as DNA damage from endogenous and exogenous sources, centrosome amplification, telomere damage, and epigenetic modifications. DNA-repair pathways can enable tumor cells to survive DNA damage. The failure to respond to DNA damage is a characteristic associated with genomic instability. Understanding of genomic instability in cancer is still very limited, but the further understanding of the molecular mechanisms through which the DNA damage response (DDR) operates, in combination with the elucidation of the genetic interactions between DDR pathways and other cell pathways, will provide therapeutic opportunities for the personalized medicine of cancer

Structures of telomerase at several steps of telomere repeat synthesis

Telomerase is unique among reverse transcriptases in containing a non-coding RNA (telomerase RNA, TER) that includes a short template used for processive synthesis of G-rich telomeric DNA repeats at the 3′ ends of most eukaryotic chromosomes(1). Telomerase maintains genomic integrity, and its activity or dysregulation are critical determinants of human longevity, stem-cell renewal, and cancer progression(2,3). Cryo electron microscopy (cryo-EM) structures at 4.8–10 Å resolution have established the general architecture, protein components and stoichiometries of Tetrahymena and human telomerase, but provided limited details of DNA– and RNA–protein interactions and insights into mechanism and recruitment(4–6). Here we report 3.3, 3.8, and 4.4 Å resolution cryo-EM structures of active Tetrahymena telomerase with telomeric DNA at different steps of nucleotide addition. Details of interactions between telomerase reverse transcriptase (TERT), TER, and DNA reveal the structural basis of 5′ and 3′ template boundary determination, template–DNA duplex handling, and product chain separation during nucleotide addition. The structure and binding interface between TERT and telomerase protein p50, a homologue of human TPP1(7,8), define conserved interactions required for telomerase activation and recruitment to telomeres. Telomerase La-related protein p65 remodels multiple regions of TER, bridging the 5′- and 3′-ends and the conserved pseudoknot to facilitate assembly of the TERT–TER catalytic core