Single cell transcriptome analysis of MCF-7 reveals consistently and inconsistently expressed gene groups each associated with distinct cellular localization and functions.

Single cell transcriptome (SCT) analysis provides superior resolution to illustrate tumor cell heterogeneity for clinical implications. We characterized four SCTs of MCF-7 using 143 housekeeping genes (HKGs) as control, of which lactate dehydrogenase B (LDHB) expression is silenced. These SCT libraries mapped to 11,423, 11,486, 10,380, and 11,306 RefSeq genes (UCSC), respectively.

TEA: the epigenome platform for Arabidopsis methylome study.

Background: Bisulfite sequencing (BS-seq) has become a standard technology to profile genome-wide DNA methylation at single-base resolution. It allows researchers to conduct genome-wise cytosine methylation analyses on issues about genomic imprinting, transcriptional regulation, cellular development and differentiation. One single data from a BS-Seq experiment is resolved into many features according to the sequence contexts, making methylome data analysis and data visualization a complex task.

Stage-Specific Demethylation in Primordial Germ Cells Safeguards against Precocious Differentiation.

Remodeling DNA methylation in mammalian genomes can be global, as seen in preimplantation embryos and primordial germ cells (PGCs), or locus specific, which can regulate neighboring gene expression. In PGCs, global and locus-specific DNA demethylation occur in sequential stages, with an initial global decrease in methylated cytosines (stage I) followed by a Tet methylcytosine dioxygenase (Tet)-dependent decrease in methylated cytosines that act at imprinting control regions (ICRs) and meiotic genes (stage II). The purpose of the two-stage mechanism is unclear.

Exosomal miR-10a derived from amniotic fluid stem cells preserves ovarian follicles after chemotherapy.

Chemotherapy (CTx)-induced premature ovarian failure (POF) in woman remains clinically irreversible. Amniotic fluid stem cells (AFSCs) have shown the potential to treat CTx-induced POF; however, the underlying mechanism is unclear. Here we demonstrate that AFSC-derived exosomes recapitulate the anti-apoptotic effect of AFSCs on CTx-damaged granulosa cells (GCs), which are vital for the growth of ovarian follicles.

Palindromic sequence impedes sequencing-by-ligation mechanism.

Background: Current next-generation sequencing (NGS) platforms adopt two types of sequencing mechanisms: by synthesis or by ligation. The former is employed by 454 and Solexa systems, while the latter by SOLiD system. Although the pros and cons for each sequencing mechanism have more or less been discussed in a number of occasions, the potential obstacle imposed by palindromic sequences has not yet been addressed.

New classification of supersecondary structures of sandwich-like proteins uncovers strict patterns of strand assemblage.

To describe the supersecondary structure (SSS) of beta sandwich-like proteins (SPs), we introduce a structural unit called the "strandon." A strandon is defined as a set of sequentially consecutive strands connected by hydrogen bonds in 3D structures. Representing beta-proteins as the assembly of strandons exposes the underlying similarities in their SSS and enables us to construct a novel classification scheme of SPs.

Early predict the outcomes of refractive accommodative esotropia by initial presentations.

Background: The differential diagnosis between fully and partially refractive accommodative esotropia (Ac-ET) depends on outcomes after intervention with refraction correction. Whether the differences exist in terms of initial clinical features between these two variants has not been fully explored.

Methods: Children between the ages of 6 months and 8 years with esotropia and spherical equivalent greater than +3.