Zea mays RNA-seq estimated transcript abundances are strongly affected by read mapping bias.

Background: Genetic variation for gene expression is a source of phenotypic variation for natural and agricultural species. The common approach to map and to quantify gene expression from genetically distinct individuals is to assign their RNA-seq reads to a single reference genome. However, RNA-seq reads from alleles dissimilar to this reference genome may fail to map correctly, causing transcript levels to be underestimated.

Cross-linked gelatin microsphere-based scaffolds as a delivery vehicle of MC3T3-E1 cells: in vitro and in vivo evaluation.

Scaffolding plays a crucial role in bone tissue engineering by not only providing interfaces for cell adhesion, proliferation, and differentiation but also guiding neotissue formation. For this purpose, microspheres (MSs) are being increasingly used alone or in combination with other scaffolds. However, few researchers have used MSs to prepare 3D scaffolds by culture with delivered cells.

Cryopreservation of Autologous Cranial Bone Flaps for Cranioplasty: A Large Sample Retrospective Study.

Objective: To clarify the clinical outcomes of cranioplasty with cryopreserved bone flaps and identify risk factors related to bone flap infection and resorption after cranioplasty with cryopreserved bone flaps.

Methods: A total of 946 patients (989 bone flaps) underwent decompressive craniectomy and delayed cranioplasty via the use of cryopreserved autogenous cranial bone flaps. Cranial bone flaps were removed during the initial craniectomy and reserved in liquid nitrogen (-196°C) with dimethyl sulfoxide as a cryoprotectant.

Identification of novel miRNAs and miRNA dependent developmental shifts of gene expression in Arabidopsis thaliana.

microRNAs (miRNAs) are small, endogenous RNAs of 20 approximately 25 nucleotides, processed from stem-loop regions of longer RNA precursors. Plant miRNAs act as negative regulators of target mRNAs predominately by slicing target transcripts, and a number of miRNAs play important roles in development. We analyzed a number of published datasets from Arabidopsis thaliana to characterize novel miRNAs, novel miRNA targets, and miRNA-regulated developmental changes in gene expression.

The plant genome's methylation status and response to stress: implications for plant improvement.

Plant improvement depends on generating phenotypic variation and selecting for characteristics that are heritable. Classical genetics and early molecular genetics studies on single genes showed that differences in chromatin structure, especially cytosine methylation, can contribute to heritable phenotypic variation. Recent molecular genetic and genomic studies have revealed a new importance of cytosine methylation for gene regulation and have identified RNA interference (RNAi)-related proteins that are necessary for methylation.

Islands of co-expressed neighbouring genes in Arabidopsis thaliana suggest higher-order chromosome domains.

Biochemical and cytogenetic experiments have led to the hypothesis that eukaryotic chromatin is organized into a series of distinct domains that are functionally independent. Two expectations of this hypothesis are: (i) adjacent genes are more frequently co-expressed than is expected by chance; and (ii) co-expressed neighbouring genes are often functionally related. Here we report that over 10% of Arabidopsis thaliana genes are within large, co-expressed chromosomal regions.