A Multiplexed Assay for Exon Recognition Reveals that an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Splicing Disruptions

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1,25-dihydroxyvitamin D3 induces biphasic NF-kappaB responses during HL-60 leukemia cells differentiation through protein induction and PI3K/Akt-dependent phosphorylation/degradation of IkappaB

1,25-dihydroxyvitamin D(3) (VD(3)) induces differentiation in a number of leukemia cell lines and under various conditions is able to either stimulate or inhibit nuclear factor kappa B (NF-kappaB) activity. Here we report a time-dependent biphasic regulation of NF-kappaB in VD(3)-treated HL-60 leukemia cells. After VD(3) treatment there was an early approximately 4 h suppression and a late 8-72 h prolonged reactivation of NF-kappaB. The reactivation of NF-kappaB was concomitant with increased IKK activities, IKK-mediated IkappaBalpha phosphorylation, p65 phosphorylation at residues S276 and S536, p65 nuclear translocation and p65 recruitment to the NF-kappaB/vitamin D responsive element promoters. In parallel with NF-kappaB stimulation, there was an up-regulation of NF-kappaB controlled inflammatory and anti-apoptotic genes such as TNFalpha, IL-1beta and Bcl-xL. VD(3)-triggered reactivation of NF-kappaB was associated with PI3K/Akt phosphorylation. PI3K/Akt antagonists suppressed VD(3)-stimulated IkappaBalpha phosphorylation as well as NF-kappaB-controlled gene expression. The early approximately 4 h VD(3)-mediated NF-kappaB suppression coincided with a prolonged increase of IkappaBalpha protein which require de novo protein synthesis, lasted for as least 72 h and was insensitive to MAPK, IKK or PI3K/Akt inhibitors. Our data suggest a novel biphasic regulation of NF-kappaB in VD(3)-treated leukemia cells and our results may have provided the first molecular explanation for the contradictory observations reported on VD(3)-mediated immune-regulation.     

CpG/CpNpG motifs in the coding region are preferred sites for mutagenesis in the breast cancer susceptibility genes

The range of BRCA1/BRCA2 gene mutations is diverse and the mechanism accounting for this heterogeneity is obscure. To gain insight into the endogenous mutational mechanisms involved, we evaluated the association of specific sequences (i.e. CpG/CpNpG motifs, homonucleotides, short repeats) and mutations within the genes. We classified 1337 published mutations in BRCA1 (1765 BRCA2 mutations) for each specific sequence, and employed computer simulation combined with mathematical calculations to estimate the true underlying tendency of mutation occurrence. Interestingly, we found no mutational bias to homonucleotides and repeats in deletions/insertions and substitutions but striking bias to CpG/CpNpG in substitutions in both genes. This suggests that methylation-dependent DNA alterations would be a major mechanism for mutagenesis.     

The roles of cyclin-dependent kinase 5 in dendrite and synapse development

Since the isolation of cyclin-dependent kinase 5 (Cdk5), this proline-directed serine/threonine kinase has been demonstrated as an important regulator of neuronal migration, neuronal survival and synaptic functions. Recently, a number of players implicated in dendrite and synapse development have been identified as Cdk5 substrates. Neurite extension, synapse and spine maturation are all modulated by a myriad of extracellular guidance cues or trophic factors. Cdk5 was recently demonstrated to regulate signaling downstream of some of these extracellular factors, in addition to modulating Rho GTPase activity, which regulates cytoskeletal dynamics. In this communication, we summarize our existing knowledge on the pathways and mechanisms through which Cdk5 affects dendrite, synapse and spine development.     

BMI and retinal vascular caliber in children

Objective: In adult populations, changes in retinal vascular caliber have been linked with obesity and metabolic syndrome. We examined the association of BMI and weight with retinal vascular caliber in children. Research Methods and Procedures: This was a school‐based, cross‐sectional study of 768 children, 7 to 9 years old, randomly sampled from the Singapore Cohort Study of the Risk Factors for Myopia. Participants had digital retinal photographs. Retinal vascular caliber was measured using a computer‐based program and combined to provide average calibers of arterioles and venules in that eye. Weight and height were measured using standardized protocol. These data were used to calculate BMI. Results: In this population, the mean retinal arteriolar and venular calibers were 156.40 μm [95% confidence interval (CI), 155.44 to 157.36] and 225.43 μm (95% CI, 224.10 to 226.74) respectively. After controlling for age, gender, race, parental monthly income, axial length, birth weight, and birth length, each 3.1 kg/m² (standard deviation) increase in BMI was associated with a 2.55‐μm (95% CI, 1.21 to 3.89; p < 0.001) larger retinal venular caliber. In multivariable analysis, greater weight was also significantly associated with larger retinal venular caliber. BMI and weight were not associated with retinal arteriolar caliber. Height was not significantly associated with retinal arteriolar or venular caliber. Discussion: Greater BMI and weight are associated with larger retinal venular caliber in healthy children.     

Effects of Fibrinolytic Inhibitors on Chondrogenesis of Bone-marrow Derived Mesenchymal Stem Cells in Fibrin Gels

The objective of this study was to examine the effect of two fibrinolytic inhibitors, aprotinin and aminohexanoic acid, on chondrogenesis of rabbit bone marrow mesenchymal stem cells (BM-MSCs). Rabbit BM-MSCs were obtained from the tibias and femurs of New Zealand White rabbits. Cell–fibrin constructs were made by mixing a cell–fibrinogen (10⁷ cells/ml; 40 mg/ml fibrinogen) solution with a thrombin (5 IU/ml) solution and then divided into four groups: aprotinin control, aprotinin + transforming growth factor β (TGF-β), aminohexanoic acid control, and aminohexanoic acid + TGF-β. Each of these groups was further treated with three different concentrations of inhibitors and the TGF-β groups were treated with 10 ng/ml of TGF-β1. The chondrogenic gene expressions, DNA content, and glycosaminoglycan content of samples were analyzed after 14 days of culture. The aprotinin groups exhibited significantly higher levels of aggrecan gene expression and glycosaminoglycan content than the aminohexanoic acid groups. However, inhibitor neither influenced gene expression of type II collagen nor proliferation (i.e., DNA content) of BM-MSCs. These findings suggest that fibrinolytic inhibitors used to control degradation of fibrin clot may influence TGF-β-induced chondrogenesis of BM-MSCs.     

A rich and bountiful harvest: Key discoveries in plant cell biology

The field of plant cell biology has a rich history of discovery, going back to Robert Hooke’s discovery of cells themselves. The development of microscopes and preparation techniques has allowed for the visualization of subcellular structures, and the use of protein biochemistry, genetics, and molecular biology has enabled the identification of proteins and mechanisms that regulate key cellular processes. In this review, seven senior plant cell biologists reflect on the development of this research field in the past decades, including the foundational contributions that their teams have made to our rich, current insights into cell biology. Topics covered include signaling and cell morphogenesis, membrane trafficking, cytokinesis, cytoskeletal regulation, and cell wall biology. In addition, these scientists illustrate the pathways to discovery in this exciting research field.

Seven senior plant cell biologists reflect on foundational contributions to a variety of topics, including pollen tube signaling, cell morphogenesis, membrane trafficking, cytokinesis, cytoskeletal regulation, and cell wall biology.     

In vitro metabolism of the cardiotonic steroids gomphogenin and calactin

The metabolism of gomphogenin and calactin was studied in vitro using respectively microsomes and the S9 fraction of homogenates from rat liver. These two substrates were previously shown to be in vitro and in vivo metabolites of gomphoside, a cardiotonic steroid belonging to a class of 5 alpha-cardenolide glycosides with doubly-linked hexosulose sugars. Structures of new metabolites were elucidated using 400 MHz 1H-NMR and chemical ionization mass spectrometry, while known compounds were identified by direct comparison. The major metabolite isolated from gomphogenin (2 alpha-hydroxyuzarigenin) metabolism was the oxidation product 2-oxo-uzarigenin which was further oxidized metabolically to 4 alpha-hydroxy-2-oxo-uzarigenin. Other metabolites were 2 alpha-hydroxyuzarigenone and its reduction product 3-epigomphogenin. Calactin was oxidized in vitro to 10-carboxyl-19-norgomphoside, the predominant metabolite, and underwent cleavage of the doubly-linked sugar to yield calotropagenin.