Intron exon boundary junctions in human genome have in-built unique structural and energetic signals

Precise identification of correct exon–intron boundaries is a prerequisite to analyze the location and structure of genes. The existing framework for genomic signals, delineating exon and introns in a genomic segment, seems insufficient, predominantly due to poor sequence consensus as well as limitations of training on available experimental data sets. We present here a novel concept for characterizing exon–intron boundaries in genomic segments on the basis of structural and energetic properties. We analyzed boundary junctions on both sides of all the exons (3 28 368) of protein coding genes from human genome (GENCODE database) using 28 structural and three energy parameters. Study of sequence conservation at these sites shows very poor consensus. It is observed that DNA adopts a unique structural and energy state at the boundary junctions. Also, signals are somewhat different for housekeeping and tissue specific genes. Clustering of 31 parameters into four derived vectors gives some additional insights into the physical mechanisms involved in this biological process. Sites of structural and energy signals correlate well to the positions playing important roles in pre-mRNA splicing.     

Temperature and Photoperiod Influence Postharvest Needle Abscission of Selected Balsam Fir (Abies balsamea L. (Mill.)) Genotypes by Modulating ABA Levels

Seasonal changes in the concentration of abscisic acid (ABA) in current-year needles of two different genotypes (AB-NSD-004 and AB-NSD-184) were monitored in branches collected from 20-year-old balsam fir (Abies balsamea L. (Mill.)) trees over a period of 11 months. A significant genotype × harvesting time interaction was observed for endogenous ABA levels and postharvest needle retention duration (NRD). A consistent pattern of seasonal variation in ABA concentration was observed in both genotypes, with the highest amount of ABA (7,887 ng g^?1 DW) accumulating in April and May. The highest levels of ABA coincided with the lowest postharvest NRD regardless of genotype. Nevertheless, genotypes differed in their ABA concentrations. Branches of genotype AB-NSD-184 sampled during August exhibited 170 days of NRD whereas those collected in May and June registered the lowest NRD of around 40 days. There was a significant negative correlation (P < 0.05) between endogenous ABA concentrations and postharvest NRD in genotype AB-NSD-184. Also, an inverse relationship was observed between the average daily photoperiod and the postharvest NRD (R ² = 0.35; P = 0.000) in the same genotype. Together with average daily temperature, the R ² value for this correlation reached the highest (0.75; P ≤ 0.00). Genotypes differed in their physiological responses to environmental cues and thus differed in their postharvest qualities. Average daily photoperiod and maximum daily temperature are strongly linked to the postharvest NRD through modulating endogenous ABA concentration.     

The Role of Carboxy-Terminal Glycosaminoglycan-binding Domain of Vitronectin in Cytoskeletal Organization and Migration of Endothelial Cells

Vitronectin is a major cell adhesion molecule present in the subendothelial matrix that mediates the attachment and spreading of a variety of cells. The carboxy-terminal end of vitronectin has a consensus sequence for glycosaminoglycan-binding. To define the functional role of this domain, we generated fragments of vitronectin that lack the glycosaminoglycan-binding domain by formic acid cleavage of plasma-derived vitronectin. In addition, we also generated similar recombinant fragments of vitronectin as glutathione S-transferase fusion proteins in E. coll. These fragments were tested for their ability to support the adhesion of human umbilical vein endothelial cells. These fragments promoted endothelial cell adhesion, reaching half maximal activity at 2-5 μg/well compared to plasma-derived vitronectin which reached at 0.2 μg/well. However, the cells that adhered to these fragments did not develop well-formed focal adhesion plaques and actin stress fibers. In addition, these fragments were poorly chemotactic for endothelial cell migration when compared to intact plasma-derived vitronectin in a modified Boyden chamber assay. The present studies show that carboxy-terminal glycosaminoglycan-binding domain of vitronectin is essential for proper cytoskeletal organization and migration of endothelial cells on vitronectin substratum.