Effect of DNA structural flexibility on promoter strength--molecular dynamics studies of E. coli promoter sequences

To study possible correlations between promoter activity and the structural flexibility of the DNA helix, we have carried out unrestrained molecular dynamics simulations of the -10 consensus region sequence and five variants forming the -10 region of various Escherichia coli promoter sequences. Analyses of the trajectories obtained from the simulations show that the consensus sequence has a pattern of two structurally flexible nucleotide steps sandwiched between two stiff steps. In the other sequences, this pattern varies in consonance with the change in the sequence. The variations in the patterns show correlation with the promoter strength.     

Diversity and distribution of terricolous lichens as indicator of habitat heterogeneity and grazing induced trampling in a temperate-alpine shrub and meadow

Lichens are among the most sensitive biomonitors of ecosystem health and human induced disturbances. Terricolous lichens of Chopta–Tungnath (Garhwal, western Himalaya, India) were analysed for their ability to indicate habitat variability and disturbances induced by livestock grazing. Terricolous lichens were sampled from 12 sites, distributed across the three macrohabitats between 2,700 and 4,001 m, using 50 × 10 cm narrow frequency grids having five 10 × 10 cm sampling units. The terricolous lichen community of the area constituted, 20 species belonging to 10 genera, five families and four growth forms. Altitude and relative humidity were the major habitat factors found influencing the terricolous lichen community of the landscape. Fruticose and compound soil lichen growth forms were found indicative of habitat disturbance largely caused by grazing induced trampling. Terricolous lichen diversity of the area was delimited by grazing pressure at mid-altitudes (3,000–3,400 m) and by decreasing soil cover at higher altitudes (>3,400 m).     

Current perspectives on stability of protein drug products during formulation, fill and finish operations

Commercialization of protein-based therapeutics is a challenging task in part due to the difficulties in maintaining protein solutions safe and efficacious throughout the drug product development process, storage, transportation and patient administration. Bulk drug substance goes through a series of formulation, fill and finish operations to provide the final dosage form in the desired formulation and container or delivery device. Different process parameters during each of these operations can affect the purity, activity and efficacy of the final product. Common protein degradation pathways and the various physical and chemical factors that can induce such reactions have been extensively studied for years. This review presents an overview of the various formulation-fill-finish operations with a focus on processing steps and conditions that can impact product quality. Various manufacturing operations including bulk freeze-thaw, formulation, filtration, filling, lyophilization, inspection, labeling, packaging, storage, transport and delivery have been reviewed. The article highlights our present day understanding of protein instability issues during biopharmaceutical manufacturing and provides guidance on process considerations that can help alleviate these concerns.     

Inhibition of aflatoxin-induced liver damage in ducklings by food additives

Inhibitory effects of food additives on toxicity induced by aflatoxin B₁ was conducted in 3-day-old ducklings. Aflatoxin B₁ at a dose of 5 μg/day per animal for 14 days induced severe liver damage which included necrosis, fatty changes, and biliary hyperplasia. These changes were found to be inhibited by the daily administration of turmeric (50mg), curcumin (10 mg), and ellagic acid (10 mg) in the diet. Addition of BHA-butylated hydroxy anisole (10 mg), BHT-butylated hydroxy toluene (10 mg), garlic (500 mg), and asafoetida (50 mg) inhibited necrosis and degeneration of the tissue, while biliary hyperplasia persisted. Biochemical and haematological parameters were not significantly altered under the conditions studied.     

CTL recognize different determinants from those defined serologically on Ld somatic cell mutants

Reciprocal Ld structural mutants have been isolated from a somatic cell line. Testing of allogeneic CTL clones on these mutants suggests that the majority of CTL clones recognize determinants different from those that elicit antibody production. Of 36 CTL clones tested, only three clones appeared to recognize a determinant that was related to the negatively selected serologic determinant. However, mAb blocking studies suggest that inhibition of CTL activity by anti-H-2 mAb does not necessarily reflect the fine specificity of the CTL activity.     

Spontaneous deletion at the B2m locus: evidence for site-specific genetic rearrangement

We have isolated 20 independent spontaneous mutants in the B2mb allele from a B2ma/b heterozygous murine cell line by immunoselection in vitro with a monoclonal antibody directed against the product of the B2mb allele. One class of mutants has undergone a deletion in the 5' end of the B2mb gene. The deletions appear to be identical in all of the independent clones, and extend an unknown distance upstream of the B2m gene from a region in the first intron. Southern blot analysis with the use of oligonucleotides to the wild type gene sequence mapped the breakpoint to within 39 base pairs. The high frequency of independent spontaneous mutants showing indistinguishable deletions suggests that the first intron of the B2m gene contains sequences that are highly susceptible to site-specific recombinations.     

Soluble Collagen VI Induces Tyrosine Phosphorylation of Paxillin and Focal Adhesion Kinase and Activates the MAP Kinase Erk2 in Fibroblasts

Signals from the extracellular matrix can modulate cellular differentiation and gene expression. We have shown previously that in contrast to other extracellular matrix molecules pepsin-solubilized collagen VI (CVI) can stimulate DNA synthesis of various mesenchymal cell types, apparently independent of integrin-mediated signal transduction. In order to further elucidate collagen VI-induced signaling events, we exposed mouse 3T3 fibroblasts and human HT1080 fibrosarcoma cells to soluble CVI. CVI induced tyrosine phosphorylation of proteins that associate with focal adhesions, such as paxillin, focal adhesion kinase (FAK), and p130CAS. Furthermore, it activated the mitogen-activated protein kinase, erk2. Kinetic analysis showed that these phosphorylations were transient, reaching a maximum after 5 min for transformed HT1080 cells and 30 min for 3T3 fibroblasts. These effects were partly inhibited by a beta1-integrin function blocking antibody and by single chains of CVI. Our results indicate that soluble fragments of native collagen VI, a ubiquitous component of the interstitial extracellular matrix, can mediate stimulation of DNA synthesis via tyrosine phosphorylation of paxillin, FAK, p130CAS, and erk2 in the absence of classical growth factors. Thus, CVI may serve as a matrix-derived sensor that allows for rapid reconstitution of a tissue defect by activating nearby mesenchymal cells.