Design of experiments applications in bioprocessing: Chromatography process development using split design of experiments

Development of a chromatographic step in a time and resource efficient manner remains a serious bottleneck in protein purification. Chromatographic performance typically depends on raw material attributes, feed material attributes, process factors, and their interactions. Design of experiments (DOE) based process development is often chosen for this purpose. A challenge is, however, in performing a DOE with such a large number of process factors. A split DOE approach based on process knowledge in order to reduce the number of experiments is proposed. The first DOE targets optimizing factors that are likely to significantly impact the process and their effect on process performance is unknown. The second DOE aims to fine-tune another set of interacting process factors, impact of whom on process performance is known from process understanding. Furthermore, modeling of a large set of output response variables has been achieved by fitting the output responses to an empirical equation and then using the parametric constants of the equation as output response variables for regression modeling. Two case studies involving hydrophobic interaction chromatography for removal of aggregates and cation exchange chromatography for separation of charge variants and aggregates have been utilized to illustrate the proposed approach. Proposed methodology reduced total number of experiments by 25% and 72% compared to a single DOE based on central composite design and full factorial design, respectively. The proposed approach is likely to result in a significant reduction in resources required as well as time taken during process development. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 35: e2730, 2019     

Palynological studies of some roadside plants under exposure to traffic stress

The diverse pollutants emitted from automobiles can have adverse effects on the health and survival of plants, animals and human beings. Different plant species have been known to possess high potential of absorption, detoxification and tolerance of high levels of pollution. Considering this, the present study was carried out to assess the impact of automobile pollution on palynology of roadside plants. Three species, viz. Cannabis sativa, Cassia fistula and Thevetia peruviana growing along the roadsides of nine sites of Amritsar city under different levels of traffic stress were selected for the study. Pollen viability and pollen size were studied by staining pollen with 2,3,5-triphenyl tetrazolium chloride stain and observed under light microscope. Scanning electron microscope was used to study the changes in morphology of the pollen grains. It was observed that the percentage of pollen viability of three species was inversely proportional to the load of traffic at a particular site. Pollen viability was observed to be minimum (C. sativa—22.58 %; C. fistula—21.30 %; and T. peruviana—6.22 %) for the plants of the three species studied growing at traffic site I, site with heavy traffic load as compared to plants growing at sites with comparatively lesser traffic load. C. sativa growing at traffic site IV showed maximum pollen viability of 79.74 %, while C. fistula and T. peruviana growing at traffic site VIII exhibited maximum pollen viability of 83.32 and 68.78 %, respectively. Pollen size and morphology did not show any significant variation and remained unaffected with the increase in traffic stress.     

Small molecule inhibitors of E. coli primase, a novel bacterial target

Bacterial primase is essential for DNA replication in Gram-positive and Gram-negative bacteria. It is also structurally distinct from eukaryotic primases, and therefore an attractive, but under-explored, target for therapeutic intervention. We applied virtual screening to discover primase inhibitors, and subsequently several commercially available analogs of these initial hits showed potent primase inhibition and in vitro antibacterial activity. This work provides a 3D pharmacophore for primase ligands, SAR trends, and leads that can be further optimized.     

Molecular analysis of CAG repeats at five different spinocerebellar ataxia loci: correlation and alternative explanations for disease pathogenesis

Spinocerebellar ataxias (SCAs) are caused by expansion of (CAG)n triplet repeats. These repeats occur as polymorphic forms in general population; however, beyond a threshold size they become pathogenic. The sizes and distributions of repeats at the SCA1, SCA2, SCA3, SCA7 and DRPLA loci were assessed by molecular analysis of 124 unrelated ataxia patients and 44 controls, and the association of larger normal (LN) alleles with disease prevalence was evaluated. Triplet repeat expansions in the disease range were detected in 8% (10/124) of the cases, with the majority having expansion at the SCA1 locus. Normal allele ranges in the cohort studied were similar to the Caucasian and North Indian populations but differed from the Korean and Japanese populations at various loci. The percentage of individuals with LN alleles at the SCA1 and SCA2 loci was higher than reported in Indians, Japanese and Caucasians. LN alleles showed a good correlation with the incidence of SCA1, indicating that SCA1 is the most prevalent ataxia in our population. The majority of cases with clinical symptoms of SCA could not be diagnosed by established CAG repeat criteria, suggesting that there may be an alternative basis for disease pathogenesis: (i) Repeats lower than the normal range may also result in abnormal phenotypes (ii) LN alleles at different loci in the same individual may contribute to symptoms (iii) Exogenous factors may play a role in triggering disease symptoms in individuals with LN alleles (iv) Triplet repeats may reach the disease range in the brain but not in the blood.     

Effect of the hydrocarbon chain and polymethylene spacer lengths on gene transfection efficacies of gemini lipids based on aromatic backbone

Design, syntheses, and gene delivery efficacies of fifteen novel gemini (dimeric) and three monomeric cationic lipids anchored on an aromatic backbone have been described. Each new lipid has been used for liposome formation, and optimal formulations were used to determine the structure-activity correlation of the gene transfection efficacies of these lipids in HeLa and HT1080 cells. The results of the present investigation bring out the effect of hydrocarbon chain lengths and the length of the spacer between the headgroups on gene transfection efficiencies of the cationic gemini lipids based on aromatic backbone. The lipids bearing n-C 14H 29 hydrocarbon chain lengths have been found to be the best transfecting agents compared to their counterparts with n-C 16H 33 and n-C 12H 25 chains in HeLa cells. On the other hand, in HT1080 cells, the lipids based on n-C 12H 25 and n-C 14H 29 chains were found to be more potent transfecting agents than lipids possessing n-C 16H 33 chains. Transmission electron microscopy examination revealed the existence of spherical lipid-DNA complexes.     

Synthesis and gene transfer activities of novel serum compatible cholesterol-based gemini lipids possessing oxyethylene-type spacers

Four novel cholesterol-based gemini cationic lipids differing in the length of oxyethylene-type spacers [-CH2-(CH2-O-CH2)n-CH2-] between each ammonium headgroup have been synthesized. These formed stable suspensions in aqueous media. Cationic liposomes were prepared from each of these lipids individually and as mixtures of cationic lipid and DOPE. These were used as nonviral gene delivery agents. All the cholesterol-based gemini lipids induced better transfection activity than their monomeric counterpart. Inclusion of DOPE in co-liposomal formulation of the cationic gemini lipid potentiates their gene transfer activity significantly. A major characteristic feature of these oxyethylene spacer based cholesterol gemini lipids was that serum does not inhibit the transfection activity of these gemini lipids, whereas the transfection activity of their monomeric counterpart decreased drastically in the presence of serum. One of the cholesterol-based gemini lipids 2a possessing a -CH2-CH2-O-CH2-CH2- spacer showed the highest transfection activity.     

Deletion of the developmentally essential gene ATR in adult mice leads to age-related phenotypes and stem cell loss

Developmental abnormalities, cancer, and premature aging each have been linked to defects in the DNA damage response (DDR). Mutations in the ATR checkpoint regulator cause developmental defects in mice (pregastrulation lethality) and humans (Seckel syndrome). Here we show that eliminating ATR in adult mice leads to defects in tissue homeostasis and the rapid appearance of age-related phenotypes, such as hair graying, alopecia, kyphosis, osteoporosis, thymic involution, fibrosis, and other abnormalities. Histological and genetic analyses indicate that ATR deletion causes acute cellular loss in tissues in which continuous cell proliferation is required for maintenance. Importantly, thymic involution, alopecia, and hair graying in ATR knockout mice were associated with dramatic reductions in tissue-specific stem and progenitor cells and exhaustion of tissue renewal and homeostatic capacity. In aggregate, these studies suggest that reduced regenerative capacity in adults via deletion of a developmentally essential DDR gene is sufficient to cause the premature appearance of age-related phenotypes.     

The complete genome sequence of Bacillus thuringiensis Al Hakam

Bacillus thuringiensis is an insect pathogen that is widely used as a biopesticide (E. Schnepf, N. Crickmore, J. Van Rie, D. Lereclus, J. Baum, J. Feitelson, D. R. Zeigler, and D. H. Dean, Microbiol. Mol. Biol. Rev. 62:775-806, 1998). Here we report the finished, annotated genome sequence of B. thuringiensis Al Hakam, which was collected in Iraq by the United Nations Special Commission (L. Radnedge, P. Agron, K. Hill, P. Jackson, L. Ticknor, P. Keim, and G. Andersen, Appl. Environ. Microbiol. 69:2755-2764, 2003).