Investigation of a failed DNA assay leads to identification of an unexpected contaminant in a commonly used chromatography buffer

For mammalian cell-derived recombinant biotherapeutics, controlling host cell DNA levels below a threshold is a regulatory requirement to ensure patient safety. DNA removal during drug substance manufacture is accomplished by a series of chromatography-based purification steps and a qPCR-based analytical method is most used to measure DNA content in the purified drug substance to enable material disposition. While the qPCR approach is mature and its application to DNA measurement is widespread in the industry, it is susceptible to trace levels of process-related contaminants that are carried forward. In this study, we observed failures in spike recovery studies that are an integral component of the qPCR-based DNA testing, suggesting the presence of an inhibitory compound in the sample matrix. We generated hypotheses around the origin of the inhibitory compound and generated multiple sample matrices and deployed a suite of analytical techniques including Raman and NMR spectroscopy to determine the origin and identity of the inhibitory compound. The caustic wash step and depth filter extractables were ruled out as root causes after extensive experimentation and DNA testing. Subsequently, 2-(N-morpholino)ethanesulfonic acid (MES), a buffer used in the chromatography unit operations, was identified as the source of the contaminant. A 500-fold concentration followed by Raman and NMR spectroscopy analysis revealed the identity of the inhibitory compound as polyvinyl sulfone (PVS), an impurity that originates in the MES manufacturing process. We have implemented PVS concentration controls for incoming MES raw material, and our work highlights the need for rigor in raw material qualification and control.     

Identification and over-expression of a thermostable lipase from Geobacillus thermoleovorans Toshki in Escherichia coli

A newly isolated thermophilic strain producing thermostable lipase was identified based on 16S rRNA sequencing, where phylogenetic analysis revealed its closeness to Geobacillus thermoleovorans. Thermostable lipase from this bacterium was cloned using consensus degenerate PCR primers. For over-expression in Escherichia coli, the lipase gene was sub-cloned in pET 15b vector with a strong T7 promotor. Lipase activity was approximately 4.5-fold higher than in the wild-type strain. The lipase enzyme was thermostable at 60 degrees C and pH 8, whereas a 30% residual activity was retained when incubated for 1h at 100 degrees C. Optimum lipase expression was obtained in 2 x YT medium after 70min of induction by IPTG.     

Complete genome sequence of the myxobacterium Sorangium cellulosum

The genus Sorangium synthesizes approximately half of the secondary metabolites isolated from myxobacteria, including the anti-cancer metabolite epothilone. We report the complete genome sequence of the model Sorangium strain S. cellulosum So ce56, which produces several natural products and has morphological and physiological properties typical of the genus. The circular genome, comprising 13,033,779 base pairs, is the largest bacterial genome sequenced to date. No global synteny with the genome of Myxococcus xanthus is apparent, revealing an unanticipated level of divergence between these myxobacteria. A large percentage of the genome is devoted to regulation, particularly post-translational phosphorylation, which probably supports the strain's complex, social lifestyle. This regulatory network includes the highest number of eukaryotic protein kinase-like kinases discovered in any organism. Seventeen secondary metabolite loci are encoded in the genome, as well as many enzymes with potential utility in industry.     

Synthesis,Characterization, and Antimicrobial Activity of Some New Thiophene Derivatives and Crystal Structure of Ethyl [4-(2-Thienylmethylene)Aminophenoxy]Acetate

Russian Journal of Bioorganic Chemistry - This work describes facile routes towards the synthesis of some novel thiophene derivatives. Thus, condensation of thiophene-2-carboxaldehyde with...     

Lipase production from a novel thermophilic Bacillus sp.: application of Plackett-Burman design for evaluating culture conditions affecting enzyme formation

A novel thermophilic Bacillus sp. capable of producing lipase was locally isolated. Phylogenetic analysis based on 16SrDNA sequence revealed its close relationship to Bacillus thermoleovorans. Plackett-Burman experimental design was used to evaluate cultural conditions affecting lipase production process. Fifteen variables and four dummy variables were examined in the experimental design. Tween 80, temperature, olive oil, aeration, beef extract and inoculum age were found to be the highest positive significant variables affecting lipase activity, whereas pH and calcium chloride were the highest negative significant variables. Moreover, Tween 80, temperature and olive oil positively affected lipase specific activity. On the other hand, gum arabic, inoculum size and calcium chloride had the highest negative effect on lipase specific activity. This study would improve the further optimization steps on the bioprocess development track.     

Sympatric morphotypes of the restricted-range Tashan Cave Garra: distinct species or a case of phenotypic plasticity?

Environmental Biology of Fishes - Among Tashan cave barb Garra tashanensis inhabiting a small cave in southwest Iran, two mental disc (sucking mouth disc) forms were observed. To assess their...     

Interactions of the natural product kendomycin and the 20S proteasome

Natural products are a valuable source for novel lead structures in drug discovery, but for the majority of isolated bioactive compounds, the cellular targets are unknown. The structurally unique ansa-polyketide kendomycin (KM) was reported to exert its potent cytotoxic effects via impairment of the ubiquitin proteasome system, but the exact mode of action remained unclear. Here, we present a systematic biochemical characterization of KM–proteasome interactions in vitro and in vivo, including complex structures of wild type and mutant yeast 20S proteasome with KM. Our results provide evidence for a polypharmacological mode of action for KM's cytotoxic effect on cancer cells.     

Insulin-releasing properties of the frog skin peptide pseudin-2 and its [Lys18]-substituted analogue

Abstract Pseudin-2 is a cationic alpha-helical peptide that was first isolated from the skin of the paradoxical frog Pseudis paradoxa on the basis of its antimicrobial activity. We have investigated the insulin-releasing properties and cytotoxicity of the peptide, together with selected analogues with increased cationicity and hydrophobicity. At concentrations in the range 10(-9)-10(-6) m, pseudin-2, and its [Lys18], [Phe8], and [d-Lys3,d-Lys10,d-Lys14] derivatives, stimulated insulin release from the BRIN-BD11 clonal beta-cell line without increasing release of lactate dehydrogenase. The [Lys18] analogue was the most potent (46% increase in insulin release at 10(-9) m) and the most effective (215% increase in insulin release at 10(-6) m). The more cationic [Lys3,Lys10,Lys14] and [Lys3,Lys10,Lys14,Lys21] analogues lacked insulinotropic action and the more hydrophobic [Phe16] analogue was cytotoxic at concentrations > or =10(-7) m. Pseudin-2 and [Lys18]-pseudin-2 had no effect on intracellular calcium concentrations and stimulated insulin release in the absence of external calcium. [Lys18]-pseudin-2 (10(-8) m) stimulated insulin release in the presence of diazoxide and verapamil. Our results demonstrate that pseudin-2 stimulates insulin secretion from BRIN-BD11 cells by a mechanism involving Ca2+-independent pathways and identify [Lys18]-pseudin-2 as a peptide that may have potential for development as a therapeutically valuable insulinotropic agent for the treatment of type 2 diabetes.     

Study of enhancement and inhibition phenomena and genes relating to degradation of petroleum polycyclic aromatic hydrocarbons in isolated bacteria

Polycyclic aromatic hydrocarbons (PAHs) are xenobiotic compounds, which being degraded by chemical, physical or biological methods. The latter is the safest and the cheapest one. Two bacterial strains ASU-01 and ASU-016 were isolated from different Egyptian petroleum contaminated sites. They were genetically identified based on the analysis of the nucleotide sequences of the 16S ribosomal PNA gene and the phylogenetic tree as Enterobacter hormaechei and Pseudomonas pseudoalcaligenes respectively. When pyrene as high molecular weight (HMW)-PAH was added as a sole carbon source, both strains could degrade it with efficiency 77.7 and 83.7% within 15 days of incubation, respectively. However, when it was mixed with low molecular weight (LMW)-PAHs, two opposite phenomena appeared. The first one was enhancement, which occurred with ASU-01. This strain shifted pyrene efficiency to 98.5%. The second phenomenon was inhibition occurred with ASU-016 which completely retarded pyrene degradation. Naphthalene dioxygenase (nahAc), and catechol dioxygenases (C12O and C23O) genes were detected in the two strains based on PCR. The detected genes were confirmed by determining the different specific activities of their translated protein (enzymes) on different PAHs. The maximum values of biosurfacatant production activity and cell-surface and percentage of cell-surface hydrophobicity (CSH) were detected during the exponential phase. These latter factors increased the bioavailability and consequently, the assimilation of PAHs.     

Desmettianosides A and B, bisdesmosidic furostanol saponins with molluscicidal activity from Yucca desmettiana

Bioactivity-guided separation of the aqueous methanolic extract of Yucca desmettiana leaves, which in a preliminary screening exhibited significant molluscicidal activity, led to the isolation and structure elucidation of two new steroidal saponins (1 and 2). The structures of desmettianosides A and B, identified as bisdesmosidic furostanol glycosides with six and five sugar units, respectively, were established by detailed spectroscopic analyses of their NMR and MS data. Compounds 1 and 2 exhibited high molluscicidal activity against Biomphalaria alexandrina snails with LC100 values of 6 and 11 mg/L, respectively.