Informatic search strategies to discover analogues and variants of natural product archetypes

Natural products are a crucial source of antimicrobial agents, but reliance on low-resolution bioactivity-guided approaches has led to diminishing interest in discovery programmes. Here, we demonstrate that two in-house automated informatic platforms can be used to target classes of biologically active natural products, specifically, peptaibols. We demonstrate that mass spectrometry-based informatic approaches can be used to detect natural products with high sensitivity, identifying desired agents present in complex microbial extracts. Using our specialised software packages, we could elaborate specific branches of chemical space, uncovering new variants of trichopolyn and demonstrating a way forward in mining natural products as a valuable source of potential pharmaceutical agents.     

Trophic plasticity among spring vs. cave populations of <Emphasis Type="Italic">Gammarus minus:</Emphasis> examining functional niches using stable isotopes and C/N ratios

In some environments, species may exhibit trophic plasticity, which allows them to extend beyond their assigned functional group. For Gammarus minus, a freshwater amphipod classified as a shredder or detritivore, cave populations have been observed consuming heterotrophs as well as shredding leaves, and therefore may be exhibiting trophic plasticity. To test this possibility, we examined the C and N stable isotope and C/N ratios for cave and spring populations of G. minus. A 15-day feeding experiment using leaves and G. minus from a spring population established that the diet-tissue discrimination factor was 3.2 ‰ for δ¹⁵N. Cave G. minus were 8 ‰ higher in δ¹⁵N relative to cave leaves, indicating they did not derive nitrogen from leaves, whereas field collected spring populations were 2–3 ‰ higher than spring leaves, indicating that they did. Cave G. minus were 2.6 ‰ higher in δ¹⁵N than the cave isopod, Caecidotea holsingeri. Relative to spring populations, Organ Cave G. minus were ¹⁵N enriched by 6 ‰, suggesting they occupied a different trophic level, or incorporated an isotopically distinct N source. While stable isotopes cannot tell what the cave G. minus are eating, the isotopes certainly show that G. minus are not eating leaves and are trophically distinct form the surface populations. Differences in C/N ratios were observed, but reflect the size of the G. minus examined and not feeding group or habitat. The isotope data strongly support the hypothesis that cave populations of G. minus have become generalist or omnivorous by including animal protein in their diet.     

Genomic Modifiers of Natural Killer Cells,Immune Responsiveness and Lymphoid Tissue Remodeling Together Increase Host Resistance to Viral Infection

The MHC class I D^k molecule supplies vital host resistance during murine cytomegalovirus (MCMV) infection. Natural killer (NK) cells expressing the Ly49G2 inhibitory receptor, which specifically binds D^k, are required to control viral spread. The extent of D^k-dependent host resistance, however, differs significantly amongst related strains of mice, C57L and MA/My. As a result, we predicted that relatively small-effect modifier genetic loci might together shape immune cell features, NK cell reactivity, and the host immune response to MCMV. A robust D^k-dependent genetic effect, however, has so far hindered attempts to identify additional host resistance factors. Thus, we applied genomic mapping strategies and multicolor flow cytometric analysis of immune cells in naive and virus-infected hosts to identify genetic modifiers of the host immune response to MCMV. We discovered and validated many quantitative trait loci (QTL); these were mapped to at least 19 positions on 16 chromosomes. Intriguingly, one newly discovered non-MHC locus (Cmv5) controlled splenic NK cell accrual, secondary lymphoid organ structure, and lymphoid follicle development during MCMV infection. We infer that Cmv5 aids host resistance to MCMV infection by expanding NK cells needed to preserve and protect essential tissue structural elements, to enhance lymphoid remodeling and to increase viral clearance in spleen.     

Impact of cell culture on recombinant monoclonal antibody product heterogeneity

Recombinant monoclonal antibodies are commonly expressed in mammalian cell culture and purified by several steps of filtration and chromatography. The resulting high purity bulk drug substance still contains product variants differing in properties such as charge and size. Posttranslational modifications and degradations occurring during cell culture are the major sources of heterogeneity in bulk drug substance of recombinant monoclonal antibodies. The focus of the current review is the impact of cell culture conditions on the types and levels of various modifications and degradations of recombinant monoclonal antibodies. Understanding the relationship between cell culture and product variants can help to make consistently safe and efficacious products. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1103–1112, 2016     

A Presence-Only Model of Suitable Roosting Habitat for the Endangered Indiana Bat in the Southern Appalachians

We know little about how forest bats, which are cryptic and mobile, use roosts on a landscape scale. For widely distributed species like the endangered Indiana bat Myotis sodalis, identifying landscape-scale roost habitat associations will be important for managing the species in different regions where it occurs. For example, in the southern Appalachian Mountains, USA, M. sodalis roosts are scattered across a heavily forested landscape, which makes protecting individual roosts impractical during large-scale management activities. We created a predictive spatial model of summer roosting habitat to identify important predictors using the presence-only modeling program MaxEnt and an information theoretic approach for model comparison. Two of 26 candidate models together accounted for >0.93 of AICc weights. Elevation and forest type were top predictors of presence; aspect north/south and distance-to-ridge were also important. The final average best model indicated that 5% of the study area was suitable habitat and 0.5% was optimal. This model matched our field observations that, in the southern Appalachian Mountains, optimal roosting habitat for M. sodalis is near the ridge top in south-facing mixed pine-hardwood forests at elevations from 260–575 m. Our findings, coupled with data from other studies, suggest M. sodalis is flexible in roost habitat selection across different ecoregions with varying topography and land use patterns. We caution that, while mature pine-hardwood forests are important now, specific areas of suitable and optimal habitat will change over time. Combining the information theoretic approach with presence-only models makes it possible to develop landscape-scale habitat suitability maps for forest bats.     

Separation of lymphokine-activated killer cell precursors and T-cells: differential growth characteristics and apparent lack of a T-cell suppressor of LAK-cell induction

Lymphokine activated killer (LAK) cell clinical effectiveness may be limited by the total cell dose and cytotoxic activity. We have, therefore, examined methods to expand the number of LAK-cells by serial passage of unfractionated and fractionated peripheral blood lymphocytes. Human purified lymphocytes were obtained by Ficoll Hypaque gradients followed by exposure of resultant mononuclear cells to phenylalanine methyl ester to remove monocytes. Lymphocytes were then fractionated on a six-step Percoll gradient (50%, 47.5%, 45%, 42.5%, 40%, and 37.5% Percoll). Unfractionated cells and fractions were cultured in standard media (RPMI-1640, 10% human sera, antibiotics and 10 mM HEPES) containing 10 nM of recombinant Interleukin-2 (rIL-2). Lymphocytes were cultured at 1 X 10(6)/ml and recultured every 3 to 4 days in fresh standard media and rIL-2. Utilizing unfractionated and fractionated lymphocytes from seven donors we made the following observations: (1) Continued passage of unfractionated lymphocytes resulted in a loss of LAK-cell activity by greater than or equal to 14 days (e.g., percent lysis of Raji at 10:1 effector:target ratio on days 0, 4, 7, and 21 was 0.38 +/- 11, 41 +/- 17, and 8 +/- 1, n = 4, respectively). (2) LAK-cell functional precursors were predominantly confined to the lymphocytes in the upper (0-4) Percoll fractions (e.g., on day 4, the percent lysis by pooled fractions 1-4 was 63 +/- 5 vs. pooled fraction 5 plus pellet, 18 +/- 7%). (3) As expected, the upper fractions (0-4) were enriched for Leu 19 positive cells (approximately 40%) and large granular lymphocytes (LGL) by morphology (approximately 30%).(ABSTRACT TRUNCATED AT 250 WORDS)     

Immunogold localization of coenzyme F420-reducing formate dehydrogenase and coenzyme F420-reducing hydrogenase in Methanobacterium formicicum

The ultrastructural locations of the coenzyme F₄₂₀-reducing formate dehydrogenase and coenzyme F₄₂₀-reducing hydrogenase of Methanobacterium formicicum were determined using immunogold labeling of thin-sectioned, Lowicryl-embedded cells. Both enzymes were located predominantly at the cell membrane. Whole cells displayed minimal F₄₂₀-dependent formate dehydrogenase activity or F₄₂₀-dependent hydrogenase activity, and little activity was released upon osmotic shock treatment, suggesting that these enzymes are not soluble periplasmic proteins. Analysis of the deduced amino acid sequences of the formate dehydrogenase subunits revealed no hydrophobic regions that could qualify as putative membrane-spanning domains.Abbreviation PBST Phosphate-buffered saline containing 0.1% (v/v) Triton X-100