Array-based evolution of DNA aptamers allows modelling of an explicit sequence-fitness landscape

Mapping the landscape of possible macromolecular polymer sequences to their fitness in performing biological functions is a challenge across the biosciences. A paradigm is the case of aptamers, nucleic acids that can be selected to bind particular target molecules. We have characterized the sequence-fitness landscape for aptamers binding allophycocyanin (APC) protein via a novel Closed Loop Aptameric Directed Evolution (CLADE) approach. In contrast to the conventional SELEX methodology, selection and mutation of aptamer sequences was carried out in silico, with explicit fitness assays for 44 131 aptamers of known sequence using DNA microarrays in vitro. We capture the landscape using a predictive machine learning model linking sequence features and function and validate this model using 5500 entirely separate test sequences, which give a very high observed versus predicted correlation of 0.87. This approach reveals a complex sequence-fitness mapping, and hypotheses for the physical basis of aptameric binding; it also enables rapid design of novel aptamers with desired binding properties. We demonstrate an extension to the approach by incorporating prior knowledge into CLADE, resulting in some of the tightest binding sequences.     

Challenging the workhorse: Comparative analysis of eukaryotic micro-organisms for expressing monoclonal antibodies

For commercial protein therapeutics, Chinese hamster ovary (CHO) cells have an established history of safety, proven capability to express a wide range of therapeutic proteins and high volumetric productivities. Expanding global markets for therapeutic proteins and increasing concerns for broadened access of these medicines has catalyzed consideration of alternative approaches to this platform. Reaching these objectives likely will require an order of magnitude increase in volumetric productivity and a corresponding reduction in the costs of manufacture. For CHO-based manufacturing, achieving this combination of targeted improvements presents challenges. Based on a holistic analysis, the choice of host cells was identified as the single most influential factor for both increasing productivity and decreasing costs. Here we evaluated eight wild-type eukaryotic micro-organisms with prior histories of recombinant protein expression. The evaluation focused on assessing the potential of each host, and their corresponding phyla, with respect to key attributes relevant for manufacturing, namely (a) growth rates in industry-relevant media, (b) adaptability to modern techniques for genome editing, and (c) initial characterization of product quality. These characterizations showed that multiple organisms may be suitable for production with appropriate engineering and development and highlighted that yeast in general present advantages for rapid genome engineering and development cycles.     

Critical photoperiod and daylength threshold differences between northern and southern populations of the butterfly Limenitis archippus

Laboratory studies show that different photoperiods induce diapause in northern (Vermont) and southern (Maryland) larval strains of the butterfly Limenitis archippus. The northern strain responds to $\text{1}\text{2}\text{hr}$ longer photoperiod thresholds and critical ranges than does the southern one. These responses are correlated with geographic differences in the ambient photoperiod of the two localities. In this facultative diapausing species, third instar larvae construct hibernacula within the basal portions of tubular leaves spun with silk, when daylength approaches either 13·5 hr (Vermont strain) or 13·0 hr (Maryland strain). When reared in total darkness some larvae develop directly to fourth inszar without diapause, although mortality is high. Among both strains different broods exhibit different incidences of diapause. Reciprocal inter-strain hybrids show intermediate diapause responses, suggesting that larval diapause is under the control of multiple genes.     

Zone collector and transfer device for thin-layer chromatography

Recently I have begun to use two-dimensional thin-layer chromatography (tlc) in place of paper chromatography for the kinetic analysis of photosynthetic incorporation of tracer carbon into plant metabolites. Because our general experimental approach (1–3) generates a large number of tlc fractions of widely different radioactivity, an economical, convenient, and rapid technique for collecting and transferring tlc zones to liquid-scintillation vials was required. Many zone collectors have been described (4–11) but were judged inadequate because of one or more of the following disadvantages: potential contamination by adsorbent from previous use adhering to the device, clogging of fritted glass filters, need for cleaning and drying prior to reuse, or need for a separate device for each sample. This report describes a device which is free of these disadvantages and is suitable for rapid collection and transfer of a series of zones.     

Variations in assimilation number of coastal marine phyto-phytoplankton: Effects of environmental co-variates

Seasonal variations in maximum specific production rate (assimilationnumber) of natural phytoplankton from a shallow marine basinwere studied in relation to environmental changes over a 22-monthperiod. Assimilation number variations were considerable (>6fold) and were correlated with both environmental and biologicalco-variates. Temperature was the most significant co-variate,accounting for 40% of the observed variation in assimilationnumber. No significant relationship was apparent between changesin assimilation number and nutrient concentrations.     

THE RELATIONSHIP BETWEEN PHOTOSYNTHESIS AND LIGHT FOR NATURAL ASSEMBLAGES OF COASTAL MARINE PHYTOPLANKTON1

In a series of 188 experiments on the, light-saturation curve for natural assemblages of phytoplankton at 3 stations in Nova Scotia coastal waters, it was found that both the initial slope (α) of the curve and the assimilation number (P_m^B) varied about 5-fold throughout the year. No differences could be detected between stations, but both α and P_m^B decreased with depth. The mean value of α for all the experiments was 0.21 mg C[mg Chl a]^?1· h^?1· W^?1· m² with a range from 0.03 to 0.63. An explanation is offered for the nonconstancy of a in terms of the effect of cell-size and shape on self-shading. An estimate is made from first principles of the physiological maximum-attainable value of α. This estimate corresponds, within the limits of experimental error, to the highest values of α observed in the study. It is deduced that on the average the phytoplankton were photosynthesizing at only 44% maximum capacity. The mean value of P_m^B for all experiments was 4.9 mg C[mg Chl a]^?1· h^?1, with a range from 0.73 to 24.8. In the matrix of partial correlation coefficients, α and P_m^B were positively correlated with each other; α was correlated with mean solar radiation averaged over the 3 days prior to the experiment, but uncorrelated with temperature; P_m^B was correlated strongly with temperature but uncorrelated with recent solar radiation. The results show that P_m^B could be estimated from α and temperature using an empirical multiple regression equation, independent of depth. It is suggested that α and P_m^B are both correlated with some other factor not measured in the study, perhaps the mean cell-size of the populations, or the nutrient status of the cells. The predictability of primary production is discussed in the light of this evidence.