web cellHTS2: A web-application for the analysis of high-throughput screening data

Background  

The analysis of high-throughput screening data sets is an expanding field in bioinformatics. High-throughput screens by RNAi generate large primary data sets which need to be analyzed and annotated to identify relevant phenotypic hits. Large-scale RNAi screens are frequently used to identify novel factors that influence a broad range of cellular processes, including signaling pathway activity, cell proliferation, and host cell infection. Here, we present a web-based application utility for the end-to-end analysis of large cell-based screening experiments by cellHTS2.     

The social parasite Phengaris (Maculinea) nausithous affects genetic diversity within Myrmica rubra host ant colonies

Evolutionary theory predicts that high genetic variation maintains plasticity in a species’ response to parasite pressure. However, higher genetic diversity might also cause easier infiltration by social parasites, because odour diversity is high and nest-mate recognition poor. Here we test if the obligate myrmecophile Lycaenid butterfly Phengaris nausithous, a parasite of colonies of the highly polygynous ant Myrmica rubra causes local adaptation by enhancing genetic variance in parasitized versus non parasitized ant populations M. rubra colonies from six infested and three uninfested sites were assayed at five microsatellite loci to quantify genetic variation. Our results reveal isolation by distance and a significantly enhanced intracolonial variance due to the parasite pressure.     

Lack of effect of photoperiod on metabolism of exogenous GA19 and GA1 in Salix pentandra seedlings

The effect of photoperiod on metabolism of 16,17-[³H₂]GA₁₉, and 1.2-[³H₂]GA₁ applied to intact seedlings of Salix pentandra, was investigated. No difference was found in conversion of 16,17-[³H₂]GA₁₉ to 16,17-[³H₂]GA₂₀, and 16,17-[³H₂]GA₁, or in metabolism of 1,2-[³H₂]GA₁ to [³H]GA₈ between plants grown in continuous light and plants exposed for 14 days to a 12-h photoperiod. Also, leaf discs from plants grown in long or short days, converted 16,17-[³H₂]GA₁₉ both in light and darkness. These data on metabolism of 16,17-[³H₂]GA₁₉, contrast with previous results, which have indicated a photoperiodic control of the metabolism of GA₁₉ to GA₂₀ in S. pentandra. Presence of these applied labelled GAs and their metabolites in different parts of seedlings was recorded, after application to intact seedlings as well as to isolated plant parts. When 16,17-[³H₂]GA₁₉ was applied through the roots of intact plants, the relative amounts of 16,17-[³H₂]GA₁ present in leaves and shoot apices were higher than in roots and stems. In corresponding experiments with 1,2-[³H₂]GA₁, relatively higher amounts of [³H₂]GA₈ were found in roots and stems than in leaves and shoot apices. Twenty-four hours after application of 16,17-[³H₂]GA₁₉ to isolated plant parts, 16,17-[³H₂]GA₂₀ and 16,17-[³H₂]GA₁ were found in leaves and roots, but not in internodes. Incubation of isolated plant parts with 1,2-[³H₂]GA₁ for 24 h resulted in presence of [³H]GA₈ in all parts. The results mentioned above were obtained by monitoring metabolites by HPLC with on-line radio counting. The conversions of 17-[²H₂]GA₁₉ to 17-[²H₂]GA₂₀ and 17-[²H₂]GA₁ in shoot apices and whole seedlings, and of 17-[²H₂]GA₈ in whole seedlings, were confirmed by GC-MS.     

Structural Properties of the Human Protease-Activated Receptor 1 Changing by a Strong Antagonist

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Diversification across biomes in a continental lizard radiation

Ecological opportunity is a powerful driver of evolutionary diversification, and predicts rapid lineage and phenotypic diversification following colonization of competitor‐free habitats. Alternatively, topographic or environmental heterogeneity could be key to generating and sustaining diversity. We explore these hypotheses in a widespread lineage of Australian lizards: the Gehyra variegata group. This clade occurs across two biomes: the Australian monsoonal tropics (AMT), where it overlaps a separate, larger bodied clade of Gehyra and is largely restricted to rocks; and in the larger Australian arid zone (AAZ) where it has no congeners and occupies trees and rocks. New phylogenomic data and coalescent analyses of AAZ taxa resolve lineages and their relationships and reveal high diversity in the western AAZ (Pilbara region). The AMT and AAZ radiations represent separate radiations with no difference in speciation rates. Most taxa occur on rocks, with small geographic ranges relative to widespread generalist taxa across the vast central AAZ. Rock‐dwelling and generalist taxa differ morphologically, but only the lineage‐poor central AAZ taxa have accelerated evolution. This accords with increasing evidence that lineage and morphological diversity are poorly correlated, and suggests environmental heterogeneity and refugial dynamics have been more important than ecological release in elevating lineage diversity.     

Exploiting mAb structure characteristics for a directed QbD implementation in early process development

In today’s biopharmaceutical industries, the lead time to develop and produce a new monoclonal antibody takes years before it can be launched commercially. The reasons lie in the complexity of the monoclonal antibodies and the need for high product quality to ensure clinical safety which has a significant impact on the process development time. Frameworks such as quality by design are becoming widely used by the pharmaceutical industries as they introduce a systematic approach for building quality into the product. However, full implementation of quality by design has still not been achieved due to attrition mainly from limited risk assessment of product properties as well as the large number of process factors affecting product quality that needs to be investigated during the process development. This has introduced a need for better methods and tools that can be used for early risk assessment and predictions of critical product properties and process factors to enhance process development and reduce costs. In this review, we investigate how the quantitative structure–activity relationships framework can be applied to an existing process development framework such as quality by design in order to increase product understanding based on the protein structure of monoclonal antibodies. Compared to quality by design, where the effect of process parameters on the drug product are explored, quantitative structure–activity relationships gives a reversed perspective which investigates how the protein structure can affect the performance in different unit operations. This provides valuable information that can be used during the early process development of new drug products where limited process understanding is available. Thus, quantitative structure–activity relationships methodology is explored and explained in detail and we investigate the means of directly linking the structural properties of monoclonal antibodies to process data. The resulting information as a decision tool can help to enhance the risk assessment to better aid process development and thereby overcome some of the limitations and challenges present in QbD implementation today.     

Auxin-Cytokinin Interactions in Wild-Type and Transgenic Tobacco

Cytokinins and auxins are important regulators of plant growthand development, but there is incomplete and conflicting evidencethat auxins affect cytokinin metabolism and vice versa. We haveinvestigated these interactions in Nicotiana tabacum L. by separatein planta manipulation of levels of the hormones followed byanalysis of the induced changes in the metabolism of the otherhormone. Cytokinin-overproducing plants (expressing the Agrobacte-riumtumefaciens ipt gene) had lower than wild-type levels of freeIAA, and reduced rates of IAA synthesis and turnover, but therewere no differences in the profiles of metabolites they producedfrom fed IAA. Similarly, auxin-overproducing plants (expressingthe A.tumefaciens iaaM and iaaH genes), had lower levels ofthe major cytokinins than wild-type plants and lower cytokininoxidase activity, but there were no differences in the profilesof metabolites they produced from fed cytokinins. The data demonstratethat cytokinin or auxin overproduction decreases the contentof the other hormone, apparently by decreasing its rate of synthesisand/or transport, rather than by increasing rates of turnoveror conjugation. Implications for the importance of cytokinin: auxin ratios in plant development are considered. (Received September 24, 1996; Accepted December 4, 1996)