Pharmacokinetic de-risking tools for selection of monoclonal antibody lead candidates

Pharmacokinetic studies play an important role in all stages of drug discovery and development. Recent advancements in the tools for discovery and optimization of therapeutic proteins have created an abundance of candidates that may fulfill target product profile criteria. Implementing a set of in silico, small scale in vitro and in vivo tools can help to identify a clinical lead molecule with promising properties at the early stages of drug discovery, thus reducing the labor and cost in advancing multiple candidates toward clinical development. In this review, we describe tools that should be considered during drug discovery, and discuss approaches that could be included in the pharmacokinetic screening part of the lead candidate generation process to de-risk unexpected pharmacokinetic behaviors of Fc-based therapeutic proteins, with an emphasis on monoclonal antibodies.     

Queueing up for enzymatic processing: correlated signaling through coupled degradation

High‐throughput technologies have led to the generation of complex wiring diagrams as a post‐sequencing paradigm for depicting the interactions between vast and diverse cellular species. While these diagrams are useful for analyzing biological systems on a large scale, a detailed understanding of the molecular mechanisms that underlie the observed network connections is critical for the further development of systems and synthetic biology. Here, we use queueing theory to investigate how ‘waiting lines’ can lead to correlations between protein ‘customers’ that are coupled solely through a downstream set of enzymatic ‘servers’. Using the E. coli ClpXP degradation machine as a model processing system, we observe significant cross‐talk between two networks that are indirectly coupled through a common set of processors. We further illustrate the implications of enzymatic queueing using a synthetic biology application, in which two independent synthetic networks demonstrate synchronized behavior when common ClpXP machinery is overburdened. Our results demonstrate that such post‐translational processes can lead to dynamic connections in cellular networks and may provide a mechanistic understanding of existing but currently inexplicable links.     

Detecting and avoiding likely false‐positive findings – a practical guide

Recently there has been a growing concern that many published research findings do not hold up in attempts to replicate them. We argue that this problem may originate from a culture of ‘you can publish if you found a significant effect’. This culture creates a systematic bias against the null hypothesis which renders meta‐analyses questionable and may even lead to a situation where hypotheses become difficult to falsify. In order to pinpoint the sources of error and possible solutions, we review current scientific practices with regard to their effect on the probability of drawing a false‐positive conclusion. We explain why the proportion of published false‐positive findings is expected to increase with (i) decreasing sample size, (ii) increasing pursuit of novelty, (iii) various forms of multiple testing and researcher flexibility, and (iv) incorrect P‐values, especially due to unaccounted pseudoreplication, i.e. the non‐independence of data points (clustered data). We provide examples showing how statistical pitfalls and psychological traps lead to conclusions that are biased and unreliable, and we show how these mistakes can be avoided. Ultimately, we hope to contribute to a culture of ‘you can publish if your study is rigorous’. To this end, we highlight promising strategies towards making science more objective. Specifically, we enthusiastically encourage scientists to preregister their studies (including a priori hypotheses and complete analysis plans), to blind observers to treatment groups during data collection and analysis, and unconditionally to report all results. Also, we advocate reallocating some efforts away from seeking novelty and discovery and towards replicating important research findings of one's own and of others for the benefit of the scientific community as a whole. We believe these efforts will be aided by a shift in evaluation criteria away from the current system which values metrics of ‘impact’ almost exclusively and towards a system which explicitly values indices of scientific rigour.     

Micropropagation of Sicilian cultivars with an aim to preserve genetic diversity in hazelnut (Corylus avellana L.)

The use of a small number of cultivars in agriculture can lead to a loss of agrobiodiversity. Since in vitro techniques are valuable tools for conserving plant biodiversity, an efficient micropropagation protocol for four Italian hazelnut cultivars, ‘Carrello’, ‘Ghirara’, ‘Minnulara’, and ‘Panottara’, was developed. The highest axillary bud survival was obtained after decontamination with 40?min 1% sodium hypochlorite followed by 40?min 0.1% sodium merthiolate in ‘Minnulara’ and ‘Ghirara’, while the 35?+?35?min treatment was the best for ‘Carrello’ and ‘Panottara’. Shoot multiplication was higher in ‘Minnulara’ and ‘Ghirara’ when 6.6?μM N⁶-benzyladenine was used, even if some hyperhydric shoots were observed, while metatopolin was more effective in the other two cultivars. In vitro rooting, performed in ‘Carrello’ and ‘Panottara’, was higher with 17.6 than with 9.8 µM indole-3-butyric. Following in vitro root induction with 17.6 µM indole-3-butyric acid for 7 days, rooting and acclimatisation in greenhouse exceeded 85% for all four cultivars.     

In silico optimization of pharmacokinetic properties and receptor binding affinity simultaneously: a ‘parallel progression approach to drug design’ applied to β-blockers

The present work exploits the potential of in silico approaches for minimizing attrition of leads in the later stages of drug development. We propose a theoretical approach, wherein ‘parallel’ information is generated to simultaneously optimize the pharmacokinetics (PK) and pharmacodynamics (PD) of lead candidates. β-blockers, though in use for many years, have suboptimal PKs; hence are an ideal test series for the ‘parallel progression approach’. This approach utilizes molecular modeling tools viz. hologram quantitative structure activity relationships, homology modeling, docking, predictive metabolism, and toxicity models. Validated models have been developed for PK parameters such as volume of distribution (log V_d) and clearance (log Cl), which together influence the half-life (t_1/2) of a drug. Simultaneously, models for PD in terms of inhibition constant pK_i have been developed. Thus, PK and PD properties of β-blockers were concurrently analyzed and after iterative cycling, modifications were proposed that lead to compounds with optimized PK and PD. We report some of the resultant re-engineered β-blockers with improved half-lives and pK_i values comparable with marketed β-blockers. These were further analyzed by the docking studies to evaluate their binding poses. Finally, metabolic and toxicological assessment of these molecules was done through in silico methods. The strategy proposed herein has potential universal applicability, and can be used in any drug discovery scenario; provided that the data used is consistent in terms of experimental conditions, endpoints, and methods employed. Thus the ‘parallel progression approach’ helps to simultaneously fine-tune various properties of the drug and would be an invaluable tool during the drug development process.     

Analysis of Resistance to Eyespot in Wheat Using Small Seed-Samples

Six different inoculation methods have been tested to determine Pseudocercosporella herpo-trichoides resistance of wheat using small seed-samples. The observed differentiation among hosts corresponds to that known from the literature:‘Diplomat’ and ‘Caribo’ are susceptible whereas ‘VPM1’, ‘Rendezvous’ and ‘Roazon’ carry resistance transferred from Aegilops ventricosa. The modified method of Frauenstein and Roskothen (1979) seems to be most efficient: it is timesaving, easy to use and only small seed-samples are necessary. Such resistance testing can be used in early generations of breeding programmes.     

Sea-level changes, river capture and the evolution of populations of the Eastern Cape and fiery redfins (Pseudobarbus afer and Pseudobarbus phlegethon, Cyprinidae) across multiple river systems in South Africa

Aim The phylogeography of the two closely related species Pseudobarbus afer and Pseudobarbus phlegethon was investigated to assess the association of evolutionary processes, inferred from mitochondrial DNA (mtDNA) sequence variation, with hypothetical palaeoriver systems and other climatic and landscape changes. Location One western and several southern river systems in South Africa. Methods We sampled known populations and confirmed known distribution gaps. This was followed by an assessment of mtDNA control region sequence variation for 31 localities across 17 river systems across the range of the species complex. A map of possible offshore drainage patterns during the last major regression event was constructed based on bathymetry and geological studies. Results The genetic distinction of four major lineages of P. afer strongly correspond with proposed palaeoriver systems. However, a western ‘Forest’ lineage, is widespread across two such proposed systems and is closely related to P. phlegethon on the west coast of South Africa. Both the ‘Krom’ and ‘St Francis’ lineages were identified in the single palaeoriver system proposed for St Francis Bay. A fourth ‘Mandela’ lineage is restricted to the one or two palaeoriver systems proposed for Nelson Mandela Bay. Four minor lineages were identified within the Forest lineage and two within the Mandela lineage. Main conclusions The close relationship between P. phlegethon and the Forest lineage of P. afer can only be explained by a series of river captures. We suggest the Gourits River system as a historical link that could account for this relationship. On the south coast, lower sea levels than at present allowed confluence between currently isolated river systems, offering opportunities for dispersal among these populations. At present, isolation between different river systems rather than dispersal appears to have a dominant influence on mtDNA diversity.     

Peroxidase and Poly-Phenol Oxidase in Brassica juncea Plants Infected with Macrophomina phaseolina (Tassai) Goid. and their Implication in Disease Resistance

Studies on the peroxidase and poly-phenol oxidase activity in relatively resistant and susceptible strains of Brassica juncea at sequential intervals after inoculation with different isolates of Macrophomina phaseolina revealed that, fungus infected tissues had relatively higher activities of these oxidative enzymes in comparison to healthy plants, and tissues inoculated with ‘Weakly Virulent’ isolates always exhibited higher activity in comparison to ‘Moderately’, ‘Highly’ and ‘MostHighly Virulent’ isolates. At the early stages of the infection on 6th day, resistant plants showed higher activities in comparison to their susceptible counterparts. Very low activity of these enzymes could be recorded in healthy plants. Findings of this, study indicate the possible involvement of these oxidative enzymes in the resistance of this disease.     

The interrelationships of Devonian lungfishes (Sarcopterygii: Dipnoi) as inferred from neurocranial evidence and new data from the genus Soederberghia Lehman, 1959

New data are presented on the neurocranial complex (endocranium plus intimately associated bones of the palate) of the Late Devonian (Famennian) ‘rhynchodipterid’ lungfish Soederberghia groenlandica from the Aina Dal Formation (Celsius Bjerg Group) of East Greenland. Only the otic and occipital regions of the braincase are ossified in Soederberghia. The neurocranium of this genus shares a series of derived features with ‘Griphognathus’whitei, including a cranial centrum, fenestrate lateral cristae, and gutters on the ventral surface of the parasphenoid interpreted as accommodating the lateral dorsal aortae. The interrelationships of early lungfishes have been the subject of considerable disagreement. New data from Soederberghia are coupled with a data set focused on the character‐rich neurocranial complex in order to examine the systematic utility of this underexploited morphological system. Different methods of phylogenetic inference (maximum parsimony, Bayesian) return broadly consistent results. The Early to Middle Devonian forms Dipnorhynchus, Stomiahykus and Uranolophus are placed among the most basal of lungfishes. ‘Holodontids’ plus ‘rhynchodipterids’ (comprising Griphognathus and Soederberghia) occupy an apical position, and are separated from the earliest lungfishes by a paraphyletic assemblage of taxa generally identified as ‘chirodipterids’ and ‘dipterids.’ This finds broad agreement with the results of previous cladistic studies focused on non‐neurocranial data sets, but diverges from functional‐adaptive scenarios that posit three lineages of early lungfishes based on aspects of the dentition. As currently defined, both ‘chirodipterids’ and the genus Chirodipterus are heterogeneous assemblages; this analysis fails to find support for the monophyly of either. While this study indicates that Griphognathus is probably paraphyletic, it nevertheless supports a close relationship between the nominal species of this genus and Soederberghia. © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 151 , 115–171.     

Population dynamics of the lichen genus Bulbothrix Hale as potential bioindicators of 'time-since-last-fire' in the cerrado of the Distrito Federal, central Brazil

This paper investigates the potential use of the corticolous lichen genus Bulbothrix Hale as a bioindicator of ‘time-since-last-fire’ in the cerrado (savannas) of central Brazil. Work was carried out at the Reserva Ecológica do IBGE and the Jardim Botãnico de Brasilia, 33 km outside Brasilia D.F., in plots of cerrado denso with known fire histories within the ‘Fire Project’ area. Measurements of abundance and thallus size were taken of all Bulbothrix individuals encountered up to 2 m on the trunks of three phorophyte species. The results show that abundances and thalli sizes of the Bulbothrix populations can be correlated with the ‘time-since-last-fire’ that had occurred in each of the plots. This study shows that is is possible to use characteristics of specific lichen populations as bioindicators of fire history.     

Oviposition behavior of orange wheat blossom midge on low- vs. high-ranked grass seed heads

The discovery of Sm1, a highly effective resistance (R) gene that targets the first instar of the orange wheat blossom midge, Sitodiplosis mosellana (Géhin) (Diptera: Cecidomyiidae), has created concerns about wheat midge adaptation. Strategies for delaying adaptation to Sm1 include the simultaneous deployment of a resistance trait targeting a different life stage, i.e., the ovipositing adult female. Previous studies have shown that adult females distinguish between wheat genotypes and seed head developmental stages and are attracted by volatiles from young wheat heads. We focused on what happens after the female lands on the seed head, comparing in three tests a seed head of the high‐ranked pre‐anthesis ‘Roblin’ wheat, Triticum aestivum L. (Poaceae), and a head of one of three lower‐ranked types: post‐anthesis ‘Roblin’, pre‐anthesis ‘Key’ wheat (T. aestivum), and pre‐anthesis ‘Robust’ barley (Hordeum vulgare L.). Within each test, high‐ and low‐ranked heads were presented in choice and no‐choice assays, with the behavior of wheat midge females scored every 5 min from 20:30 to 23:00 hours, under mid‐summer natural light conditions and sunset occurring between 20:50 and 21:20 hours. Head type influenced both proportions of females observed on the head and proportions of females probing with the ovipositor. Head*assay interactions occurred only in the test comparing wheat to barley, with barley reducing females observed on the wheat head and wheat increasing females probing on barley. Results indicate that the wheat midge female detects plant cues while examining the seed head and that this detection contributes to differences in egg counts.     

Further evidence of the African antiquity of hyaenodontid (‘Creodonta’, Mammalia) evolution

We report here the new ‘creodont’ Lahimia selloumi gen. et sp. nov. from the late Palaeocene of the Ouled Abdoun Basin (Morocco) as the oldest known Hyaenodontidae with Tinerhodon from the Ouarzazate Basin (Morocco). By contrast to Tinerhodon, Lahimia is unexpectedly derived. Most of its specializations, such as the shortening of the anterior dentition (e.g. loss of P₁) and the talonid reduction and simplification, are strikingly shared with Boualitomus from the Ypresian of the Ouled Abdoun Basin, and are distinctive from other hyaenodontids, including ‘proviverrines’. They are interpreted as synapomorphies evidencing a precociously specialized early African hyaenodontid lineage. Although Lahimia and Boualitomus remain known only by the lower dentition, their relationships with Koholia are suggested by comparison of their molar occlusal pattern. Lahimia and Boualitomus are referred to the Koholiinae, which is representative of an old African endemic lineage, as initially recognized. This remarkable lineage is characterized by synapomorphies of Lahimia and Boualitomus, and also by a shared original prevallum/postvallid shearing. The discovery of Lahimia provides direct evidence for the antiquity of the African evolution of the Hyaenodontidae. This is in agreement with an African origin of the Hyaenodontidae, and with the probable diphyletism of the ‘Creodonta’. Lahimia and the Koholiinae, as well as the diversity of the first Laurasian hyaenodontid lineages, emphasize our poor knowledge of the striking early African hyaenodontid radiation.     

Systematics and evolution of the cutworm moths (Lepidoptera: Noctuidae): evidence from two protein-coding nuclear genes

Abstract. A broad molecular systematic survey of Noctuidae was undertaken to test recent hypotheses on the problematic definitions and relationships of the subfamilies, with special emphasis on the ‘trifines.’ An initial hypothesis of noctuid classification to the subtribal level was synthesized from recent reviews, and then sampled as broadly as possible. Concatenated sequences for the nuclear genes elongation factor‐1α (EF‐1α; 1200 bp) and dopa decarboxylase (DDC; 700–1100 bp) were analysed for a total of 146 exemplar species, twice that of a previous study. Trees were estimated using likelihood, distance, and both equally weighted and ‘six‐parameter’ parsimony. Of the 144 possible nodes, bootstrap support (BP) was ≥ 50% for ～80, and ≥ 80% for ～60. There was very strong support (BP ≥ 90%) for an ‘L.A.Q.’ clade encompassing nearly all quadrifine noctuids plus Arctiidae and Lymantriidae, decisively rendering Noctuidae paraphyletic. We present a new classification for Noctuoidea in which Noctuidae sensu stricto is restricted to trifines; most quadrifine subfamilies are raised to full families. Within the ‘L.A.Q.’ clade, Aganainae and Herminiinae were strongly grouped, but other relationships were weakly supported, probably due to limited taxon sampling. Nolidae and Euteliinae + Stictopterinae are generally grouped with the ‘L.A.Q.’ clade, but with weak support. All analyses favour the broadest definitions proposed for the trifine clade (our Noctuidae sensu stricto) although support is not strong, except that the exemplar of Eustrotiinae: Eublemmini is placed securely in the ‘L.A.Q.’ clade. Numerous recent proposals for dismantling and recombining the ‘Hampsonian’ traditional trifine subfamilies are strongly supported, most notably a broadly defined ‘true cutworm’ clade (Noctuinae s.l.), encompassing the greater part of the traditional subfamilies Amphipyrinae, Cuculliinae, Hadeninae and Noctuinae s.s. (BP ≥ 95%). Within this clade there is strong support for Apameini s.s.+ Xylenini s.l. and for Noctuinae s.s. and divisions thereof, but little support for monophyly or subdivision of Hadeninae. Noctuinae s.l. invariably are allied with Heliothinae, scattered remnants of the traditional Amphipyrinae, and several smaller groups in a broader ‘pest clade’, albeit with weak support. Relationships among the remaining ‘lower’ trifines are not strongly resolved. Mapping of a preliminary synopsis of species diversities, host use patterns and latitudinal distributions on the phylogeny suggests that the diversification of trifines may have been promoted, to a degree unique among Macrolepidoptera, by the Tertiary expansion of seasonal, open habitats and their associated herbaceous floras.     

Eunotia amazonica sp. nov. (Bacillariophyta), a common stalk-forming species from the Rio Negro basin (Brazilian Amazon)

A new stalk-forming diatom was observed at high relative abundances on periphytic samples collected in the Rio Negro hydrographic basin (Brazilian Amazon) and is here described using light and scanning electron microscopy. We also present ecological preferences of the new species. Eunotia amazonica sp. nov. co-dominated periphytic samples collected during the rainy seasons of 2013 and 2014 near the city of Manaus (Amazonas, Brazil). The main diagnostic feature of the new species is the stalk-forming growth form (‘Cymbella-like’) illustrated here for the first time in the genus Eunotia Ehrenberg. Previous reports on growth forms in common European databases for this genus included colonial (‘ribbon-like’) but also ‘mobile’, ‘fixed by pads’ or ‘without structures of fixation’. We demonstrated that the three dominant Eunotia species in periphytic samples from the Rio Negro all exhibited distinct ‘growth forms’ or habits: Eunotia amazonica sp. nov. (stalked), Eunotia intricans Metzeltin & Lange-Bertalot (ribbon-like) and Eunotia rabenhorstiana (Grunow) Hustedt (branched-arborescent). The high diversity of species, many of which are unknown to science, as well as the poorly known life-forms and habits of the Eunotiaceae in the region, partially prevent the use of metrics based on life-form to assess ecological changes. Generic assumptions based on robust statistical methods may obscure reality and lead to biased conclusions of diatom community changes in poorly explored regions such as Neotropical freshwater rivers, where the Eunotiaceae are largely dominant, particularly in the Amazon basin.     

Elimination of Apple Mosaic Virus and Raspberry Bushy Dwarf Virus from Infected Red Raspberry (Rubus idaeus L.) by Tissue Culture

Experiments with ApMV infected ‘Malling Landmark’ and RBDV infected ‘Schamp;önemannamp;’ and ‘Trentamp;’ plants were carried out to evaluate a) the dependence of virus eradication on explant size and mass propagation. b) the reliability of results of ELISA tests on in vitro plantlets. With ApMV a correlation between virus elimination and explant size was observed, whereas with RBDV even plantlets from the smallest established explants were still infected. With ApMV, in vitro multiplication for three subsequent subcultures did not lead to further virus elimination, with RBDV this was observed in two cases. ELISA test results for both viruses, ApMV and RBDV, were identical when small in vitro plantlets, long-term stored plants, or potted plants from the same origin were tested, indicating that virus tests are possible with very young plant material and can be used to select virus-free plants in vitro. Tissue culture permits long-term storage of plant viruses. It is also suitable tor plant virus propagation and could be a useful aid in plant virus purification. For commercial multiplication only virus-indexed plant material should be used for establishment and further propagation in vitro.     

The Effects of Co-Infection by Sunn-Hemp Mosaic Virus (SHMV) and Fusarium oxysporum on the Growth of French Bean

In the seedlings of three cultivars of French bean (Phaseolus vulgaris), ‘Prince,’‘Masterpiece’ and ‘Pinto’, co-infection by Sunn-hemp mosaic virus (SHMV) with either of the vascular wilt pathogens, Fusarium oxysporum f. sp. phaseoh (Fop) or f. sp. tracbeiphilum (Fot) caused greater losses in total fresh weight and in leaf area compared with uninfected plants or plants infected singly with any one of these pathogens. Co-infection of a fourth cultivar (‘Canadian Wonder’) had no greater effects on growth reduction than single infection. The concentration of SHMV in the leaves of ‘Prince’ and to a greater extent in the leaves of ‘Masterpiece’ increased more after double infection than with infection by the virus alone. The nature and possible mechanisms of the pathogenic effects in French bean are discussed.     

New generation water quality guidelines for ecosystem protection

1. Water quality guidelines are important for the management of water resources. Initially, guidelines focused on quality for domestic drinking water and for agricultural, recreational and industrial purposes. More recently, the emphasis has been on ecosystem protection, as well. 2. This paper discusses the key elements of new risk-based water quality guidelines being developed in Australia and New Zealand, that should lead to more effective management and protection of aquatic ecosystems. 3. There are three essential elements to this new approach: (i) it is ecosystem-based— ideally the guidelines should be, as far as possible, ecosystem-specific; (ii) it is issue-based— the guidelines should focus on the actual issues or problems caused by physical, chemical and biological stressors rather than on the individual indicators, as at present; and (iii) it is risk-based. There is generally great difficulty in deciding whether adverse biological effects will result from various stressors added to an ecosystem. The new approach develops guideline ‘packages’ for each issue and, where possible, for each ecosystem type. Each ‘package’ consists of specified key performance indicators, trigger levels for these indicators (that is, levels which indicate the degree of risk that adverse biological effects may occur), and for high risk situations (where trigger levels are exceeded) a protocol for considering the effect of ecosystem-specific factors in reducing (or enhancing) the biological effects. 4. This paper presents a case study related to a highly relevant aquatic ecosystem issue in Australia, namely the excessive growth of cyanobacteria (blue-green algal blooms), to illustrate how the new risk-based guidelines might be applied.