Advances in Fasciola hepatica research using ‘omics’ technologies

The liver fluke Fasciola hepatica is an economically important pathogen of livestock worldwide, as well as being an important neglected zoonosis. Parasite control is reliant on the use of drugs, particularly triclabendazole, which is effective against multiple parasite stages. However, the spread of parasites resistant to triclabendazole has intensified the pursuit for novel control strategies. Emerging 'omics' technologies are helping advance our understanding of liver fluke biology, specifically the molecules that act at the host-parasite interface and are central to infection, virulence and long-term survival within the definitive host. This review discusses the technological sequencing advances that have facilitated the unbiased analysis of liver fluke biology, resulting in an extensive range of ‘omics’ datasets. In addition, we highlight the ‘omics’ studies of host responses to F. hepatica infection that, when combined with the parasite datasets, provide the opportunity for integrated analyses of host-parasite interactions. These extensive datasets will form the foundation for future in-depth analysis of F. hepatica biology and development, and the search for new drug or vaccine interventions.     

Comprehensive analysis of the roles of ‘black’ and ‘gray’ clusters in structure and function of rat β-parvalbumin

Recently we found two highly conserved structural motifs in the proteins of the EF-hand calcium binding protein family. These motifs provide a supporting scaffold for the Ca²⁺ binding loops and contribute to the hydrophobic core of the EF-hand domain. Each structural motif forms a cluster of three amino acids called cluster I (‘black’ cluster) and cluster II (‘grey’ cluster). Cluster I is much more conserved and mostly incorporates aromatic amino acids. In contrast, cluster II includes a mix of aromatic, hydrophobic, and polar amino acids. The ‘black’ and ‘gray’ clusters in rat β-parvalbumin consist of F48, A100, F103 and G61, L64, M87, respectively. In the present work, we sequentially substituted these amino acids residues by Ala, except Ala100, which was substituted by Val. Physical properties of the mutants were studied by circular dichroism, scanning calorimetry, dynamic light scattering, chemical crosslinking, and fluorescent probe methods. The Ca²⁺ and Mg²⁺ binding affinities of these mutants were evaluated by intrinsic fluorescence and equilibrium dialysis methods. In spite of a rather complicated pattern of contributions of separate amino acid residues of the ‘black’ and ‘gray’ clusters into maintenance of rat β-parvalbumin structural and functional status, the alanine substitutions in the cluster I cause noticeably more pronounced changes in various structural parameters of proteins, such as hydrodynamic radius of apo-form, thermal stability of Ca²⁺/Mg²⁺-loaded forms, and total energy of Ca²⁺ binding in comparison with the changes caused by amino acid substitutions in the cluster II. These findings were further supported by the outputs of computational analysis of the effects of these mutations on the intrinsic disorder predisposition of rat β-parvalbumin, which also indicated that local intrinsic disorder propensities and the overall levels of predicted disorder were strongly affected by mutations in the cluster I, whereas mutations in cluster II had less pronounced effects. These results demonstrate that amino acids of the cluster I provide more essential contribution to the maintenance of structuraland functional properties of the protein in comparison with the residues of the cluster II.     

Genetic and biochemical studies on perchloroethylene ‘in vitro’ and ‘in vivo’

Perchloroethylene (PCE) was tested in a diploid strain (D7) of the yeast Saccharomyces cerevisiae in suspension tests with and without a mammalian microsomal activation system (S9) and ‘in vivo’ by the intrasanguineous host-mediated assay. In addition, enzyme alteration studies were performed in mice non-pretreated or pretreated with phenobarbital + β-naphthoflavone. PCE did not induce any genetic effect either ‘in vitro’ or ‘in vivo’. In the suspension test, PCE was more toxic without metabolic activation and less toxic with mammalian microsomal activation. The enzymatic determinations showed an increase of the aminopyrine demethylase activity and of the level of cytochrome P-450.     

Molecular studies in Pelargonium (Geraniaceae). A taxonomic appraisal of section Ciconium and the origin of the ‘Zonal’ and ‘Ivy-leaved’ cultivars

An RFLP analysis of chloroplast and nuclear DNA was followed in this taxonomic appraisal of section Ciconium. The section appears to be a monophyletic one, which divides into two groups, or sub-sections. The Zonal Geranium, P. × hortorum is derived from section Ciconium, and the species most likely to be its ancestors are shown to be P. inquinans and P. zonale. Maternal inheritance of chloroplasts was demonstrated by comparing chloroplast DNA from interspecific hybrids with their parents. These data also suggest that P. inquinans was probably the maternal parent of P. × hortorum in the original crosses. The Ivy-leaved cultivars appear to be derived from P. peltatum, with some contribution from P. zonale and/or P. × hortorum.     

Impact of the ‘tubulin economy’ on the formation and function of the microtubule cytoskeleton

The microtubule cytoskeleton is assembled from a finite pool of α,β-tubulin, the size of which is controlled by an autoregulation mechanism. Cells also tightly regulate the architecture and dynamic behavior of microtubule arrays. Here, we discuss progress in our understanding of how tubulin autoregulation is achieved and highlight work showing that tubulin, in its unassembled state, is relevant for regulating the formation and organization of microtubules. Emerging evidence suggests that tubulin regulates microtubule-associated proteins and kinesin motors that are critical for microtubule nucleation, dynamics, and function. These relationships create feedback loops that connect the tubulin assembly cycle to the organization and dynamics of microtubule networks. We term this concept the ‘tubulin economy’, which emphasizes the idea that tubulin is a resource that can be deployed for the immediate purpose of creating polymers, or alternatively as a signaling molecule that has more far-reaching consequences for the organization of microtubule arrays.     

Universality in neural networks: the importance of the ‘mean firing rate’

We present a general analysis of highly connected recurrent neural networks which are able to learn and retrieve a finite number of static patterns. The arguments are based on spike trains and their interval distribution and require no specific model of a neuron. In particular, they apply to formal two-state neurons as well as to more refined models like the integrate-and-fire neuron or the Hodgkin-Huxley equations. We show that the mean firing rate defined as the inverse of the mean interval length is the only relevant parameter (apart from the synaptic weights) that determines the existence of retrieval solutions with a large overlap with one of the learnt patterns. The statistics of the spiking noise (Gaussian, Poisson or other) and hence the shape of the interval distribution does not matter. Thus our unifying approach explains why, and when, all the different associative networks which treat static patterns yield basically the same results, i.e., belong to the same universality class.     

Structure and seasonal distribution of litterfall in young plantations of Populus ‘Tristis#1’

Litterfall was sampled in 3- to 7-year-old irrigated and fertilized plantings of Populus Tristis#1 in northern Wisconsin. Leaves accounted for more than 90 per cent of the total litter and reached an asymptotic value of about 4,000 to 4,200 kg/ha. Leaf litterfall culminated in late September or first half of October. Inadequate light appeared to be responsible for an early (June) leaf fall in dense plantings. The maximum cumulative leaf area index ranged from 8.4 to 8.7. The pattern of foliation and defoliation was similar: it started with small leaves in the lower canopy and ended with large leaves of the upper canopy. Longevity of the small leaves was shorter than that of the large leaves. Leaf size was positively affected by fertilization but was not affected by a discontinuation of irrigation by mid-July during the droughty 1976. The specific leaf weight ranged from 2.6 mg/cm² in the lower canopy to 10.2 mg/cm² in the upper canopy. The specific leaf weight of litter leaves was 4 to 38 per cent lower than that of green leaves of the same size.     

Regulation of biotechnology in the United States: One and a half years of using the ‘coordinated framework’

There are several organizations in the US with responsibilities for regulatory oversight of the planned introduction of recombinant DNA organisms into the environment. Equally, there are many kinds of projects which require assessment. The policies, recommendations and rulings of the various authorities have been integrated into a ‘Coordinated Framework’ which defines the operation of flexible case-by-case risk assessment. Additions to and revision of the guidelines are being made, a process which will continue in the light of new experience.     

Comparative studies of a new microbial bate and the commercial bate ‘Oropon’ in leather treatment

An extracellular protease ofBacillus subtilis K2, when compared with the pancreatic bate Oropon used at comparable protease activity, produced a finer grain and greater elasticity of goat pelt. Quality of the processed, finished leather after microbial bating showed <41% and <14% increases in tensile and tear strengths, respectively, compared with Oropon-bated leather.     

N-Acetamideindolecarboxylic acid allosteric ‘finger-loop’ inhibitors of the hepatitis C virus NS5B polymerase: discovery and initial optimization studies

SAR studies at the N¹-position of allosteric indole-based HCV NS5B inhibitors has led to the discovery of acetamide derivatives with good cellular potency in subgenomic replicons (EC₅₀ <200 nM). This class of inhibitors displayed improved physicochemical properties and favorable ADME-PK profiles over previously described analogs in this class.     

Estimating the first flowering and full blossom dates of Yoshino cherry (Cerasus × yedoensis ‘Somei-yoshino’) in Japan using machine learning algorithms

Climate change alters the phenology of various plants. For example, increasing temperatures shift the first flowering and full blossom days of Yoshino cherry trees and affect cultural events related to cherry blossoms. We developed models to estimate the first flowering and full blossom dates of Yoshino cherry in Japan based on temperature and phenological data observed at 82 stations in Japan for 68 years (1953–2020). Three machine learning algorithms, namely, the random forest (RF), artificial neural network (ANN), and gradient boosting decision tree (GBDT) algorithms, were utilized, and the hyperparameters were optimized using Optuna. The GBDT models produced the best estimation accuracy, with an overall root mean square error (RMSE) = 1.53 and 1.48 days for the first flowering date and full blossom date, respectively. Furthermore, our analysis using Shapley Additive Explanations (SHAP) revealed that in the RF and GBDT models, the low temperature in winter and high temperature in spring would advance the estimated first flowering and full blossom dates.     

Combination of ‘omics’ data to investigate the mechanism(s) of hydrazine-induced hepatotoxicity in Rats and to identify potential biomarkers

To gain novel insight into the molecular mechanisms underlying hydrazine-induced hepatotoxicity, mRNAs, proteins and endogenous metabolites were identified that were altered in rats treated with hydrazine compared with untreated controls. These changes were resolved in a combined genomics, proteomics and metabonomics study. Sprague–Dawley rats were assigned to three treatment groups with 10 animals per group and given a single oral dose of vehicle, 30 or 90 mg?kg^?1 hydrazine, respectively. RNA was extracted from rat liver 48 h post-dosing and transcribed into cDNA. The abundance of mRNA was investigated on cDNA microarrays containing 699 rat-specific genes involved in toxic responses. In addition, proteins from rat liver samples (48 and 120/168 h post-dosing) were resolved by two-dimensional differential gel electrophoresis and proteins with changed expression levels after hydrazine treatment were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry peptide mass fingerprinting. To elucidate how regulation was reflected in biochemical pathways, endogenous metabolites were measured in serum samples collected 48 h post-dosing by 600-MHz ¹H-NMR. In summary, a single dose of hydrazine caused gene, protein and metabolite changes, which can be related to glucose metabolism, lipid metabolism and oxidative stress. These findings support known effects of hydrazine toxicity and provide potential new biomarkers of hydrazine-induced toxicity.     

Assessment of ‘top-down’ and ‘bottom-up’ forces as determinants of rotifer distribution among lakes in Ontario,Canada

Predation and food supply are generally perceived as important determinants of spatial and temporal variations of populations. The population dynamics of freshwater rotifers have been well researched in this aspect. However, their spatial variations have attracted less attention and have not been studied by simultaneously considering both predation and food supply. We studied spatial variations of rotifer abundance among 34 Canadian boreal lakes. A large part of the variance of rotifer abundance was associated with variables related to trophic status including chlorophyll a and total phosphorus. However, abundances of mesozooplankton such as potential predators and competitors did not correlate with rotifer abundance and did not explain the residual of the regression between rotifer abundance and chlorophyll a. The results of the present study indicated that variation in rotifer abundance among lakes was caused by bottom-up forces related to food supply and not by top-down predatory interactions. This provides a contrast to previous empiric and experimental studies that reported that temporal variations of rotifer abundance were mainly regulated by top-down interactions. This discrepancy suggests that overall differences in rotifer abundance among lakes are mainly determined by bottom-up forces while temporal changes in single lakes are shaped by top-down forces. Meanwhile, the composition of rotifer species was correlated with mesozooplankton abundance as well as trophic status. Rotifer species with long spines or rigid loricae were found in the lakes where mesozooplankton were abundant, which suggests that defensive morphology could have affected the rotifer species distribution among the study lakes.     

Getting to the guts of the matter: The status and potential of ‘omics’ research of parasitic protists of the human gastrointestinal system

Parasitic protists are a major cause of diarrhoeal illnesses in humans globally. Collectively, enteric pathogens exceed all other forms of infectious disease, in terms of their estimated global prevalence and socioeconomic impact. They have a disproportionately high impact on children in impoverished communities, leading to acute (diarrhoea, vomiting, dehydration and death) and chronic disease (malabsorption, malnutrition, physical and cognitive stunting and predisposition to chronic, non-communicable disease) consequences. However, historically, investment in research and disease control measures has been disproportionately poor, leading to their current classification as neglected pathogens. A sound understanding of their biology is essential in underpinning detection, treatment and control efforts. One major tool in rapidly improving our knowledge of these parasites is the use of biological systems, including ‘omic’ technologies. In recent years, these tools have shown significant success when applied to enteric protists. This review summarises much of this knowledge and highlights the significant remaining knowledge gaps. A major focus of the present review was to provide a perspective on a way forward to address these gaps using advanced biotechnologies.     

Comparison of ‘ignition’ and ‘extraction’ methods for the determination of organic phosphate in rocks and soils

Summary Ignition markedly increased the solubility in dilute acid of iron- and aluminium-bound inorganic phosphate in samples of weathered New Zealand greywacke rock. This observation supports the view that ignition methods may sometimes overestimate the total organic phosphate of soils.     

‘Time’ and the expression of temporality in eastern Sumba

In this article the author attempts to show the rationale behind the ideology of the Fijian political movement called Taukei, i.e. “owners of the land”. The fundamentalist current within the Fijian political scene in later years has made powerful use of indigenous concepts related to the land (vanua). In contrast to other ethnic groups in the country Fijians consider themselves to be upholders of indisputable moral principles also embraced by the concept vanua. On the one hand their preoccupation with everything that vanua stands for makes Fijians easy prey to political manipulation. On the other hand, the moral standards represented by vanua give them a sense of identity in a situation of rapid social and political change.