Richards's equation and nonlinear mixed models applied to avian growth: why use them?

Postnatal growth is an important life‐history trait that varies widely across avian species, and several equations with a sigmoidal shape have been used to model it. Classical three‐parameter models have an inflection point fixed at a percentage of the upper asymptote which could be an unrealistic assumption generating biased fits. The Richards model emerged as an interesting alternative because it includes an extra parameter that determines the location of the inflection point which can move freely along the growth curve. Recently, nonlinear mixed models (NLMM) have been used in modeling avian growth because these models can deal with a lack of independence among data as typically occurs with multiple measurements on the same individual or on groups of related individuals. Here, we evaluated the usefulness of von Bertalanffy, Gompertz, logistic, U₄ and Richards's equations modeling chick growth in the imperial shag Phalacrocorax atriceps. We modelled growth in commonly used morphological traits, including body mass, bill length, head length and tarsus length, and compared the performance of models by using NLMM. Estimated adult size, age at maximum growth and maximum growth rates markedly differed across models. Overall, the most consistent performance in estimated adult size was obtained by the Richards model that showed deviations from mean adult size within 5%. Based on AICc values, the Richards equation was the best model for all traits analyzed. For tarsus length, both Richards and U₄ models provided indistinguishable fits because the relative inflection value estimated from the Richards model was very close to that assumed by the U₄ model. Our results highlight the bias incurred by three‐parameter models when the assumed inflection placement deviates from that derived from data. Thus, the application of the Richards equation using the NLMM framework represents a flexible and powerful tool for the analysis of avian growth.     

Sporobolomyces and Sporidiobolus – non-conventional yeasts for use in industries

The search for new, biotechnologically useful yeast strains has been carried out in many research centers in the world. Sporobolomyces and Sporidiobolus are examples of such useful yeasts, that can be used as a source of many valuable metabolites in industries. This article describes the modern taxonomy of these yeasts, which resulted from many years of research, including both classical microbiology and genetic analyses. Subsequently, the paper presents a review of scientific studies on the biosynthesis of various extracellular and intracellular metabolites produced by Sporobolomyces and Sporidiobolus yeasts, which are of great importance in the contemporary food, feed, and pharmaceutical industries. Such metabolites include exopolysaccharides, lipids, carotenoids, enzymes, and γ-decalactone. Aiming at developing a sustainable circular bioeconomy, this study considers two directions of use of these yeasts, i.e., as a feed additive and as an antagonist in the biocontrol of plant materials. This article is one of the first to organize the knowledge collected from published studies and present the contemporary scientific achievements and prospects for the biotechnological use of Sporobolomyces and Sporidiobolus yeasts.     

Exploiting amyloid: how and why bacteria use cross-β fibrils

Many bacteria produce protein fibrils that are structurally analogous to those associated with protein misfolding diseases such as Alzheimer's disease. However, unlike fibrils associated with disease, bacterial amyloids have beneficial functions including conferring stability to biofilms, regulating development or imparting virulence. In the present review, we consider what makes amyloid fibrils so suitable for these roles and discuss recent developments in the study of bacterial amyloids, in particular the chaplins from Streptomyces coelicolor. We also consider the broader impact of the study of bacterial amyloids on our understanding of infection and disease and on developments in nanotechnology.     

Single nucleotide polymorphism libraries: why and how are we building them?

A great deal of time and money is currently being invested in the production of large libraries of single nucleotide polymorphisms (SNPs) - variations of one nucleotide between the DNA sequence of individuals. This review compares and contrasts the available sources of SNP data, and describes the rationale behind the SNP mapping efforts, from the study of common diseases to unraveling an individual's response to medication.     

Exosomes at a glance – common nominators for cancer hallmarks and novel diagnosis tools

Cancer represents a heterogeneous disease with multiple levels of regulation and a dynamic environment that sustains the evolution of the malignant mass. This dynamic is in part sustained by a class of extracellular vesicles termed exosomes that are able to imprint the pathological state by incorporating differential cargos in order to facilitate cell-to-cell communication. Exosomes are stable within the extracellular medium and function as shuttles secreted by healthy or pathological cells, being further taken by the accepting cell with direct effects on its phenotype. The exosomal trafficking is deeply involved in multiple levels of cancer development with roles in all cancer hallmarks. Nowadays, studies are constantly exploring the ability of exosomes to sustain the malignant progression in order to attack this pathological trafficking and impair the ability of the tumor mass to expand within the organisms. As important, the circulatory characteristics of exosomes represent a steady advantage regarding the possibility of using them as minimally invasive diagnosis tools, where cancer patients’ present modified exosomal profiles compared to the healthy ones. This last characteristic, as novel diagnosis tools, has the advantage of a possible rapid transition within the clinic, compared to the studies that evaluate the therapeutic meaning.     

Horseradish and soybean peroxidases: comparable tools for alternative niches?

Horseradish and soybean peroxidases (HRP and SBP, respectively) are useful biotechnological tools. HRP is often termed the classical plant heme peroxidase and although it has been studied for decades, our understanding has deepened since its cloning and subsequent expression, enabling numerous mutational and protein engineering studies. SBP, however, has been neglected until recently, despite offering a real alternative to HRP: SBP actually outperforms HRP in terms of stability and is now used in numerous biotechnological applications, including biosensors. Review of both is timely. This article summarizes and discusses the main insights into the structure and mechanism of HRP, with special emphasis on HRP mutagenesis, and outlines its use in a variety of applications. It also reviews the current knowledge and applications to date of SBP, particularly biosensors. The final paragraphs speculate on the future of plant heme-based peroxidases, with probable trends outlined and explored.     

Parentally biased favouritism: why should parents specialize in caring for different offspring?

'Parentally biased favouritism' occurs when the two parents differentially care for individual offspring or kinds of offspring. Examples in birds include brood division and differential investment by the two parents in relation to the size or sex of the offspring. This paper uses mathematical models to investigate which ideas can, in theory, explain parentally biased favouritism. One previous explanation is that the parents differ in their cost of reproduction and that the parent who consequently invests least concentrates its care on the more valuable offspring. However, a mathematical model predicts the total care given by each parent and received by each offspring, not how much each parent cares for each offspring, and hence does not explain parentally biased favouritism. Parentally biased favouritism towards particular types of offspring can be explained by a difference between the parents in the benefits of caring for a given type of offspring or in the effort incurred in providing care to a given type of offspring, but then it is extreme, with at least one of the parents providing care to only one type of offspring. Parentally biased favouritism towards particular individual offspring (brood division) can be explained by parent-offspring conflict or sexual conflict.     

YANA – a software tool for analyzing flux modes,gene-expression and enzyme activities

Background  

A number of algorithms for steady state analysis of metabolic networks have been developed over the years. Of these, Elementary Mode Analysis (EMA) has proven especially useful. Despite its low user-friendliness, METATOOL as a reliable high-performance implementation of the algorithm has been the instrument of choice up to now. As reported here, the analysis of metabolic networks has been improved by an editor and analyzer of metabolic flux modes. Analysis routines for expression levels and the most central, well connected metabolites and their metabolic connections are of particular interest.     

Self-efficacy and diabetes: why is emotional 'education' important and how can it be achieved?

Adequate age-appropriate diabetes knowledge and skills are essential to the success of diabetes self- and parental care. Health professionals have a central role in providing diabetes education. A direct link between diabetes knowledge and diabetes regimen behaviour cannot be assumed. Health professionals have to help children and their parents to develop the emotional concept of 'self-efficacy for diabetes self-care', to ensure optimal diabetes control.     

Open source tools and toolkits for bioinformatics: significance, and where are we?

This review summarizes important work in open-source bioinformatics software that has occurred over the past couple of years. The survey is intended to illustrate how programs and toolkits whose source code has been developed or released under an Open Source license have changed informatics-heavy areas of life science research. Rather than creating a comprehensive list of all tools developed over the last 2-3 years, we use a few selected projects encompassing toolkit libraries, analysis tools, data analysis environments and interoperability standards to show how freely available and modifiable open-source software can serve as the foundation for building important applications, analysis workflows and resources.     

A multi-body model for comparative study of cervical traction simulation – development,improvement and validation

A computer simulation model was developed to study the dynamic behavior of the cervical spine during cervical traction therapy in inclined and sitting traction positions. The model improved upon an old model with additional components to represent the behavior of the intervertebral discs and the posterior ligaments. The simulation result of the new model was compared against the cervical traction data from a radiographic experiment in both positions. The simulation results of the old model and new model were compared to illustrate the improvement. Using the new model, we compared the timing response of cervical traction in the inclined and sitting positions.     

Discrimination abilities for nutrients: which difference matters for choosy birds and why?

Fine-tuned discrimination abilities are a prerequisite for optimal diet theory (ODT) and the concept of nutrient regulation as alternative models of food choice. These abilities have rarely been determined, and neither has been applied to frugivorous consumers. We investigated nutrient choices of four tanagers (Tachyphonus cristatus, Dacnis cayana, Chlorophanes spiza and Cyanerpes nitidus) for different lipid or carbohydrate concentrations, and determined discrimination abilities by reducing in steps the difference between two foods ranging from 2.5 to 12%. Three species detected differences in sugar concentrations of only 1% and differences in lipid content of 2%. Hence, frugivorous tanagers were able to select the more rewarding food based on fine-scale differences in nutritional content. Tanagers also consumed more carbohydrates than proteins or lipids in isocaloric trials, but were indifferent to equicaloric solutions of 20% of either glucose or sucrose. In contrast to foods with low sugar contents, intake of foods high in lipids or carbohydrates was limited to a protein intake of 0.75 g/7 h. Lipid and carbohydrates were treated as though they were interchangeable nutrients for birds at low, but not at high, sugar concentrations. Furthermore, the tanagers discriminated foods containing the same amount of protein but differing in the type of protein. Preference for boviserine serum albumin (BSA) over casein was not related to moult. We supplemented the food consisting of casein with the essential amino acid cysteine to match cysteine concentrations of BSA. The birds then consumed more of the casein food than of the cysteine-supplemented casein food. Overall, the birds' consistent choices in the experiments with foods of different energy density are interpretable by both ODT and the nutrient regulation theory. However, only the latter accounts for the birds' choices of isocaloric foods differing in macro- or micronutritional content. Models of food selection should therefore focus on nutrient geometry and consumer-specific requirements. Copyright 2003 Published by Elsevier Science Ltd on behalf of The Association for the Study of Animal Behaviour.      

Adenosyltransferase: an enzyme and an escort for coenzyme B12?

Many organic cofactors are both rare and reactive. They are usually in low abundance, which poses problems for efficient collision-based targeting to dependent enzymes, whereas their reactivity is problematic for side reactions. Sequestration and escorted delivery presents one solution to this conundrum, but such porters, if they exist, are mostly unknown. In humans, the mitochondrial enzyme methylmalonyl-coenzyme A mutase uses coenzyme B(12) (adenosylcobalamin) but would be inactive if bound to the cofactor precursor that is delivered to the mitochondrion. Adenosyltransferase converts cob(II)alamin to coenzyme B(12). Based on kinetic evidence for interaction between the two enzymes, the 40-fold greater affinity for coenzyme B(12) and the higher coordination number for cobalt in the mutase, we propose that the adenosyltransferase is a dual-function protein: an enzyme that synthesizes coenzyme B(12) and a chaperone that delivers it.