Alternative oxidase in the branched mitochondrial respiratory network: an overview on structure, function, regulation, and role

Plants and some other organisms including protists possess a complex branched respiratory network in their mitochondria. Some pathways of this network are not energy-conserving and allow sites of energy conservation to be bypassed, leading to a decrease of the energy yield in the cells. It is a challenge to understand the regulation of the partitioning of electrons between the various energy-dissipating and -conserving pathways. This review is focused on the oxidase side of the respiratory chain that presents a cyanide-resistant energy-dissipating alternative oxidase (AOX) besides the cytochrome pathway. The known structural properties of AOX are described including transmembrane topology, dimerization, and active sites. Regulation of the alternative oxidase activity is presented in detail because of its complexity. The alternative oxidase activity is dependent on substrate availability: total ubiquinone concentration and its redox state in the membrane and O2 concentration in the cell. The alternative oxidase activity can be long-term regulated (gene expression) or short-term (post-translational modification, allosteric activation) regulated. Electron distribution (partitioning) between the alternative and cytochrome pathways during steady-state respiration is a crucial measurement to quantitatively analyze the effects of the various levels of regulation of the alternative oxidase. Three approaches are described with their specific domain of application and limitations: kinetic approach, oxygen isotope differential discrimination, and ADP/O method (thermokinetic approach). Lastly, the role of the alternative oxidase in non-thermogenic tissues is discussed in relation to the energy metabolism balance of the cell (supply in reducing equivalents/demand in energy and carbon) and with harmful reactive oxygen species formation.

A conceptual and practical overview of cDNA microarray technology: implications for basic and clinical sciences

cDNA microarray is an innovative technology that facilitates the analysis of the expression of thousands of genes simultaneously. The utilization of this methodology, which is rapidly evolving, requires a combination of expertise from the biological, mathematical and statistical sciences. In this review, we attempt to provide an overview of the principles of cDNA microarray technology, the practical concerns of the analytical processing of the data obtained, the correlation of this methodology with other data analysis methods such as immunohistochemistry in tissue microarrays, and the cDNA microarray application in distinct areas of the basic and clinical sciences.

Overview of Zika virus (ZIKV) infection in regards to the Brazilian epidemic

Zika virus (ZIKV), a mosquito-borne flavivirus, belongs to the Flaviviridae family, genus Flavivirus. ZIKV was initially isolated in 1947 from a sentinel monkey in the Zika forest, Uganda. Little clinical importance was attributed to ZIKV, once only few symptomatic cases were reported in some African and Southeast Asiatic countries. This situation changed in 2007, when a large outbreak was registered on the Yap Island, Micronesia, caused by the Asian ZIKV lineage. Between 2013 and 2014, ZIKV spread explosively and caused many outbreaks in different islands of the Southern Pacific Ocean and in 2015 autochthonous transmission was reported in Brazil. Currently, Brazil is the country with the highest number of ZIKV-positive cases in Latin America. Moreover, for the first time after the discovery of ZIKV, the Brazilian scientists are studying the possibility for the virus to cause severe congenital infection related to microcephaly and serious birth defects due to the time-spatial coincidence of the alarming increase of newborns with microcephaly and the Brazilian ZIKV epidemic. The present review summarizes recent information for ZIKV epidemiology, clinical picture, transmission, diagnosis and the consequences of this emerging virus in Brazil.

Putting plays (and more) in cyberspace : an overview of the British women playwrights around 1800 project

The british women playwrights around 1800 Web project has had a split allegiance from its beginning. Its beginnings lay in our interest in sustaining over time a community that had begun exploring the histories and writing of women in late-eighteenth and early-nineteenth century British theater. [...]

Handwritten Character Recognition of South Indian Scripts: A Review

Handwritten character recognition is always a frontier area of research in the field of pattern recognition and image processing and there is a large demand for OCR on hand written documents. Even though, sufficient studies have performed in foreign scripts like Chinese, Japanese and Arabic characters, only a very few work can be traced for handwritten character recognition of Indian scripts especially for the South Indian scripts. This paper provides an overview of offline handwritten character recognition in South Indian Scripts, namely Malayalam, Tamil, Kannada and Telungu

A review of research on working memory and its importance in education of the deaf

This independent study provides an overview of working memory as it pertains to deaf and hard of hearing students.

Water quality and ecology of the River Lee: mass balance and a review of temporal and spatial data

A regional overview of the water quality and ecology of the River Lee catchment is presented. Specifically, data describing the chemical, microbiological and macrobiological water quality and fisheries communities have been analysed, based on a division into river, sewage treatment works, fish-farm, lake and industrial samples. Nutrient enrichment and the highest concentrations of metals and micro-organics were found in the urbanised, lower reaches of the Lee and in the Lee Navigation. Average annual concentrations of metals were generally within environmental quality standards although, oil many occasions, concentrations of cadmium, copper, lead, mercury and zinc were in excess of the standards. Various organic substances (used as herbicides, fungicides, insecticides, chlorination by-products and industrial solvents) were widely detected in the Lee system. Concentrations of ten micro-organic substances were observed in excess of their environmental quality standards, though not in terms of annual averages. Sewage treatment works were the principal point source input of nutrients. metals and micro-organic determinands to the catchment. Diffuse nitrogen sources contributed approximately 60% and 27% of the in-stream load in the upper and lower Lee respectively, whereas approximately 60% and 20% of the in-stream phosphorus load was derived from diffuse sources in the upper and lower Lee. For metals, the most significant source was the urban runoff from North London. In reaches less affected by effluent discharges, diffuse runoff from urban and agricultural areas dominated trends. Flig-h microbiological content, observed in the River Lee particularly in urbanised reaches, was far in excess of the EC Bathing Water Directive standards. Water quality issues and degraded habitat in the lower reaches of the Lee have led to impoverished aquatic fauna but, within the mid-catchment reaches and upper agricultural tributaries, less nutrient enrichment and channel alteration has permitted more diverse aquatic fauna.

Integrating socio-economics and ecology: a taxonomy of quantitative methods and a review of their use in agro-ecology

Answering many of the critical questions in conservation, development and environmental management requires integrating the social and natural sciences. However, understanding the array of available quantitative methods and their associated terminology presents a major barrier to successful collaboration. We provide an overview of quantitative socio-economic methods that distils their complexity into a simple taxonomy. We outline how each has been used in conjunction with ecological models to address questions relating to the management of socio-ecological systems. We review the application of social and ecological quantitative concepts to agro-ecology and classify the approaches used to integrate the two disciplines. Our review included all published integrated models from 2003 to 2008 in 27 journals that publish agricultural modelling research. Although our focus is on agro-ecology, many of the results are broadly applicable to other fields involving an interaction between human activities and ecology. We found 36 papers that integrated social and ecological concepts in a quantitative model. Four different approaches to integration were used, depending on the scale at which human welfare was quantified. Most models viewed humans as pure profit maximizers, both when calculating welfare and predicting behaviour. Synthesis and applications. We reached two main conclusions based on our taxonomy and review. The first is that quantitative methods that extend predictions of behaviour and measurements of welfare beyond a simple market value basis are underutilized by integrated models. The second is that the accuracy of prediction for integrated models remains largely unquantified. Addressing both problems requires researchers to reach a common understanding of modelling goals and data requirements during the early stages of a project.

Overview of mathematical approaches used to model bacterial chemotaxis I: the single cell

Mathematical modeling of bacterial chemotaxis systems has been influential and insightful in helping to understand experimental observations. We provide here a comprehensive overview of the range of mathematical approaches used for modeling, within a single bacterium, chemotactic processes caused by changes to external gradients in its environment. Specific areas of the bacterial system which have been studied and modeled are discussed in detail, including the modeling of adaptation in response to attractant gradients, the intracellular phosphorylation cascade, membrane receptor clustering, and spatial modeling of intracellular protein signal transduction. The importance of producing robust models that address adaptation, gain, and sensitivity are also discussed. This review highlights that while mathematical modeling has aided in understanding bacterial chemotaxis on the individual cell scale and guiding experimental design, no single model succeeds in robustly describing all of the basic elements of the cell. We conclude by discussing the importance of this and the future of modeling in this area.

Overview of mathematical approaches used to model bacterial chemotaxis II: bacterial populations

We review the application of mathematical modeling to understanding the behavior of populations of chemotactic bacteria. The application of continuum mathematical models, in particular generalized Keller-Segel models, is discussed along with attempts to incorporate the microscale (individual) behavior on the macroscale, modeling the interaction between different species of bacteria, the interaction of bacteria with their environment, and methods used to obtain experimentally verified parameter values. We allude briefly to the role of modeling pattern formation in understanding collective behavior within bacterial populations. Various aspects of each model are discussed and areas for possible future research are postulated.

The Mammalian cell cycle: an overview

In recent years, we have witnessed major advances in our understanding of the mammalian cell cycle and how it is regulated. Normal mammalian cellular proliferation is tightly regulated at each phase of the cell cycle by the activation and deactivation of a series of proteins that constitute the cell cycle machinery. This review article describes the various phases of the mammalian cell cycle and focuses on the cell cycle regulatory molecules that act at each stage to ensure normal cellular progression.

The mammalian cell cycle: an overview

In recent years, we have witnessed major advances in our understanding of the mammalian cell cycle and how it is regulated. Normal mammalian cellular proliferation is tightly regulated at each phase of the cell cycle by the activation and deactivation of a series of proteins that constitute the cell cycle machinery. This review article describes the various phases of the mammalian cell cycle and focuses on the cell cycle regulatory molecules that act at each stage to ensure normal cellular progression.

Model selection approaches for non-linear system identification: a review

The identification of non-linear systems using only observed finite datasets has become a mature research area over the last two decades. A class of linear-in-the-parameter models with universal approximation capabilities have been intensively studied and widely used due to the availability of many linear-learning algorithms and their inherent convergence conditions. This article presents a systematic overview of basic research on model selection approaches for linear-in-the-parameter models. One of the fundamental problems in non-linear system identification is to find the minimal model with the best model generalisation performance from observational data only. The important concepts in achieving good model generalisation used in various non-linear system-identification algorithms are first reviewed, including Bayesian parameter regularisation and models selective criteria based on the cross validation and experimental design. A significant advance in machine learning has been the development of the support vector machine as a means for identifying kernel models based on the structural risk minimisation principle. The developments on the convex optimisation-based model construction algorithms including the support vector regression algorithms are outlined. Input selection algorithms and on-line system identification algorithms are also included in this review. Finally, some industrial applications of non-linear models are discussed.

Porcine models for the metabolic syndrome, digestive and bone disorders: a general overview

The aim of this review article is to provide an overview of the role of pigs as a biomedical model for humans. The usefulness and limitations of porcine models have been discussed in terms of metabolic, cardiovascular, digestive and bone diseases in humans. Domestic pigs and minipigs are the main categories of pigs used as biomedical models. One drawback of minipigs is that they are in short supply and expensive compared with domestic pigs, which in contrast cost more to house, feed and medicate. Different porcine breeds show different responses to the induction of specific diseases. For example, ossabaw minipigs provide a better model than Yucatan for the metabolic syndrome as they exhibit obesity, insulin resistance and hypertension, all of which are absent in the Yucatan. Similar metabolic/physiological differences exist between domestic breeds (e.g. Meishan v. Pietrain). The modern commercial (e.g. Large White) domestic pig has been the preferred model for developmental programming due to the 2- to 3-fold variation in body weight among littermates providing a natural form of foetal growth retardation not observed in ancient (e.g. Meishan) domestic breeds. Pigs have been increasingly used to study chronic ischaemia, therapeutic angiogenesis, hypertrophic cardiomyopathy and abdominal aortic aneurysm as their coronary anatomy and physiology are similar to humans. Type 1 and II diabetes can be induced in swine using dietary regimes and/or administration of streptozotocin. Pigs are a good and extensively used model for specific nutritional studies as their protein and lipid metabolism is comparable with humans, although pigs are not as sensitive to protein restriction as rodents. Neonatal and weanling pigs have been used to examine the pathophysiology and prevention/treatment of microbial-associated diseases and immune system disorders. A porcine model mimicking various degrees of prematurity in infants receiving total parenteral nutrition has been established to investigate gut development, amino acid metabolism and non-alcoholic fatty liver disease. Endoscopic therapeutic methods for upper gastrointestinal tract bleeding are being developed. Bone remodelling cycle in pigs is histologically more similar to humans than that of rats or mice, and is used to examine the relationship between menopause and osteoporosis. Work has also been conducted on dental implants in pigs to consider loading; however with caution as porcine bone remodels slightly faster than human bone. We conclude that pigs are a valuable translational model to bridge the gap between classical rodent models and humans in developing new therapies to aid human health.