Oxidoreductases for the remediation of organic pollutants in water – a critical review

Water contamination by various recalcitrant organic aromatic compounds is an emerging environmental issue that is increasingly attracting the attention of environmental scientists. A great majority of these recalcitrant pollutants are industrial wastes, textile dyes, pharmaceuticals, hormones, and personal care products that are discharged into wastewater. Not surprisingly, various chemical, physical, and biological strategies have been proposed and developed to remove and/or degrade these pollutants from contaminated water bodies. Biological approaches, specifically using oxidoreductase enzymes (such as peroxidases and laccases) for pollutant degradation are a relatively new and a promising research area that has potential advantages over other methods due to their higher efficiency and the ease of handling. This review focuses on the application of different classes of oxidoreductase enzymes to degrade various classes of organic pollutants. In addition to classifying these enzymes based on structural differences, the major factors that can affect their remediation ability, such as the class of peroxidases employed, pH, molecular structure of the pollutant, temperature, and the presence of redox mediators are also examined and discussed. Interestingly, a literature survey combined with our unpublished data suggests that “peroxidases” are a very heterogeneous and diverse family of enzymes and have different pH profiles, temperature optima, thermal stabilities, requirements for redox mediators, and substrate specificities as well as varying detoxification abilities. Additionally, remediation of real-life polluted samples by oxidoreductases is also highlighted as well as a critical look at current challenges and future perspectives.     

Population-based neuropathological studies of dementia: design, methods and areas of investigation – a systematic review

Background  

Prospective population-based neuropathological studies have a special place in dementia research which is under emphasised.     

Exhaled breath analysis: a review of ‘breath-taking’ methods for off-line analysis

Background

The potential of exhaled breath sampling and analysis has long attracted interest in the areas of medical diagnosis and disease monitoring. This interest is attributed to its non-invasive nature, access to an unlimited sample supply (i.e., breath), and the potential to facilitate a rapid at patient diagnosis. However, progress from laboratory setting to routine clinical practice has been slow. Different methodologies of breath sampling, and the consequent difficulty in comparing and combining data, are considered to be a major contributor to this. To fulfil the potential of breath analysis within clinical and pre-clinical medicine, standardisation of some approaches to breath sampling and analysis will be beneficial.

Objectives

The aim of this review is to investigate the heterogeneity of breath sampling methods by performing an in depth bibliometric search to identify the current state of art in the area. In addition, the review will discuss and critique various breath sampling methods for off-line breath analysis.

Methods

Literature search was carried out in databases MEDLINE, BIOSIS, EMBASE, INSPEC, COMPENDEX, PQSCITECH, and SCISEARCH using the STN platform which delivers peer-reviewed articles. Keywords searched for include breath, sampling, collection, pre-concentration, volatile. Forward and reverse search was then performed on initially included articles. The breath collection methodologies of all included articles was subsequently reviewed.

Results

Sampling methods differs between research groups, for example regarding the portion of breath being targeted. Definition of late expiratory breath varies between studies.

Conclusions

Breath analysis is an interdisciplinary field of study using clinical, analytical chemistry, data processing, and metabolomics expertise. A move towards standardisation in breath sampling is currently being promoted within the breath research community with a view to harmonising analysis and thereby increasing robustness and inter-laboratory comparisons.

     

Regulation and expression of transgenes in fish—a review

Transgenic fish, owing to a number of advantages which they offer over other species, are proving to be valuable model systems for the study of gene regulation and developmental genetics in addition to being useful targets for the genetic manipulation of commercially important traits. Despite having begun only a decade ago, the production of transgenic fish has become commonplace in a number of laboratories world-wide and considerable progress has been made. In this review, we initially consider the various regulatory elements and coding genes which have been used in fish, and subsequently discuss and compare both the transient and long-term fate and expression patterns of injected DNA sequences in the context of the different factors which are likely to have an effect on the expression of transgenes.     

Host cell protein analysis in therapeutic protein bioprocessing – methods and applications

The analysis of host cell proteins (HCPs) is one of the most important analytical requirements during bioprocess development of therapeutic moieties. In this review, we focus on the comparison of different methods for the analysis of HCPs and how cell lines, fermentation conditions, and unit operations influence HCP distribution during the process chain. Current guidelines typically require reduction of HCPs to the ppm level, depending on the intended use, the route of administration of the product, and the production system. A range of immunospecific and non-specific methods are available that have been globally accepted by regulatory bodies. Immunospecific methods, such as ELISA, are simple to use in routine analysis and can quantify low levels of HCPs when specific antibodies are available. Non-specific methods are more complex; however, they provide a holistic view of the HCP profile and qualitative information of the composition of HCP in the sample. Different methods for the comparison of bioprocessing strategies during scale-up and purification development are compared herein. The methods include immunospecific methods, such as ELISA, western blot, and threshold, and non-specific methods, such as 2D-DIGE and 2D-HPLC combined with MS.     

Reproductive traits of Pinus halepensis in the light of fire – a critical review

Fire is known to be a major factor in shaping plants and vegetation worldwide. Many plant traits have been described as adaptations for surviving fire, or regenerating after it. However, many of the traits are also advantageous for overcoming other disturbances. The fact that fire in the Mediterranean Basin has been almost exclusively of anthropogenic origin, and thus is of short duration in an evolutionary time scale, cast doubt on the possibility that fire can act as a selective force in the Mediterranean Basin. Our aim here is to review the ecological advantages of Pinus halepensis traits and their possibility to be selected by fire. The non-self pruning of cones and branches, and the high resin content increase the probability of canopy fires and consequent death of P. halepensis trees. Post-fire regeneration of P. halepensis depends totally upon its canopy-stored seed bank. The seedlings grow quickly and they first reproduce at an early age. Young reproductive trees function first as females with a high percentage of serotinous cones. Thus, young P. halepensistrees allocate many resources to seed production, reducing their `immaturity risk' in a case of an early successive fire. The proportion of serotinous cones is higher in post-fire naturally regenerating stands than in unburned stands, and seeds from serotinous cones germinate better under simulated post-fire conditions. The extremely high pH of the ash-bed under the burned canopies creates the post-fire regeneration niche of P. halepensis exactly under their parent trees. All these traits are advantageous for post-fire regeneration, but could they also be selected during the time scale of anthropogenic fires in the Mediterranean Basin? Pinus halepensis is a relatively short living tree with almost no recruitment under forest canopy. The longest estimated fire-return interval and generation length are about 125 years. The earliest solid evidence for the first hominid-controlled fire in the Mediterranean basin is 780,000 years ago, and thus the estimated number of post-fire generations is 6240. We suggest that such a number of generations is sufficient for the selection and radiation of fire adaptive traits in P. halepensis.

     

The shape and mobility of the thoracic spine in asymptomatic adults – A systematic review of in vivo studies

A comprehensive knowledge of the thoracic shape and kinematics is essential for effective risk prevention, diagnose and proper management of thoracic disorders and assessment of treatment or rehabilitation strategies as well as for in silico and in vitro models for realistic applications of boundary conditions.After an extensive search of the existing literature, this study summarizes 45 studies on in vivo thoracic kyphosis and kinematics and creates a systematic and detailed database. The thoracic kyphosis over T1–12 determined using non-radiological devices (34°) was relatively less than measured using radiological devices (40°) during standing. The majority of kinematical measurements are based on non-radiological devices. The thoracic range of motion (RoM) was greatest during axial rotation (40°), followed by lateral bending (26°), and flexion (21°) when determined using non-radiological devices during standing. The smallest RoM was identified during extension (13°). The lower thoracic level (T8–12) contributed more to the RoM than the upper (T1–4) and middle (T4–8) levels during flexion and lateral bending. During axial rotation and extension, the middle level (T4–8) contributed the most. Coupled motion was evident, mostly during lateral bending and axial rotation. With aging, the thoracic kyphosis increased by about 3° per decade, whereas the RoM decreased by about 5° per decade for all load directions. These changes with aging mainly occurred in the lower region (T6–12). The influence of sex on thoracic kyphosis and the RoM has been described as partly contradictory. Obesity was found to decrease the thoracic RoM. Studies comparing standing, sitting and lying reported the effect of posture as significant.     

How is ecosystem health defined and measured? A critical review of freshwater and estuarine studies

Assessing ecosystem health is an ongoing priority for governments, scientists and managers worldwide. There are several decades of scientific literature discussing ecosystem health and approaches to assess it, with applications to aquatic and terrestrial environments incorporating economic, environmental and social processes. We conducted a systematic review of studies that assess ecosystem health to update our current understanding of how ecosystem health is being defined, and provide new ideas and directions on how it can be measured. We focused the review on studies that used the term ‘ecosystem health’ or the equivalent terms ‘ecosystem integrity’, ‘ecosystem quality’ and ‘ecosystem protection’, in lotic freshwater and estuarine environments, and examined how many of these included explicit definitions of what ecosystem health means for their study system. We collected information about the temporal and geographical distribution of studies, and the types of indicators (biological, physical or chemical) used in the assessments. We found few studies clearly defined ecosystem health and justified the choice of indicators. Given the broad use of the term it seems impractical to have an overarching definition of ecosystem health, but rather an approach that is able to define and measure health on a case by case basis. A combination of biological, physical and chemical indicators was commonly used to assess ecosystem health in both estuarine and freshwater studies, with a strong bias towards fish and macroinvertebrate community metrics (e.g. diversity, abundance and composition). We found only two studies that simultaneously considered both freshwater and estuarine sections of the ecosystem, highlighting the significant knowledge gap in our understanding of the transfer of flow, nutrients and biota between the different systems—all key factors that influence ecosystem health. This review is the first to combine knowledge from both freshwater and estuarine ecosystem assessments and critically review how aquatic ecosystem health is defined and measured since the late-1990s, providing the basis for setting achievable management goals relating to ecosystem health into the future.     

Workflow management systems for gene sequence analysis and evolutionary studies – A Review

Post ‘omic’ era has resulted in the development of many primary, secondary and derived databases. Many analytical and visualization bioinformatics tools have been developed to manage and analyze the data available through large sequencing projects. Availability of heterogeneous databases and tools make it difficult for researchers to access information from varied sources and run different bioinformatics tools to get desired analysis done. Building integrated bioinformatics platforms is one of the most challenging tasks that bioinformatics community is facing. Integration of various databases, tools and algorithm is a challenging problem to deal with. This article describes the bioinformatics analysis workflow management systems that are developed in the area of gene sequence analysis and phylogeny. This article will be useful for biotechnologists, molecular biologists, computer scientists and statisticians engaged in computational biology and bioinformatics research.     

Lignans of sesame: Purification methods,biological activities and biosynthesis – A review

Lignans are a group of compounds consisting of dimers of phenyl propane units. They are found in diverse forms distributed in a variety of plants. Sesame lignans in particular are obtained from Sesamum indicum, a highly prized oilseed crop cultivated widely in many countries in the east. The plant is the main source of clinically important antioxidant lignans such as sesamin, sesamolin, sesaminol and sesamol. These lignans exhibit antihypertensive, anticancerous and hypocholesterolemic activities as well especially in humans due to which they have become compounds of tremendous research interest in recent times. Sesamin is synthesized from shikimic acid through phenylpropanoid pathway and metabolised into enterolignans which play a pivotal role in protection against several hormone related diseases. In this paper we present an overview of current status of research on sesame lignans with respect to the analytical methods employed, the biological activities and biosynthesis of sesame lignans.     

Comparison of derivatization and chromatographic methods for GC–MS analysis of amino acid enantiomers in physiological samples

GC–MS analysis of fluorinated and non-fluorinated chloroformate and anhydride derivatives of amino acid (AA) enantiomers on two different chiral columns was compared for the direct quantification of free l- and d-AAs in human serum and urine in a single analytical run. Best sensitivity was achieved with pentafluoropropionic anhydride/heptafluorobutanol derivatives separated on a Chirasil-l-Val column. However, the occurrence of racemization during derivatization precluded accurate quantification of AA enantiomers. Derivatization with methyl chloroformate/methanol and separation on an Rt-γDEXsa column did not exhibit racemization and yielded ten baseline separated racemates of proteinogenic AAs with resolution values greater than 2.4. However, protein and peptide hydrolysis occurred in serum and urine during the highly exothermal derivatization reaction under alkaline conditions. Removing serum proteins by precipitation before derivatization and performing the reaction at neutral pH enabled the determination of accurate free AA enantiomer concentrations. Accuracy of quantification was validated by an established nonchiral GC–MS method for AA analysis. Reliable quantification was achieved using stable-isotope labeled l-AAs as internal standards. Limits of detection (LOD) and lower limits of quantification (LLOQ) for the d-AAs were in the range of 3.2–446 nM and 0.031–1.95 μM, respectively. Relative standard deviations (N = 6) for the measurement of AAs in urine and serum ranged from 0.49–11.10% to 0.70–3.87%, respectively. The method was applied to the analysis of urine from 19 patients with renal insufficiency. In comparison to healthy probands, D-ratios of Ala, Val, Pro, Thr, Asp, and Asn were significantly increased.     

Horizontal distribution of cladocerans in arctic Greenland lakes – impact of macrophytes and fish

Submerged macrophytes may play an important role as a refuge for zooplankton against predators. However, a recent study suggests that their importance depends on the trophic state of the lake. We studied the impact of fish and macrophytes on the horizontal distribution of pelagic cladocerans in 56 oligotrophic arctic Greenland lakes. In north-east and western Greenland, zooplankton was sampled in the near-shore (littoral) and central (pelagial) part of all lakes and fish were sampled with multiple mesh-sized gill nets. Macrophytes were visually estimated in the littoral. In north-east Greenland, 5 taxa of cladocerans were found, while 14 taxa were recorded in western Greenland. Daphnia pulex occurred only in fishless lakes in both northeast and western Greenland and avoided the near-shore areas in the shallow and deep lakes. Bosmina spp. and Holopedium gibberum were evenly distributed between the littoral and the pelagial in the deep and shallow fishless lakes. However, their near-shore density was lowest in the presence of fish. Macrophyte-related and benthic cladocerans concentrated either in the littoral or were evenly distributed between the littoral and the pelagial, irrespective of depth and fish presence or absence. Macrophytes had no impact on the horizontal distribution of pelagic cladocerans. Thus, it is concluded that horizontal heterogeneity of Bosmina spp. and Holopedium gibberum might be affected by the presence of fish.     

Hormones and root-shoot relationships in flooded plants — an analysis of methods and results

Two aspects of root to shoot communication in flooded plants are discussed (i) the formation of porous aerenchyma that enhances the passage of oxygen, and other gases, from shoots to roots and (ii) the movement of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) from roots to shoots in the transpiration stream, and the effect of this on ethylene production and epinastic curvature in the shoots. For aerenchyma studies a highly sensitive photoacoustic laser detector for ethylene was used to avoid interference associated with other methods of ethylene measurement that require tissue excision. ACC concentrations in xylem sap were measured by physico-chemical means to ensure correct identification and account for processing losses. Solute concentrations, e.g., abscisic acid (ABA), in xylem sap are shown to be distorted by temporary contamination caused by the method used to collect sap. Concentrations of solutes in xylem sap (e.g., ACC) are also altered by changes in sap flow brought about by conventional methods of sap collection or by experimental treatments such as flooding the soil. Ways of for overcoming these problems are described together with a summary of preliminary results.     

Statistical methods for temporal and space–time analysis of community composition data

This review focuses on the analysis of temporal beta diversity, which is the variation in community composition along time in a study area. Temporal beta diversity is measured by the variance of the multivariate community composition time series and that variance can be partitioned using appropriate statistical methods. Some of these methods are classical, such as simple or canonical ordination, whereas others are recent, including the methods of temporal eigenfunction analysis developed for multiscale exploration (i.e. addressing several scales of variation) of univariate or multivariate response data, reviewed, to our knowledge for the first time in this review. These methods are illustrated with ecological data from 13 years of benthic surveys in Chesapeake Bay, USA. The following methods are applied to the Chesapeake data: distance-based Moran''s eigenvector maps, asymmetric eigenvector maps, scalogram, variation partitioning, multivariate correlogram, multivariate regression tree, and two-way MANOVA to study temporal and space–time variability. Local (temporal) contributions to beta diversity (LCBD indices) are computed and analysed graphically and by regression against environmental variables, and the role of species in determining the LCBD values is analysed by correlation analysis. A tutorial detailing the analyses in the R language is provided in an appendix.     

Cadmium induced bioaccumulation,histopathology, gene regulation in fish and its amelioration – A review

Different anthropogenic activities as well as natural sources contribute enormously towards various heavy metal contaminations in aquatic habitats. Cadmium (Cd) is one of most prevalent and toxic heavy metals with a long half life. Unlike terrestrial animals, exposure of Cd in fishes may happen not only through feeds but also from its habitat water. Bioaccumulation of Cd in fishes occurs in many tissues, but mainly in gill, liver, kidney, skin, and muscle. The concentrations of Cd in fish tissues depend upon the extent and duration of Cd exposure, species and age of fishes, dietary minerals and antioxidant concentrations, and habitat water quality. Specific histopathological observations in liver, kidney, and gill are useful to understand the effects of Cd, which could help to determine the ameliorating methods to be adopted. Exposure of Cd exerts several adverse effects on general growth and development, reproductive processes, osmoregulation, morphological and histological structures, stress tolerance, and endocrine system, mainly due to changes in biological functions induced by differential expressions of several genes related to oxidative stress, apoptosis, inflammation, immunosuppressions, genotoxicity, Cd chelation and carbohydrate metabolism. Chronic biomagnifications of Cd exceeding the permitted level may be harmful not only to the fishes itself but also to humans through food chains. Amelioration of such toxic heavy metal that has been categorized as a potent carcinogenic in humans is of utmost importance. Main modes of amelioration encompas reducing oxidative damages by promoting the antioxidative defenses, decreasing Cd absorption, increasing excretion through excretory system and improving the tolerance of fishes to Cd toxicity. Many amelioration measures such as use of minerals (for example, zinc, calcium, and iron), vitamins (vitamin C, A, and E), different herbs, probiotics and other agents (taurine, bentonite, chitosan, zeolite, and metallothionein) have been explored for their effective roles to reduce Cd bioaccumulation and toxicity symptoms in fishes. The present review discusses bioaccumulation of Cd, histopathological alterations, oxidative stress, synergism-antagonism, and gene regulation in different tissues, and its amelioration measures in fishes.     

Measurements of peripheral and deep body temperature in cattle – A review

Automation of the measurement of the physiological and behavioural parameters of livestock has become an important goal for both scientists and farmers. Accurate data and knowledge about farmed animals, especially in cattle breeding, are needed. Proper early diagnosis of a cow's health status in real time allows for preventing the development of infection, oestrus detection and leads to reduced environmental stress. Thus, it contributes to more effective herd management. Among the physiological parameters, body temperature and its fluctuations are key indicators of health and well-being in animals. Currently, along with the development of technical solutions and their implementation, increasingly more attention is being paid to the continuously measurement of body core and peripheral temperature in animals. Recently there has been an increased number of publications devoted to this subject. However, there is a need to systematise this knowledge as these studies have had different purposes, have been performed in various environmental conditions, and the measurements were taken using different methods and equipment. As such, the results obtained by the different authors often may not be comparable. For this reason, this paper has two main purposes: to present the most widely used continuous methods of peripheral and body core temperature measurement, and to show its references values which characterise the individual locations of the cattle body in thermoneutral ambient. An analysis of the professional publications regarding measurements of peripheral and deep body temperature led to the conclusion that these methods have high research and diagnostic potential. However, it is necessary to standardised research to enable better and more comparable results, including among others; different cattle groups, animal age, health and environmental conditions.     

Thirty-four years of dendrochronological studies in Perú: A review of advances and challenges

The development of tree-ring chronologies of tropical trees allows to reconstruct the environmental history of the Neotropics on extensive temporal and spatial scales. This article presents a historic, state-of -the-art overview/review of dendrochronological studies in Perú, a megadiverse country in its flora, types of climate and ecosystems. We reviewed all available information on dendrochronological studies by assessing scientific articles in indexed, and non-indexed journals as well university thesis repositories. Dendrochronological studies began in the late 1980s and have botanically involved 20 families, 34 genera and 52 tree species. The most studied families are Fabaceae (16 studies), Meliaceae (12), Rosaceae (06), and Bignoniaceae (04), and the most studied genera were Cedrela (13), Polylepis (08) and Prosopis (06). The development of chronologies was mainly applied in climatic reconstructions, forest conservation and management. We identify underrepresentation or sampling gaps regarding climatic and geographic complexity. The high tree diversity of Perú constitutes a natural laboratory to develop tree-ring studies to better understand the growth and functioning of tropical tree species, their interaction with climate, and to derive climate reconstructions during the last centuries. This review aims to contribute to the direction of future dendrochronological studies in Perú.