The potential of microbial ecological indicators to guide ecosophisticated management of hydrocarbon-contaminated soils

Soil is an unrenewable natural resource under increasing anthropogenic pressure. One of the main threats to soils, compromising their ability to provide us with the goods and ecosystem services we expect, is pollution. Oil hydrocarbons are the most common soil contaminants, and they disturb not just the biota but also the physicochemical properties of soils. Indigenous soil micro-organisms respond rapidly to changes in the soil ecosystem, and are chronically in direct contact with the hydrophobic pollutants on the soil surfaces. Soil microbial variables could thus serve as an intrinsically relevant indicator of soil quality, to be used in the ecological risk assessment of contaminated and remediated soils. Two contrasting studies were designed to investigate soil microbial ecological responses to hydrocarbons, together with parallel changes in soil physicochemical and ecotoxicological properties. The aim was to identify quantitative or qualitative microbiological variables that would be practicable and broadly applicable for the assessment of the quality and restoration of oil-polluted soil. Soil bacteria commonly react on hydrocarbons as a beneficial substrate, which lead to a positive response in the classical microbiological soil quality indicators; negative impacts were accurately reflected only after severe contamination. Hydrocarbon contaminants become less bioavailable due to weathering processes, and their potentially toxic effects decrease faster than the total concentration. Indigenous hydrocarbon degrader bacteria, naturally present in any terrestrial environment, use specific mechanisms to improve access to the hydrocarbon molecules adsorbed on soil surfaces. Thus when contaminants are unavailable even to the specialised degraders, they should pose no hazard to other biota either. Change in the ratio of hydrocarbon degrader numbers to total microbes was detected to predictably indicate pollutant effects and bioavailability. Also bacterial diversity, a qualitative community characteristic, decreased as a response to hydrocarbons. Stabilisation of community evenness, and community structure that reflected clean reference soil, indicated community recovery. If long-term temporal monitoring is difficult and appropriate clean reference soil unavailable, such comparison could possibly be based on DNA-based community analysis, reflecting past+present, and RNA-based community analysis, showing exclusively present conditions. Microbial ecological indicators cannot replace chemical oil analyses, but they are theoretically relevant and operationally practicable additional tools for ecological risk assessment. As such, they can guide ecologically informed and sustainable ecosophisticated management of oil-contaminated lands.

The variants of the protein toxins abrin and ricin A useful guide to understanding the processing events in the toxin transport

Kinetic data on inhibition of protein synthesis in thymocyte by three abrins and ricin have been obtained. The intrinsic efficiencies of A chains of four toxins to inactivate ribosomes, as analyzed by k1-versus-concentration plots were abrin II, III > ricin > abrin I. The lag times were 90, 66, 75 and 105 min at a 0.0744 nM concentration of each of abrin I, II, III and ricin, respectively. To account for the observed differences in the dose-dependent lag time, functional and structural variables of toxins such as binding efficiency of B chains to receptors and low-pH-induced structural alterations have been analyzed. The association constants obtained by stopped flow studies showed that abrin-I (4.13 × 105 M−1 s−1) association with putative receptor (4-methylumbelliferyl-α-D-galactoside) is nearly two times more often than abrin III (2.6 × 105 M−1 s−1) at 20°C. Equillibrium binding constants of abrin I and II to thymocyte at 37°C were 2.26 × 107 M−1 and 2.8 × 107 M−1 respectively. pH-induced structural alterations as studied by a parallel enhancement in 8-anilino-L-naphthalene sulfonate fluorescence revealed a high degree of qualitative similarity. These results taken with a nearly identical concentration-independent lag time (minimum lag of 41–42 min) indicated that the binding efficiencies and internalization efficiencies of these toxins are the same and that the observed difference in the dose-dependent lag time is causally related to the proposed processing event. The rates of reduction of inter-subunit disulfide bond, an obligatory step in the intoxication process, have been measured and compared under a variety of conditions. Intersubunit disulfide reduction of abrin I is fourfold faster than that of abrin II at pH 7.2. The rate of disulfide reduction in abrin I could be decreased 1 I-fold by adding lactose, compared to that without lactose. The observed differences in the efficiencies of A chains, the dose-dependent lag period, the modulating effect of lactose on the rates of disulfide reduction and similarity in binding properties make the variants a valuable tool to probe the processing events in toxin transport in detail.

Pictorial Guide to Frogs and Toads of the Western Ghats

A unique colour pictorial guide exclusively on frogs and toads of the Western Ghats of India. The guide illustrates 73 species with quality photographs, pointers to key features, pictograms, distribution maps, habitat photographs and with minimal text. Scientific and common names, museum record, actual and relative sizes, habitats and current IUCN status of each species are also provided. Species are grouped on their habitat preferences, making it easy to use in the field.

An overview of recent advances in structural bioinformatics of protein-protein interactions and a guide to their principles

Rich data bearing on the structural and evolutionary principles of protein protein interactions are paving the way to a better understanding of the regulation of function in the cell. This is particularly the case when these interactions are considered in the framework of key pathways. Knowledge of the interactions may provide insights into the mechanisms of crucial `driver' mutations in oncogenesis. They also provide the foundation toward the design of protein protein interfaces and inhibitors that can abrogate their formation or enhance them. The main features to learn from known 3-D structures of protein protein complexes and the extensive literature which analyzes them computationally and experimentally include the interaction details which permit undertaking structure-based drug discovery, the evolution of complexes and their interactions, the consequences of alterations such as post-translational modifications, ligand binding, disease causing mutations, host pathogen interactions, oligomerization, aggregation and the roles of disorder, dynamics, allostery and more to the protein and the cell. This review highlights some of the recent advances in these areas, including design, inhibition and prediction of protein protein complexes. The field is broad, and much work has been carried out in these areas, making it challenging to cover it in its entirety. Much of this is due to the fast increase in the number of molecules whose structures have been determined experimentally and the vast increase in computational power. Here we provide a concise overview. (C) 2014 Elsevier Ltd. All rights reserved.

Whales, dolphins, and porpoises of the eastern North Pacific and adjacent Arctic waters: a guide to their identification

This is an identification guide for cetaceans (whales, dolphins, and porpoises), that was designed to assist laymen in identifying cetaceans encountered in eastern North Pacific and Arctic waters. It was intended for use by ongoing cetacean observer programs. This is a revision of an earlier guide with the same title published in 1972 by the Naval Undersa Center and the National Marine Fisheries Service. It includes sections on identifying cetaceans at sea as well as stranded animals on shore. Species accounts are divided by body size and presence or lack of a dorsal fin. Appendices include illustrations of tags on whales, dolphins, and porpoises, by Larry Hobbs; how to record data from observed cetaceans at sea and for stranded cetaceans; and a list of cetacean names in Japanese and Russian. (Document contains 245 pages - file takes considerable time to open)

Whales, dolphins, and porpoises of the western North Atlantic: a guide to their identification

This is an identification guide for cetaceans (whales, dolphins, and porpoises). It was designed to assist laypersons in identifying cetaceans encountered in the western North Atlantic Ocean and was intended for use by ongoing cetacean observer programs. This publication includes sections on identifying cetaceans at sea as well as stranded animals on shore. Species accounts are divided by body size and presence or lack of a dorsal fin. Appendices cover tags used on cetacean species; how to record and report cetacean observations at see and for stranded cetaceans; and a list of contacts for reporting cetacean strandings. (Document pdf contains 183 pages - file takes considerable time to open)

Guide to best practices for ocean CO2 measurements

CHAP 1 - Introduction to the Guide CHAP 2 - Solution chemistry of carbon dioxide in sea water CHAP 3 - Quality assurance CHAP 4 - Recommended standard operating procedures (SOPs) SOP 1 - Water sampling for the parameters of the oceanic carbon dioxide system SOP 2 - Determination of total dissolved inorganic carbon in sea water SOP 3a - Determination of total alkalinity in sea water using a closed-cell titration SOP 3b - Determination of total alkalinity in sea water using an open-cell titration SOP 4 - Determination of p(CO2) in air that is in equilibrium with a discrete sample of sea water SOP 5 - Determination of p(CO2) in air that is in equilibrium with a continuous stream of sea water SOP 6a - Determination of the pH of sea water using a glass/reference electrode cell SOP 6b - Determination of the pH of sea water using the indicator dye m-cresol purple SOP 7 - Determination of dissolved organic carbon and total dissolved nitrogen in sea water SOP 7 en Español - Determinacion de carbono organico disuelto y nitrogeno total disuelto en agua de mar SOP 11 - Gravimetric calibration of the volume of a gas loop using water SOP 12 - Gravimetric calibration of volume delivered using water SOP 13 - Gravimetric calibration of volume contained using water SOP 14 - Procedure for preparing sodium carbonate solutions for the calibration of coulometric CT measurements SOP 21 - Applying air buoyancy corrections SOP 22 - Preparation of control charts SOP 23 - Statistical techniques used in quality assessment SOP 24 - Calculation of the fugacity of carbon dioxide in the pure gas or in air CHAP 5 - Physical and thermodynamic data Errata - to the hard copy of the Guide to best practices for ocean CO2 measurements