Bioremediation of mercury: not properly exploited in contaminated soils!

Applied Microbiology and Biotechnology - Contamination of land and water caused by heavy metal mercury (Hg) poses a serious threat to biota worldwide. The seriousness of toxicity of this neurotoxin...     

Relationship between river water quality and land use in a small river basin running through the urbanizing area of Central Japan

In this study, the relationship between water quality (as represented by major inorganic ion concentrations) and land use characteristics is examined for a small river basin which runs through the urbanizing area of central Japan. Water samples were taken from 24 sites at base flow and analyzed, and the proportions of the various land uses associated with the respective drainage basins were calculated using a digital land-use map (scale: 1:25000). The electrical conductivity (EC) of the water ranged from 84.5 to 600 μS cm⁻¹. Ca²⁺ and Na⁺ were the major cations, accounting for 77% of all cations. Among the anions, HCO₃ ⁻ was dominant (56%), followed by Cl⁻ (24%), SO₄ ²⁻ (13%) and NO₃ ⁻ (7%). Applying principal component analysis to land use in the drainage basin yielded three principal components. The first principal component expressed the degree of occupation by residential areas, the second indicated the degree of urban developing area (i.e., fast-developing and industrial areas), and the third showed the degree of coverage with farmland and green space. The residential area showed significant positive correlations with K⁺, Mg²⁺, Ca²⁺, NO₃ ⁻, HCO₃ ⁻, EC and TMI (total major ions). Urban developing area showed significant positive correlations with Ca²⁺, Cl⁻, HCO₃ ⁻, EC and TMI as well as weak negative correlations with NO₃ ⁻ and SO₄ ²⁻. Industrial area showed weak positive correlations with Na⁺ and Cl⁻ and a moderate negative correlation with NO₃ ⁻. Farmland showed significant positive correlations with NO₃ ⁻ and SO₄ ²⁻; these ions are present due to fertilizers and the biological activity of plants. Forest area is inversely related to almost all ions, indicating the need for this form of land use in order to maintain river water quality.     

Syntheses and anti-depressant activity of 5-amino-1, 3, 4-thiadiazole-2-thiol imines and thiobenzyl derivatives

A number of new imine derivatives of 5-amino-1, 3, 4-thiadiazole-2-thiol have been synthesized, and their anti-depressant activity was tested using imipramine as reference drug. Two compounds namely 5-{[1-(4-chlorophenyl)-3-(4-methoxy-phenyl)prop-2-en-1-ylidene]-amino}-5-benzylthio-1, 3,4 -thiadiazole 4i(b) and 5-{[1-(4-chlorophenyl)-3-(4-dimethyl-aminophenyl)-prop-2-en-1-ylidene]amino}-5-benzylthio-1,3,4-thiadiazole 4i(c) have shown significant anti-depressant activity, which decreased immobility time by 77.99% and 76.26% compared to the standard imipramine (82%). All the compounds in the series have passed neurotoxicity tests.     

Mutation Size Optimizes Speciation in an Evolutionary Model

The role of mutation rate in optimizing key features of evolutionary dynamics has recently been investigated in various computational models. Here, we address the related question of how maximum mutation size affects the formation of species in a simple computational evolutionary model. We find that the number of species is maximized for intermediate values of a mutation size parameter μ; the result is observed for evolving organisms on a randomly changing landscape as well as in a version of the model where negative feedback exists between the local population size and the fitness provided by the landscape. The same result is observed for various distributions of mutation values within the limits set by μ. When organisms with various values of μ compete against each other, those with intermediate μ values are found to survive. The surviving values of μ from these competition simulations, however, do not necessarily coincide with the values that maximize the number of species. These results suggest that various complex factors are involved in determining optimal mutation parameters for any population, and may also suggest approaches for building a computational bridge between the (micro) dynamics of mutations at the level of individual organisms and (macro) evolutionary dynamics at the species level.     

Effect of TNF-α and IL-1β genetic variants on the development of myocardial infarction in Turkish population

Tumor necrosis factor-alpha (TNF-α) and interleukin 1 beta (IL-1β) genetic variants which resulting in TNF-α and IL-1 overproduction may increase susceptibility to autoimmune diseases such as atherosclerosis. We have studied the association of TNF-α G308A and IL-1β (+3953) C/T polymorphism with myocardial infarction in Turkish population. 143 patients with myocardial infarction and 213 age-matched healthy controls were included in the study. In univariant analysis, the frequencies of IL-1β, TNF-α genotype or allele, and haplotype of C:A and T:A were significantly elevated in patients when compared with those of controls. GA genotype of TNF-α, T allele of IL-1β and A of TNF-α allele seem to be risk factors for myocardial infarction. In contrast, CC genotype of IL-1β and GG genotype of TNF-α have protective effect against myocardial infarction. In multivariate logistic regression analysis, TNF-α A allele, gender and smoking were associated with myocardial infarction. In conclusion, we can state that TNF-α A allele might be associated with myocardial infarction.     

ATPase Subdomain IA Is a Mediator of Interdomain Allostery in Hsp70 Molecular Chaperones

The versatile functions of the heat shock protein 70 (Hsp70) family of molecular chaperones rely on allosteric interactions between their nucleotide-binding and substrate-binding domains, NBD and SBD. Understanding the mechanism of interdomain allostery is essential to rational design of Hsp70 modulators. Yet, despite significant progress in recent years, how the two Hsp70 domains regulate each other''s activity remains elusive. Covariance data from experiments and computations emerged in recent years as valuable sources of information towards gaining insights into the molecular events that mediate allostery. In the present study, conservation and covariance properties derived from both sequence and structural dynamics data are integrated with results from Perturbation Response Scanning and in vivo functional assays, so as to establish the dynamical basis of interdomain signal transduction in Hsp70s. Our study highlights the critical roles of SBD residues D481 and T417 in mediating the coupled motions of the two domains, as well as that of G506 in enabling the movements of the α-helical lid with respect to the β-sandwich. It also draws attention to the distinctive role of the NBD subdomains: Subdomain IA acts as a key mediator of signal transduction between the ATP- and substrate-binding sites, this function being achieved by a cascade of interactions predominantly involving conserved residues such as V139, D148, R167 and K155. Subdomain IIA, on the other hand, is distinguished by strong coevolutionary signals (with the SBD) exhibited by a series of residues (D211, E217, L219, T383) implicated in DnaJ recognition. The occurrence of coevolving residues at the DnaJ recognition region parallels the behavior recently observed at the nucleotide-exchange-factor recognition region of subdomain IIB. These findings suggest that Hsp70 tends to adapt to co-chaperone recognition and activity via coevolving residues, whereas interdomain allostery, critical to chaperoning, is robustly enabled by conserved interactions.     

Thermal Tolerance Limits of Diamondback Moth in Ramping and Plunging Assays

Thermal sensitivity is a crucial determinant of insect abundance and distribution. The way it is measured can have a critical influence on the conclusions made. Diamondback moth (DBM), Plutella xylostella (L.) (Lepidoptera: Plutellidae) is an important insect pest of cruciferous crops around the world and the thermal responses of polyphagous species are critical to understand the influences of a rapidly changing climate on their distribution and abundance. Experiments were carried out to the lethal temperature limits (ULT₀ and LLT₀: temperatures where there is no survival) as well as Upper and Lower Lethal Temperature (ULT₂₅ and LLT₂₅) (temperature where 25% DBM survived) of lab-reared adult DBM population to extreme temperatures attained by either two-way ramping (ramping temperatures from baseline to LT₂₅ and ramping back again) or sudden plunging method. In this study the ULT₀ for DBM was recorded as 42.6°C and LLT₀ was recorded as −16.5°C. DBM had an ULT₂₅ of 41.8°C and LLT₂₅ of −15.2°C. The duration of exposure to extreme temperatures had significant impacts on survival of DBM, with extreme temperatures and/or longer durations contributing to higher lethality. Comparing the two-way ramping temperature treatment to that of direct plunging temperature treatment, our study clearly demonstrated that DBM was more tolerant to temperature in the two-way ramping assay than that of the plunging assay for cold temperatures, but at warmer temperatures survival exhibited no differences between ramping and plunging. These results suggest that DBM will not be put under physiological stress from a rapidly changing climate, rather access to host plants in marginal habitats has enabled them to expand their distribution. Two-way temperature ramping enhances survival of DBM at cold temperatures, and this needs to be examined across a range of taxa and life stages to determine if enhanced survival is widespread incorporating a ramping recovery method.     

The olfactory receptor gene superfamily: data mining, classification, and nomenclature

The vertebrate olfactory receptor (OR) subgenome harbors the largest known gene family, which has been expanded by the need to provide recognition capacity for millions of potential odorants. We implemented an automated procedure to identify all OR coding regions from published sequences. This led us to the identification of 831 OR coding regions (including pseudogenes) from 24 vertebrate species. The resulting dataset was subjected to neighbor-joining phylogenetic analysis and classified into 32 distinct families, 14 of which include only genes from tetrapodan species (Class II ORs). We also report here the first identification of OR sequences from a marsupial (koala) and a monotreme (platypus). Analysis of these OR sequences suggests that the ancestral mammal had a small OR repertoire, which expanded independently in all three mammalian subclasses. Classification of ``fish-like' (Class I) ORs indicates that some of these ancient ORs were maintained and even expanded in mammals. A nomenclature system for the OR gene superfamily is proposed, based on a divergence evolutionary model. The nomenclature consists of the root symbol `OR', followed by a family numeral, subfamily letter(s), and a numeral representing the individual gene within the subfamily. For example, OR3A1 is an OR gene of family 3, subfamily A, and OR7E12P is an OR pseudogene of family 7, subfamily E. The symbol is to be preceded by a species indicator. We have assigned the proposed nomenclature symbols for all 330 human OR genes in the database. A WWW tool for automated name assignment is provided. Received: / Accepted: