Geochemistry of Virus–Prokaryote Interactions in Freshwater and Acid Mine Drainage Environments,Ontario, Canada

An extensive water sample survey was conducted in southern Ontario, Canada across a variety of freshwater systems in order to further understand the role of viruses in aquatic environments. Backwards stepwise multiple regression analysis found that VLP (virus-like particle) abundance, phosphate, pH, sulfate, and magnesium are predictors of prokaryotic abundance with the model describing 90% of the variability in the data (R² = 0.90). Statistically significant (P < 0.05) predictors of VLP abundance were mineral saturation indices (SI) of goethite (R² = 0.78) although moderate Pearson component analysis correlations (r) were noted with ferrihydrite, jarosite, and pyrolusite. These relationships indicate that viral inactivation through mineral attachment may be a contributor to the moderate relationship between VLP and prokaryotic abundance (r_s = 0.45). In addition, VLP abundance is shown to have a stronger correlation with minerals SI values than prokaryotes indicating a stronger mineral influence with viruses.     

Sediment Microbial Community Composition and Methylmercury Pollution at Four Mercury Mine–Impacted Sites

Mercury pollution presents a globally significant threat to human and ecosystem health. An important transformation in the mercury cycle is the conversion of inorganic mercury to methylmercury, a toxic substance that negatively affects neurological function and bioaccumulates in food chains. This transformation is primarily bacterially mediated, and sulfate-reducing bacteria (SRB) have been specifically implicated as key mercury methylators in lake and estuarine sediments. This study used phospholipid fatty acid (PLFA) analysis to investigate sediment microbial community composition at four abandoned mercury mine–impacted sites in the California Coast Range: the Abbott, Reed, Sulphur Bank, and Mt. Diablo mines. Differences in watershed and hydrology among these sites were related to differences in microbial community composition. The Abbott and Sulphur Bank mines had the highest levels of methylmercury. Floc (a type of precipitate that forms when acid mine drainage contacts lake or river water) and sediment samples differed in terms of several important environmental variables and microbial community composition, but did not have statistically different methylmercury concentrations. Quantification of PLFA biomarkers for SRB (10Mel6:0 for Desulfobacter and i17:1 for Desulfovibrio) revealed that Desulfobacter and Desulfovibrio organisms made up higher percentages of overall microbial biomass at the Sulphur Bank and Mt. Diablo mines than at the Abbott and Reed mines. Correlations between these SRB biomarker fatty acids and methylmercury concentrations suggest that Desulfobacter and Desulfovibrio organisms may contribute to methylmercury production in the Abbott, Reed, and Sulphur Bank mines but may not be important contributors to methylmercury in the Mt. Diablo Mine.     

Use of Arbuscular Mycorrhiza and Organic Amendments to Enhance Growth of Macaranga peltata (Roxb.) Müll. Arg. in Iron Ore Mine Wastelands

Macaranga peltata (Roxb.) Mull. Arg. is a disturbance tolerant plant species with potential in mine wasteland reclamation. Our study aims at studying the phyto-extraction potential of M. peltata and determining plant-soil interaction factors effecting plant growth in iron ore mine spoils. Plants were grown in pure mine spoil and spoil amended with Farm Yard Manure (FYM) and Vermicompost (VC) along with arbuscular mycorrhizal (AM) species Rhizophagus irregularis. Pure and amended mine spoils were evaluated for nutrient status. Plant growth parameters and foliar nutrient contents were determined at the end of one year. FYM amendment in spoil significantly increased plant biomass compared to pure mine spoil and VC amended spoil. Foliar Fe accumulation was recorded highest (594.67μg/g) in pure spoil with no mortality but considerably affecting plant growth, thus proving to exhibit phyto-extraction potential. FYM and VC amendments reduced AM colonization (30.4% and 37% resp.) and plants showed a negative mycorrhizal dependency (–30.35 and –39.83 resp.). Soil pH and P levels and, foliar Fe accumulation are major factors determining plant growth in spoil. FYM amendment was found to be superior to VC as a spoil amendment for hastening plant growth and establishment in iron ore mine spoil     

In-Situ Remediation of Lead–Zinc Polymetallic Mine Contaminated Soils by MnFe2O4 Microparticles

In-situ remediation is a practical approach to remediate soils contaminated with heavy metals. The MnFe₂O₄ microparticles (MM) were prepared for the in-situ remediation of contaminated soils from a lead–zinc polymetallic mine in Inner Mongolia province, China. The effects of MM dosage, pH on remediation efficiency, were determined with static vibration leaching experiment, and the release risk of heavy metals of treated soil was studied by column leaching experiment. The results showed that the leached Cu, Pb, Zn, and As concentration decreased drastically with increasing MM dosage, when the dosage was lower than 10 g/kg. Moreover, the decrease of pH caused increase of leached concentration of Cu, Pb, Zn, but slight decrease of leached As concentration. For the amended soil, concentrations of leached heavy metals were lower than Grade III limit of Chinese Environmental Quality Standards for Ground and Surface water (GB3838-2002) under simulated acid rain leaching condition. In comparison with non-amended soils, the total amount of Cu, Pb, Zn, and As release from amended soils was reduced by 93.6%, 69.2%, 57.0%, and 99.7%, respectively. The MM is a kind of promising amendment for heavy metals contaminated soil.     

Synthesis and Cytotoxicity of О- and N-Acyl Derivatives of Azepanobetulin

Russian Journal of Bioorganic Chemistry - A five-stage synthesis of azepanobetulin from betulin with a total yield of 47% has been carried out. The acylation of azepanobetulin with anhydrides or...     

First Report of Fungal Strains from Afşin–Elbistan Mine for Microbial Lignite Process

Abstract

Today, the need for energy is increasing and fossil fuels are constituting one of the most important energy sources in the world. Therefore, the efficient use of fossil fuels has become inevitable. In order to better use the opportunities offered by nature, we have turned to nature’s own resources. In this study, fungal strains of potential use in coal processing technology, isolated from Turkey’s largest lignite mine and identified. Our goal was to obtain active isolates for the biotechnological applications using the mine’s own source. For this aim, lignite samples were collected from different regions of the Af?in–Elbistan lignite mine, isolation studies were done and eventually, distinguished fungal isolates were identified by using conventional and molecular techniques. Hereby, fungal biodiversity of Turkey’s largest lignite mine has been investigated for the first time. Furthermore, 20 fungal isolates belong to Alternaria, Aspergillus, and Penicillium genera were cultured to provide resources for the development of future biotechnological coal processing techniques.     

Community Genomic and Proteomic Analyses of Chemoautotrophic Iron-Oxidizing “Leptospirillum rubarum” (Group II) and “Leptospirillum ferrodiazotrophum” (Group III) Bacteria in Acid Mine Drainage Biofilms

We analyzed near-complete population (composite) genomic sequences for coexisting acidophilic iron-oxidizing Leptospirillum group II and III bacteria (phylum Nitrospirae) and an extrachromosomal plasmid from a Richmond Mine, Iron Mountain, CA, acid mine drainage biofilm. Community proteomic analysis of the genomically characterized sample and two other biofilms identified 64.6% and 44.9% of the predicted proteins of Leptospirillum groups II and III, respectively, and 20% of the predicted plasmid proteins. The bacteria share 92% 16S rRNA gene sequence identity and >60% of their genes, including integrated plasmid-like regions. The extrachromosomal plasmid carries conjugation genes with detectable sequence similarity to genes in the integrated conjugative plasmid, but only those on the extrachromosomal element were identified by proteomics. Both bacterial groups have genes for community-essential functions, including carbon fixation and biosynthesis of vitamins, fatty acids, and biopolymers (including cellulose); proteomic analyses reveal these activities. Both Leptospirillum types have multiple pathways for osmotic protection. Although both are motile, signal transduction and methyl-accepting chemotaxis proteins are more abundant in Leptospirillum group III, consistent with its distribution in gradients within biofilms. Interestingly, Leptospirillum group II uses a methyl-dependent and Leptospirillum group III a methyl-independent response pathway. Although only Leptospirillum group III can fix nitrogen, these proteins were not identified by proteomics. The abundances of core proteins are similar in all communities, but the abundance levels of unique and shared proteins of unknown function vary. Some proteins unique to one organism were highly expressed and may be key to the functional and ecological differentiation of Leptospirillum groups II and III.To understand how microorganisms contribute to biogeochemical cycling, it is necessary to determine the roles of uncultivated as well as cultivated groups and to establish how these roles vary during ecological succession and when environmental conditions change. Shotgun genomic sequencing (metagenomics) has opened new opportunities for culture-independent studies of microbial communities. Examples include investigations of acid mine drainage (AMD) biofilm communities (4, 43, 75), symbiosis in a marine worm involving sulfur-oxidizing and sulfate-reducing bacteria (85), and enhanced biological phosphorous removal by sludge communities (32). From these genomic data sets, it has been possible to reconstruct aspects of the metabolism of individual organisms (32) and coexisting community members (29, 75) and to identify which organisms contribute community-essential functions (75). An interesting question relates to how differences in metabolic potential between organisms from the same lineage allow them to occupy distinct niches. Identification of potentially adaptive traits in closely related organisms is also important from an evolutionary perspective.Genomic data do not reveal how organisms alter their metabolisms in response to the presence of other organisms or environmental conditions. Proteomics methods for analysis of metabolic responses of isolates (16, 17, 42, 80, 81) have been extended to analyze the functioning of the dominant members of natural consortia (56, 69), with strain-level resolution (43, 82). In these studies, peptides are separated by liquid chromatography (LC) and identified by tandem mass spectrometry (MS-MS) through reference to appropriate genomic databases. Proteomic analysis is possible even if the genome sequences are not identical to those of the organisms present (24); however, missing sequence information reduces the resolution of such proteogenomic studies.Due to dominance by a few organism types, chemoautotrophic microbial AMD biofilms from Richmond Mine, Iron Mountain, CA, are tractable model systems used to develop cultivation-independent metagenomic and proteogenomic methods for analysis of community structure, function, and ecology (13). Acidophilic Leptospirillum bacteria dominate this AMD system (15), other AMD systems (54), and bioleaching systems used for recovery of metals (19, 53, 86). These bacteria play pivotal roles in sulfide mineral dissolution because they are iron oxidizers (53, 75), and ferric iron drives sulfide oxidation, leading to formation of metal-rich sulfuric acid solutions. According to a recent microscopy-based study (83), Leptospirillum group II are the first colonists in AMD biofilm communities whereas Leptospirillum group III generally appear later, sometimes partitioned within biofilm interiors. Because only Leptospirillum group III appear to be able to fix nitrogen, they may be keystone species in AMD ecosystems (75). This observation enabled the isolation of one representative, “Leptospirillum ferrodiazotrophum” (76). In prior work, we reported near-complete genome sequences of two Leptospirillum group II types (43, 65), but detailed functional annotations and metabolic analyses have not been published. Genomic data have been used to explore the metabolism of Leptospirillum bacteria in one biofilm community (56), but proteomic and genomic analyses of the same biofilm community have not been performed.Here, we report a near-complete genomic sequence for Leptospirillum group III, derived from a biofilm obtained from the UBA site within the Richmond Mine, Iron Mountain, CA; a detailed functional annotation of the genomes of Leptospirillum groups II and III; and a genomic and proteomic comparison of them. In addition, we report the sequence of an extrachromosomal plasmid associated with these organisms. This study represents the first comprehensive genomics-based analysis of the metabolism of bacteria in the Nitrospirae phylum and the first environmental community proteogenomic study where the genomic and proteomic data were derived from the same sample. We compared the proteomic profiles of three different biofilm communities to evaluate the importance of shared and unique genes and pathways in environmental adaptation.     

Archaeal diversity: temporal variation in the arsenic-rich creek sediments of Carnoulès Mine, France

The Carnoulès mine is an extreme environment located in the South of France. It is an unusual ecosystem due to its acidic pH (2-3), high concentration of heavy metals, iron, and sulfate, but mainly due to its very high concentration of arsenic (up to 10 g L?1 in the tailing stock pore water, and 100-350 mg L?1 in Reigous Creek, which collects the acid mine drainage). Here, we present a survey of the archaeal community in the sediment and its temporal variation using a culture-independent approach by cloning of 16S rRNA encoding genes. The taxonomic affiliation of Archaea showed a low degree of biodiversity with two different phyla: Euryarchaeota and Thaumarchaeota. The archaeal community varied in composition and richness throughout the sampling campaigns. Many sequences were phylogenetically related to the order Thermoplasmatales represented by aerobic or facultatively anaerobic, thermoacidophilic autotrophic or heterotrophic organisms like the organotrophic genus Thermogymnomonas. Some members of Thermoplasmatales can also derive energy from sulfur/iron oxidation or reduction. We also found microorganisms affiliated with methanogenic Archaea (Methanomassiliicoccus luminyensis), which are involved in the carbon cycle. Some sequences affiliated with ammonia oxidizers, involved in the first and rate-limiting step in nitrification, a key process in the nitrogen cycle were also observed, including Candidatus Nitrososphaera viennensis and Candidatus nitrosopumilus sp. These results suggest that Archaea may be important players in the Reigous sediments through their participation in the biochemical cycles of elements, including those of carbon and nitrogen.     

Cloning and sequencing of inulinase and β-fructofuranosidase genes of a deep-sea Microbulbifer species and properties of recombinant enzymes

An inulinase-producing Microbulbifer sp. strain, JAM-3301, was isolated from a deep-sea sediment. An inulin operon that contained three open reading frames was cloned and sequenced. Two of the three genes were expressed. One product was an endo-inulinase, and the other was a β-fructofuranosidase. Both enzymes worked together to effectively degrade inulin.     

Identification and Characterisation of the α and β Subunits of Succinyl CoA Ligase of Tomato

Despite the central importance of the TCA cycle in plant metabolism not all of the genes encoding its constituent enzymes have been functionally identified. In yeast, the heterodimeric protein succinyl CoA ligase is encoded for by two single-copy genes. Here we report the isolation of two tomato cDNAs coding for α- and one coding for the β-subunit of succinyl CoA ligase. These three cDNAs were used to complement the respective Saccharomyces cerevisiae mutants deficient in the α- and β-subunit, demonstrating that they encode functionally active polypeptides. The genes encoding for the subunits were expressed in all tissues, but most strongly in floral and leaf tissues, with equivalent expression of the two α-subunit genes being expressed to equivalent levels in all tissues. In all instances GFP fusion expression studies confirmed an expected mitochondrial location of the proteins encoded. Following the development of a novel assay to measure succinyl CoA ligase activity, in the direction of succinate formation, the evaluation of the maximal catalytic activities of the enzyme in a range of tissues revealed that these paralleled those of mRNA levels. We also utilized this assay to perform a preliminary characterisation of the regulatory properties of the enzyme suggesting allosteric control of this enzyme which may regulate flux through the TCA cycle in a manner consistent with its position therein.     

Rate of utilization of glucose and `compartmentation'' of α-oxoglutarate and glutamate in rat brain

1. The rate of incorporation of ¹⁴C into pyruvate, α-oxoglutarate, lactate and glucose of rat tissues was measured after the subcutaneous injection of uniformly labelled glucose. 2. In rat brain the specific radioactivities of lactate and glucose were similar to that of alanine. In liver the specific radioactivity of glucose was considerably higher than that of lactate or alanine. 3. The specific radioactivities of α-oxo acids of rat brain were lower than those of corresponding amino acids, alanine and glutamate. These findings have been explained in relation to metabolic compartments in vivo. 4. The approximate estimated rate of glucose utilization in rat brain in vivo is 0·96μmole/g. of brain/min.     

Preparation and Characterization of Oligonucleotides of D- and L-2’ Deoxyuridine

Abstract

The synthesis of oligonucleotides of 2'deoxyuridine containing both the natural D-2'deoxyribose and the unnatural L-2'deoxyribose is described. Units up to the 18-mer have been made via a modified triester procedure and characterized by HPLC.     

Summer-autumn ichthyoplankton of the Sea of Okhotsk and the Sea of Japan and special traits of feeding of fish larvae and fry in 2003–2004

In summer-autumn of 2003–2004, the ichthyoplankton of the Sea of Okhotsk comprised 35 species. In this period the most widely distributed and numerous were larvae of the lord Hemilepidotus gilberti, the Pacific stout sand lance Ammodytes hexapterus, and the Sakhalin dab Limanda sakhalinensis. The maximum catches of fish larvae were attributed to coastal waters off eastern Sakhalin and to the shelf of the northern part of the Sea of Okhotsk. In November of 2003, the ichthyoplankton of the Sea of Japan was represented by fish larvae belonging mainly to the boreal ichthyocomplex. The catches consisted predominantly of larvae of the arabesque greenling Pleurogrammus azonus, the ronquil Bathymaster derjugini, and the rockfish Sebastes owstoni. Fish larvae and fry in the northwestern part of the Sea of Japan were caught principally within 43°–45° N and 137°–139° E above the depth 1500–2000 m. The food spectrum of fish larvae in the Sea of Okhotsk and the Sea of Japan comprised over 20 plankters of various size belonging to seven taxa. Irrespective of fish species, the food items common of all fish were copepods Pseudocalanus minutus and Oithona similis. The daily rations were calculated for mass species (Hemilepidotus gilberti, Ammodytes hexapterus, Hexagrammos stelleri, Pleurogrammus azonus, Bathymaster derjugini, and Sebastes owstoni). The larvae of all considered species in the Sea of Japan and in the Sea of Okhotsk fed predominantly in the light period of the day.     

Potential ‘Ecological Traps’ of Restored Landscapes: Koalas Phascolarctos cinereus Re-Occupy a Rehabilitated Mine Site

With progressively increasing anthropogenic habitat disturbances, restoration of impacted landscapes is becoming a critical element of biodiversity conservation. Evaluation of success in restoration ecology rarely includes faunal components, usually only encompassing abiotic and floral components of the ecosystems. Even when fauna is explicitly included, it is usually only species presence/absence criteria that are considered. If restoration is to have a positive outcome, however, populations in restored habitats should exhibit comparable survival and reproductive rates to populations found in undisturbed surroundings. If a species recolonises restored areas but later experiences decreased fitness, restored areas could become ecological sinks or traps. We investigated this possibility in a case study of koalas Phascolarctos cinereus occupying rehabilitated mining areas on North Stradbroke Island, Australia. Our holistic approach compared rehabilitated and undisturbed areas on the basis of their vegetation characteristics, of koalas'' body condition, roosting trees, diet, as well as predator index. Koalas using rehabilitated areas appeared to be able to access an adequate supply of roosting and fodder trees, were in good condition and had high reproductive output. We did not find any significant differences in predator density between rehabilitated areas and undisturbed surroundings. The results presented in this study showed there was no evidence that the post-mining rehabilitated areas constitute ecological sinks or traps. However, to reach a definitive conclusion as to whether areas rehabilitated post-mining provide at least equivalent habitat to undisturbed locations, additional research could be undertaken to assess foliar nutrient/water/toxin differences and predation risk in rehabilitated areas compared with undisturbed areas. More generally, the evaluation of whether restoration successfully produces a functional ecological community should include criteria on the fitness of faunal populations reoccupying such sites, so as to ensure functioning ecosystems, rather than ecological sinks or traps, are the outcome.     

α-Lactalbumin binding and membrane integrity—effect of charge and degree of unsaturation of glycerophospholipids

Several studies have shown that the physical state of the phospholipid membrane has an important role in protein-membrane interactions, involving both electrostatic and hydrophobic forces. We have investigated the influence of the interaction of the calcium-depleted, (apo)-conformation of bovine α-lactalbumin (BLA) on the integrity of anionic glycerophospholipid vesicles by leakage experiments using fluorescence spectroscopy. The stability of the membranes was also studied by measuring surface tension/molecular area relationships with phospholipid monolayers. We show that the degree of unsaturation of the acyl chains and the proportion of charged phospholipid species in the membranes made of neutral and acidic glycerophospholipids are determinants for the association of BLA with liposomes and for the impermeability of the bilayer. Particularly, tighter packing counteracted interaction with BLA, while unsaturation—leading to looser packing—promoted interaction and leakage of contents. Equimolar mixtures of neutral and acidic glycerophospholipids were more permeable upon protein binding than pure acidic lipids. The effect of lipid structure on BLA-membrane interaction and bilayer integrity may throw new light on the membrane disrupting mechanism of a conformer of human α-lactalbumin (HAMLET) that induces death of tumour cells but not of normal cells.     

Hydrophilicity and antigenicity of proteins — A case study of myoglobin and hemoglobin

Hydrophilicity index is used to locate antigenic determinants on two related groups of proteins-myoglobin and hemoglobin. The data on 41 species (including 34 mammals) of myoglobin show that average hydrophilicity for the complete myoglobin molecules as well as the average hydrophilicity for all hydrophilic regions put together seem to remain constant; the variation in the size and location of the antigenic determinants in these species is very small indicating that the antigenic sites are not shifted during evolution. In the case of both the proteins there is a good agreement between the antigenic sites picked up by using hydrophilicity index and the experimentally determined antigenic sites. The data on 56 species of hemoglobin α-chains and 44 species of hemoglobinβ-chains showed that although there are few sites on hemoglobin which have remained invariant during evolution, there is a significant variation in other sites in terms of either a splitting of a site, or a drastic change in the hydrophilicity values and/or a length of the site. Comparison of the hydrophilicity data on these two groups of proteins suggests that hemoglobins which perform a variety of functions as compared to myoglobins are evolving faster than myoglobins supporting the contention of earlier workers.     

Analysis and modeling of time-variant amplitude–frequency couplings of and between oscillations of EEG bursts

Low-frequency (0.5-2.5 Hz) and individually defined high-frequency (7-11 or 8-12 Hz; 11-15 or 14-18 Hz) oscillatory components of the electroencephalogram (EEG) burst activity derived from thiopental-induced burst-suppression patterns (BSP) were investigated in seven sedated patients (17-26 years old) with severe head injury. The predominant high-frequency burst oscillations (>7 Hz) were detected for each patient by means of time-variant amplitude spectrum analysis. Thereafter, the instantaneous envelope (IE) and the instantaneous frequency (IF) were computed for these low- and high-frequency bands to quantify amplitude-frequency dependencies (envelope-envelope, envelope-frequency, and frequency-frequency correlations). Time-variant phase-locking, phase synchronization, and quadratic phase couplings are associated with the observed amplitude-frequency characteristics. Additionally, these time-variant analyses were carried out for modeled burst patterns. Coupled Duffing oscillators were adapted to each EEG burst and by means of these models data-based burst simulations were generated. Results are: (1) strong envelope-envelope correlations (IE courses) can be demonstrated; (2) it can be shown that a rise of the IE is associated with an increase of the IF (only for the frequency bands 0.5-2.5 and 7-11 or 8-12 Hz); (3) the rise characteristics of all individually averaged envelope-frequency courses (IE-IF) are strongly correlated; (4) for the 7-11 or 8-12 Hz oscillation these associations are weaker and the variation between the time courses of the patients is higher; (5) for both frequency ranges a quantitative amplitude-frequency dependency can be shown because higher IE peak maxima are accompanied by stronger IF changes; (6) the time range of significant phase-locking within the 7-11 or 8-12 Hz frequency bands and of the strongest quadratic phase couplings (between 0.5-2.5 and 7-11 or 8-12 Hz) is between 0 and 1,000 ms; (7) all phase coupling characteristics of the modeled bursts accord well with the corresponding characteristics of the measured EEG burst data. All amplitude-frequency dependencies and phase locking/coupling properties described here are known from and can be discussed using coupled Duffing oscillators which are characterized by autoresonance properties.