New perspectives on the use of nucleic acids in pharmacological applications: inhibitory action of extracellular self-DNA in biological systems

The research for new products against pathogens, parasites and infesting species, in both agriculture and medicine, implies huge and increasing scientific, industrial and economic efforts. Traditional approaches are based on random screening procedures searching for bioactive compounds. However, the success of such methodologies in most cases has been strongly limited by side-effects of the potential new drugs, especially toxicity and pharmacological resistance. The use of nucleic acids in drug development has been introduced searching for target-specific effect. In addition, a recent discovery revealed that randomly fragmented extracellular self-DNA may act as highly species-specific inhibitory product for different species, suggesting an unprecedented use of DNA for biological control. On this base, a new scenario of pharmacological applications is discussed.     

Legionella oakridgensis: unusual new species isolated from cooling tower water.

We describe a new species of Legionella represented by 10 strains isolated from industrial cooling towers. Legionella oakridgensis differed genetically from the other seven species of Legionella in DNA hybridization studies and differed serologically in direct fluorescent-antibody tests. The new species, unlike all other species except L. jordanis, did not require added L-cysteine for growth in serial transfer on charcoal-yeast extract agar. L. oakridgensis, as well as three other species tested, required L-cysteine for primary isolation from animal tissues. L. oakridgensis was the only species of Legionella that failed to produce alkaline phosphatase at pH 8.5. In all other respects, it resembled other species of Legionella, including having a high content of branched-chain cellular fatty acids and being pathogenic for guinea pigs. These bacteria have not yet been associated with human disease, but they are potential causes of legionellosis.     

Isolation and taxonomic study of a new canthaxanthin-containing bacterium, Gordonia jacobaea MV-1 sp. nov.

This article describes the isolation and taxonomic study of a coryneform isolate of a new Gordonia species (G. jacobaea), strain MV-1, which accumulates several carotenoids, including the ketocarotenoid trans-canthaxanthin. Identification of this new isolate by morphobiochemical methods did not allow unambiguous taxon assignment, but sequencing of the 16S rRNA gene clearly pointed to the genus Gordonia, Gordonia sputi being the closest fit. Differences in certain transversions/transitions in otherwise very well-conserved sequences of the described Gordonia species supported the proposal of this new taxon. The fact that both the best growth and best pigmentation were obtained with glucose, an inexpensive carbon source and at an industrially suitable temperature, suggests that this new bacterial strain may have good potential for the industrial production of canthaxanthin.     

Diversity of some insect fauna in industrial and non-industrial areas of West Bengal, India

The present work is designed to study diversity of five insect orders (viz., Hemiptera, Orthoptera, aculeate Hymenoptera, Lepidoptera and Coleoptera) in the industrial region of Haldia (India) and in non-industrial area of the same district and to evaluate the impact of industrialization on the biodiversity of those insect orders. The objective also extended to find out the possibility of existence of bioindicator, if any. Eight study sites were selected from the East part of Midnapur district covering 40 km aerial distance. Out of eight different study sites, five were distributed in and around Haldia industrial complex and three in industry-free area. During this study, a total of 120 species under 98 genera in 37 families of insects were collected. Binary data of 5 orders revealed that the species richness of Hemiptera, Orthoptera and Lepidoptera is higher in non-industrial zone in comparison to that of industrial zone. Aculeate Hymenoptera shows no particular trend whereas Coleoptera shows higher species richness in industrial areas. Results of multivariate analyses are compared with the species richness data for all the eight study sites. It is concluded that even in an apparently homogeneous ecological condition species richness may drastically change with the influence of industries. Total insect fauna decline by at least 23.33% is noticed in industrial areas. It is found that some species of lepidopteran, hemipteran and orthopteran insects are susceptible to industrial pollution and some of the members of these orders may be considered as a bioindicator group.     

PRELIMINARY OBSERVATIONS ON THE MACROCRUSTACEA OF COASTAL LAKES IN THE VICINITY OF RICHARDS BAY,ZULULAND, SOUTH AFRICA

SUMMARY

A limited amount of research has been carried out on the four coastal lakes in the Richards Bay area. Due to the impending threat of water pollution from industrial, mining and residential areas within the catchments of these lakes there is an urgent need for the collection of baseline data before it is too late.

This paper reports on preliminary observations on Macrocrustacea of the lakes. A total of 27 species were recorded, of which 8 are new distribution records for the species in fresh water and one, an isopod, is a species new to science from a family previously unrecorded on the African continent. Sixteen of the Macrocrustacea recorded were found to be relict estuarine species.

The relationship between the Macrocrustacea are discussed in terms of habitat and dietary associations. The former category was found to be variable in the shallower Richards Bay lakes as opposed to Lake Sibaya whose depth (40 m) plays an important role in species distribution. Information is provided on habitat, substrata preference, associations with plant communities, and known depth distribution. Dietary data on the Macrocrustacea present in the four coastal lakes showed that seven major feeding groups are present: benthic filter feeders, nektonic filter feeders, periphyton grazers, shredders of dead macrophytes, benthic scavengers, partial carnivores and fish ectoparasites.     

Engineering industrial fatty acids in oilseeds

More than 300 types of modified fatty acids (mFA) are produced in triacylglycerols (TAG) by various plant species, with many of these unusual structures rendering unique physical and chemical properties that are desirable for a variety of bio-based industrial uses. Attempts to produce these mFA in crop species have thus far failed to reach the desired levels of production and highlighted the need to better understand how fatty acids are synthesized and accumulated in seed oils. In this review we discuss how some of the progress made in recent years, such as the improved TAG synthesis model to include acyl editing and new enzymes such as PDCT, may be utilized to achieve the goal of effectively modifying plant oils for industrial uses. Co-expressing several key enzymes may circumvent the bottlenecks for the accumulation of mFA in TAG through efficient removal of mFA from phosphatidylcholine. Other approaches include the prevention of feedback inhibition of fatty acid synthesis and improving primary enzyme activity in host transgenic plants. In addition, genomic approaches are providing unprecedented power to discover more factors that may facilitate engineering mFA in oilseeds. Based on the results of the last 20 years, creating a high mFA accumulating plant will not be done by simply inserting one or two genes; it is necessary to stack genes encoding enzymes with favorable kinetic activity or specificity along with additional complementary transgenes in optimized plant backgrounds to produce industrial fatty acids at desirable levels. Finally, we discuss the potential of Camelina as an industrial oilseed platform.     

Preliminary assessment of changes in the structure of small mammal communities caused by industrial pollution in the North Kazakhstan Region

This paper presents new data on small mammal communities in the industrial area of Pavlodar (Kazakhstan) for the first time. We have analyzed and compared diversity characteristics of small mammal communities found in a reference area and in an area of anthropogenic disturbance. The total abundance has been shown to increase with distance to the sources of pollution. A depauperate composition and single-dominance structure of species characterize the communities of small mammals in significantly disturbed areas. With a moderately intense level of anthropogenic stressors, species diversity increases, but the number of individual species decreases due to the fragmentation of habitats.     

新型可再生工业用油脂的代谢工程

植物种子油是一种可再生资源,亦用作生物燃油和化学工业原料. 一些野生植物能高水平合成积累羟化、环氧化和共轭脂肪酸等具有重要工业应用价值的特异脂肪酸.催化这些特异脂肪酸合成的酶主要是类脂肪酸去胞和酶2(类FAD2). 由特异脂肪酸合成到三酰基甘油脂 (TAG) 形成还需要酰基转移酶 (如DGAT) 的参与. 在油料作物种子中表达类FAD2酶及其相关基因(如DGAT),已培育出了能合成积累一定含量特异脂肪酸的工程油料品系,为基于农作物生产高附加值工业用油脂开辟了新途径. 本文论述了参与特异脂肪酸生物合成途径的关键酶基因、油料作物代谢工程策略,以及应用工程油料作物大规模生产重要工业用脂肪酸的研究进展、存在问题和应用前景等.     

Systematic and biotechnological aspects of halophilic and halotolerant actinomycetes

More than 70 species of halotolerant and halophilic actinomycetes belonging to at least 24 genera have been validly described. Halophilic actinomycetes are a less explored source of actinomycetes for discovery of novel bioactive secondary metabolites. Degradation of aliphatic and aromatic organic compounds, detoxification of pollutants, production of new enzymes and other metabolites such as antibiotics, compatible solutes and polymers are other potential industrial applications of halophilic and halotolerant actinomycetes. Especially new bioactive secondary metabolites that are derived from only a small fraction of the investigated halophilic actinomycetes, mainly from marine habitats, have revealed the huge capacity of this physiological group in production of new bioactive chemical entities. Combined high metabolic capacities of actinomycetes and unique features related to extremophilic nature of the halophilic actinomycetes have conferred on them an influential role for future biotechnological applications.     

Carbonylation of milk powder proteins as a consequence of processing conditions

During industrial treatments, milk proteins could be oxidatively modified, thus leading to the formation of modified/oxidised amino acid residues. The apparition of such modified residues may contribute to the formation of new immunologically reactive structures. Some of these adducts could, in an advanced stage, lead to cross-linked protein species whose proteolytic susceptibility would be drastically decreased. Such protein species, that are resistant to digestion, could also constitute major food allergens. Therefore, these oxidative protein modifications tend to increase the natural allergenicity of milk proteins. For these reasons, monitoring milk protein oxidative modifications could be very useful regarding both product quality and allergenicity issues. In the present paper, we highlight, using different analytical approaches, the preferential carbonylation of beta-lactoglobulin (beta-Lg) during industrial treatments of milk. This result is particularly interesting since native beta-Lg represents one of the major milk allergens.     

The influence of urban land use on seed dispersal and wetland invasibility

Urban habitats are generally considered highly invaded by exotic species due to the frequency and extent of disturbance caused by human activities and development. Our previous study had demonstrated that forested wetlands within residential areas are more extensively invaded than wetlands within industrial–commercial areas. In this study, we investigate whether the structure of the forest edge and seed dispersal can explain the differential in the invasion of wetlands surrounded by industrial and residential land use. Our results indicate that edges of industrially bordered wetlands are denser, with vegetation concentrated at the boundary of tree growth, whereas the edges of residentially bordered wetlands are more open and diffuse. This difference influences the number of seeds and species capable of dispersing into the wetland. Less dense edges resulted in a higher number of seeds entering residential wetlands; however, there were no differences in the numbers of exotic seeds or exotic species in the seed rain residential and industrial wetlands. Although seed dispersal could not directly explain differences in the current extent of invasion of these sites, seed dispersal did follow corridor pathways, including ditches and trails that breach the edges and extend through the wetlands. These disturbances act as corridors for seed dispersal into both types wetlands and may play a role in introducing new species to the interior of the wetland, an outcome supported by a higher number of exotic species in the seed banks of residential sites. Our results suggest that both the type of adjoining land use and the provision of access to people on trails in urban wetlands can affect the composition of these communities.     

Metabolic engineering of fatty acid biosynthesis in plants.

Fatty acids are the most abundant form of reduced carbon chains available from nature and have diverse uses ranging from food to industrial feedstocks. Plants represent a significant renewable source of fatty acids because many species accumulate them in the form of triacylglycerol as major storage components in seeds. With the advent of plant transformation technology, metabolic engineering of oilseed fatty acids has become possible and transgenic plant oils represent some of the first successes in design of modified plant products. Directed gene down-regulation strategies have enabled the specific tailoring of common fatty acids in several oilseed crops. In addition, transfer of novel fatty acid biosynthetic genes from noncommercial plants has allowed the production of novel oil compositions in oilseed crops. These and future endeavors aim to produce seeds higher in oil content as well as new oils that are more stable, are healthier for humans, and can serve as a renewable source of industrial commodities. Large-scale new industrial uses of engineered plant oils are on the horizon but will require a better understanding of factors that limit the accumulation of unusual fatty acid structures in seeds.     

New yeast expression platforms based on methylotrophic Hansenula polymorpha and Pichia pastoris and on dimorphic Arxula adeninivorans and Yarrowia lipolytica - a comparison

Yeasts combine the ease of genetic manipulation and fermentation of a microbial organism with the capability to secrete and to modify proteins according to a general eukaryotic scheme. Yeasts thus provide attractive platforms for the production of recombinant proteins. Here, four important species are presented and compared: the methylotrophic Hansenula polymorpha and Pichia pastoris, distinguished by an increasingly large track record as industrial platforms, and the dimorphic species Arxula adeninivorans and Yarrrowia lipolytica, not yet established as industrial platforms, but demonstrating promising technological potential, as discussed in this article.     

Influence of environmental abiotic factors on the content of saponins in plants

Saponins are a large group of secondary metabolites occurring in significant amounts in many plant species. However, the saponin content of plants is variable and it can be influenced by the surrounding environment. The local geoclimate, seasonal changes, external conditions such as light, temperature, humidity and soil fertility, as well as cultivation techniques, affect both the quantitative amount and qualitative composition of saponins. Such variation substantially impacts on the quality and properties of wild and cultivated plants exploited for pharmaceutical, nutritional and industrial applications. This review summarizes the available data on the effects of abiotic environmental factors on saponin level in plants, especially those of considerable economic importance, highlighting current problems such as the reduction in natural plant resources, over-exploitation and destruction of wild habitats, climate shifts as well as the consequences of the growing demand for plant-derived medicinal and industrial products. The need for a theoretical basis for a reasonable harvest, attempts at the domestication of wild plant species and the development of new agricultural technologies allowing high production under optimized conditions are also discussed.     

A formal scheme of adsorptional receptors in <Emphasis Type="Italic">Pseudomonas aeruginosa</Emphasis> and possibilities for its practical implementation

In recent years, a revival of interest to study of bacteriophages has been observed. Bacteriophages and phage-coded products can be used instead of antibiotics in the treatment of some human and animal infections caused by antibiotic-resistant bacterial strains. Bacteriophages may serve as an excellent method for monitoring anthropogenic changes in bacterial communities, which are connected with the contamination by industrial sewages or infection of water reservoirs with pathogenic bacteria. Technical applicability of bacteriophages may be successful for combating bacterial biofilms, for example, in pipelines. And finally, comparative basic and systemic genomic studies of bacteriophages belonging to various bacterial species are conclusive in understanding and assessing their role in the joint evolution (coevolution) with host bacteria; particularly, this research is important for elucidating mechanisms of phage participation in the horizontal exchange of genetic modules. Possibly, these studies may be useful for the prediction of not only the direction of coevolution of certain bacterial species and their phages but also the time of new pathogenic bacteria origination.     

Quantitative estimation of insect diversity inhabiting Calotropis procera in industrial and nonindustrial areas of West Bengal, India

This paper compares the species richnesses, Bray–Curtis similarities, species diversities, evennesses, and the results of various analyses (multivariate, logarithmic series, and lognormal distribution analyses) of insects from four orders (viz., Hemiptera, Orthoptera, aculeate Hymenoptera, and Coleoptera) inhabiting a medicinal plant, Calotropis procera among eight sites within industrial and nonindustrial zones in the Purba Medinipur district (erstwhile Midnapore), West Bengal, India. Both cluster analysis and principal component analysis indicate an effect of industrialization on the diversity of the four insect orders. The species community at each site exhibits an almost pure lognormal distribution. Bootstrap estimation of species diversity also points to the effect of industrialization. A comparison of the values of x and N/S of the logarithmic series indicates a typical relationship between the species community and its diversity. The number of unique species among the eight study sites is 6 according to jackknife estimation. Beta-diversity analysis of the samples shows the impact of industrialization on the abundances and species richness of the insects. Altogether, 16 types of analytical procedure are applied for this purpose, and their suitabilities for this kind of data set are assessed. Disturbance, probably due to industrial emissions, has changed the compositions and structures of the insect communities out to a distance of at least 6 km from the core industrial area.     

Lysine biosynthesis in microbes: relevance as drug target and prospects for β-lactam antibiotics production

Plants as well as pro- and eukaryotic microorganisms are able to synthesise lysine via de novo synthesis. While plants and bacteria, with some exceptions, rely on variations of the meso-diaminopimelate pathway for lysine biosynthesis, fungi exclusively use the α-aminoadipate pathway. Although bacteria and fungi are, in principle, both suitable as lysine producers, current industrial fermentations rely on the use of bacteria. In contrast, fungi are important producers of β-lactam antibiotics such as penicillins or cephalosporins. The synthesis of these antibiotics strictly depends on α-aminoadipate deriving from lysine biosynthesis. Interestingly, despite the resulting industrial importance of the fungal α-aminoadipate pathway, biochemical reactions leading to α-aminoadipate formation have only been studied on a limited number of fungal species. In this respect, just recently an essential isomerisation reaction required for the formation of α-aminoadipate has been elucidated in detail. This review summarises biochemical pathways leading to lysine production, discusses the suitability of interrupting lysine biosynthesis as target for new antibacterial and antifungal compounds and emphasises on biochemical reactions involved in the formation of α-aminoadipate in fungi as an essential intermediate for both, lysine and β-lactam antibiotics production.     

Tardigrades of the Taimyr peninsula with descriptions of two new species

This is the first report on tardigrades from the Taimyr peninsula. Seventy-one species of tardigrades were recorded, new to Russian fauna and two of which are new to science. Diphascon boreale sp. nov. is closely related to D. brevipes (Marcus, 1936) but easily distinguished from it by claw structure and the absence of cuticular bars on the legs. Isohypsibius roberti sp. nov. belongs to the elegans group of the genus Isohypsibius ; it diners from other species in the group by having a long and thin buccal tube and large lunulae with small teeth on leg IV. The eggs of Ramazzottius montivagus are here described for the first time. The almost complete absence of tardigrades in and around Norilsk is noted. This is related to the heavy industrial pollution from a local nickel-copper plant.     

A comparison of trap type and height for capturing cerambycid beetles (Coleoptera)

Wood-boring beetles in the family Cerambycidae (Coleoptera) play important roles in many forest ecosystems. However, increasing numbers of invasive cerambycid species are transported to new countries by global commerce and threaten forest health in the United States and worldwide. Our goal was to identify effective detection tools for a broad array of cerambycid species by testing some known cerambycid attractants and a pheromone in different trap designs placed across a range of habitats. We compared numbers and species richness of cerambycid beetles captured with cross-vane panel traps and 12-unit Lindgren multiple-funnel traps, placed either at ground level (1.5 m high) or canopy level (approximately 3-10 m high), at eight sites classified as either residential, industrial, deciduous forest, or conifer forest. We captured 3,723 beetles representing 72 cerambycid species from 10 June to 15 July 2010. Species richness was highest for the subfamilies Cerambycinae and Lamiinae, which accounted for 33 and 46% of all species captured, respectively. Overall, the cross-vane panel traps captured approximately 1.5 times more beetles than funnel traps. Twenty-one species were captured exclusively in traps at one height, either in the canopy or at ground level. More species were captured in hardwood sites (59 species) where a greater diversity of host material was available than in conifer (34 species), residential (41 species), or industrial (49) sites. Low numbers of beetles (n < 5) were recorded for 28 of the beetle species. The number of species captured per week ranged from 49 species on 21 June to 37 species on 12 July. Cross-vane panel traps installed across a vertical gradient should maximize the number of cerambycid species captured.     

High-Efficiency Genome Editing and Allele Replacement in Prototrophic and Wild Strains of Saccharomyces

Current genome editing techniques available for Saccharomyces yeast species rely on auxotrophic markers, limiting their use in wild and industrial strains and species. Taking advantage of the ancient loss of thymidine kinase in the fungal kingdom, we have developed the herpes simplex virus thymidine kinase gene as a selectable and counterselectable marker that forms the core of novel genome engineering tools called the Haploid Engineering and Replacement Protocol (HERP) cassettes. Here we show that these cassettes allow a researcher to rapidly generate heterogeneous populations of cells with thousands of independent chromosomal allele replacements using mixed PCR products. We further show that the high efficiency of this approach enables the simultaneous replacement of both alleles in diploid cells. Using these new techniques, many of the most powerful yeast genetic manipulation strategies are now available in wild, industrial, and other prototrophic strains from across the diverse Saccharomyces genus.