Pervasiveness of UVC254-resistant Geobacillus strains in extreme environments

Applied Microbiology and Biotechnology - We have characterized a broad collection of extremophilic bacterial isolates from a deep subsurface mine, compost dumping sites, and several hot spring...     

Engineered whole-cell biocatalyst-based detoxification and detection of neurotoxic organophosphate compounds

The development of efficient tools is required for the eco-friendly detoxification and effective detection of neurotoxic organophosphates (OPs). Although enzymes have received significant attention as biocatalysts because of their high specific activity, the uneconomic and labor-intensive processes of enzyme production and purification make their broad use in practical applications difficult. Because whole-cell systems offer several advantages compared with free enzymes, including high stability, a reduced purification requirement, and low preparation cost, they have been suggested as promising biocatalysts for the detoxification and detection of OPs. To develop efficient whole-cell biocatalysts with enhanced activity and a broad spectrum of substrate specificity, several factors have been considered, namely the selected strains, the chosen OP-hydrolyzing enzymes, where enzymes are localized in a cell, and which enhancer will assist the expression, function, and folding of the enzyme. In this article, we review the current investigative progress in the development of engineered whole-cell biocatalysts with excellent OP-hydrolyzing activity, a broad spectrum of substrate specificity, and outstanding stability for the detoxification and detection of OPs.     

Pollen limitation and the evolution of androdioecy from dioecy

Androdioecy is an unusual breeding system in which populations consist of separate male and hermaphrodite individuals. The evolution of androdioecy is still poorly understood; however, there is evidence from several androdioecious species that the breeding system may have evolved from dioecy (males and females). This article presents a simple deterministic model showing that androdioecy can evolve from dioecy under a broad range of realistic conditions. For the evolution of androdioecy from dioecy, hermaphrodites must be able to invade the dioecious population. Then, males must be maintained, while females are eliminated. Hermaphrodite invasion is favored when females are pollen limited and hermaphrodites have high overall fertility and are self-fertile. Male maintenance is favored when hermaphrodites resemble females, having high seed production and low pollen fitness, and when the selfing rate is not too high. These conditions were satisfied over a broad and realistic range of parameter values, suggesting that the evolution of androdioecy from dioecy is highly plausible.     

多糖化合物抗HIV活性及应用

多糖类化合物种类繁多 ,许多多糖化合物在体内或体外表现出良好的抗HIV活性 ,多糖能够作用于HIV复制周期的多个环节 ,影响tat、gp1 2 0、RT等多个病毒蛋白的功能。目前 ,已有多糖被用于杀微生物剂、抗病毒辅助治疗、抗机会性感染等临床研究中 ,多糖在临床上存在抗凝血活性、生物利用度低等问题 ,但丰富的多糖类化合物因其作用多效性仍有广阔的抗HIV应用前景。     

植物精油化学成分及其抗菌活性的研究进展

植物精油是一类从植物中萃取的芳香味油状液体,是一类优良的天然抗菌材料。作为抗菌材料,植物精油具有以下优点:具有广谱高效的抗菌活性;具有熏蒸特性、气味芳香;取自天然植物,绿色环保;来源广,提取容易。植物精油因其多种优点,在抗菌领域具有巨大的潜在应用价值。本文从植物精油的分布及化学成分、抗细菌活性和抗真菌活性的研究,以及植物精油化学成分与抗菌活性之间的联系等方面对植物精油的抗菌性能进行评述,以期促进植物精油在抗菌领域的广泛应用,同时给从事植物精油抗菌研究的科研工作者提供参考。     

In vitro and in vivo replication of seal gammaherpesviruses in cells of multiple species

Phocid herpesvirus virus type 2 (PhHV-2), a putative gammaherpesvirus of seals, has been isolated from harbor seals (Phoca vitulina) and grey seals (Halichoerus grypus). In the present study, different PhHV-2 isolates were shown to have a broad in vitro tropism for various cell types from several mammalian species. Inbred mice and two species of non-human primates proved to be susceptible to experimental infection with PhHV-2. The development of myoepitheliomas and spleen hyperplasia upon cyclosporin A treatment in some of the PhHV-2-infected animals warrants further investigation of the oncogenic and zoonotic potential of this virus.     

Polyphenoloxidase in higher plants: immunological detection and analysis of in vitro translation products

Antibodies to broad bean polyphenoloxidase (PPO) were used to detect and demonstrate that the PPOs found in several different plants have many similarities in common. Crude extracts from leaves of broad bean, bush bean, lettuce, mung bean, pea, soybean, spinach, tobacco, and tomato contained enzyme which cross-reacted with polyclonal anti-PPO in Ouchterlony double diffusion analysis. The results suggested that plant polyphenoloxidase from a wide range of species may contain similar antigen determinants. Poly A⁺ mRNA was isolated from leaves of each plant species and translated in vitro using a rabbit reticulocyte translation system. An in vitro synthesized product corresponding to PPO from each species was identified after specific immunoprecipitation with anti-PPO. The molecular weight of this in vitro product was similar in all plants examined and found to be approximately 45 kilodaltons. Peptide maps of the in vitro synthesized product from all plant species were similar and showed at least three peptides in common. Plant PPOs may have more structural similarities than commonly though in spite of the great variety in observed isoenzyme forms.     

Broad antigenic coverage induced by vaccination with virus-based cDNA libraries cures established tumors

Effective cancer immunotherapy requires the release of a broad spectrum of tumor antigens in the context of potent immune activation. We show here that a cDNA library of normal tissue, expressed from a highly immunogenic viral platform, cures established tumors of the same histological type from which the cDNA library was derived. Immune escape occurred with suboptimal vaccination, but tumor cells that escaped the immune pressure were readily treated by second-line virus-based immunotherapy. This approach has several major advantages. Use of the cDNA library leads to presentation of a broad repertoire of (undefined) tumor-associated antigens, which reduces emergence of treatment-resistant variants and also permits rational, combined-modality approaches in the clinic. Finally, the viral vectors can be delivered systemically, without the need for tumor targeting, and are amenable to clinical-grade production. Therefore, virus-expressed cDNA libraries represent a novel paradigm for cancer treatment addressing many of the key issues that have undermined the efficacy of immuno- and virotherapy to date.     

Phylogenetic diversity and specificity of bacteria closely associated with Alexandrium spp. and other phytoplankton

While several studies have suggested that bacterium-phytoplankton interactions have the potential to dramatically influence harmful algal bloom dynamics, little is known about how bacteria and phytoplankton communities interact at the species composition level. The objective of the current study was to determine whether there are specific associations between diverse phytoplankton and the bacteria that co-occur with them. We determined the phylogenetic diversity of bacterial assemblages associated with 10 Alexandrium strains and representatives of the major taxonomic groups of phytoplankton in the Gulf of Maine. For this analysis we chose xenic phytoplankton cultures that (i) represented a broad taxonomic range, (ii) represented a broad geographic range for Alexandrium spp. isolates, (iii) grew under similar cultivation conditions, (iv) had a minimal length of time since the original isolation, and (v) had been isolated from a vegetative phytoplankton cell. 16S rRNA gene fragments of most Bacteria were amplified from DNA extracted from cultures and were analyzed by denaturing gradient gel electrophoresis and sequencing. A greater number of bacterial species were shared by different Alexandrium cultures, regardless of the geographic origin, than by Alexandrium species and nontoxic phytoplankton from the Gulf of Maine. In particular, members of the Roseobacter clade showed a higher degree of association with Alexandrium than with other bacterial groups, and many sequences matched sequences reported to be associated with other toxic dinoflagellates. These results provide evidence for specificity in bacterium-phytoplankton associations.     

Crystal structure of a Vip3B family insecticidal protein reveals a new fold and a unique tetrameric assembly

Vegetatively expressed insecticidal proteins (VIPs) produced by Bacillus thuringiensis fall into several classes of which the third, VIP3, is known for their activity against several key Lepidopteran pests of commercial broad acre crops and because their mode of action does not overlap with that of crystalline insecticidal proteins. The details of the VIP3 structure and mode of action have remained obscure for the quarter century that has passed since their discovery. In the present article, we report the first crystal structure of a full‐length VIP3 protein. Crystallization of this target required multiple rounds of construct optimization and screening—over 200 individual sequences were expressed and tested. This protein adopts a novel global fold that combines domains with hitherto unreported topology and containing elements seemingly borrowed from carbohydrate‐binding domains, lectins, or from other insecticidal proteins.     

Broad‐scale vegetation‐environment relationships in Eurasian high‐latitude areas

Question: How is tundra vegetation related to climatic, soil chemical, geological variables and grazing across a very large section of the Eurasian arctic area? We were particularly interested in broad‐scale vegetation‐environment relationships and how well do the patterns conform to climate‐vegetation schemes. Material and Methods: We sampled vegetation in 1132 plots from 16 sites from different parts of the Eurasian tundra. Clustering and ordination techniques were used for analysing compositional patterns. Vegetation‐environment relationships were analysed by fitting of environmental vectors and smooth surfaces onto non‐metric multidimensional scaling scattergrams. Results: Dominant vegetation differentiation was associated with a complex set of environmental variables. A general trend differentiated cold and continental areas from relatively warm and weakly continental areas, and several soil chemical and physical variables were associated with this broad‐scaled differentiation. Especially soil chemical variables related to soil acidity (pH, Ca) showed linear relationships with the dominant vegetation gradient. This was closely related to increasing cryoperturbation, decreasing precipitation and cooler conditions. Remarkable differences among relatively adjacent sites suggest that local factors such as geological properties and lemming grazing may strongly drive vegetation differentiation. Conclusions: Vegetation differentiation in tundra areas conforms to a major ecocline underlain by a complex set of environmental gradients, where precipitation, thermal conditions and soil chemical and physical processes are coupled. However, local factors such as bedrock conditions and lemming grazing may cause marked deviations from the general climate‐vegetation models. Overall, soil chemical factors (pH, Ca) turned out to have linear relationship with the broad‐scale differentiation of arctic vegetation.     

Reproductive condition in two Malayan freshwater viviparid gastropods

Siamopaludina martensi and Filopaludina sumatrensis have typical viviparid reproductive systems with dimorphic spermatozoa and copulatory right tentacle in the male, and a large pallial brood-pouch in the female. Females outnumber males as in several other viviparids. Brood-pouches contained overall monthly averages of 0–14 developing young in S. martensi , 9–23 in F. sumatrensis , more than half of which were well-developed, later juveniles. Brood-pouch counts and ovary condition of both species varied in broad accordance with monthly rainfall, giving an irregularly seasonal pattern of annual change resembling those of several terrestrial Malayan snails. Juveniles emerge from the brood-pouch mostly at night. Alteration of aquarium conditions leads to temporarily accelerated release of young but does not permanently raise brood-pouch counts or rates of release.     

Genetic analysis of endogenous xenotropic murine leukemia viruses: association with two common mouse mutations and the viral restriction locus Fv-1.

We have defined 40 endogenous xenotropic virus (Xmv) loci from several common inbred strains of mice by examining provirus-cell DNA junction fragments in recombinant inbred mice. Some inbred strains carried unique proviruses, but most Xmv loci were present in several strains, indicating that many Xmv integration events preexisted modern inbreeding. It was also clear that most Xmv junction fragment variation between inbred strains resulted from independent integration events and not modification or restriction site polymorphism following integration. Chromosomal assignments were determined for 32 Xmv loci by comparing their recombinant inbred strain distribution patterns to those of known genetic markers. The Xmv loci were generally dispersed throughout the genome, but several chromosomal regions contained more than one provirus. Furthermore, several close genetic associations with cellular genes were discovered. Four Xmv loci were closely linked to Fv-1b, a dominant viral resistance gene present in C57BL/6J, BALB/cJ, A/J, and several other strains. Xmv-28 was closely linked to rd (retinal degeneration), and Xmv-10 was closely linked to a (non-agouti), both of which are old mutations as inferred from their broad distribution in mice. We suggest that Xmv integration contributed to genetic diversity in the past and that much of this diversity exists today in common laboratory strains.     

Expanding the repertoire of nitrilases with broad substrate specificity and high substrate tolerance for biocatalytic applications

Enzymatic conversion of nitriles to carboxylic acids by nitrilases has gained significance in the green synthesis of several pharmaceutical precursors and fine chemicals. Although nitrilases from several sources have been characterized, there exists a scope for identifying broad spectrum nitrilases exhibiting higher substrate tolerance and better thermostability to develop industrially relevant biocatalytic processes. Through genome mining, we have identified nine novel nitrilase sequences from bacteria and evaluated their activity on a broad spectrum of 23 industrially relevant nitrile substrates. Nitrilases from Zobellia galactanivorans, Achromobacter insolitus and Cupriavidus necator were highly active on varying classes of nitriles and applied as whole cell biocatalysts in lab scale processes. Z. galactanivorans nitrilase could convert 4-cyanopyridine to achieve yields of 1.79 M isonicotinic acid within 3 h via fed-batch substrate addition. The nitrilase from A. insolitus could hydrolyze 630 mM iminodiacetonitrile at a fast rate, effecting 86 % conversion to iminodiacetic acid within 1 h. The arylaliphatic nitrilase from C. necator catalysed enantioselective hydrolysis of 740 mM mandelonitrile to (R)-mandelic acid in 4 h. Significantly high product yields suggest that these enzymes would be promising additions to the suite of nitrilases for upscale biocatalytic application.     

Grooved Stones from Zawi Chemi Shanidar, a Protoneolithic Site in Northern Iraq

Grooved stones appear as a new cultural element in Epipaleolithic-Protoneolithic sites (dating from ca. 9000–6000 B.C.) in a broad geographic zone from Southwest Asia to North Africa. Similar objects have been recorded from archeological and ethnographic contexts in both the Old World and the New World. Ethnographic and other evidence has shown that the several types of grooved stones are associated with a variety of functions, mainly related to the manufacture and use of arrows and arrow shafts. It is suggested that these tools may be associated with the discovery and diffusion of the bow and arrow .     

Small object detection neurons in female hoverflies

While predators such as dragonflies are dependent on visual detection of moving prey, social interactions make conspecific detection equally important for many non-predatory insects. Specialized 'acute zones' associated with target detection have evolved in several insect groups and are a prominent male-specific feature in many dipteran flies. The physiology of target selective neurons associated with these specialized eye regions has previously been described only from male flies. We show here that female hoverflies (Eristalis tenax) have several classes of neurons within the third optic ganglion (lobula) capable of detecting moving objects smaller than 1 degrees . These neurons have frontal receptive fields covering a large part of the ipsilateral world and are tuned to a broad range of target speeds and sizes. This could make them suitable for detecting targets under a range of natural conditions such as required during predator avoidance or conspecific interactions.     

The evolving genetic landscape of congenital disorders of glycosylation

Congenital Disorders of Glycosylation (CDG) are an expanding and complex group of rare genetic disorders caused by defects in the glycosylation of proteins and lipids. The genetic spectrum of CDG is extremely broad with mutations in over 140 genes leading to a wide variety of symptoms ranging from mild to severe and life-threatening. There has been an expansion in the genetic complexity of CDG in recent years. More specifically several examples of alternate phenotypes in recessive forms of CDG and new types of CDG following an autosomal dominant inheritance pattern have been identified. In addition, novel genetic mechanisms such as expansion repeats have been reported and several already known disorders have been classified as CDG as their pathophysiology was better elucidated. Furthermore, we consider the future and outlook of CDG genetics, with a focus on exploration of the non-coding genome using whole genome sequencing, RNA-seq and multi-omics technology.     

Phylogenetic Diversity and Specificity of Bacteria Closely Associated with Alexandrium spp. and Other Phytoplankton

While several studies have suggested that bacterium-phytoplankton interactions have the potential to dramatically influence harmful algal bloom dynamics, little is known about how bacteria and phytoplankton communities interact at the species composition level. The objective of the current study was to determine whether there are specific associations between diverse phytoplankton and the bacteria that co-occur with them. We determined the phylogenetic diversity of bacterial assemblages associated with 10 Alexandrium strains and representatives of the major taxonomic groups of phytoplankton in the Gulf of Maine. For this analysis we chose xenic phytoplankton cultures that (i) represented a broad taxonomic range, (ii) represented a broad geographic range for Alexandrium spp. isolates, (iii) grew under similar cultivation conditions, (iv) had a minimal length of time since the original isolation, and (v) had been isolated from a vegetative phytoplankton cell. 16S rRNA gene fragments of most Bacteria were amplified from DNA extracted from cultures and were analyzed by denaturing gradient gel electrophoresis and sequencing. A greater number of bacterial species were shared by different Alexandrium cultures, regardless of the geographic origin, than by Alexandrium species and nontoxic phytoplankton from the Gulf of Maine. In particular, members of the Roseobacter clade showed a higher degree of association with Alexandrium than with other bacterial groups, and many sequences matched sequences reported to be associated with other toxic dinoflagellates. These results provide evidence for specificity in bacterium-phytoplankton associations.     

Isolation and Characterization of Numerous Novel Phages Targeting Diverse Strains of the Ubiquitous and Opportunistic Pathogen Achromobacter xylosoxidans

The clinical relevance of nosocomially acquired infections caused by multi-resistant Achromobacter strains is rapidly increasing. Here, a diverse set of 61 Achromobacter xylosoxidans strains was characterized by MultiLocus Sequence Typing and Phenotype MicroArray technology. The strains were further analyzed in regard to their susceptibility to 35 antibiotics and to 34 different and newly isolated bacteriophages from the environment. A large proportion of strains were resistant against numerous antibiotics such as cephalosporines, aminoglycosides and quinolones, whereas piperacillin-tazobactam, ticarcillin, mezlocillin and imipenem were still inhibitory. We also present the first expanded study on bacteriophages of the genus Achromobacter that has been so far a blank slate with respect to phage research. The phages were isolated mainly from several waste water treatment plants in Germany. Morphological analysis of all of these phages by electron microscopy revealed a broad diversity with different members of the order Caudovirales, including the families Siphoviridae, Myoviridae, and Podoviridae. A broad spectrum of different host ranges could be determined for several phages that lysed up to 24 different and in part highly antibiotic resistant strains. Molecular characterisation by DNA restriction analysis revealed that all phages contain linear double-stranded DNA. Their restriction patterns display distinct differences underlining their broad diversity.     

Broad HIV-1 neutralization mediated by CD4-binding site antibodies

We have identified several patient sera showing potent and broad HIV-1 neutralization. Using antibody adsorption and elution from selected gp120 variants, the neutralizing specificities of the two most broadly reactive sera were mapped to the primary receptor CD4-binding region of HIV-1 gp120. Novel antibodies to the CD4-binding site are elicited in some HIV-1-infected individuals, and new approaches to present this conserved region of gp120 to the immune system may result in improved vaccine immunogens.