N-Domain of ArdA Antirestriction Proteins Inhibits the Repression Activity of the Histone-Like H-NS Protein

Molecular Biology - DNA mimicking ArdA anti-restriction proteins specifically inhibit restriction (endonuclease) activity of the type I restriction-modification (RM) system. An ArdA monomer is...     

Evidence for the existence of a restriction-modification system common to several species of the family Vibrionaceae

A broad-host-range vibriophage KVP40 originally isolated on Vibrio parahaemolyticus 1010 was restricted and modified by strains of at least five Vibrio and one Photobacterium species. 1010 was a non-restricting host. An anti-restriction mutant KVP40 aar1 was isolated after propagating the phage on a restricting host, V. anguillarum VIB36. KVP40 aar1 grown on either 1010 or VIB36, as well as the parental phage grown on VIB36, showed much higher efficiencies of plating on all the restricting hosts as compared with the parental phage grown on 1010, indicating that these restricting hosts probably share a common restriction-modification system active in vivo on KVP40.     

Physical mapping and cloning of bacteriophage T4 anti-restriction endonuclease gene.

We have proposed that the ability of T4 to produce non-glucosylated progeny after a single cycle of growth on a galU rglA rglB+ mutant of Escherichia coli is due to the initiation of the rglB+ function by a phage-coded, anti-restriction endonuclease protein. Based on this hypothesis, we screened T4 deletion mutants for failure to give a burst in this host. The absence of an arn gene in phage mutants lacking the 55.5- to 58.4-kilobase region is verified by their inability to protect secondary infecting non-glucosylated phage from rglB-controlled cleavage. A functional arn gene was cloned on plasmid pBR325, and the 0.8-kilobase insert DNA was shown to be homologous to the DNA missing in the arn deletion phage.     

Single-stranded DNA binding and methylation by EcoP1I DNA methyltransferase

EcoP1I methyltransferase (M.EcoP1I) belongs to the type III restriction-modification system encoded by prophage P1 that infects Escherichia coli. Binding of M.EcoP1I to double-stranded DNA and single-stranded DNA has been characterized. Binding to both single- and double-stranded DNA could be competed out by unlabeled single-stranded DNA. Metal ions did not influence DNA binding. Interestingly, M.EcoP1I was able to methylate single-stranded DNA. Kinetic parameters were determined for single- and double-stranded DNA methylation. This feature of the enzyme probably functions in protecting the phage genome from restriction by type III restriction enzymes and thus could be considered as an anti-restriction system. This study describing in vitro methylation of single-stranded DNA by the type III methyltransferase EcoP1I allows understanding of the mechanism of action of these enzymes and also their role in the biology of single-stranded phages.     

Vibrational dynamics and heat capacity in polyglycine II

The earlier works on the vibrational dynamics of polyglycine II (PG II) suffer from several infirmities, which not only suppress the dynamical nature of normal modes, but also lead to several incorrect assignments and interactive constants of the potential field. In this study, we have re-examined the phonon dispersion profiles of PG II using Higgs method for evaluation of phase-related normal modes and have attempted to remove the infirmities, as far as possible. The Wilson's GF matrix method combined with the Urey-Bradley force field has been used for normal mode analysis. This potential field leads to correct assignments of Raman, infrared and inelastic neutron scattering frequencies. Characteristic features of the dispersion curve (v versus delta/pi plot), such as repulsion and regions of high density-of-states have been interpreted. In addition, the heat capacity as a function of temperature has been obtained via density-of-states. It agrees well with the experimental data and is being reported for the first time.     

Various characteristics of the anti-restriction mechanism in bacteriophage T5

Bacteriophage T5 is not confined by the restriction systems of the second type EcoRII and EcoRV. Bacteriophage T5 DNA is not modified by EcoRII and EcoRV methylases in vivo. The sites of recognition for restriction endonuclease EcoRV are mapped at 24.4; 57.6; 68.5; 70.2% of T5 DNA, while the sites at 5.1; 7.6% are recognized by EcoRII, the sites at 5.75; 6.0 and 6.5% are recognized by HpaI in FST. A high activity of restriction endonucleases EcoRI and EcoRV is demonstrated in crude extracts of E. coli B834 (RI) and E. coli B834 (RV) cells infected by bacteriophage T5. The simultaneous infection of E. coli B834 (RI) or E. coli B834 (RV) cells by the amber mutants of bacteriophage T5 and the suppressing phage lambda NM761 does not result in the protection of lambda DNA by the T5 anti-restriction mechanism. The presented data support the hypothesis that the anti-restriction mechanism of bacteriophage T5 is based on prevention of T5 DNA contacts with restriction enzymes by a specific phage protein.     

Static Magnetic Field Influence on the Activity of some Respiratory Enzymes in Wheat

Most of the published studies on magnetic field action on biological systems have examined reactions in animals, while a smaller number of studies have reported magnetic field effects in plants. The effects of static magnetic field on the activity of several key enzymes in plant metabolism, such as malate dehydrogenase, succinate oxidase, succinate dehydrogenase, and cytochrome oxidase in young wheat seedlings, have been investigated in this study. It appears that the observed changes in enzyme activity could be considered to be a result of the influence of the magnetic field on the reactivity of these enzymes, including effects on metal cations that regulate enzyme activity. The results support the idea of the existence of “biological windows,” particularly with respect to exposure time.     

Recombinant viral insecticides: Delivery of environmentally safe and cost-effective products

Biological control agents such as baculovirus insecticides have many attributes which make them attractive alternatives to synthetic chemical pesticides. However, there have been several economic and agronomic barriers to their widespread use. Among the obstacles to commercialization of viral insecticides have been high production costs, the lack of efficacious formulation and application technologies, and a slow speed of action. Biotechnology has contributed several advances toward overcoming these obstacles. The high cost ofin vivo production can be reduced significantly using a newly developed high-density rearing system termed HeRD. The HeRD technology can be used to rear many different species of lepidopterous larvae for production of viral insecticides, as hosts for parasitoid production, or for sterile-male release programs. Using this technology, the baculovirus production costs are equivalent to sprayable Bt toxins. The field efficacy of viral pesticides and other biological control agents requires cost effective, biologically based formulation and application technologies. Based on current field efficacy evaluations of baculovirus pesticides, formulation/application technologies must be improved for viral pesticides to compete effectively and consistently in most pesticide markets. Through recombinant DNA technology, it is now possible to insert foreign pesticidal genes into viral pesticides, resulting in faster time to death or, more importantly, time to cessation of feeding of the target pests. However, the commercial use of recombinant pesticides has raised several potential environmental issues, including possible effects on non-target organisms, ecological interactions, mitigation and genetic stability. Genetic strategies have been developed to mitigate most of the potential problems associated with recombinant baculovirus pesticides. Five field tests have been conducted in the U.S. to evaluate these strategies. The laboratory and field results illustrate that the genetic strategies employed ensure environmental safety while also reducing production costs.     

Engineering skeletal muscle tissue--new perspectives in vitro and in vivo

Muscle tissue engineering (TE) has not yet been clinically applied because of several problems. However, the field of skeletal muscle TE has been developing tremendously and new approaches and techniques have emerged. This review will highlight recent developments in the field of nanotechnology, especially electrospun nanofibre matrices, as well as potential cell sources for muscle TE. Important developments in cardiac muscle TE and clinical studies on Duchenne muscular dystrophy (DMD) will be included to show their implications on skeletal muscle TE.     

Comparative analysis of anti-restriction activities of ArdA (ColIb-P9) and Ocr (T7) proteins

Anti-restriction proteins ArdA and Ocr are specific inhibitors of type I restriction-modification enzymes. The IncI1 transmissible plasmid ColIb-P9 ardA and bacteriophage T7 0.3(ocr) genes were cloned in pUC18 vector. Both ArdA (ColIb-P9) and Ocr (T7) proteins inhibit both restriction and modification activities of the type I restriction-modification enzyme (EcoKI) in Escherichia coli K12 cells. ColIb-P9 ardA, T7 0.3(ocr), and the Photorhabdus luminescens luxCDABE genes were cloned in pZ-series vectors with the P(ltetO-1) promoter, which is tightly repressible by the TetR repressor. Controlling the expression of the lux-genes encoding bacterial luciferase demonstrates that the P(ltetO-1) promoter can be regulated over an up to 5000-fold range by supplying anhydrotetracycline to the E. coli MG1655Z1 tetR(+) cells. Effectiveness of the anti-restriction activity of the ArdA and Ocr proteins depended on the intracellular concentration. It is shown that the dissociation constants K(d) for ArdA and Ocr proteins with EcoKI enzyme differ 1700-fold: K(d) (Ocr) = 10(-10) M, K(d) (ArdA) = 1.7.10(-7) M.     

Molecular recognition of anions by synthetic receptors

Over the past year, several significant developments have been made in the field of anion binding. The fundamental principles of molecular recognition are increasingly being better understood, and of particular interest are reports of several synthetic anion receptors able to perform their task in complex natural media. Additionally, macroscopic devices such as anion specific electrodes and membranes based on a molecular recognition approach are now being made.     

Conservation genetics in a globally changing environment: present problems,paradoxes and future challenges

Despite recent advances in conservation genetics and related disciplines and the growing impact that conservation genetics is having in conservation biology, our knowledge on several key issues in the field is still insufficient. Here we identify some of these issues together with addressing several paradoxes which have to be solved before conservation genetics can face new challenges that are appearing in the transitory phase from the population genetics into the population genomics era. Most of these issues, paradoxes and challenges, like the central dogma of conservation genetics, the computational, theoretical and laboratory experiment achievements and limitations in the conservation genetics field have been discussed. Further knowledge on the consequences of inbreeding and outbreeding depression in wild populations as well as the capacity of small populations to adapt to local environmental conditions is also urgently needed. The integration of experimental, theoretical and applied conservation genetics will contribute to improve our understanding of methodological and applied aspects of conservation genetics.     

Protein kinases 1988: a current perspective

This review focuses on several recent developments in the field of protein kinases. In the area of protein serine/threonine kinases, much has been learned recently about protein kinase C structure and function. Novel lipid mediators, both stimulatory and inhibitory, have been discovered, and kinase has been shown to be an increasingly large family of gene products. Heterogeneity of cellular localization and function has been documented. Calcium/calmodulin-dependent protein kinases are now believed to consist of at least five enzymes, which range from those with extreme substrate specificity such as phosphorylase kinase and myosin light-chain kinases to calcium calmodulin kinase II, with several known substrates. Several of these enzymes appear to be important in synaptic transmission and, for calcium/calmodulin kinase III, in the regulation of protein synthesis. Several new examples of pseudosubstrate prototopes as endogenous kinase inhibitors have been described, including regions intrinsic to kinase primary sequences, which could serve as constitutive inhibitors of enzyme activity. In the field of protein tyrosine kinases, new enzyme species are being discovered at a rapid rate. There are several well-documented examples of kinase autophosphorylation on tyrosine leading to stimulation of catalytic activity. For the growth factor receptors with intrinsic protein tyrosine kinase activity, it now seems clear that kinase catalytic activity is necessary for most hormone effects on cells, with the general exceptions of ligand binding and, possibly, receptor cycling. Finally, several groups have recently described a close association between protein tyrosine kinases and a phosphatidylinositol kinase activity, a link that might eventually explain some of the initial steps in signal transduction that occur after kinase activation.     

Umbilical cord blood stem cells: Towards a proteomic approach

The first umbilical cord blood (UCB) transplant to a sibling with Fanconi's anaemia in 1988 represented a breakthrough in the field of transplantation. Thereon, several transplants have been performed with UCB-derived hematopoietic stem cells (HSCs) and a plethora of studies have investigated the plasticity of UCB-derived stem and progenitor cells. However, these studies have not been hitherto translated into clinical trials and, although UCB is routinely used as an alternative source of HSCs, no substantial advances have been made in the field of clinical regenerative medicine. The real deal is the lack of knowledge about the molecular processes governing the events of differentiation which transform immature UCB stem cells into terminally-committed hematopoietic, muscle, bone and nervous cells. In order to fill this void, several studies have been recently focused on the identification of the peculiar proteomic profile of UCB-derived stem cells.Hereby, we concisely review recent proteomic surveys addressing UCB-derived stem and progenitor cells.Notably, comparative studies detected a wider spectrum of proteins in immature cells rather than in more differentiated populations, as if maturation events could represent a bottleneck to protein expression. Future research projects should try to shed light on these processes and their completion could pave the way for unprecedented treatments.     

The bright frontiers of microbial metabolic optogenetics

In recent years, light-responsive systems from the field of optogenetics have been applied to several areas of metabolic engineering with remarkable success. By taking advantage of light's high tunability, reversibility, and orthogonality to host endogenous processes, optogenetic systems have enabled unprecedented dynamical controls of microbial fermentations for chemical production, metabolic flux analysis, and population compositions in co-cultures. In this article, we share our opinions on the current state of this new field of metabolic optogenetics.We make the case that it will continue to impact metabolic engineering in increasingly new directions, with the potential to challenge existing paradigms for metabolic pathway and strain optimization as well as bioreactor operation.     

Multiscale determinants of parasite abundance: A quantitative hierarchical approach for coral reef fishes

During recent decades, there have been numerous attempts to identify the key determinants of parasite communities and several influential variables have been clarified at either infra-, component or compound community scales. However, in view of the possible complexity of interactions among determinants, the commonly-used exploratory and statistical modelling techniques have often failed to find meaningful ecological patterns from such data. Moreover, quantitative assessments of factors structuring species richness, abundance, community structure and species associations in parasite communities remain elusive. Recently, because they are ideally suited for the analysis of complex and highly interactive data, there has been increasing interest in the use of classification and regression tree analyses in several ecological fields. To date, such approaches have never been used by parasitologists for field data. This study aims to both introduce and illustrate the use of multivariate regression trees in order to investigate the determinants of parasite abundance in a multi-scale quantitative context. To do this, we used new field epidemiological data from 1489 coral reef fishes collected around two islands in French Polynesia. We evaluated the relative effect and interactions of several host traits and environmental factors on the abundance of metazoan parasite assemblage at several scales and assessed the impact of major factors on each parasite taxon. Our results suggest that the islands sampled, the host species and host size are equal predictors of parasite abundance at a global scale, whereas other factors proved to be significant predictors of a local pattern, depending on host family. We also discuss the potential use of regression trees for parasitologists as both an explorative and a promising predictive tool.     

Medical perspectives of adults and embryonic stem cells

In the last 30 years, allogeneic bone marrow transplantation has become the treatment of choice for many hematologic malignancies or inherited disorders and a number of changes have been registered in terms of long-term survival rate of transplanted patients as well as of available sources of hematopoietic stem cell (HSC). In parallel to the publication of better results in HSC transplantation, several recent discoveries have opened a scientific and ethical debate on the therapeutical potential of stem cells isolated from adult or embryonic tissues. One of the major discoveries in this field is the capacity of bone marrow-derived stem cells to treat a genetic liver disease in a mouse model, thus justifying the concept of transdifferentiation of adult stem cell and raising hopes on its possible therapeutical applications. We have tried here to summarise the advances in this field and to discuss the limits of these biological data.     

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。     

High-performance photovoltaic behavior of oriented purple membrane polymer composite films

The photovoltaic behavior of films in which bacteriorhodopsin molecules are embedded in a polyvinyl alcohol matrix has been investigated by using both pulsed laser excitation and regular light illumination. Response times as short as milliseconds, photocurrents as great as 120 micro A/cm(2), and photovoltages as large as 3.8 V have been obtained. A theoretical model has been developed and used to extract several physical parameters and fit the experimental results. Some important intrinsic parameters have been obtained. Theoretical results indicate that the average displacement of the excited protons is on the order of several tens of microns. Other curve fits show that photocurrent and photovoltage increase linearly with external field, but increase exponentially with flash power. These theoretical models and results can be extended to other kinds of photoactive polymeric materials.