Genomic sequence and receptor for the Vibrio cholerae phage KSF-1phi: evolutionary divergence among filamentous vibriophages mediating lateral gene transfer

KSF-1phi, a novel filamentous phage of Vibrio cholerae, supports morphogenesis of the RS1 satellite phage by heterologous DNA packaging and facilitates horizontal gene transfer. We analyzed the genomic sequence, morphology, and receptor for KSF-1phi infection, as well as its phylogenetic relationships with other filamentous vibriophages. While strains carrying the mshA gene encoding mannose-sensitive hemagglutinin (MSHA) type IV pilus were susceptible to KSF-1phi infection, naturally occurring MSHA-negative strains and an mshA deletion mutant were resistant. Furthermore, d-mannose as well as a monoclonal antibody against MSHA inhibited infection of MSHA-positive strains by the phage, suggesting that MSHA is the receptor for KSF-1phi. The phage genome comprises 7,107 nucleotides, containing 14 open reading frames, 4 of which have predicted protein products homologous to those of other filamentous phages. Although the overall genetic organization of filamentous phages appears to be preserved in KSF-1phi, the genomic sequence of the phage does not have a high level of identity with that of other filamentous phages and reveals a highly mosaic structure. Separate phylogenetic analysis of genomic sequences encoding putative replication proteins, receptor-binding proteins, and Zot-like proteins of 10 different filamentous vibriophages showed different results, suggesting that the evolution of these phages involved extensive horizontal exchange of genetic material. Filamentous phages which use type IV pili as receptors were found to belong to different branches. While one of these branches is represented by CTXphi, which uses the toxin-coregulated pilus as its receptor, at least four evolutionarily diverged phages share a common receptor MSHA, and most of these phages mediate horizontal gene transfer. Since MSHA is present in a wide variety of V. cholerae strains and is presumed to express in the environment, diverse filamentous phages using this receptor are likely to contribute significantly to V. cholerae evolution.     

The seasonality of phytoplankton in the North American Great Lakes,a comparative synthesis

The phytoplankton and productivity of the North American Great Lakes has been studied extensively by Fisheries and Oceans Canada during the past 15 years to monitor the impact of nutrient and contaminant loading on the plankton of the ecosystem. Lakewide cruises were conducted at monthly intervals mainly during the spring to fall period. This provided extensive biomass, species, size, productivity and nutrient concentration data for the Great Lakes. These data were collected using the Utermöhl inverted microscope technique together with standardized taxonomic, productivity and data-handling procedures. These standardized methodologies were applied to all the Great Lakes which resulted in a comprehensive phycological and ecological data base for the first time. These data form the basis for the evaluation of the complex phenomenon of seasonality.The eutrophic/mesotrophic Lower Great Lakes exhibited well-developed seasonal peaks of high biomass, with inshore-offshore differentiation and spring maxima most pronounced in the inshore region. However, the oligotrophic Upper Great Lakes had low biomass and generally lacked well-developed seasonal patterns. No marked seasonal trends were observed in the ultra-oligotrophic Lake Superior. The seasonality of biomass and various taxonomic groups of phytoplankton showed differentiation between individual lakes and is discussed in detail. The seasonal succession of species provided interesting comparisons between the Lower Great Lakes, which harbour eutrophic and mesotrophic species, and the Upper Great Lakes, which harbour oligotrophic species.Due to the voluminous nature of our data, a general overview has been given for all the Great Lakes with Lake Ontario treated in detail as a case study. The Lake Ontario case study provides the state-of-the-art status ranging from the lakewide surveys of 1970 to the current research with minute organisms such as ultraplankton and picoplankton.     

Web-based applications for building, managing and analysing kinetic models of biological systems

Mathematical modelling and computational analysis play an essentialrole in improving our capability to elucidate the functionsand characteristics of complex biological systems such as metabolic,regulatory and cell signalling pathways. The modelling and concomitantsimulation render it possible to predict the cellular behaviourof systems under various genetically and/or environmentallyperturbed conditions. This motivates systems biologists/bioengineers/bioinformaticiansto develop new tools and applications, allowing non-expertsto easily conduct such modelling and analysis. However, amonga multitude of systems biology tools developed to date, onlya handful of projects have adopted a web-based approach to kineticmodelling. In this report, we evaluate the capabilities andcharacteristics of current web-based tools in systems biologyand identify desirable features, limitations and bottlenecksfor further improvements in terms of usability and functionality.A short discussion on software architecture issues involvedin web-based applications and the approaches taken by existingtools is included for those interested in developing their ownsimulation applications.      

Enhanced tolerance of transgenic tall fescue plants overexpressing 2-Cys peroxiredoxin against methyl viologen and heat stresses

Plant 2-Cys peroxiredoxins (2-Cys Prx) has both peroxidase and chaperon function. We overexpressed an Arabidopsis 2-Cys Prx in transgenic tall fescue (Festuca arundinacea) plants to confer tolerance against heat and methyl viologen (MV) stress. Transgenic plants were generated by Agrobacterium-mediated genetic transformation, and integration and expression of the transgene was confirmed by Southern, northern and western blot analyses. Compared to control plants, transgenic plants had significantly less electrolyte leakage and thiobarbituric acid-reactive substances (TBARS) when exposed to heat or MV. Under heat stress (42°C), transgenic plants maintained their chlorophyll fluorescence (Fv/Fm) for 24 h while control plants lost chlorophyll fluorescence very quickly. We conclude that the high levels of 2-Cys Prx proteins in transgenic plants protect leaves from oxidative damage probably due to chaperon activity.     

Pharmacokinetic allometric scaling of oligonucleotides

The objective of this study was to evaluate the predictive performance of interspecies scaling of oligonucleotides to predict clearance and volume of distribution at steady state in humans from animal data. The human pharmacokinetic parameters were predicted using 1, 2, or at least 3 animal species. The results of the study indicated that the pharmacokinetic parameters of oligonucleotides can be predicted with reasonable accuracy in humans when at least 3 animal species are employed. On the other hand, allometric scaling based on 1 or 2 species or fixed coefficient or fixed exponent can be erratic and unreliable. Further work should be conducted in this direction.     

Glyphosate-induced oxidative stress in rice leaves revealed by proteomic approach

Glyphosate is one of the most widely used herbicides in cereal-growing regions worldwide. In the present work, the protein expression profile of rice leaves exposed to glyphosate was analyzed in order to investigate the alternative effects of glyphosate on plants. Two-week-old rice leaves were subjected to glyphosate or a reactive oxygen species (ROS) inducing herbicide paraquat, and total soluble proteins were extracted and analyzed by two-dimensional gel electrophoresis (2-DE) coupled with matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry (MS) analysis. A total of 25 differentially expressed proteins were identified from the glyphosate treated sample, wherein 18 proteins were up-regulated and 7 proteins were down-regulated. These proteins had shown a parallel expression pattern in response to paraquat. Results from the 2-DE analysis, combined with immunoblotting, clearly revealed that ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) large subunit was significantly decreased by the treatment of both herbicides. An increased accumulation of antioxidant enzymes including ascorbate peroxidase, glutathione S-transferase, thioredoxin h-type, nucleoside diphosphate kinase 1, peroxiredoxin and a superoxide dismutase [Cu–Zn] chloroplast precursor in the glyphosate-treated sample suggests that a glyphosate treatment possibly generates oxidative stress in plants. Moreover, a gene expression analysis of five antioxidant enzymes by Northern blot confirmed their mRNA levels in the rice leaves. A histo-cytochemical investigation with DAB (3,3-diaminobenzidine) to localize H₂O₂ and increases of the thiobarbituric acid reactive substances (TBARS) concentration revealed that the glyphosate application generates ROS, which resulted in the peroxidation and destruction of lipids in the rice leaves.     

Absence of nonlinear responses in cells and tissues exposed to RF energy at mobile phone frequencies using a doubly resonant cavity

A doubly resonant cavity was used to search for nonlinear radiofrequency (RF) energy conversion in a range of biological preparations, thereby testing the hypothesis that living tissue can demodulate RF carriers and generate baseband signals. The samples comprised high‐density cell suspensions (human lymphocytes and mouse bone marrow cells); adherent cells (IMR‐32 human neuroblastoma, G361 human melanoma, HF‐19 human fibroblasts, N2a murine neuroblastoma (differentiated and non‐differentiated) and Chinese hamster ovary (CHO) cells) and thin sections or slices of mouse tissues (brain, kidney, muscle, liver, spleen, testis, heart and diaphragm). Viable and non‐viable (heat killed or metabolically impaired) samples were tested. Over 500 cell and tissue samples were placed within the cavity, exposed to continuous wave (CW) fields at the resonant frequency (f) of the loaded cavity (near 883 MHz) using input powers of 0.1 or 1 mW, and monitored for second harmonic generation by inspection of the output at 2f. Unwanted signals were minimised using low pass filters (≤1 GHz) at the input to, and high pass filters (≥1 GHz) at the output from, the cavity. A tuned low noise amplifier allowed detection of second harmonic signals above a noise floor as low as −169 dBm. No consistent second harmonic of the incident CW signals was detected. Therefore, these results do not support the hypothesis that living cells can demodulate RF energy, since second harmonic generation is the necessary and sufficient condition for demodulation. Bioelectromagnetics 31:556–565, 2010. © 2010 Wiley‐Liss, Inc.     

Proteome analysis of soybean roots under waterlogging stress at an early vegetative stage

To gain better insight into how soybean roots respond to waterlogging stress, we carried out proteomic profiling combined with physiological analysis at two time points for soybean seedlings in their early vegetative stage. Seedlings at the V2 stage were subjected to 3 and 7 days of waterlogging treatments. Waterlogging stress resulted in a gradual increase of lipid peroxidation and in vivo H₂O₂ level in roots. Total proteins were extracted from root samples and separated by two-dimensional gel electrophoresis (2-DE). A total of 24 reproducibly resolved, differentially expressed protein spots visualized by Coomassie brilliant blue (CBB) staining were identified by matrix assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry or electrospray ionization tandem mass spectrometry (ESI-MS/MS) analysis. Of these, 14 proteins were upregulated; 5 proteins were decreased; and 5 were newly induced in waterlogged roots. The identified proteins include well-known classical anaerobically induced proteins as well as novel waterlogging-responsive proteins that were not known previously as being waterlogging responsive. The novel proteins are involved in several processes, i.e. signal transduction, programmed cell death, RNA processing, redox homeostasis and metabolisms of energy. An increase in abundance of several typical anaerobically induced proteins, such as glycolysis and fermentation pathway enzymes, suggests that plants meet energy requirement via the fermentation pathway due to lack of oxygen. Additionally, the impact of waterlogging on the several programmed cell death- and signal transduction-related proteins suggest that they have a role to play during stress. RNA gel blot analysis for three programmed cell death-related genes also revealed a differential mRNA level but did not correlate well with the protein level. These results demonstrate that the soybean plant can cope with waterlogging through the management of carbohydrate consumption and by regulating programmed cell death. The identification of novel proteins such as a translation initiation factor, apyrase, auxin-amidohydrolase and coproporphyrinogen oxidase in response to waterlogging stress may provide new insight into the molecular basis of the waterlogging-stress response of soybean.     

Olfactory bulb axonal outgrowth is inhibited by draxin

Olfactory bulb (OB) projection neurons receive sensory input from olfactory receptor neurons and precisely relay it through their axons to the olfactory cortex. Thus, olfactory bulb axonal tracts play an important role in relaying information to the higher order of olfactory structures in the brain. Several classes of axon guidance molecules influence the pathfinding of the olfactory bulb axons. Draxin, a recently identified novel class of repulsive axon guidance protein, is essential for the formation of forebrain commissures and can mediate repulsion of diverse classes of neurons from chickens and mice. In this study, we have investigated the draxin expression pattern in the mouse telencephalon and its guidance functions for OB axonal projection to the telencephalon. We have found that draxin is expressed in the neocortex and septum at E13 and E17.5 when OB projection neurons form the lateral olfactory tract (LOT) rostrocaudally along the ventrolateral side of the telencephalon. Draxin inhibits axonal outgrowth from olfactory bulb explants in vitro and draxin-binding activity in the LOT axons in vivo is detected. The LOT develops normally in draxin−/− mice despite subtle defasciculation in the tract of these mutants. These results suggest that draxin functions as an inhibitory guidance cue for OB axons and indicate its contribution to the formation of the LOT.