The proper functioning of biomolecules in living cells requires them to assume particular structures and to undergo conformational changes. Both biomolecular structure and motion can be studied using a wide variety of techniques, but none offers the level of detail as do molecular dynamics (MD) simulations. Integrating two widely used modeling programs, namely NAMD and VMD, we have created a robust, user-friendly software, QwikMD, which enables novices and experts alike to address biomedically relevant questions, where often only molecular dynamics simulations can provide answers. Performing both simple and advanced MD simulations interactively, QwikMD automates as many steps as necessary for preparing, carrying out, and analyzing simulations while checking for common errors and enabling reproducibility. QwikMD meets also the needs of experts in the field, increasing the efficiency and quality of their work by carrying out tedious or repetitive tasks while enabling easy control of every step. Whether carrying out simulations within the live view mode on a small laptop or performing complex and large simulations on supercomputers or Cloud computers, QwikMD uses the same steps and user interface. QwikMD is freely available by download on group and personal computers. It is also available on the cloud at Amazon Web Services.

/pdf/qwikmd-integrative-molecular-dynamics-toolkit-for-novices-2cq41yu48i.pdf

QwikMD — Integrative Molecular Dynamics Toolkit for Novices and Experts

Nitrate-dependent ferrous iron [Fe(II)] oxidation (NDFO) is a well-recognized chemolithotrophic pathway in anoxic sediments. The neutrophilic chemolithoautotrophic enrichment culture KS originally obtained from a freshwater sediment (K. L. Straub, M. Benz, B. Schink, and F. Widdel, Appl Environ Microbiol 62:1458-1460, 1996) has been used as a model system to study NDFO. However, the primary Fe(II) oxidizer in this culture has not been isolated, despite extensive efforts to do so. Here, we present a metagenomic analysis of this enrichment culture in order to gain insight into electron transfer pathways and the roles of different bacteria in the culture. We obtained a near-complete genome of the primary Fe(II) oxidizer, a species in the family Gallionellaceae, and draft genomes from its flanking community members. A search of the putative extracellular electron transfer pathways in these genomes led to the identification of a homolog of the MtoAB complex [a porin-multiheme cytochromec system identified in neutrophilic microaerobic Fe(II)-oxidizing Sideroxydans lithotrophicus ES-1] in a Gallionellaceae sp., and findings of other putative genes involving cytochromecand multicopper oxidases, such as Cyc2 and OmpB. Genome-enabled metabolic reconstruction revealed that this Gallionellaceae sp. lacks nitric oxide and nitrous oxide reductase genes and may partner with flanking populations capable of complete denitrification to avoid toxic metabolite accumulation, which may explain its resistance to growth in pure culture. This and other revealed interspecies interactions and metabolic interdependencies in nitrogen and carbon metabolisms may allow these organisms to cooperate effectively to achieve robust chemolithoautotrophic NDFO. Overall, the results significantly expand our knowledge of NDFO and suggest a range of genetic targets for further exploration.

Metagenomic Analyses of the Autotrophic Fe(II)-Oxidizing, Nitrate-Reducing Enrichment Culture KS

The paralytic shellfish poisoning toxins (PSTs) were, as their name suggests, discovered as a result of human poisoning after consumption of contaminated shellfish. More recently, however, the same toxins have been found to be produced by freshwater cyanobacteria. These organisms have worldwide distribution and are common in our sources of drinking water, thus presenting another route of potential human exposure. However, the regulatory limits for PSTs in drinking water are considerably lower than in shellfish. This has increased the need to find alternatives to the mouse bioassay, which, apart from being ethically questionable, does not have a limit of detection capable of detecting the PSTs in water at the regulated concentrations. Additionally, the number of naturally occurring PSTs has grown substantially since saxitoxin was first characterised, markedly increasing the analytical challenge of this group of compounds. This paper summarises the development of chromatographic, toxicity, and molecular sensor binding methodologies for detection of the PSTs in shellfish, cyanobacteria, and water contaminated by these toxins. It then summarises the advantages and disadvantages of their use for particular applications. Finally it recommends some future requirements that will contribute to their improvement for these applications.

/pdf/comparison-of-analytical-tools-and-biological-assays-for-4unnm77vzt.pdf

Comparison of analytical tools and biological assays for detection of paralytic shellfish poisoning toxins.

Cell adhesion to the extracellular matrix is essential for cellular processes, such as migration and invasion. In response to cues from the microenvironment, integrin-mediated adhesions alter cellular behaviour through cytoskeletal rearrangements. The tight association of the actin cytoskeleton with adhesive structures has been extensively studied, whereas the microtubule network in this context has gathered far less attention. In recent years, however, microtubules have emerged as key regulators of cell adhesion and migration through their participation in adhesion turnover and cellular signalling. In this Review, we focus on the interactions between microtubules and integrin-mediated adhesions, in particular, focal adhesions and podosomes. Starting with the association of microtubules with these adhesive structures, we describe the classical role of microtubules in vesicular trafficking, which is involved in the turnover of cell adhesions, before discussing how microtubules can also influence the actin-focal adhesion interplay through RhoGTPase signalling, thereby orchestrating a very crucial crosstalk between the cytoskeletal networks and adhesions.

Microtubules at focal adhesions - a double-edged sword

Purpose: The membrane of erythrocyte can be affected by consumption of bioactive compounds from herbs and medicinal plants. Hemolytic activities of nine extracts from different species on human erythrocytes were investigated. Methods: The toxicity of methanolic extracts of nine plants from arid and sub-arid area on human erythrocytes was measured by in vitro hemolytic assay. The absorbance of hemoglobin release was read by spectrophotometer at 540 nm. Results: our results show that hemolytic activity in all extracts is not more than15% and not significant alteration on erythrocyte membrane was observed at low concentrations while hemolytic activity is concentration-dependent. Hemolytic effect was amplified at increased concentration and it is function of extract. The higher hemolytic activity is showing with extract from the Saharan species Morettia canescens (14.80%). In addition, none hemolytic activity was observed against human erythrocytes with Paronychia chlorothyrsa extract. The present study show that majority of extracts of different plants manifest hemolytic activity < 15%. Conclusion: These results explain that parameters of red blood membrane cell are not altered if therapeutic formulations from these plants are used at low concentration, but a great attention will take with greatest concentrations.

/pdf/hemolytic-activity-of-different-herbal-extracts-used-in-2azbtp67fy.pdf

Hemolytic activity of different herbal extracts used in Algeria

Cell Biology: Structure, Biochemistry and Function

CELLS AND CELL GROWTH: The Cell: An Introduction Cell Growth and Proliferation MOLECULAR CONSTITUENTS OF CELLS: Cellular Chemistry The Cellular Macromolecules: Proteins The Cellular Macromolecules: Polysaccharides The Cellular Macromolecules: Lipids The Cellular Macromolecules: Nucleic Acids CELL METABOLISM: Enzymes Bioenergetics Cell Metabolism Metabolic Regulation TOOLS AND METHODS OF CELL BIOLOGY: Fractionation of Tissues and Cells The Isolation and Characterization of Cellular Macromolecules Radioactive Isotopes as Tracers in Cell Biology STRUCTURE AND FUNCTION OF THE MAJOR CELL ORGANELLES: The Plasma Membrane and the Endoplasmic Reticulum The Mitochondrion The Chloroplast The Golgi Apparatus Lysosomes and Microbodies The Nucleus: Organization and Division The Nucleus and Molecular Genetics Ribosomes and the Synthesis of Proteins The Cytoplasmic Matrix SPECIAL CELL FUNCTIONS: Cellular Differentiation and Specialization Immunity and Cancer.

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Cell Biology: Structure, Biochemistry and Function

Cell and Molecular Biology