gamma-Turn types prediction in proteins using the support vector machines

Recently, two different models have been developed for predicting gamma-turns in proteins by Kaur and Raghava [2002. An evaluation of beta-turn prediction methods. Bioinformatics 18, 1508-1514; 2003. A neural-network based method for prediction of gamma-turns in proteins from multiple sequence alignment. Protein Sci. 12, 923-929]. However, the major limitation of previous methods is inability in predicting gamma-turns types. Thus, there is a need to predict gamma-turn types using an approach which will be useful in overall tertiary structure prediction. In this work, support vector machines (SVMs), a powerful model is proposed for predicting gamma-turn types in proteins. The high rates of prediction accuracy showed that the formation of gamma-turn types is evidently correlated with the sequence of tripeptides, and hence can be approximately predicted based on the sequence information of the tripeptides alone.     

Toward nanoscale genome sequencing

This article reports on the state-of-the-art technologies that sequence DNA using miniaturized devices. The article considers the miniaturization of existing technologies for sequencing DNA and the opportunities for cost reduction that 'on-chip' devices can deliver. The ability to construct nano-scale structures and perform measurements using novel nano-scale effects has provided new opportunities to identify nucleotides directly using physical, and not chemical, methods. The challenges that these technologies need to overcome to provide a US$1000-genome sequencing technology are also presented.     

Biophysical characterization of an integrin-targeted lipopolyplex gene delivery vector

Nonviral gene delivery vectors now show good therapeutic potential: however, detailed characterization of the composition and macromolecular organization of such particles remains a challenge. This paper describes experiments to elucidate the structure of a ternary, targeted, lipopolyplex synthetic vector, the LID complex. This consists of a lipid component, Lipofectin (L) (1:1 DOTMA:DOPE), plasmid DNA (D), and a dual-function, cationic peptide component (I) containing DNA condensation and integrin-targeting sequences. Fluorophore-labeled lipid, peptide, and DNA components were used to formulate the vector, and the stoichiometry of the particles was established by fluorescence correlation spectroscopy (FCS). The size of the complex was measured by FCS, and the sizes of LID, L, LD, and ID complexes were measured by dynamic light scattering (DLS). Fluorescence quenching experiments and freeze-fracture electron microscopy were then used to demonstrate the arrangement of the lipid, peptide, and DNA components within the complex. These experiments showed that the cationic portion of the peptide, I, interacts with the plasmid DNA, resulting in a tightly condensed DNA-peptide inner core; this is surrounded by a disordered lipid layer, from which the integrin-targeting sequence of the peptide partially protrudes.     

Development of fast Fourier transformation continuous cyclic voltammetry as a highly sensitive detection system for ultra trace monitoring of penicillin V

Fast continuous cyclic voltammetry was used as a detection method for penicillin V in a flow injection system. Additionally, a special computer-based numerical calculation method (using fast Fourier transformation) providing enhancement of the analyte signal and noise reduction is introduced here. During the measurements, the potential waveform (consisting of the potential steps of cleaning, stripping, and the potential ramp) was continuously applied to an Au disk microelectrode (12.5 microm in radius). In particular, the effects of accumulation potential, sweep rate, and delay time on the sensitivity and selectivity of the method were investigated. Eventually, the stripping time was found to be less than 300 ms, the detection limit of the method was 7.0x10(-12) M, and the associated relative standard deviation at 5.0x10(-6) M penicillin V was 2.3 for eight runs.     

Targeting lipopolyplexes using bifunctional peptides incorporating hydrophobic spacer amino acids: synthesis, transfection, and biophysical studies

We have developed efficient synthetic routes to two hydrophobic amino acids, suitably protected for solid-phase peptide synthesis, and have successfully synthesized peptides containing these or other hydrophobic amino acids as spacers between a Lys16 moiety and an integrin-targeting motif. These peptides have in turn been used to formulate a range of lipopolyplex vectors with Lipofectin and plasmid DNA. The transfection efficiencies of these vectors and their aggregation behavior in buffers and in serum have been studied. We have shown that vectors containing peptides incorporating long linkers that are entirely hydrophobic are less efficient transfection agents. However, linkers of equivalent length that are in part hydrophobic show improved transfection properties, which is probably due to the improved accessibility of the integrin-binding motif.     

Importance of probiotics in the prevention and treatment of colorectal cancer

Colorectal cancer (CRC) remains one of the most common and deadly cancers. Intestinal gut microflora is important to maintain and contributes to several intestinal functions, including the development of the mucosal immune system, absorption of complex macromolecules, synthesis of amino acids/vitamins and the protection against pathogenic microorganisms. It is well known that the gut microbiota changes or dysbiosis may have an essential impact in the initiation and promotion of chronic inflammatory pathways and also have a profound different genetic and epigenetic alterations leading to dysplasia, clonal expansion, and malignant transformation. Probiotic bacteria has antitumor activity with various mechanisms such as nonspecific physiological and immunological mechanisms. This review evaluates the effects of microbiota and probiotics in clinical trials, in vitro and animal model studies that have explored how probiotic against cancer development and also discusses the possible immunomodulatory mechanisms. Several mechanisms alteration of the intestinal microflora; inactivation of cancerogenic compounds; competition with putrefactive and pathogenic microbiota; improvement of the host's immune response; antiproliferative effects via regulation of apoptosis and cell differentiation; fermentation of undigested food; inhibition of tyrosine kinase; reduces the enteropathogenic complications before and after colon cancer surgery and improve diarrhea and it's have been able to create the integrity of gut mucosal and have stimulatory effects on the systemic immune system and prevent the CRC metastasis. Research in clinical trials encouraging findings that support a role of probiotics in CRC prevention and improve the safety and effectiveness of cancer therapy even though additional clinical research is still necessary.     

Concurrence of ionic homeostasis alteration and dry mass sustainment in emmer wheats exposed to saline water: implications for tackling irrigation water salinity

Plant and Soil - Dicranopteris linearis is a fern that accumulates unusually high concentrations (up to 0.3% dry weight) of rare earth elements (REEs) in China. Previously, we reported that D....