Multiplex de novo sequencing of peptide antibiotics

Proliferation of drug-resistant diseases raises the challenge of searching for new, more efficient antibiotics. Currently, some of the most effective antibiotics (i.e., Vancomycin and Daptomycin) are cyclic peptides produced by non-ribosomal biosynthetic pathways. The isolation and sequencing of cyclic peptide antibiotics, unlike the same activity with linear peptides, is time-consuming and error-prone. The dominant technique for sequencing cyclic peptides is nuclear magnetic resonance (NMR)-based and requires large amounts (milligrams) of purified materials that, for most compounds, are not possible to obtain. Given these facts, there is a need for new tools to sequence cyclic non-ribosomal peptides (NRPs) using picograms of material. Since nearly all cyclic NRPs are produced along with related analogs, we develop a mass spectrometry approach for sequencing all related peptides at once (in contrast to the existing approach that analyzes individual peptides). Our results suggest that instead of attempting to isolate and NMR-sequence the most abundant compound, one should acquire spectra of many related compounds and sequence all of them simultaneously using tandem mass spectrometry. We illustrate applications of this approach by sequencing new variants of cyclic peptide antibiotics from Bacillus brevis, as well as sequencing a previously unknown family of cyclic NRPs produced by marine bacteria. Supplementary Material is available online at www.liebertonline.com/cmb.     

Neurofeedback Training for Opiate Addiction: Improvement of Mental Health and Craving

Psychological improvements in patients with substance use disorders have been reported after neurofeedback treatment. However, neurofeedback has not been commonly accepted as a treatment for substance dependence. This study was carried out to examine the effectiveness of this therapeutic method for opiate dependence disorder. The specific aim was to investigate whether treatment leads to any changes in mental health and substance craving. In this experimental study with a pre-post test design, 20 opiate dependent patients undergoing Methadone or Buprenorphine maintenance treatment were examined and matched and randomized into two groups. While both experimental and control groups received their usual maintenance treatment, the experimental group received 30 sessions of neurofeedback treatment in addition. The neurofeedback treatment consisted of sensory motor rhythm training on Cz, followed by an alpha-theta protocol on Pz. Data from the general health questionnaire and a heroin craving questionnaire were collected before and after treatment. Multivariate analysis of covariance showed that the experimental group achieved improvement in somatic symptoms, depression, and total score in general mental health; and in anticipation of positive outcome, desire to use opioid, and relief from withdrawal of craving in comparison with the control group. The study supports the effectiveness of neurofeedback training as a therapeutic method in opiate dependence disorder, in supplement to pharmacotherapy.     

Monte Carlo characterizations mapping of the (γ,n) and (n,γ) photonuclear reactions in the high energy X-ray radiation therapy

Aim

The aim of this work was to map the characteristics of (n,γ) and (γ,n) reactions in a high energy photon radiation therapy.

Background

Photoneutrons produced in the high energy X-Ray radiation therapy may damage patients and staff. It is due to high RBE of the produced neutrons according to their energy and isotropic emission. Characterization of the photoneutrons can help us in appropriate shielding.

Materials and methods

This study focused on the photoneutron and capture gamma ray phenomena. Characteristics such as dose value, fluence and spectra of both the neutrons and the by produced prompt gamma ray were described.

Results and discussion

Neutron and prompt gamma spectra in different points showed the neutrons to be thermalized when increasing the distance from the linac. Energy of the neutrons changed from about 0.6 MeV at the isocentre to around 10⁻⁰⁸ MeV at the outer door position. Although the neutrons were found as fast neutrons, their spectra showed they were thermal neutrons at the outer door position. Additionally, it was seen that the energy of the gamma rays is higher than the scattered X-ray energy. The energy of gamma rays was seen to be up to 10 MeV while the linac photons had energy lower than 1 MeV. Neutron source strength obtained in this work was in good agreement with the published data, which may be a confirmation of our simulation accuracy.

Conclusion

The study showed that the Monte Carlo simulation can be applied in the radiotherapy and industrial radiation works as a useful and precise estimator. We also concluded that the dose from the prompt gamma ray at the outer door location is higher than the scattered radiation from the linac and should be considered in the shielding.     

Response of macroinvertebrate communities to anthropogenic pressures in Tajan River (Iran)

The Tajan River was investigated for one year in seven stations, analyzing the relationships between physical properties, water chemistry and aquatic macroinvertebrates. Biotic and diversity indices were compared with canonical unconstrained (CA) and constrained (CCA) ordination to test different methods able to estimate river ecology status. An upstream-downstream gradient was emphasized, in presence of anthropogenic stressors, coming from trout farms, paper factory, agriculture, urbanization, river regulation; the first CCA axis emphasized a natural gradient, bound to altitude, source distance, water temperature, the second CCA axis a pollution gradient. Biotic and diversity indices detected three polluted stations: S3, downstream the Korcha tributary, S6 downstream a paper factory and S7 situated after the Sari town. S4 showed high macroinvertebrates densities, which were attributed to the presence of a dam. Both multimetric and multivariate methods emphasized the need to separate the influence of natural variables from anthropogenic stressors in the Tajan River. To separate the influence of longitudinal gradient from the influence of pollution, it was suggested to evaluate the anthropogenic impact as deviation from a regression line, considering a multimetric index as dependent variable and source distance as predictor variable. The definition of reference sites was problematic in this poorly investigated area and a progress in taxonomic resolution is in any case recommended to better define the ecological status of these waters.     

Identification of Druggable Cancer Driver Genes Amplified across TCGA Datasets

The Cancer Genome Atlas (TCGA) projects have advanced our understanding of the driver mutations, genetic backgrounds, and key pathways activated across cancer types. Analysis of TCGA datasets have mostly focused on somatic mutations and translocations, with less emphasis placed on gene amplifications. Here we describe a bioinformatics screening strategy to identify putative cancer driver genes amplified across TCGA datasets. We carried out GISTIC2 analysis of TCGA datasets spanning 14 cancer subtypes and identified 461 genes that were amplified in two or more datasets. The list was narrowed to 73 cancer-associated genes with potential “druggable” properties. The majority of the genes were localized to 14 amplicons spread across the genome. To identify potential cancer driver genes, we analyzed gene copy number and mRNA expression data from individual patient samples and identified 40 putative cancer driver genes linked to diverse oncogenic processes. Oncogenic activity was further validated by siRNA/shRNA knockdown and by referencing the Project Achilles datasets. The amplified genes represented a number of gene families, including epigenetic regulators, cell cycle-associated genes, DNA damage response/repair genes, metabolic regulators, and genes linked to the Wnt, Notch, Hedgehog, JAK/STAT, NF-KB and MAPK signaling pathways. Among the 40 putative driver genes were known driver genes, such as EGFR, ERBB2 and PIK3CA. Wild-type KRAS was amplified in several cancer types, and KRAS-amplified cancer cell lines were most sensitive to KRAS shRNA, suggesting that KRAS amplification was an independent oncogenic event. A number of MAP kinase adapters were co-amplified with their receptor tyrosine kinases, such as the FGFR adapter FRS2 and the EGFR family adapter GRB7. The ubiquitin-like ligase DCUN1D1 and the histone methyltransferase NSD3 were also identified as novel putative cancer driver genes. We discuss the patient tailoring implications for existing cancer drug targets and we further discuss potential novel opportunities for drug discovery efforts.     

Size Control in the Nanoprecipitation Process of Stable Iodine (127I) Using Microchannel Reactor—Optimization by Artificial Neural Networks

In this study, nanosuspension of stable iodine (¹²⁷I) was prepared by nanoprecipitation process in microfluidic devices. Then, size of particles was optimized using artificial neural networks (ANNs) modeling. The size of prepared particles was evaluated by dynamic light scattering. The response surfaces obtained from ANNs model illustrated the determining effect of input variables (solvent and antisolvent flow rate, surfactant concentration, and solvent temperature) on the output variable (nanoparticle size). Comparing the 3D graphs revealed that solvent and antisolvent flow rate had reverse relation with size of nanoparticles. Also, those graphs indicated that the solvent temperature at low values had an indirect relation with size of stable iodine (¹²⁷I) nanoparticles, while at the high values, a direct relation was observed. In addition, it was found that the effect of surfactant concentration on particle size in the nanosuspension of stable iodine (¹²⁷I) was depended on the solvent temperature.

Graphical Abstract

Open in a separate windowNanoprecipitation process of stable iodine (127I) and optimization of particle size using ANNs modeling.KEY WORDS: ANNs, microfluidic, nanoprecipitation, particle size, stable iodine     

Concentration and distribution characteristics of airborne fungi in indoor and outdoor air of Tehran subway stations

The concentration and distribution characteristics of airborne fungi were investigated in indoor and outdoor air of two metro stations (Imam Khomeini and Sadeghiyeh stations) in Tehran subway. Samples were taken from indoor air at each station from platform and ticket office area also from adjacent outdoor air of each station. Indoor sampling was conducted for two types of trains, old and new. The concentration of airborne fungi ranged from 21 CFU/m³ at the outdoor air of Imam Khomeini station to 1,402 CFU/m³ in the air samples collected from the platform of this station. Results showed that airborne fungi concentrations at indoor air were higher than the outdoor air (p < 0.05), and fungal levels significantly correlated with the number of passengers (p < 0.05; r = 0.68) and RH % (p < 0.05; r = 0.43). Sixteen genera of fungi were isolated in all sampled environments. The predominant genera identified in indoor and outdoor air were Penicillium spp. (34.88 % of total airborne fungi) and Alternaria spp. (29.33 % of total airborne fungi), respectively. The results of this study showed that the indoor air quality in subway is worse than the outdoor air.     

Spatial distributions of the red palm mite, Raoiella indica (Acari: Tenuipalpidae) on coconut and their implications for development of efficient sampling plans

The red palm mite (Raoiella indica), an invasive pest of coconut, entered the Western hemisphere in 2004, then rapidly spread through the Caribbean and into Florida, USA. Developing effective sampling methods may aid in the timely detection of the pest in a new area. Studies were conducted to provide and compare intra tree spatial distribution of red palm mite populations on coconut in two different geographical areas, Trinidad and Puerto Rico, recently invaded by the mite. The middle stratum of a palm hosted significantly more mites than fronds from the upper or lower canopy and fronds from the lower stratum, on average, had significantly fewer mites than the two other strata. The mite populations did not vary within a frond. Mite densities on the top section of the pinna had significantly lower mite densities than the two other sections, which were not significantly different from each other. In order to improve future sampling plans for the red palm mite, the data was used to estimate the variance components associated with the various levels of the hierarchical sampling design. Additionally, presence-absence data were used to investigate the probability of no mites being present in a pinna section randomly chosen from a frond inhabited by mites at a certain density. Our results show that the most precise density estimate at the plantation level is to sample one pinna section per tree from as many trees as possible.