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[en] Highlights: • Many methods available to graphically and numerically characterise DNA/RNA sequences. • We used 7 graphical representation methods to compute sequence descriptors. • Only 2 of 7 methods could discriminate between closely related genes, others broadly. • Implies that method to be chosen depends upon the nature of the application. • No single descriptor is universally applicable, need combined “super-descriptor”. - Abstract: Graphical representation methods constitute a class of alignment-free techniques for comparative study of biomolecular sequences. In this brief commentary, we study how well some of these methods can discriminate among closely related genes.
[en] The damage caused by ionizing radiation to DNA and proteins is the reason to treat cancer by radiation therapy. A better understanding of the molecular processes and quantification of the different damaging mechanisms is the prerequisite to develop more efficient therapies. Hereby the understanding of the processes involved in the damage to DNA are of key interest due to its central role in reproduction and mutation. Due to the high amount of water in biological tissue, most of the damage is caused by the secondary particles produced by scattering of the ionizing radiation with water. Thereby a multitude of species such as are produced, where especially kinetic low energy electrons, pre hydrated electrons, OH radicals and ions are of importance. The quantification of the contribution to DNA damage of these different species is of interest. Here we present an approach to disentangle their relative contributions to the DNA strand break yield. Experimentally it is based on the direct irradiation of DNA in liquid with high energy electrons by a scanning electron microscope. The plasmid DNA is irradiated in water with electrons under the presence of different scavengers. The presented results reveal the relative contributions of OH-radicals, low energy electrons and pre hydrated electrons to the DNA single and double strand break yield. (author)
[en] The marriage of biomolecular recognition and magnetic nanoparticle creates tremendous opportunities in the development of advanced technology both in academic research and in industrial sectors. In this paper, we review current progress on the magnetic nanoparticle-biomolecule hybrid systems, particularly employing the recognition pairs of DNA-DNA, DNA-protein, protein-protein, and protein-inorganics in several nanobiotechnology application areas, including molecular biology, diagnostics, medical treatment, industrial biocatalysts, and environmental separations.
[en] Natural products play a significant role in the design of anticancer drugs acting on DNA replication. Different classes of natural products include meroterpene, phenol, flavonoid and coumestan isolated from Psoralea corylifolia plant have been found active against cancer disease. DNA polymerase and topoisomerase are the important reported targets for cancer chemotherapy. In the present work, docking analysis of total fifteen different phenol-based (1-12) and furanocoumarin-based (13-15) natural products from P. corylifolia were studied against DNA polymerase α. The objective of this study was to find the potential binding residues of phenol-based inhibitors against DNA polymerase α. In the light of docking results, it can be suggested that crucial interactions of inhibitor’s phenolic group with the amino acid residues of DNA polymerase α are responsible for their activity. In particular, hydrogen bond interaction between phenol-based natural products with the carboxylate oxygen of Asp1004 residue is of prime importance as the mutated enzyme has no polymerase activity at all. Moreover, hydrophobic and π-π stacking interactions between phenol-based inhibitors and Tyr865, DG110, DG111, and DC11 side chains of DNA polymerase α are also observed which may play an additional role. It is further elucidated that furanocoumarin-based natural products did not show any significant interaction with the ASP1004 due to the absence of phenolic OH group. Docking results disclose the reason behind the activity of phenol-based and inactivity of furanocoumarin-based natural products against DNA polymerase α. (author)
[en] We present Farseer-NMR ( https://git.io/vAueU ), a software package to treat, evaluate and combine NMR spectroscopic data from sets of protein-derived peaklists covering a range of experimental conditions. The combined advances in NMR and molecular biology enable the study of complex biomolecular systems such as flexible proteins or large multibody complexes, which display a strong and functionally relevant response to their environmental conditions, e.g. the presence of ligands, site-directed mutations, post translational modifications, molecular crowders or the chemical composition of the solution. These advances have created a growing need to analyse those systems’ responses to multiple variables. The combined analysis of NMR peaklists from large and multivariable datasets has become a new bottleneck in the NMR analysis pipeline, whereby information-rich NMR-derived parameters have to be manually generated, which can be tedious, repetitive and prone to human error, or even unfeasible for very large datasets. There is a persistent gap in the development and distribution of software focused on peaklist treatment, analysis and representation, and specifically able to handle large multivariable datasets, which are becoming more commonplace. In this regard, Farseer-NMR aims to close this longstanding gap in the automated NMR user pipeline and, altogether, reduce the time burden of analysis of large sets of peaklists from days/weeks to seconds/minutes. We have implemented some of the most common, as well as new, routines for calculation of NMR parameters and several publication-quality plotting templates to improve NMR data representation. Farseer-NMR has been written entirely in Python and its modular code base enables facile extension.
[en] The land-hopper, Talitroides topitotum, is a talitrid amphipod distributed worldwide in subtropical and template regions, with a wide range of altitudinal distribution, temperature and humidity. Specimens were collected and processed since 2012 until 2016, by collection-filtration of wet substrates. Specimens were taxonomically identified using diagnostic phenotypic characteristics, and the developmental stage and sex were recorded. DNA was extracted from whole amphipods, followed by PCR of cytochrome oxidase subunit 1 and ribosomal RNA subunit 16S genes. Partial genetic sequences were obtained and a maximum-likelihood phylogenetic tree was calculated based on a GTR-GAMMA model. The analysis of potential distribution of T. topitotum was estimated using 19 bioclimatic variables. This study extends the previously reported distribution and elevations between 1900 and 595 m a.s.l. Thirty-nine localities were analyzed, where the following categories were registered: 1) T. topitotum is present, 2) terrestrial amphipods are not present, 3) T. topitotum is not present, but the native amphipod is present. The relative abundance of T. topitotum corresponds to adult females, a high proportion of juveniles and no males were collected. The bioinformatic analysis established the taxonomic position of T. topitotum within a group of terrestrial amphipods; moreover, the invasive species diverges of Cerrorchestia hyloraina, demonstrating the phylogenetic separation between these species that could be sharing habitats. Based on the model of maximum entropy, T. topitotum shows a high dispersion capacity and its establishment and propagation are been improved by climatic elements such as temperature, precipitation, humidity, and elevation. Our findings are relevant for management policies and monitoring the distribution of native species of terrestrial amphipods in the region.
[en] We review the status of protein-based molecular electronics. First, we define and discuss fundamental concepts of electron transfer and transport in and across proteins and proposed mechanisms for these processes. We then describe the immobilization of proteins to solid-state surfaces in both nanoscale and macroscopic approaches, and highlight how different methodologies can alter protein electronic properties. Because immobilizing proteins while retaining biological activity is crucial to the successful development of bioelectronic devices, we discuss this process at length. We briefly discuss computational predictions and their connection to experimental results. We then summarize how the biological activity of immobilized proteins is beneficial for bioelectronic devices, and how conductance measurements can shed light on protein properties. Finally, we consider how the research to date could influence the development of future bioelectronic devices. (review)
[en] Eleven indigenous arsenic-tolerant fungi were isolated from arsenic-contaminated mine tailing and identified by molecular biology methods. Among them, Aspergillus oryzae (denoted as A. oryzae TLWK-09) had high tolerance and bioaccumulation of As(V). The maximum tolerance to As(V) concentration of A. oryzae TLWK-09 reached 5000 mg/L. As(V) bioaccumulation on A. oryzae TLWK-09 in the aqueous system was investigated under different environmental conditions such as mycelia dosage, contact time, pH, and ionic strength. Bioaccumulation data of As(V) were fitted to Langmuir model, and the maximum uptake capacity of A. oryzae TLWK-09 for As(V) was 54.12 mg/g at 301 K. The morphological structures of mycelia changed obviously under As(V) stress by scanning electron microscope (SEM) and transmission electron microscope (TEM) analysis. The analysis of Fourier transform infrared spectroscopy (FTIR) indicated the presence of carboxyl, hydroxyl, and amino groups on the fungal mycelia, which showed that these groups accounted for As(V) bioaccumulation. These results suggested that A. oryzae TLWK-09 could be an efficient and promising bioremediation material for As(V) pollution.
[en] Adaptive landscapes represent a mapping between genotype and fitness. Rugged adaptive landscapes contain two or more adaptive peaks: allele combinations with higher fitness than any of their neighbors in the genetic space. How do populations evolve on such rugged landscapes? Evolutionary biologists have struggled with this question since it was first introduced in the 1930s by Sewall Wright. Discoveries in the fields of genetics and biochemistry inspired various mathematical models of adaptive landscapes. The development of landscape models led to numerous theoretical studies analyzing evolution on rugged landscapes under different biological conditions. The large body of theoretical work suggests that adaptive landscapes are major determinants of the progress and outcome of evolutionary processes. Recent technological advances in molecular biology and microbiology allow experimenters to measure adaptive values of large sets of allele combinations and construct empirical adaptive landscapes for the first time. Such empirical landscapes have already been generated in bacteria, yeast, viruses, and fungi, and are contributing to new insights about evolution on adaptive landscapes. In this Key Issues Review we will: (i) introduce the concept of adaptive landscapes; (ii) review the major theoretical studies of evolution on rugged landscapes; (iii) review some of the recently obtained empirical adaptive landscapes; (iv) discuss recent mathematical and statistical analyses motivated by empirical adaptive landscapes, as well as provide the reader with instructions and source code to implement simulations of evolution on adaptive landscapes; and (v) discuss possible future directions for this exciting field. (key issues review)
[en] Purpose: This study aimed to investigate in vivo effects of estradiol on the regulation of hepatic inducible nitric oxide synthase (iNOS) expression in the high fat (HF) diet-induced obesity. Also, we aimed to investigate whether activation of the extracellular signal-regulated kinase (ERK1/2), adenosine monophosphate-activated protein kinase (AMPK), Src kinase, and miR-221 is involved in estradiol-mediated regulation of iNOS in the liver of obese male Wistar rats. Male Wistar rats were fed a standard laboratory diet or a HF diet for 10 weeks. Half of HF rats were treated with estradiol intraperitoneally (40 μg/kg), whereas the other half were placebo-treated 24 H before euthanasia. Results show that estradiol treatment of HF rats decreased hepatic iNOS mRNA (P < 0.05) and protein expression (P < 0.01), the protein levels of p65 subunit of nuclear factor κB (P < 0.05) and ERα (P < 0.05), ERK1/2 phosphorylation (P < 0.001), and ERα/Src kinase association (P < 0.05). By contrast, hepatic Src protein level (P < 0.05), AMPKα phosphorylation (P < 0.05), and miR-221 expression (P < 0.05) were increased in HF rats after estradiol treatment. Our results indicate that estradiol in vivo regulates hepatic iNOS expression in obese rats via molecular mechanisms involving ERK1/2, AMPK, Src, and miR-221 signaling. © 2018 International Union of Biochemistry and Molecular Biology, Inc.