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[en] The structural analysis of glycoproteins is a challenging endeavor and is under steadily increasing demand, but only a very limited number of labs have the expertise required to accomplish this task. This tutorial is aimed at researchers from the fields of molecular biology and biochemistry that have discovered that glycoproteins are important in their biological research and are looking for the tools to elucidate their structure. It provides brief descriptions of the major and most common analytical techniques used in glycomics and glycoproteomics analysis, including explanations of the rationales for individual steps and references to published literature containing the experimental details necessary to carry out the analyses. Glycomics includes the comprehensive study of the structure and function of the glycans expressed in a given cell or organism along with identification of all the genes that encode glycoproteins and glycosyltransferases. Glycoproteomics which is subset of both glycomics and proteomics is the identification and characterization of proteins bearing carbohydrates as posttranslational modification. This tutorial is designed to ease entry into the glycomics and glycoproteomics field for those without prior carbohydrate analysis experience.
[en] A description of the upgraded beamline X25 at the NSLS, operated by the PXRR and the Photon Sciences Directorate serving the Macromolecular Crystallography community, is presented. Beamline X25 at the NSLS is one of the five beamlines dedicated to macromolecular crystallography operated by the Brookhaven National Laboratory Macromolecular Crystallography Research Resource group. This mini-gap insertion-device beamline has seen constant upgrades for the last seven years in order to achieve mini-beam capability down to 20 µm × 20 µm. All major components beginning with the radiation source, and continuing along the beamline and its experimental hutch, have changed to produce a state-of-the-art facility for the scientific community
[en] Recent progress in the determination of genomic sequences has yielded many millions of gene sequences. But what do these sequences tell us and what are the generalities and rules that are governed by them? It seems that we understand very little about genetic contexts required to ''read'' them. There is more to life than the genomic blueprint of each organism. Life functions within the natural laws that we know and the ones we do not know. Mathematics can be used to understand life from the molecular to the biosphere level. This paper provides a brief overview of major historical events of molecular biology and genetics, current interface of emerging field of bioinformatics, and future challenges and perspectives between mathematics and biology
[en] Crystal structures of a membrane protein transporter in three different conformational states provide insights into the transport mechanism. Secondary active transporters move molecules across cell membranes by coupling this process to the energetically favourable downhill movement of ions or protons along an electrochemical gradient. They function by the alternating access model of transport in which, through conformational changes, the substrate binding site alternately faces either side of the membrane. Owing to the difficulties in obtaining the crystal structure of a single transporter in different conformational states, relatively little structural information is known to explain how this process occurs. Here, the structure of the sodium-benzylhydantoin transporter, Mhp1, from Microbacterium liquefaciens, has been determined in three conformational states; from this a mechanism is proposed for switching from the outward-facing open conformation through an occluded structure to the inward-facing open state
[en] Hydration water is essential in determining the optimal conditions for the development of the biological activity of biological systems. Indeed the physical properties of hydration water are responsible for and determine the region of biological stability of proteins. By means of Nuclear Magnetic Resonance, we probe some thermodynamical properties of the first hydration shell of lysozyme from 200K to 360 K. In particular, we study the thermal behavior of the nuclear magnetization and of the apparent spin-spin relaxation time (T"∗_2 ). We find the existence of two thermal borders with two corresponding evident crossovers at low and high temperatures signaling the thresholds of the native state of lysozyme and therefore of its functionality.
[en] Mechanisms of phytoremediation in the uranium contaminated environment are described, and a worldwide overview of the content and progress of the related research topics is provided. Based on the analysis, it is pointed out that we should strengthen the research of plant-microbial coexistence system as well as the research of the related molecular biology and genetic engineering in order to enhance the phytoremediation's efficiency in the uranium contaminated environment. (authors)
[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)