Mapping DNA conformations and interactions within the binding cleft of bacteriophage T4 single-stranded DNA binding protein (gp32) at single nucleotide resolution

12 pagesIn this study, we use single-stranded DNA (oligo-dT) lattices that have been position-specifically labeled with monomer or dimer 2-aminopurine (2-AP) probes to map the local interactions of the DNA bases with the nucleic acid binding cleft of gp32, the single-stranded binding (ssb) protein of bacteriophage T4. Three complementary spectroscopic approaches are used to characterize these local interactions of the probes with nearby nucleotide bases and amino acid residues at varying levels of effective protein binding cooperativity, as manipulated by changing lattice length. These include: (i) examining local quenching and enhancing effects on the fluorescence spectra of monomer 2-AP probes at each position within the cleft; (ii) using acrylamide as a dynamic-quenching additive to measure solvent access to monomer 2-AP probes at each ssDNA position; and (iii) employing circular dichroism spectra to characterize changes in exciton coupling within 2-AP dimer probes at specific ssDNA positions within the protein cleft. The results are interpreted in part by what we know about the topology of the binding cleft from crystallographic studies of the DNA binding domain of gp32 and provide additional insights into how gp32 can manipulate the ssDNA chain at various steps of DNA replication and other processes of genome expression.NIH-NIGMS grant [GM-15792 to P.H.v.H., Andrew H. Marcus, co-PIs]; Dreyfus Senior Mentor Undergraduate Research Award (to P.H.v.H,) that provided partial support for B.C. and A.D.; Monmouth University Creativity and Research Grant (to D.J., in part). Funding for open access charge: University of Oregon Library System; NIH Grant

Macrosegregation During Dendritic Arrayed Growth of Hypoeutectic Pb-Sn Alloys: Influence of Primary Arm Spacing and Mushy Zone Length

Thermosolutal convection in the dendritic mushy zone occurs during directional solidification of hypoeutectic lead tin alloys in a positive thermal gradient, with the melt on the top and the solid below. This results in macrosegregation along the length of the solidified samples. The extent of macrosegregation increases with increasing primary dendrite spacings for constant mushy zone length. For constant primary spacings, the macrosegregation increases with decreasing mushy zone length. Presence of convection reduces the primary dendrite spacings. However, convection in the interdendritic melt has significantly more influence on the spacings as compared with that in the overlying melt, which is caused by the solutal buildup at the dendrite tips

Numerical study of Gezon experiment

International audienceTo prepare the microgravity experiment of crystal growth by floating zone method, GEZON, numerical studies of hydrodynamics of the melt are carried out. Calculations of zone length and convection driven by surface-tension gradients are presented for germanium floating zone operating under microgravity conditions. Results of linear stability analysis show the instability of intense thermocapillarity convection needed to be damped by using a magnetic field; the critical magnetic induction is obtained. it is expected to grow a striation-free crystal with this magnetic fiel

Advanced glycoxidation and lipoxidation end products (AGEs and ALEs): an overview of their mechanisms of formation

Advanced lipoxidation end products (ALEs) and advanced glycation end products (AGEs) have a pathogenetic role in the development and progression of different oxidative-based diseases including diabetes, atherosclerosis, and neurological disorders. AGEs and ALEs represent a quite complex class of compounds that are formed by different mechanisms, by heterogeneous precursors and that can be formed either exogenously or endogenously. There is a wide interest in AGEs and ALEs involving different aspects of research which are essentially focused on set-up and application of analytical strategies (1) to identify, characterize, and quantify AGEs and ALEs in different pathophysiological conditions ; (2) to elucidate the molecular basis of their biological effects ; and (3) to discover compounds able to inhibit AGEs/ALEs damaging effects not only as biological tools aimed at validating AGEs/ALEs as drug target, but also as promising drugs. All the above-mentioned research stages require a clear picture of the chemical formation of AGEs/ALEs but this is not simple, due to the complex and heterogeneous pathways, involving different precursors and mechanisms. In view of this intricate scenario, the aim of the present review is to group the main AGEs and ALEs and to describe, for each of them, the precursors and mechanisms of formation

Hydrogen storage in liquid hydrogen carriers: recent activities and new trends

Efficient storage of hydrogen is one of the biggest challenges towards a potential hydrogen economy. Hydrogen storage in liquid carriers is an attractive alternative to compression or liquefaction at low temperatures. Liquid carriers can be stored cost-effectively and transportation and distribution can be integrated into existing infrastructures. The development of efficient liquid carriers is part of the work of the International Energy Agency Task 40: Hydrogen-Based Energy Storage. Here, we report the state-of-the-art for ammonia and closed CO2-cycle methanol-based storage options as well for liquid organic hydrogen carriers

Scientific drilling projects in ancient lakes: integrating geological and biological histories

Sedimentary sequences in ancient or long-lived lakes can reach several thousands of meters in thickness and often provide an unrivalled perspective of the lake's regional climatic, environmental, and biological history. Over the last few years, deep drilling projects in ancient lakes became increasingly multi- and interdisciplinary, as, among others, seismological, sedimentological, biogeochemical, climatic, environmental, paleontological, and evolutionary information can be obtained from sediment cores. However, these multi- and interdisciplinary projects pose several challenges. The scientists involved typically approach problems from different scientific perspectives and backgrounds, and setting up the program requires clear communication and the alignment of interests. One of the most challenging tasks, besides the actual drilling operation, is to link diverse datasets with varying resolution, data quality, and age uncertainties to answer interdisciplinary questions synthetically and coherently. These problems are especially relevant when secondary data, i.e., datasets obtained independently of the drilling operation, are incorporated in analyses. Nonetheless, the inclusion of secondary information, such as isotopic data from fossils found in outcrops or genetic data from extant species, may help to achieve synthetic answers. Recent technological and methodological advances in paleolimnology are likely to increase the possibilities of integrating secondary information, e.g., through molecular dating of molecular phylogenies. Some of the new approaches have started to revolutionize scientific drilling in ancient lakes, but at the same time, they also add a new layer of complexity to the generation and analysis of sediment core data. The enhanced opportunities presented by new scientific approaches to study the paleolimnological history of these lakes, therefore, come at the expense of higher logistic, communication, and analytical efforts. Here we review types of data that can be obtained in ancient lake drilling projects and the analytical approaches that can be applied to empirically and statistically link diverse datasets for creating an integrative perspective on geological and biological data. In doing so, we highlight strengths and potential weaknesses of new methods and analyses, and provide recommendations for future interdisciplinary deep drilling projects

Reactive infiltration by Si: Infiltration versus wetting

International audienceThis paper focuses on spontaneous infiltration by liquid metals in reactive metal/ceramic systems. Two cases of reactive infiltration, where a molten silicon drop is in contact with two different porous bodies, graphite and (oxidized) silicon nitride, are briefly described and discussed. For each solid, the dynamics of wetting on the solid surface is compared to the dynamics of infiltration into the porou