UV Spectra and Excitation Delocalization in DNA: Influence of the Spectral Width

The singlet excited states of the model DNA duplex (dA)10.(dT)10 are studied. Calculations are performed in the exciton theory framework. Molecular dynamics calculations provide the duplex geometry. The dipolar coupling is determined using atomic transition charges. The monomer transition energies are simulated by Gaussian functions resembling the absorption bands of nucleosides in aqueous solutions. Most of the excited states are found to be delocalized over at least two bases and result from the mixing of different monomer states. Their properties are only weakly affected by conformational changes of the double helix. On average, the highest oscillator strength is carried by the upper eigenstates. The duplex absorption spectra are shifted a few nanometers to higher energies with respect to the spectra of noninteracting monomers. The states with larger spatial extent are located close to the maximum of the absorption spectrum

Exciton States of Dynamic DNA Double Helices: Alternating dCdG Sequences

The present communication deals with the excited states of the alternating DNA oligomer (dCdG)5·(dCdG)5 which correspond to the UV absorption band around 260 nm. Their properties are studied in the frame of the exciton theory, combining molecular dynamics simulations and quantum chemistry data. It is shown that the dipolar coupling undergoes important variations with the site and the helix geometry. In contrast, the energy of the monomer transitions within the double helix is not sensitive to the local environment. It is thus considered to be distributed over Gaussian curves whose maximum and width are derived from the experimental absorption spectra of nucleosides in aqueous solution. The influence of the spectral width on the excited state delocalization and the absorption spectra is much stronger than that of the oligomer plasticity. About half of the excited states are delocalized over at least two bases. Many of them result from the mixing of different monomer states and extend on both strands. The trends found in the simulated spectra, when going from non-interacting monomers to the duplex, are in agreement with experimental observations. Conformational changes enhance the diversity of the states which can be populated upon excitation at a given energy. The states with larger spatial extent are located close to the maximum of the absorption spectrum

Hachimoji DNA and RNA: A genetic system with eight building blocks

Reported here are DNA and RNA-like systems built from eight (hachi-) nucleotide letters (-moji) that form four orthogonal pairs. This synthetic genetic biopolymer meets the structural requirements needed to support Darwinism, including a polyelectrolyte backbone, predictable thermodynamic stability, and stereoregular building blocks that fit a Schrödinger aperiodic crystal. Measured thermodynamic parameters predict the stability of hachimoji duplexes, allowing hachimoji DNA to double the information density of natural terran DNA. Three crystal structures show that the synthetic building blocks do not perturb the aperiodic crystal seen in the DNA double helix. Hachimoji DNA was then transcribed to give hachimoji RNA in the form of a functioning fluorescent hachimoji aptamer. These results expand the scope of molecular structures that might support life, including life throughout the cosmos

A Comparative Analysis of Print-Of-View Modeling For Industrial and Technology Education Courses

(First paragraph): Enrollment in technology education at the college level has been declining (Isbell & Lovedahl, 1989; Volk, 1997; Daugherty, 1998; Hill, 1999; Ndahi & Ritz, 2003; Moye, 2009). It is essential for technology teacher educators to investigate ways to increase the enrollment in their programs, or the profession may fail to provide technology teachers in the future (Ndahi & Ritz, 2003). A solution that several institutions with technology education programs have adopted is the offering of the program via distance learning. Distance learning “allows participants to collapse time and space” (Cole, 2000, p. ix). According to Flowers (2003) technology education programs “with a history of hands-on learning at the undergraduate level” have been slow to implement distance learning techniques and strategies (p. 64). Therefore, it is important to explore the extent to which distance-learning technologies such as video modeling can be used by industrial and technical teacher education faculty. The intention of this study is to add to the body of knowledge on effective video modeling procedures and, in particular, the point of view used when recording instructional videos

A host–guest approach for determining drug–DNA interactions: an example using netropsin

Netropsin is a well-characterized DNA minor groove binding compound that serves as a model for the study of drug–DNA interactions. Our laboratory has developed a novel host–guest approach to study drug–DNA interactions in which the host, the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase (MMLV RT) is co-crystallized with a DNA oligonucleotide guest in the presence and absence of drug. We have co-crystallized netropsin with the RT fragment bound to the symmetric 16mer d(CTTAATTCGAATTAAG)(2) and determined the structure of the complex at 1.85 Å. In contrast to previously reported netropsin–DNA structures, our oligonucleotide contains two AATT sites that bind netropsin with flanking 5′ and 3′ sequences that are not symmetric. The asymmetric unit of the RT fragment–DNA–netropsin crystals contains one protein molecule and one-half of the 16mer with one netropsin molecule bound. The guanidinium moiety of netropsin binds in a narrow part of the minor groove, while the amidinium is bound in the widest region within the site. We compare this structure to other Class I netropsin–DNA structures and find that the asymmetry of minor groove widths in the AATT site contributes to the orientation of netropsin within the groove while hydrogen bonding patterns vary in the different structures

A European lens upon adult and lifelong learning in Asia

In this article, we seek to assess the extent to which adult and lifelong learning policies and practices in Asia have distinctiveness by comparison to those found in western societies, through an analysis of inter-governmental, national and regional policies in the field. We also inform our study through the analysis of the work of organisations with an international remit with a specific focus on Asia and Europe. In one case, the Asia–Europe Meeting Lifelong Learning (ASEM LLL) Hub has a specific function of bringing together researchers in Asia and Europe. In another, the PASCAL Observatory has had a particular focus on one aspect of lifelong learning, that of learning cities, with a concentration in its work on Asia and Europe. We focus on learning city development as a particular case of distinction in the field. We seek to identify the extent to which developments in the field in Asia have influenced and have been influenced by practices elsewhere in world, especially in Europe, and undertake our analysis using theories of societal learning/the learning society, learning communities and life-deep learning. We complement our analysis through assessment of material contained in three dominant journals in the field, the International Journal of Lifelong Education, the International Review of Education and Adult Education Quarterly, each edited in the west

Public drunkenness as a nuisance in Ghent (Belgium) and Trento (Italy)

This article explores the reality of the nuisance of public drunkenness in one nightlife location of Ghent (Belgium) and in one of Trento (Italy) and inspects the way alcohol-related disorder is viewed and tackled by police officers there. Drawing on the literature arguing for the existence of different "cultures of drinking" in western and southern European countries, a distinct reality of the nuisance of public drunkenness was hypothesized to be present in these two cities. Against the backdrop of cultural criminology scholarship and of the national literature on policing practices, it was expected that the physical/aesthetic appearance of street drinkers would differently impact on the way police officers there represent alcohol-related disorder and enforce national and local nuisance regulations. The gathered data indicate that while drinking patterns and connected disorderly behavior do not significantly vary in Ghent and in Trento, the aesthetic/physical characteristics of certain groups of people play a role in shaping the representations of some police officers in Trento. The study concludes that cultural and context-specific factors, including those linked to the cultures of drinking and to aesthetics, should be considered in criminological research to more fully understand and explain the different policing views on and attitudes to alcohol-related disorder in inner-city nightlife areas. In its conclusions, the article also highlights some directions for future research

Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms

© 2015 Kim, Nowack, Olsen, Becraft, Wood, Thiel, Klapper, Kühl, Fredrickson, Bryant, Ward and Metz. Dynamic environmental factors such as light, nutrients, salt, and temperature continuously affect chlorophototrophic microbial mats, requiring adaptive and acclimative responses to stabilize composition and function. Quantitative metabolomics analysis can provide insights into metabolite dynamics for understanding community response to such changing environmental conditions. In this study, we quantified volatile organic acids, polar metabolites (amino acids, glycolytic and citric acid cycle intermediates, nucleobases, nucleosides, and sugars), wax esters, and polyhydroxyalkanoates, resulting in the identification of 104 metabolites and related molecules in thermal chlorophototrophic microbial mat cores collected over a diel cycle in Mushroom Spring, Yellowstone National Park. A limited number of predominant taxa inhabit this community and their functional potentials have been previously identified through metagenomic and metatranscriptomic analyses and in situ metabolisms, and metabolic interactions among these taxa have been hypothesized. Our metabolomics results confirmed the diel cycling of photorespiration (e.g. glycolate) and fermentation (e.g. acetate, propionate, and lactate) products, the carbon storage polymers polyhydroxyalkanoates, and dissolved gases (e.g. H2 and CO2) in the waters overlying the mat, which were hypothesized to occur in major mat chlorophototrophic community members. In addition, we have formulated the following new hypotheses: 1) the morning hours are a time of biosynthesis of amino acids, DNA, and RNA; 2) photo-inhibited cells may also produce lactate via fermentation as an alternate metabolism; 3) glycolate and lactate are exchanged among Synechococcus and Roseiflexus spp.; and 4) fluctuations in many metabolite pools (e.g. wax esters) at different times of day result from species found at different depths within the mat responding to temporal differences in their niches

Hormonal Contraception Use is Common Among Patients with Inflammatory Bowel Diseases and an Elevated Risk of Deep Vein Thrombosis:

Persons with inflammatory bowel disease (IBD) have an increased risk of venous thromboembolism (VTE). We sought to examine whether self-report of hormonal contraception (HC), as a proxy for exposure to estrogen-based contraception, was less common for women with multiple risk factors for VTE

Cytomegalovirus viral load in the colon and risk of colectomy in hospitalized patients with inflammatory bowel diseases

To the Editor: We read with interest the article of Lee et al1 describing the risk factors for adverse outcomes in hospitalized patients with ulcerative colitis (UC) with concurrent cytomegalovirus (CMV) colitis. CMV reactivation and resolution can be spontaneous in patients with UC regardless of antiviral therapy; however, inconsistencies between CMV detection methods of various studies and criteria for defining CMV positivity may be leading to these disparate findings.2,3 In the study by Lee et al, CMV colitis was defined by the presence of 1 or more inclusion bodies on hematoxylin and eosin staining or CMV immunohistochemistry on colonic biopsies. The most accurate approach for detection of clinically significant CMV infection has not been firmly established and guidelines differ in their recommendations.3,4 A recent study using quantitative colonic PCR in consecutive patients with UC undergoing endoscopy in the setting of a moderate to severe flare demonstrated a correlation between higher viral load and resistance to immunosuppressive therapy with significant differences found when using a cutoff viral load of .250 per milligram tissue.