Influence of base stacking and hydrogen bonding on the fluorescence of 2-aminopurine and pyrrolocytosine in nucleic acids

Fluorescent nucleobase analogues are used extensively to probe the structure and dynamics of nucleic acids. The fluorescence of the adenine analogue 2-aminopurine and the cytosine analogue pyrrolocytosine is significantly quenched when the bases are located in regions of double-stranded nucleic acids. To allow more detailed structural information to be obtained from fluorescence studies using these bases, we have studied the excited-state properties of the bases at the CIS and TDB3LYP level in hydrogen-bonded and base-stacked complexes. The results reveal that the first excited state (the fluorescent state) of a hydrogen-bonded complex containing 2-aminopurine and thymine is just the first excited state of 2-aminopurine alone. However, the same cannot be said for structures in which 2-aminopurine is base stacked with other nucleobases. Stacking causes the molecular orbitals involved in the fluorescence transition to spread over more than one base. The predicted rate for the fluorescence transition is reduced, thus reducing the fluorescence quantum yield. The decrease in radiative rate varies with the stacking arrangement (e.g., A- or B-form DNA) and with the identity of the nucleobase with which 2-aminopurine is stacked. Stacking 2-aminopurine between two guanine moieties is shown to significantly decrease the energy gap between the first and second excited states. We do not find reliable evidence for a low-energy charge-transfer state in any of the systems that were studied. In the case of pyrrolocytosine, base stacking was found to reduce the oscillator strength for the fluorescence transition, but very little spreading of molecular orbitals across more than one base was observed.     

The effects of chronic immune stimulation on muscle growth in rainbow trout

Successful production of aquaculture species depends on efficient growth with low susceptibility to disease. Therefore, selection programs have focused on rapid growth combined with disease resistance. However, chronic immune stimulation diminishes muscle growth (a syndrome referred to as cachexia), and decreases growth efficiency in production animals, including rainbow trout. In mammals, recent results show that increased levels of pro-inflammatory cytokines, such as those seen during an immune assault, specifically target myosin and MyoD and inhibit muscle growth. This suggests that increased disease resistance in fish, a desired trait for production, may actually decrease the growth of muscle, the main aquacultural commodity. To test this possibility, a rainbow trout model of cachexia was developed and characterized. A six-week study was conducted in which rainbow trout were chronically immune stimulated by repeated injections of LPS. Growth indices were monitored, and whole body and muscle proximate analyses, real-time PCR, and Western blotting were conducted to examine the resulting cachectic phenotype. Muscle ratio was decreased in fish chronically immunostimulated, however expression levels of MyoD2 and myosin were not decreased compared to fish that were not immunostimulated, indicating that while muscle accretion was altered, the mechanism by which it occurred was somewhat different than that characterized in mammals. Microarray analysis was used to compare gene expression in fish that had been chronically immunostimulated versus those that had not to identify possible alternative mechanisms of cachexia in fish.     

Quality control for terms and definitions in ontologies and taxonomies

Background  

Ontologies and taxonomies are among the most important computational resources for molecular biology and bioinformatics. A series of recent papers has shown that the Gene Ontology (GO), the most prominent taxonomic resource in these fields, is marked by flaws of certain characteristic types, which flow from a failure to address basic ontological principles. As yet, no methods have been proposed which would allow ontology curators to pinpoint flawed terms or definitions in ontologies in a systematic way.     

Are mild head injuries as mild as we think? Neurobehavioral concomitants of chronic post-concussion syndrome

Background  

Mild traumatic brain injury (MTBI) can sometimes lead to persistent postconcussion symptoms. One well accepted hypothesis claims that chronic PCS has a neural origin, and is related to neurobehavioral deficits. But the evidence is not conclusive. In the attempt to characterise chronic MTBI consequences, the present experiment used a group comparison design, which contrasted persons (a) with MTBI and PCS, (b) MTBI without PCS, and (c) matched controls. We predicted that participants who have experienced MTBI but show no signs of PCS would perform similar to controls. At the same time, a subgroup of MTBI participants would show PCS symptoms and only these volunteers would have poorer cognitive performance. Thereby, the performance deficits should be most noticeable in participants with highest PCS severity.     

Chloroplast division: a work of ARTEMIS

Chloroplasts contain three membrane systems that constrict together during division of the organelle. A newly identified protein, ARTEMIS, may shed light on the nuclear control of chloroplast division, and also on the mechanism of thylakoid membrane fission and how this is coordinated with fission of the two envelope membranes.     

Predictions of fate from rosette size in four “biennial” plant species: Verbascum thapsus,Oenothera biennis,Daucus carota,and Tragopogon dubius

Summary Individual plants were marked in field populations of four biennial plant species, Verbascum thapsus L., Oenothera biennis L., Daucus carota L., and Tragopogon dubius Scop., and followed for 2 or 3 years. The relationship of both rosette size and age to the probability of an individual dying, remaining vegetative, or flowering was determined for each species. In all four species, a minimum size must be reached before flowering can be induced and above that minimum the probability of flowering increases directly with rosette size. Conversely, the probability of dying decreases with increasing rosette size. In general, the fate of a rosette appears to be independent of its age although in populations where the probability of death is high for individuals above the minimum size for flowering, the age of a rosette may influence its fate to some extent.     

Extended scrapie incubation time in goats singly heterozygous for PRNP S146 or K222

Scrapie is the transmissible spongiform encephalopathy (TSE) of sheep and goats, and scrapie eradication in sheep is based in part on strong genetic resistance to classical scrapie. Goats may serve as a scrapie reservoir, and to date there has been no experimental inoculation confirming strong genetic resistance in goats. Two prion protein variants (amino acid substitutions S146 and K222) in goats have been significantly underrepresented in scrapie cases though present in scrapie-exposed flocks, and have demonstrated low cell-free protein conversion efficiency to the disease form (PrP(D)). To test degree of genetic resistance conferred in live animals with consistent exposure, we performed the first oral scrapie challenge of goats singly heterozygous for either PRNP S146 or K222. All N146-Q222 homozygotes became clinically scrapie positive by an average of 24months, but all S146 and K222 heterozygotes remain scrapie negative by both rectal biopsy and clinical signs at significantly longer incubation times (P<0.0001 for both comparisons). Recent reports indicate small numbers of S146 and K222 heterozygous goats have become naturally infected with scrapie, suggesting these alleles do not confer complete resistance in the heterozygous state but rather extend incubation. The oral challenge results presented here confirm extended incubation observed in a recent intracerebral challenge of K222 heterozygotes, and to our knowledge provide the first demonstration of extended incubation in S146 heterozygotes. These results suggest longer relevant trace-back histories in scrapie-eradication programs for animals bearing these alleles and strengthen the case for additional challenge experiments in both homozygotes to assess potential scrapie resistance.     

Characterizing upper limb muscle volume and strength in older adults: a comparison with young adults

Aging is associated with the loss of muscle volume (MV) and force leading to difficulties with activities of daily living. However, the relationship between upper limb MV and joint strength has not been characterized for older adults. Quantifying this relationship may help our understanding of the functional declines of the upper limb that older adults experience. Our objective was to assess the relationship between upper limb MV and maximal isometric joint moment-generating capacity (IJM) in a single cohort of healthy older adults (age ≥ 65 years) for 6 major functional groups (32 muscles). MV was determined from MRI for 18 participants (75.1±4.3 years). IJM at the shoulder (abduction/adduction), elbow (flexion/extension), and wrist (flexion/extension) was measured. MV and IJM measurements were compared to previous reports for young adults (28.6±4.5 years). On average older adults had 16.5% less total upper limb MV compared to young adults. Additionally, older adult wrist extensors composed a significantly increased percentage of upper limb MV. Older adult IJM was reduced across all joints, with significant differences for shoulder abductors (p<0.0001), adductors (p=0.01), and wrist flexors (p<0.0001). Young adults were strongest at the shoulder, which was not the case for older adults. In older adults, 40.6% of the variation in IJM was accounted for by MV changes (p≤0.027), compared to 81.0% in young adults. We conclude that for older adults, MV and IJM are, on average, reduced but the significant linear relationship between MV and IJM is maintained. These results suggest that older adult MV and IJM cannot be simply scaled from young adults.