Not so crystal clear: the structure of the human telomere G-quadruplex in solution differs from that present in a crystal

The structure of human telomere DNA is of intense interest because of its role in the biology of both cancer and aging. The sequence [5′-AGGG(TTAGGG)(3)] has been used as a model for telomere DNA in both NMR and X-ray crystallographic studies, the results of which show dramatically different structures. In Na(+) solution, NMR revealed an antiparallel G-quadruplex structure that featured both diagonal and lateral TTA loops. Crystallographic studies in the presence of K(+) revealed a flattened, propeller-shaped structure featuring a parallel-stranded G-quadruplex with symmetrical external TTA loops. We report the results of biophysical experiments in solution and computational studies that are inconsistent with the reported crystal structure, indicating that a different structure exists in K(+) solutions. Sedimentation coefficients were determined experimentally in both Na(+) and K(+) solutions and were compared with values calculated using bead models for the reported NMR and crystal structures. Although the solution NMR structure accurately predicted the observed S-value in Na(+) solution, the crystal structure predicted an S-value that differed dramatically from that experimentally observed in K(+) solution. The environments of loop adenines were probed by quantitative fluorescence studies using strategic and systematic single-substitutions of 2-aminopurine for adenine bases. Both fluorescence intensity and quenching experiments in K(+) yielded results at odds with quantitative predictions from the reported crystal structure. Circular dichroism and fluorescence quenching studies in the presence of the crowding agent polyethylene glycol showed dramatic changes in the quadruplex structure in K(+) solutions, but not in Na(+) solutions, suggesting that the crystal environment may have selected for a particular conformational form. Molecular dynamics simulations were performed to yield model structures for the K(+) quadruplex form that are consistent with our biophysical results and with previously reported chemical modification studies. These models suggest that the biologically relevant structure of the human telomere quadruplex in K(+) solution is not the one determined in the published crystalline state

The spectral dimension of generic trees

We define generic ensembles of infinite trees. These are limits as $N\to\infty$ of ensembles of finite trees of fixed size $N$, defined in terms of a set of branching weights. Among these ensembles are those supported on trees with vertices of a uniformly bounded order. The associated probability measures are supported on trees with a single spine and Hausdorff dimension $d_h =2$. Our main result is that their spectral dimension is $d_s=4/3$, and that the critical exponent of the mass, defined as the exponential decay rate of the two-point function along the spine, is 1/3

A comparison of the CARATKids and CARAT10 questionnaires for the evaluation of control of asthma and allergic rhinitis in adolescents

[Excerpt] The Control of Allergic Rhinitis and Asthma Test (CARAT) was introduced to assess control of allergic rhinitis and asthma (ARA) simultaneously. It is the first tool to implement ARIA guidelines in clinical practice [1-5].CARAT10 was developed for adults [5], and CARATKids was designed for children aged 6 to 12 years [6]. There is no validated questionnaire to assess control of ARA in patients between the ages of 12 to 17 years.Financial support for this work was provided by FEDER funds through the Operational Programme Competitiveness Factors—COMPETE and National Funds through FCT— Foundation for Science and Technology under project POCI-01-0145-FEDER--007038 and project NORTE-01-0145-FEDER-000013, supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF)

Specific Soluble Oligomers of Amyloid-β Peptide Undergo Replication and Form Non-Fibrillar Aggregates in Interfacial Environments

Aggregates of amyloid-β (Aβ) peptides have been implicated in the etiology of Alzheimer disease. Among the different forms of Aβ aggregates, low molecular weight species ranging between ∼2- and 50-mers, also called “soluble oligomers,” have emerged as the species responsible for early synaptic dysfunction and neuronal loss. Emerging evidence suggests that the neurotoxic oligomers need not be formed along the obligatory nucleation-dependant fibril formation pathway. In our earlier work, we reported the isolation of one such “off-pathway” 12–18-mer species of Aβ42 generated from fatty acids called large fatty acid-derived oligomers (LFAOs) (Kumar, A., Bullard, R. L., Patel, P., Paslay, L. C., Singh, D., Bienkiewicz, E. A., Morgan, S. E., and Rangachari, V. (2011) PLoS One 6, e18759). Here, we report the physiochemical aspects of LFAO-monomer interactions as well as LFAO-LFAO associations in the presence of interfaces. We discovered that LFAOs are a replicating strain of oligomers that recruit Aβ42 monomers and quantitatively convert them into LFAO assemblies at the expense of fibrils, a mechanism similar to prion propagation. We also found that in the presence of hexane-buffer or chloroform-buffer interfaces LFAOs are able to associate with themselves to form larger but non-fibrillar aggregates. These results further support the hypothesis that low molecular weight oligomers can be generated via non-fibril formation pathways. Furthermore, the unique replicating property of off-pathway oligomers may hold profound significance for Alzheimer disease pathology

Plate versus bulk trolley food service in a hospital: comparison of patients’ satisfaction

Objective The aim of this research was to compare plate with bulk trolley food service in hospitals in terms of patient satisfaction. Key factors distinguishing satisfaction with each system would also be identified. Methods A consumer opinion card (n = 180), concentrating on the quality indicators of core foods, was used to measure patient satisfaction and compare two systems of delivery, plate and trolley. Binary logistic regression analysis was used to build a model that would predict food service style on the basis of the food attributes measured. Further investigation used multinomial logistic regression to predict opinion for the assessment of each food attribute within food service style. Results Results showed that the bulk trolley method of food distribution enables all foods to have a more acceptable texture, and for some foods (potato, P = 0.007; poached fish, P = 0.001; and minced beef, P ≤ 0.0005) temperature, and for other foods (broccoli, P ≤ 0.0005; carrots, P ≤ 0.0005; and poached fish, P = 0.001) flavor, than the plate system of delivery, where flavor is associated with bad opinion or dissatisfaction. A model was built indicating patient satisfaction with the two service systems. Conclusion This research confirms that patient satisfaction is enhanced by choice at the point of consumption (trolley system); however, portion size was not the controlling dimension. Temperature and texture were the most important attributes that measure patient satisfaction with food, thus defining the focus for hospital food service managers. To date, a model predicting patient satisfaction with the quality of food as served has not been proposed, and as such this work adds to the body of knowledge in this field. This report brings new information about the service style of dishes for improving the quality of food and thus enhancing patient satisfaction

Fisetin derivatives exhibit enhanced anti-inflammatory activity and modulation of endoplasmic reticulum stress

Fisetin (FST) is a dietary flavonol that is known to possess multiple relevant bioactivities, raising the question of its potential health benefits and even its use in novel pharmacological approaches. To attain this prospect, some limitations to this molecule, namely its poor bioavailability and solubility, must be addressed. Inflammation and endoplasmic reticulum (ER) stress are often hand in hand in the context of chronic disease. Both are activated upon perceived disturbances in homeostasis but can be deleterious when intensely or chronically activated. We have synthesized a set of FST derivatives trying to improve the biological properties of the parent molecule. These new molecules were tested along with the original compound for their ability to mitigate the activation of these signaling pathways. FST has proven to be effective against the onset of inflammation, reducing NF-κB activation, cytokine release, inflammasome activation and ROS generation, as well as decreasing the activation of the unfolded protein response (UPR). Some of the tested derivatives are also described as new caspase-1 inhibitors, being also capable of reducing pro-inflammatory cytokines and ER stress markers.(undefined

Folding and Hydrodynamics of a DNA i-Motif from the c-MYC Promoter Determined by Fluorescent Cytidine Analogs

AbstractThe four-stranded i-motif (iM) conformation of cytosine-rich DNA has importance to a wide variety of biochemical systems that range from their use in nanomaterials to potential roles in oncogene regulation. The iM structure is formed at slightly acidic pH, where hemiprotonation of cytosine results in a stable C-C+ basepair. Here, we performed fundamental studies to examine iM formation from a C-rich strand from the promoter of the human c-MYC gene. We used a number of biophysical techniques to characterize both the hydrodynamic properties and folding kinetics of a folded iM. Our hydrodynamic studies using fluorescence anisotropy decay and analytical ultracentrifugation show that the iM structure has a compact size in solution and displays the rigidity of a double strand. By studying the rates of circular dichroism spectral changes and quenching of fluorescent cytidine analogs, we also established a mechanism for the folding of a random coil oligo into the iM. In the course of determining this folding pathway, we established that the fluorescent dC analogs tC° and PdC can be used to monitor individual residues of an iM structure and to determine the pKa of an iM. We established that the C-C+ hydrogen bonding of certain bases initiates the folding of the iM structure. We also showed that substitutions in the loop regions of iMs give a distinctly different kinetic signature during folding compared with bases that are intercalated. Our data reveal that the iM passes through a distinct intermediate form between the unfolded and folded forms. Taken together, our results lay the foundation for using fluorescent dC analogs to follow structural changes during iM formation. Our technique may also be useful for examining folding and structural changes in more complex iMs

The occurrence of ecto-parasitic Leptus sp. mites on Africanised honey bees

Honey bee-mite-pathogen associations have led to the widespread collapse of Apis mellifera colonies in various parts of the world. The global trade in bees continues to expose honey bees to new pests and pathogens. Here we highlight to the beekeeping community a potential new mite-pathogen association. In South America ecto-parasitic Leptus mite larvae have been recorded parasitising adult honey bees and these mites are known to transmit Spiroplasma bacteria the causative agent of 'Mays disease' in bees. Here we provide new data and review past studies on Leptus mites and discuss the potential risk to A. mellifera this mite may pose in the future

The respiratory research agenda in primary care in Portugal: a Delphi study

Background: A research agenda can help to stimulate and guide research. The International Primary Care Respiratory Group (IPCRG) published a Research Needs Statement (RNS) in 2010 in which 145 research questions were identified. In 2012, priorities for respiratory research were established, based on these questions. To date, there has been no statement on primary care respiratory research needs in Portugal. The aim of the study was to develop a national consensus on research priorities in respiratory diseases in primary care in Portugal and to assess the applicability of the priorities for respiratory research set by the IPCRG. Method: We conducted a Delphi study by electronic mail with a panel of experts on respiratory disease from primary and secondary care in Portugal. In the first round, the research needs in respiratory disease in Portugal were identified. In the second round, 196 research questions in six disease areas, derived from the first round and from the IPCRG Respiratory needs statement, were prioritised on a five-point Likert-type scale. In the third round, the questions were prioritized again with feed-back provided on the median scores for each item in the second round. Consensus was considered to have been reached when 80 % of the participants gave a score of 4 or 5 out of five on a given item. Results: The 40 experts identified 121 respiratory research questions in Round 1 and expressed their views on 196 questions in Rounds 2 and 3. Twelve research questions (6 %) reached consensus. There were five questions in the asthma domain on early diagnosis, pulmonary function tests, the use of inhalers, and adherence to treatment. There were four questions in the chronic obstructive pulmonary disease domain on vaccinations, on routine monitoring and evaluation of treatment, on diagnosis, and on adherence to treatments. There was one question in the smoking domain on the effects of brief counselling. There were two questions on respiratory tract infections on the treatment of children and on the prescription of antibiotics. An additional 23 research questions (12 %) achieved consensus between 75 and 79 %. Conclusion: The results reflect the Portuguese reality in response the international agenda for research on respiratory diseases published by the IPCRG. They can support the development of future respiratory disease research in Portugal.Financial support for this work was provided by FEDER funds through the Operational Programme Competitiveness Factors - COMPETE and National Funds through FCT - Foundation for Science and Technology under the project POCI-01-0145-FEDER-007038; and by the project NORTE-01-0145-FEDER-000013, supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). PMT is partially supported by a grant from the International Primary Care Respiratory Group