Selected reading from Treatise on Friendship

Course reading ebook, adapted by Ian D. Dunkle from Project Gutenberg’s Treatises on Friendship and Old Age, by Marcus Tullius Cicero, translated by E.S. Shuckburgh: http://www.gutenberg.org/ebooks/2808Cicero describes the necessary features, the value, and the limits of friendship through a short dialogue

Deuterated nucleotides as chemical probes of RNA structure: a detailed protocol for the enzymatic synthesis of a complete set of nucleotides specifically deuterated at ribose carbons

We describe here a detailed protocol for the synthesis of ribonucleotides specifically deuterated at each ribose carbon atom. We synthesized 20 specifically deuterated ribonucleotides: ATP, CTP, GTP, and UTP, each of which contained one of five deuterated riboses (either 1′-D, 2″-D, 3′-D, 4′-D, or 5′,5″-D2). Our synthetic approach is inspired by the pioneering work of Tolbert and Williamson, who developed a method for the convenient one-pot enzymatic synthesis of nucleotides (Tolbert, T. J. and Williamson, J. R. (1996) J. Am. Chem. Soc. 118, 7929–7940). Our protocol consists of a comprehensive list of required chemical and enzymatic reagents and equipment, detailed procedures for enzymatic assays and nucleotide synthesis, and chromatographic procedures for purification of deuterated nucleotides. As an example of the utility of specifically deuterated nucleotides, we used them to synthesize specifically deuterated sarcin/ricin loop (SRL) RNA and measured the deuterium kinetic isotope effect on hydroxyl radical cleavage of the SRL.https://www.scienceopen.com/document/read?vid=eb44f1b0-c408-4336-a2c0-aed203250898Published versio

Informatics Inside : Grenzen überwinden - Virtualität erweitert Realität : Informatik-Konferenz an der Hochschule Reutlingen, 11. Mai 2011

Die Informatics Inside-Konferenz findet in diesem Jahr zum dritten Mal statt. Mit dem Thema "Grenzen überwinden – Virtualität erweitert Realität" stellt sich die Veranstaltung einem aktuellen Schwerpunkt, der viele Interessierte aus Wirtschaft, Wissenschaft und Forschung anzieht. Die Konferenz hat sich von einer Veranstaltung für die Masterstudenten des Studiengangs Medien- und Kommunikationsinformatik zu einer offenen Studentenkonferenz entwickelt. Um die Qualität weiter zu steigern wurde parallel dazu ein zweistufiges Review-Verfahren für Beiträge dieses Tagungsbandes eingeführt

Where Is Waldo? Visual search behavior in "Wimmelpictures"

In order to explore an image, the human eye functions like a spotlight, scanning the content from one object to the next. This visual search behavior is implemented with the help of attention control. The following work surveys the visual search behavior in "Wimmelpictures", a special type of busy pictures. The research objective is to analyze different search strategies and to work out possible differences concerning age and gender. The university experiment is carried out by an eye tracker that records the fixations and saccades of the test persons. The results indicate three forms of search strategy: based on a pattern, based on feature selection, or a mixture of both. Our data shows the search for special features of the target is the most successful. Furthermore there are no differences concerning gender but some concerning age. All age groups need more time to locate the target with an increasing number of distractors in the image. The size of the target is also relevant as a larger target is found more quickly than the smaller one

Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations

Recognition of DNA by proteins depends on DNA sequence and structure. Often unanswered is whether the structure of naked DNA persists in a protein–DNA complex, or whether protein binding changes DNA shape. While X-ray structures of protein–DNA complexes are numerous, the structure of naked cognate DNA is seldom available experimentally. We present here an experimental and computational analysis pipeline that uses hydroxyl radical cleavage to map, at single-nucleotide resolution, DNA minor groove width, a recognition feature widely exploited by proteins. For 11 protein–DNA complexes, we compared experimental maps of naked DNA minor groove width with minor groove width measured from X-ray co-crystal structures. Seven sites had similar minor groove widths as naked DNA and when bound to protein. For four sites, part of the DNA in the complex had the same structure as naked DNA, and part changed structure upon protein binding. We compared the experimental map with minor groove patterns of DNA predicted by two computational approaches, DNAshape and ORChID2, and found good but not perfect concordance with both. This experimental approach will be useful in mapping structures of DNA sequences for which high-resolution structural data are unavailable. This approach allows probing of protein family-dependent readout mechanisms.National Institutes of Health [R01GM106056 to R.R., T.D.T.; U54CA121852 in part to T.D.T.]; Boston University Undergraduate Research Opportunities Program [Faculty Matching Grants to D.O. and Y.J.]; USC Graduate School [Research Enhancement Fellowship and Manning Endowed Fellowship to T.P.C.]. R.R. is an Alfred P. Sloan Research Fellow. Funding for open access charge: Boston University. (R01GM106056 - National Institutes of Health; U54CA121852 - National Institutes of Health; Boston University Undergraduate Research Opportunities Program; USC Graduate School; Boston University)https://academic.oup.com/nar/article/46/5/2636/4829691?searchresult=1https://academic.oup.com/nar/article/46/5/2636/4829691?searchresult=1Published versio

Current status of vascularized composite tissue allotransplantation

Vascularized composite tissue allotransplantation (VCA) offers treatment options of complex functional deficiencies that cannot be repaired with conventional reconstructive methods. VCAs consist of blocks of functional units comprising different tissue types such as skin, bone, muscle, nerves, blood vessels, tendons, ligaments and others, and are thus substantially different from the composition of organ transplants. The field of VCA has made fascinating progresses in the recent past. Among other VCAs, numerous successful hand, face and limb transplants have been performed in the world. At the same time, specific questions in regard to innate and adaptive immunity, consequences of ischemia/reperfusion injury, immunosuppression, preservation, and regenerative capacity remain. In spite of this, the field is poised to make significant advances in the near future

Biomacromolecular stereostructure mediates mode hybridization in chiral plasmonic nanostructures

The refractive index sensitivity of plasmonic fields has been exploited for over 20 years in analytical technologies. While this sensitivity can be used to achieve attomole detection levels, they are in essence binary measurements that sense the presence/absence of a predetermined analyte. Using plasmonic fields, not to sense effective refractive indices but to provide more “granular” information about the structural characteristics of a medium, provides a more information rich output, which affords opportunities to create new powerful and flexible sensing technologies not limited by the need to synthesize chemical recognition elements. Here we report a new plasmonic phenomenon that is sensitive to the biomacromolecular structure without relying on measuring effective refractive indices. Chiral biomaterials mediate the hybridization of electric and magnetic modes of a chiral solid-inverse plasmonic structure, resulting in a measurable change in both reflectivity and chiroptical properties. The phenomenon originates from the electric-dipole–magnetic-dipole response of the biomaterial and is hence sensitive to biomacromolecular secondary structure providing unique fingerprints of α-helical, β-sheet, and disordered motifs. The phenomenon can be observed for subchiral plasmonic fields (i.e., fields with a lower chiral asymmetry than circularly polarized light) hence lifting constraints to engineer structures that produce fields with enhanced chirality, thus providing greater flexibility in nanostructure design. To demonstrate the efficacy of the phenomenon, we have detected and characterized picogram quantities of simple model helical biopolymers and more complex real proteins

Criteria for and Appropriateness of Renal Transplantation in Elderly Patients With End-Stage Renal Disease : A Literature Review and Position Statement on Behalf of the European Renal Association-European Dialysis and Transplant Association Descartes Working Group and European Renal Best Practice

During the last 20 years, waiting lists for renal transplantation (RT) have grown significantly older. However, elderly patients (ie ≥65 years of age) are still more rarely referred or accepted to waiting lists and, if enlisted, have less chances of actually receiving a kidney allograft, than younger counterparts. In this review, we looked at evidence for the benefits and risks of RT in the elderly trying to answer the following questions: Should RT be advocated for elderly patients? What should be the criteria to accept elderly patients on the waiting list for RT? What strategies might be used to increase the rate of RT in waitlisted elderly candidates? For selected elderly patients, RT was shown to be superior to dialysis in terms of patient survival. Virtually all guidelines recommend that patients should not be deemed ineligible for RT based on age alone, although a short life expectancy generally might preclude RT. Concerning the assessment of comorbidities in the elderly, special attention should be paid to cardiac evaluation and screening for malignancy. Comorbidity scores and frailty assessment scales might help the decision making on eligibility. Psychosocial issues should also be evaluated. To overcome the scarcity of organ donors, elderly RT candidates should be encouraged to consider expanded criteria donors and living donors, as alternatives to deceased standard criteria donors. It has been demonstrated that expanded criteria donor RT in patients 60 years or older is associated with higher survival rates than remaining on dialysis, whereas living donor RT is superior to all other options.Peer reviewe