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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

Abstract 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.

Disrupting the subscription journals’ business model for the necessary large-scale transformation to open access

Abstract This paper makes the strong, fact-based case for a large-scale transformation of the current corpus of scientific subscription journals to an open access business model. The existing journals, with their well-tested functionalities, should be retained and developed to meet the demands of 21st-century research, while the underlying payment streams undergo a major restructuring. There is sufficient momentum for this decisive push toward open access publishing. The diverse existing initiatives must be coordinated so as to converge on this clear goal. The international nature of research implies that this transformation will be achieved on a truly global scale only through a consensus of the world’s most eminent research organizations. All the indications are that the money already invested in the research publishing system is sufficient to enable a transformation that will be sustainable for the future. There needs to be a shared understanding that the money currently locked in the journal subscription system must be withdrawn and re-purposed for open access publishing services. The current library acquisition budgets are the ultimate reservoir for enabling the transformation without financial or other risks. The goal is to preserve the established service levels provided by publishers that are still requested by researchers, while redefining and reorganizing the necessary payment streams. By disrupting the underlying business model, the viability of journal publishing can be preserved and put on a solid footing for the scholarly developments of the future.

Review of ‘Intersubject information mapping: revealing canonical representations of complex natural stimuli’

ScienceOpen SO Reviews Review    Rated 3 of 5. Wei-Tang Chang on 2015-07-30 (2015)
somewhat interesting but more emperical and quantitative results are needed

Review of ‘Twin pregnancy in each half of a didelphys uterus with delayed delivery and review of literature’

ScienceOpen SO Reviews Review    Rated 3 of 5. maddalena mallozzi on 2015-07-21 (2015)
Useful to know the possible clinical outcome

Periventricular heterotopia and white matter abnormalities in a girl with mosaic ring chromosome 6

     Review now
Ring chromosome 6 is a rare chromosome abnormality that arises typically de novo. The phenotypes can be highly variable, ranging from almost normal to severe malformations and neurological defects. We report a case of a 3-year-old girl with mosaic ring chromosome 6 who presented with being small for gestational age and intellectual disability, and whose brain MRI later revealed periventricular heterotopia and white matter abnormalities. Mosaicism was identified in peripheral blood cells examined by standard G-bands, mos 46,XX,r(6)(p25q27)[67]/45,XX,-6[25]/46,XX,dic r(6:6)(p25q27:p25q27)[6]/47,XX,r(6)(p25q27) × 2[2]. Using array-comparative genomic hybridization, we identified terminal deletion of 6q27 (1.5 Mb) and no deletion on 6p. To our knowledge, this is the first report of periventricular heterotopia and white matter abnormalities manifested in a patient with ring chromosome 6. These central nervous system malformations are further discussed in relation to molecular genetics.

Assessment of adverse events via a telephone consultation service for cancer patients receiving ambulatory chemotherapy

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Background An increasing number of cancer patients are receiving ambulatory chemotherapy to improve their quality of life and reduce medical expenses. During outpatient chemotherapy, adverse events (AEs) occurring at home must be carefully monitored. We investigated the use of our institution’s telephone consultation service that is available to patients and their caregivers for advice on and the management of AEs and complications arising from cancer treatment. Patients and methods Telephone consultants assessed and graded AEs according to the Common Terminology Criteria for Adverse Events (CTCAE). All patient characteristics, AEs, and background factors were analyzed using logistic regression analyses. Results Between August 2011 and August 2012, we included 253 patients and 344 telephone consultations regarding AEs during chemotherapy for analysis in this study. Grade 1 AEs were assessed in 223 consultations (65%); grade 2 AEs, in 90 consultations (26%); and grade 3 AEs, in 31 consultations (9%). A multivariate logistic regression analysis revealed an association between a change in patient schedules and the occurrence of grade 2 or worse AEs (Hazard ratio = 6.58, P < 0.001). Changes in planned chemotherapy occurred more often in cases involving male patients (Hazard ratio = 2.70, P = 0.02) and in cases of grade 2 or worse AEs (Hazard ratio = 6.58, P < 0.001). Conclusion We found that AE assessment using CTCAE via a telephone consultation service is useful for both the triage of patients and the prediction of severe AEs that may change clinical schedules. Electronic supplementary material The online version of this article (doi:10.1186/s13104-015-1292-8) contains supplementary material, which is available to authorized users.