The structure of an endogenous Drosophila centromere reveals the prevalence of tandemly repeated sequences able to form i-motifs

Centromeres are the chromosomal loci at which spindle microtubules attach to mediate chromosome segregation during mitosis and meiosis. In most eukaryotes, centromeres are made up of highly repetitive DNA sequences (satellite DNA) interspersed with middle repetitive DNA sequences (transposable elements). Despite the efforts to establish complete genomic sequences of eukaryotic organisms, the so-called 'finished' genomes are not actually complete because the centromeres have not been assembled due to the intrinsic difficulties in constructing both physical maps and complete sequence assemblies of long stretches of tandemly repetitive DNA. Here we show the first molecular structure of an endogenous Drosophila centromere and the ability of the C-rich dodeca satellite strand to form dimeric i-motifs. The finding of i-motif structures in simple and complex centromeric satellite DNAs leads us to suggest that these centromeric sequences may have been selected not by their primary sequence but by their ability to form noncanonical secondary structures.Peer Reviewe

Tetramolecular G-quadruplex formation pathways studied by electrospray mass spectrometry

Electrospray mass spectrometry was used to investigate the mechanism of tetramolecular G-quadruplex formation by the DNA oligonucleotide dTG5T, in ammonium acetate. The intermediates and products were separated according to their mass (number of strands and inner cations) and quantified. The study of the temporal evolution of each species allows us to propose the following formation mechanism. (i) Monomers, dimers and trimers are present at equilibrium already in the absence of ammonium acetate. (ii) The addition of cations promotes the formation of tetramers and pentamers that incorporate ammonium ions and therefore presumably have stacked guanine quartets in their structure. (iii) The pentamers eventually disappear and tetramers become predominant. However, these tetramers do not have their four strands perfectly aligned to give five G-quartets: the structures contain one ammonium ion too few, and ion mobility spectrometry shows that their conformation is more extended. (iv) At 4°C, the rearrangement of the kinetically trapped tetramers with presumably slipped strand(s) into the perfect G-quadruplex structure is extremely slow (not complete after 4 months). We also show that the addition of methanol to the monomer solution significantly accelerates the cation-induced G-quadruplex assembly

Applying Research Results to Production Chemistry in the Galapagos Research Center Ltd., Zagreb

Tvrtka Galapagos istraživački centar d. o. o. privatna je znanstvena organizacija, aktivna u područjima kemije, biologije, biomedicine, veterine i farmacije. Za potrebe ovog članka posvećenog Međunarodnoj godini kemije, obuhvaćen je pregled područja kojim se bave kemičari u ovom istraživačkom centru, a iznesene su i tehnike i tehnologije koje se primjenjuju u provedbi istraživačko-razvojnih projekata. Aktivnosti kemičara usmjerene su na sintezu novih organskih spojeva, potencijalnih novih lijekova, na njihovu identifikaciju i strukturnu karakterizaciju, na procese pročišćavanja, uvećanja sinteze (scale up), na primijenjenu analitiku u biološkim materijalima (DMPK - metabolizam lijekova i farmakokinetika) te na farmaceutski razvoj pretkliničkih kandidata. Projektni timovi u Galapagosu obuhvaćaju istraživače svih relevantnih struka za istraživanje potencijalnih novih lijekova, kao što su kemičari (kemijski inženjeri i tehnolozi), biolozi, medicinari, veterinari, farmaceuti. Konačni cilj svakog od projekata je djelotvoran, dobro definiran pretklinički kandidat, koji se dalje razvija u suradnji s drugim dijelovima Galapagosa (Belgija, Francuska, Velika Britanija) ili u partnerstvu s velikim farmaceutskim kompanijama. U članku su područja istraživanja i tehnologije potkrijepljeni konkretnim primjerima i rezultatima objavljenim u člancima.Galapagos Research Center Ltd., is a private research organization, active in the field of chemistry, biology, biomedicine, veterinary science and pharmacy. This article is devoted to the International Year of Chemistry; this review includes the areas of study undertaken by the chemists in the research center. Also presented are the current techniques and technologies applied in the implementation of research and development projects. The main activities of chemists are directed to the synthesis of new organic compounds resulting in potentially new medicines, their subsequent identification, structural characterization, purification process, magnification (scale up), the applied analysis of biological materials (DMPK – Drug Metabolism and Pharmacokinetics) and the pharmaceutical development of preclinical candidates. Project teams at Galapagos incorporate researchers of all relevant professions to explore the potential of new medicines. These include chemists (chemical engineers and technologists), biologists, medical doctors, veterinarians and pharmacists. The ultimate goal of each of the projects is to establish an effective, well-defined preclinical candidate, which is further developed in other parts of the organization (Belgium, France, Great Britain), otherwise in the development laboratories of large partner organizations. This research article includes research and technology supported by concrete examples, and the results published in previous articles

Protocol for a national audit on self-reported confidence levels, training requirements and current practice among trainee doctors in the UK: The Trainees Own Perception of Delivery of Care in Diabetes (TOPDOC) Study

Background: As the incidence and prevalence of diabetes increases across the world, resource pressures require doctors without specialist training to provide care for people with diabetes. In the UK, national standards have been set to ensure quality diabetes care from diagnosis to the management of complications. In a multi-centre pilot study, we have demonstrated a lack of confidence among UK trainee doctors in managing diabetes. Suboptimal confidence was identified in a number of areas, including the management of diabetes emergencies. A national survey would clarify whether the results of our pilot study are representative and reproducible. Methods/Design: Target cohort: All postgraduate trainee doctors in the UK. Domains Studied: The self reported online survey questionnaire has 5 domains: (1) confidence levels in the diagnosis and management of diabetes, (2) working with diabetes specialists, (3) perceived adequacy of training in diabetes (4) current practice in optimising glycaemic control and (5) perceived barriers to seeking euglycaemia. Assessment tools: Self-reported confidence is assessed using the 'Confidence Rating' (CR) scale for trainee doctors developed by the Royal College of Physicians. This scale has four points - ('not confident' (CR1), 'satisfactory but lacking confidence' (CR2), 'confident in some cases (CR3) and 'fully confident in most cases' (CR4). Frequency of aspects of day-to-day practice is assessed using a six-point scale. Respondents have a choice of 'always' (100%), 'almost always' (80-99%), 'often' (50-79%), 'not very often' (20-49%) and 'rarely' (5-19%) or never (less than 5%). Discussion: It is anticipated that the results of this national study will clarify confidence levels and current practice among trainee doctors in the provision of care for people with diabetes. The responses will inform efforts to enhance postgraduate training in diabetes, potentially improving the quality of care for people with diabetes.</p