DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Sequencing projects have traditionally employed long (400–800 bp) reads, but the existence of reference sequences for the human and many other genomes makes it possible to develop new, fast approaches to re-sequencing, whereby shorter reads are compared to a reference to identify intra-species genetic variation. We report an approach that generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high quality sequence. We demonstrate application of this approach to human genome sequencing on flow-sorted X chromosomes and then scale the approach to determine the genome sequence of a male Yoruba from Ibadan, Nigeria. We build an accurate consensus sequence from >30x average depth of paired 35-base reads. We characterise four million SNPs and four hundred thousand structural variants, many of which are previously unknown. Our approach is effective for accurate, rapid and economical whole genome re-sequencing and many other biomedical applications.

Summary1. Biological capacities to respond to changing environments dictate success or failure of populations and species over time. The major environmental feature in this context is often temperature, and organisms across the planet vary widely in their capacity to cope with temperature variation. With very few exceptions, Antarctic marine species are more sensitive to temperature variation than marine groups elsewhere, having survivable temperature envelopes between 5 °C and 12 °C above the minimum sea temperature of −2 °C. 2. Our findings show that in biological functions important to long-term survival these animals are even more tightly constrained. The Antarctic bivalve mollusc Laternula elliptica and limpet Nacella concinna both survive a few days in experiments at 9-10 °C, but suffer 50% failure in essential biological activities at 2-3 °C and complete loss at 5 °C. The Antarctic scallop Adamussium colbecki is even more sensitive, and loses the ability to swim as temperature approaches 2 °C. 3. These failures of activity are caused by a loss of aerobic capacity, and the animals investigated are so sensitive that a 2 °C rise in sea temperature could cause population or species removal from the Southern Ocean.

The derivatization of 3-amino-9-ethylcarbazole with a diamino-alkyl anchor affords a fluorescent dye suitable for indicator displacement from cucurbituril macrocycles. The novel compound 1 shows, due to a complexation-induced pKa shift, a large and predictable dual fluorescence response (100-fold increase at 375 nm and 9-fold decrease at 458 nm) upon supramolecular encapsulation and a strong affinity for cation-receptor macrocycles, in particular cucurbit[6]uril (CB6). A direct application is presented by monitoring the enzymatic activity of lysine decarboxylase.

A combination of moderately selective host-guest binding with the impressive specificity of enzymatic transformations allows the real-time monitoring of enzymatic reactions in a homogeneous solution. The resulting enzyme assays ("supramolecular tandem assays") exploit the dynamic binding of a fluorescent dye with a macrocyclic host in competition with the binding of the substrate and product. Two examples of enzymatic reactions were investigated: the hydrolysis of arginine to ornithine catalyzed by arginase and the oxidation of cadaverine to 5-aminopentanal by diamine oxidase, in which the substrates have a higher affinity to the macrocycle than the products ("substrate-selective assays"). The depletion of the substrate allows the fluorescent dye to enter the macrocycle in the course of the enzymatic reaction, which leads to the desired fluorescence response. For arginase, p-sulfonatocalix[4]arene was used as the macrocycle, which displayed binding constants of 6400 M(-1) with arginine, 550 M(-1) with ornithine, and 60,000 M(-1) with the selected fluorescent dye (1-aminomethyl-2,3-diazabicyclo[2.2.2]oct-2-ene); the dye shows a weaker fluorescence in its complexed state, which leads to a switch-off fluorescence response in the course of the enzymatic reaction. For diamine oxidase, cucurbit[7]uril (CB7) was used as the macrocycle, which showed binding constants of 4.5 x 10(6) M(-1) with cadaverine, 1.1 x 10(5) M(-1) with 1-aminopentane (as a model for the thermally unstable 1-aminopentanal), and 2.9 x 10(5) M(-1) with the selected fluorescent dye (acridine orange, AO); AO shows a stronger fluorescence in its complexed state, which leads to a switch-on fluorescence response upon enzymatic oxidation. It is demonstrated that tandem assays can be successfully used to probe the inhibition of enzymes. Inhibition constants were estimated for the addition of known inhibitors, i.e., S-(2-boronoethyl)-L-cysteine and 2(S)-amino-6-boronohexanoic acid for arginase and potassium cyanide for diamine oxidase. Through the sequential coupling of a "product-selective" with a "substrate-selective" assay it was furthermore possible to monitor a multistep biochemical pathway, namely the decarboxylation of lysine to cadaverine by lysine decarboxylase followed by the oxidation of cadaverine by diamine oxidase. This "domino tandem assay" was performed in the same solution with a single reporter pair (CB7/AO).

The coupling of an enzymatic transformation with dynamic host-guest exchange allows the unselective binding of macrocycles to be used for highly selective analyte sensing. The resulting supramolecular tandem enzyme assays require the enzymatic substrate and its corresponding product to differ significantly in their affinity for macrocycles, for example, cation receptors, and to show a differential propensity to displace a fluorescent dye from its host-guest complex. The enzymatic transformation results in a concomitant dye displacement that can be accurately followed by optical spectroscopy, specifically fluorescence. By exploiting this label-free continuous enzyme assay principle with the fluorescent dye Dapoxyl and the macrocyclic host cucurbit[7]uril, a multiparameter sensor array has been designed, which is capable of detecting the presence of amino acids (e.g. histidine, arginine, lysine, and tyrosine) and their decarboxylases. Only in the presence of both, the particular amino acid and the corresponding decarboxylase, is the amine or diamine product formed. These products are more highly positively charged than the substrate, have a higher affinity for the macrocycle and, therefore, displace the dye from the complex. The extension of the high selectivity and muM sensitivity of the tandem assay principle has also allowed for the accurate measurement of D-lysine enantiomeric excesses of up to 99.98 %, as only the L-enantiomer is accepted by the enzyme as a substrate and is converted to the product that is responsible for the observed fluorescence signal.

Objectives: To measure morbidity and mortality rates following insertion of gastrostomy tubes in head and neck cancer patients. To determine evidence for any relationship between gastrostomy insertion technique and complication rates. Design: A prospective cohort study and qualitative systematic review. Setting: Multi-cancer networks in the South West of England, Hampshire and the Isle of White. Participants: One hundred and seventy-two patients with head and neck cancer undergoing gastrostomy tube insertion between 2004 and 2005. Percutaneous endoscopic gastrostomy (PEG) was performed in 121 patients. Fifty-one patients had radiologically inserted gastrostomy (RIG). Twenty-seven studies reporting outcomes following 2353 gastrostomy procedures for head and neck cancer. Main outcome measures: Post-procedure mortality, major and minor complications. Results: In the present series, mortality rates were 1.0% (1 ⁄ 121) for PEG and 3.9% (2 ⁄ 51) for RIG. Overall major complication rates following PEG and RIG were 3.3% (4 ⁄ 121) and 15.6% (9 ⁄ 51) respectively. In our systematic review and meta-analysis of 2379 head and neck cancer patients, we observed fatality rates of 2.2% (95% CI 0.014-0.034) following PEG and 1.8% (95% CI 0.010-0.032) following RIG. Furthermore, major complication rates following PEG were 7.4% (95% CI 5.9-9.3%) and 8.9% (95% CI 7.0-11.2%) after RIG. Conclusions: Procedure related mortality rates following gastrostomy in head and neck cancer patients are higher than those in mixed patient populations. Major complication rates following RIG in head and neck cancer patients are greater than those following PEG. Major complications following PEG in patients with head and neck cancer appear no worse than in mixed pathology groups. We have identified that RIG is associated with increased morbidity and mortality in patients who are ineligible for PEG. The serious nature of the complications associated with gastrostomy particularly in patients with head and neck cancer requires careful consideration by the referring physician.The optimum technique for gastrostomy placement in patients with head and neck cancer remains controversial.1-4 Examination of the literature relating to complication and success rates of gastrostomy is made difficult by patient and pathology diversity and modifications of insertion technique. In 1995, Wollman et al.5 reported a metaanalysis investigating outcomes of 5752 patients following radiologic, endoscopic and surgical gastrostomy for all types of pathology. The authors concluded that radiologically inserted gastrostomies (RIG) were slightly more successful than percutaneous endoscopic gastrostomy (PEG) (99.2% versus 95.7%) and also safer, with statistically significant lower rates of major complications (5.9% versus 9.4%). Cancer comprised only 24-29% of the study populations and interpretation of the results in the context of head and neck cancer practice remains exigent. In this study, we examine outcomes following gastrostomy tube insertion in 172 consecutive patients trea...

The deep ocean below 200 m water depth is the least observed, but largest habitat on our planet by volume and area. Over 150 years of exploration has revealed that this dynamic system provides critical climate regulation, houses a wealth of energy, mineral, and biological resources, and represents a vast repository of biological diversity. A long history of deep-ocean exploration and observation led to the initial concept for the Deep-Ocean Observing Strategy (DOOS), under the auspices of the Global Ocean Observing System (GOOS). Here we discuss the scientific need for globally

Human mitochondrial DNA polymerase, encoded by POLG, contains a polyglutamine tract encoded by a CAG microsatellite repeat. Analysis of POLG genotypes in different populations identified an association between absence of the common, ten-repeat allele and male infertility typified by a range of sperm quality defects but excluding azoospermia.