The sequence of the human genome

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

The genome sequence of Drosophila melanogaster

The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes approximately 13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with comparable functional diversity.

ER stress induces cleavage of membrane-bound ATF6 by the same proteases that process SREBPs

ATF6 is a membrane-bound transcription factor that activates genes in the endoplasmic reticulum (ER) stress response. When unfolded proteins accumulate in the ER, ATF6 is cleaved to release its cytoplasmic domain, which enters the nucleus. Here, we show that ATF6 is processed by Site-1 protease (S1P) and Site-2 protease (S2P), the enzymes that process SREBPs in response to cholesterol deprivation. ATF6 processing was blocked completely in cells lacking S2P and partially in cells lacking S1P. ATF6 processing required the RxxL and asparagine/proline motifs, known requirements for S1P and S2P processing, respectively. Cells lacking S2P failed to induce GRP78, an ATF6 target, in response to ER stress. ATF6 processing did not require SCAP, which is essential for SREBP processing. We conclude that S1P and S2P are required for the ER stress response as well as for lipid synthesis.

Direct splitting of water under visible light irradiation with an oxide semiconductor photocatalyst

The photocatalytic splitting of water into hydrogen and oxygen using solar energy is a potentially clean and renewable source for hydrogen fuel. The first photocatalysts suitable for water splitting, or for activating hydrogen production from carbohydrate compounds made by plants from water and carbon dioxide, were developed several decades ago. But these catalysts operate with ultraviolet light, which accounts for only 4% of the incoming solar energy and thus renders the overall process impractical. For this reason, considerable efforts have been invested in developing photocatalysts capable of using the less energetic but more abundant visible light, which accounts for about 43% of the incoming solar energy. However, systems that are sufficiently stable and efficient for practical use have not yet been realized. Here we show that doping of indium-tantalum-oxide with nickel yields a series of photocatalysts, In(1-x)Ni(x)TaO(4) (x = 0-0.2), which induces direct splitting of water into stoichiometric amounts of oxygen and hydrogen under visible light irradiation with a quantum yield of about 0.66%. Our findings suggest that the use of solar energy for photocatalytic water splitting might provide a viable source for 'clean' hydrogen fuel, once the catalytic efficiency of the semiconductor system has been improved by increasing its surface area and suitable modifications of the surface sites.

Complementation cloning of S2P, a gene encoding a putative metalloprotease required for intramembrane cleavage of SREBPs

We report the cloning of a gene, S2P, that encodes a putative metalloprotease required for intramembrane proteolysis of sterol-regulatory element-binding proteins (SREBPs) at Site-2. SREBPs are membrane-bound transcription factors that activate genes regulating cholesterol metabolism. The active NH2-terminal domains of SREBPs are released from membranes by sequential cleavage at two sites: Site-1, within the lumen of the endoplasmic reticulum; and Site-2, within a transmembrane segment. The human S2P gene was cloned by complementation of mutant CHO cells that cannot cleave SREBPs at Site-2 and are cholesterol auxotrophs. S2P defines a new family of polytopic membrane proteins that contain an HEXXH sequence characteristic of zinc metalloproteases. Mutation of the putative zinc-binding residues abolishes S2P activity. S2P encodes an unusual metalloprotease that cleaves proteins within transmembrane segments.

Quantum-state controlled chemical reactions of ultracold potassium-rubidium molecules

How does a chemical reaction proceed at ultralow temperatures? Can simple quantum mechanical rules such as quantum statistics, single partial-wave scattering, and quantum threshold laws provide a clear understanding of the molecular reactivity under a vanishing collision energy? Starting with an optically trapped near-quantum-degenerate gas of polar 40K87Rb molecules prepared in their absolute ground state, we report experimental evidence for exothermic atom-exchange chemical reactions. When these fermionic molecules were prepared in a single quantum state at a temperature of a few hundred nanokelvin, we observed p-wave-dominated quantum threshold collisions arising from tunneling through an angular momentum barrier followed by a short-range chemical reaction with a probability near unity. When these molecules were prepared in two different internal states or when molecules and atoms were brought together, the reaction rates were enhanced by a factor of 10 to 100 as a result of s-wave scattering, which does not have a centrifugal barrier. The measured rates agree with predicted universal loss rates related to the two-body van der Waals length.

Direct link between microwave and optical frequencies with a 300 THz femtosecond laser comb

We demonstrate a great simplification in the long-standing problem of measuring optical frequencies in terms of the cesium primary standard. An air-silica microstructure optical fiber broadens the frequency comb of a femtosecond laser to span the optical octave from 1064 to 532 nm, enabling us to measure the 282 THz frequency of an iodine-stabilized Nd:YAG laser directly in terms of the microwave frequency that controls the comb spacing. Additional measurements of established optical frequencies at 633 and 778 nm using the same femtosecond comb confirm the accepted uncertainties for these standards.

Association between rates of caesarean section and maternal and neonatal mortality in the 21st century: a worldwide population-based ecological study with longitudinal data

Objective

Caesarean section was initially performed to save the lives of the mother and/or her baby. Caesarean section rates have risen substantially worldwide over the past decades. In this study, we set out to compile all available caesarean section rates worldwide at the country level, and to identify the appropriate caesarean section rate at the population level associated with the minimal maternal and neonatal mortality.

Design

Ecological study using longitudinal data.

Setting

Worldwide country‐level data.

Population

A total of 159 countries were included in the analyses, representing 98.0% of global live births (2005).

Methods

Nationally representative caesarean section rates from 2000 to 2012 were compiled. We assessed the relationship between caesarean section rates and mortality outcomes, adjusting for socio‐economic development by means of human development index (HDI) using fractional polynomial regression models.

Main outcome measures

Maternal mortality ratio and neonatal mortality rate.

Results

Most countries have experienced increases in caesarean section rate during the study period. In the unadjusted analysis, there was a negative association between caesarean section rates and mortality outcomes for low caesarean section rates, especially among the least developed countries. After adjusting for HDI, this effect was much smaller and was only observed below a caesarean section rate of 5–10%. No important association between the caesarean section rate and maternal and neonatal mortality was observed when the caesarean section rate exceeded 10%.

Conclusions

Although caesarean section is an effective intervention to save maternal and infant lives, based on the available ecological evidence, caesarean section rates higher than around 10% at the population level are not associated with decreases in maternal and neonatal mortality rates, and thus may not be necessary to achieve the lowest maternal and neonatal mortality.

Tweetable abstract

The caesarean section rate of around 10% may be the optimal rate to achieve the lowest mortality.

The caesarean section rate of around 10% may be the optimal rate to achieve the lowest mortality.

PERK promotes cancer cell proliferation and tumor growth by limiting oxidative DNA damage

To proliferate and expand in an environment with limited nutrients, cancer cells co-opt cellular regulatory pathways that facilitate adaptation and thereby maintain tumor growth and survival potential. The endoplasmic reticulum (ER) is uniquely positioned to sense nutrient deprivation stress and subsequently engage signaling pathways that promote adaptive strategies. As such, components of the ER stress-signaling pathway represent potential antineoplastic targets. However, recent investigations into the role of the ER resident protein kinase, RNA-dependent protein kinase (PKR)-like ER kinase (PERK) have paradoxically suggested both pro- and anti-tumorigenic properties. We have used animal models of mammary carcinoma to interrogate the contribution of PERK in the neoplastic process. The ablation of PERK in tumor cells resulted in impaired regeneration of intracellular antioxidants and accumulation of reactive oxygen species triggering oxidative DNA damage. Ultimately, PERK deficiency impeded progression through the cell cycle because of the activation of the DNA damage checkpoint. Our data reveal that PERK-dependent signaling is used during both tumor initiation and expansion to maintain redox homeostasis, thereby facilitating tumor growth.

Transcatheter aortic valve implantation: durability of clinical and hemodynamic outcomes beyond 3 years in a large patient cohort

BACKGROUND

Although short- and medium-term outcomes after transcatheter aortic valve implantation are encouraging, long-term data on valve function and clinical outcomes are limited.

METHODS AND RESULTS

Consecutive high-risk patients who had been declined as surgical candidates because of comorbidities but who underwent successful transcatheter aortic valve implantation with a balloon-expandable valve between January 2005 and December 2006 and survived past 30 days were assessed. Clinical, echocardiographic, and computed tomographic follow-up examinations were performed. Seventy patients who underwent successful procedures and survived longer than 30 days were evaluated at a minimum follow-up of 3 years. At a median follow-up of 3.7 years (interquartile range 3.4 to 4.3 years), survival was 57%. Survival at 1, 2, and 3 years was 81%, 74%, and 61%, respectively. Freedom from reoperation was 98.5% (1 patient with endocarditis). During this early procedural experience, 11 patients died within 30 days, and 8 procedures were unsuccessful. When these patients were included, overall survival was 51%. Transaortic pressure gradients increased from 10.0 mm Hg (interquartile range 8.0 to 12.0 mm Hg) immediately after the procedure to 12.1 mm Hg (interquartile range 8.6 to 16.0 mm Hg) after 3 years (P=0.03). Bioprosthetic valve area decreased from a mean of 1.7±0.4 cm(2) after the procedure to 1.4±0.3 cm(2) after 3 years (P<0.01). Aortic incompetence after implantation was trivial or mild in 84% of cases and remained unchanged or improved over time. There were no cases of structural valvular deterioration, stent fracture, deformation, or valve migration.

CONCLUSIONS

Transcatheter aortic valve implantation demonstrates good medium- to long-term durability and preserved hemodynamic function, with no evidence of structural failure. The procedure appears to offer an adequate and lasting resolution of aortic stenosis in selected patients.

An optical lattice clock with accuracy and stability at the 10(-18) level

Progress in atomic, optical and quantum science has led to rapid improvements in atomic clocks. At the same time, atomic clock research has helped to advance the frontiers of science, affecting both fundamental and applied research. The ability to control quantum states of individual atoms and photons is central to quantum information science and precision measurement, and optical clocks based on single ions have achieved the lowest systematic uncertainty of any frequency standard. Although many-atom lattice clocks have shown advantages in measurement precision over trapped-ion clocks, their accuracy has remained 16 times worse. Here we demonstrate a many-atom system that achieves an accuracy of 6.4 × 10(-18), which is not only better than a single-ion-based clock, but also reduces the required measurement time by two orders of magnitude. By systematically evaluating all known sources of uncertainty, including in situ monitoring of the blackbody radiation environment, we improve the accuracy of optical lattice clocks by a factor of 22. This single clock has simultaneously achieved the best known performance in the key characteristics necessary for consideration as a primary standard-stability and accuracy. More stable and accurate atomic clocks will benefit a wide range of fields, such as the realization and distribution of SI units, the search for time variation of fundamental constants, clock-based geodesy and other precision tests of the fundamental laws of nature. This work also connects to the development of quantum sensors and many-body quantum state engineering (such as spin squeezing) to advance measurement precision beyond the standard quantum limit.

Phase-coherent optical pulse synthesis from separate femtosecond lasers

We generated a coherently synthesized optical pulse from two independent mode-locked femtosecond lasers, providing a route to extend the coherent bandwidth available for ultrafast science. The two separate lasers (one centered at 760 nanometers wavelength, the other at 810 nanometers) are tightly synchronized and phase-locked. Coherence between the two lasers is demonstrated via spectral interferometry and second-order field cross-correlation. Measurements reveal a coherently synthesized pulse that has a temporally narrower second-order autocorrelation width and that exhibits a larger amplitude than the individual laser outputs. This work represents a new and flexible approach to the synthesis of coherent light.

Role of reactive oxygen species and p53 in chromium(VI)-induced apoptosis

Apoptosis is a programmed cell death mechanism to control cell number in tissues and to eliminate individual cells that may lead to disease states. The present study investigates chromium(VI) (Cr(VI))-induced apoptosis and the role of reactive oxygen species (ROS) and p53 in this response. Treatment of human lung epithelial cells (A549) with Cr(VI) caused apoptosis as measured by DNA fragmentation, mitochondria damage, and cell morphology. Cr(VI)-induced apoptosis is contributed to ROS generation, resulting from cellular reduction of Cr(VI) as measured by flow cytometric analysis of the stained cells, oxygen consumption, and electron spin resonance spin trapping. Scavengers of ROS, such as catalase, aspirin, and N-acetyl-L-cysteine, decreased Cr(VI)-induced apoptosis, whereas NADPH and glutathione reductase, enhancers of Cr(VI)-induced ROS generation, increased it. p53 is activated by Cr(VI), mostly by ROS-mediated free radical reactions. Cr(VI)-induced ROS generation occurred within a few minutes after Cr(VI) treatment of the cells, whereas p53 induction took at least 5 h. The level of Cr(VI)-induced apoptosis was similar in both p53-positive cells and p53-negative cells independent of p53 status in the early stage (0-3 h) of Cr(VI) treatment. However, at the later stage (3-24 h), the level of the apoptosis is higher in p53-positive cells than in p53-negative cells. These results suggest that ROS generated through Cr(VI) reduction is responsible to the early stage of apoptosis, whereas p53 contributes to the late stage of apoptosis and is responsible for the enhancement of Cr(VI)-induced apoptosis at this stage.

Dark Matter Search Results from a One Ton-Year Exposure of XENON1T

We report on a search for weakly interacting massive particles (WIMPs) using 278.8 days of data collected with the XENON1T experiment at LNGS. XENON1T utilizes a liquid xenon time projection chamber with a fiducial mass of (1.30±0.01)  ton, resulting in a 1.0 ton yr exposure. The energy region of interest, [1.4,10.6]  keV_{ee} ([4.9,40.9] keV_{nr}), exhibits an ultralow electron recoil background rate of [82_{-3}^{+5}(syst)±3(stat)]  events/(ton yr keV_{ee}). No significant excess over background is found, and a profile likelihood analysis parametrized in spatial and energy dimensions excludes new parameter space for the WIMP-nucleon spin-independent elastic scatter cross section for WIMP masses above 6  GeV/c^{2}, with a minimum of 4.1×10^{-47}  cm^{2} at 30  GeV/c^{2} and a 90% confidence level.

The role of intramuscular lipid in insulin resistance

There is interest in how altered lipid metabolism could contribute to muscle insulin resistance. Many animal and human states of insulin resistance have increased muscle triglyceride content, and there are now plausible mechanistic links between muscle lipid accumulation and insulin resistance, which go beyond the classic glucose-fatty acid cycle. We postulate that muscle cytosolic accumulation of the metabolically active long-chain fatty acyl CoAs (LCACoA) is involved, leading to insulin resistance and impaired insulin signalling or impaired enzyme activity (e.g. glycogen synthase or hexokinase) either directly or via chronic translocation/activation of mediators such as a protein kinase C (particularly PKC theta and epsilon ). Ceramides and diacylglycerols (DAGs) have also been implicated in forms of lipid-induced muscle insulin resistance. Dietary lipid-induced muscle insulin resistance in rodents is relatively easily reversed by manipulations that lessen cytosolic lipid accumulation (e.g. diet change, exercise or fasting). PPAR agonists (both gamma and alpha) also lower muscle LCACoA and enhance insulin sensitivity. Activation of AMP-activated protein kinase (AMPK) by AICAR leads to muscle enhancement (especially glycolytic muscle) of insulin sensitivity, but involvement of altered lipid metabolism is less clear cut. In rodents there are similarities in the pattern of muscle lipid accumulation/PKC translocation/altered insulin signalling/insulin resistance inducible by 3-5-h acute free fatty acid elevation, 1-4 days intravenous glucose infusion or several weeks of high-fat feeding. Recent studies extend findings and show relevance to humans. Muscle cytosolic lipids may accumulate either by increased fatty acid flux into muscle, or by reduced fatty acid oxidation. In some circumstances muscle insulin resistance may be an adaptation to optimize use of fatty acids when they are the predominant available energy fuel. The interactions described here are fundamental to optimizing therapy of insulin resistance based on alterations in muscle lipid metabolism.

Dipolar collisions of polar molecules in the quantum regime

Ultracold polar molecules offer the possibility of exploring quantum gases with interparticle interactions that are strong, long-range and spatially anisotropic. This is in stark contrast to the much studied dilute gases of ultracold atoms, which have isotropic and extremely short-range (or 'contact') interactions. Furthermore, the large electric dipole moment of polar molecules can be tuned using an external electric field; this has a range of applications such as the control of ultracold chemical reactions, the design of a platform for quantum information processing and the realization of novel quantum many-body systems. Despite intense experimental efforts aimed at observing the influence of dipoles on ultracold molecules, only recently have sufficiently high densities been achieved. Here we report the experimental observation of dipolar collisions in an ultracold molecular gas prepared close to quantum degeneracy. For modest values of an applied electric field, we observe a pronounced increase in the loss rate of fermionic potassium-rubidium molecules due to ultracold chemical reactions. We find that the loss rate has a steep power-law dependence on the induced electric dipole moment, and we show that this dependence can be understood in a relatively simple model based on quantum threshold laws for the scattering of fermionic polar molecules. In addition, we directly observe the spatial anisotropy of the dipolar interaction through measurements of the thermodynamics of the dipolar gas. These results demonstrate how the long-range dipolar interaction can be used for electric-field control of chemical reaction rates in an ultracold gas of polar molecules. Furthermore, the large loss rates in an applied electric field suggest that creating a long-lived ensemble of ultracold polar molecules may require confinement in a two-dimensional trap geometry to suppress the influence of the attractive, 'head-to-tail', dipolar interactions.