The 2007 Census Test: a major step towards the 2011 Census

The Office for National Statistics (ONS) is planning a major Census field test in 2007. It will form part of the planning and testing programme leading to up the next Census of Population for England and Wales in 2011, which will also include a Rehearsal in 2009. The 2007 Test will be a large-scale test in five local authority (LA) areas selected to reflect a range of field conditions, covering some 100,000 households in total. Within England the Test will cover parts of Bath and North East Somerset, Camden, Liverpool and Stoke-on-Trent. In Wales the Test will take place in Carmarthenshire. The selected LAs have been chosen to provide a varied cross-section of the population and types of housing that would be covered in a full census. This article sets out the main aims for the Test and describes the design and location of the sampled areas and the basis for their selection. It goes on to detail the ways (previously reported in Population Trend 1251) in which the ONS Census team and the LAs involved are working in partnership in planning the census enumeration with the long-term view of improving overall census coverage and user confidence in the results. The article notes that decisions on the topics to be covered in the 2007 Test have only recently been decided, and concludes with an overview of the qustions to be included in the 2007 Test questionnaire.     

Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome

Genomic disorders are characterized by the presence of flanking segmental duplications that predispose these regions to recurrent rearrangement. Based on the duplication architecture of the genome, we investigated 130 regions that we hypothesized as candidates for previously undescribed genomic disorders. We tested 290 individuals with mental retardation by BAC array comparative genomic hybridization and identified 16 pathogenic rearrangements, including de novo microdeletions of 17q21.31 found in four individuals. Using oligonucleotide arrays, we refined the breakpoints of this microdeletion, defining a 478-kb critical region containing six genes that were deleted in all four individuals. We mapped the breakpoints of this deletion and of four other pathogenic rearrangements in 1q21.1, 15q13, 15q24 and 17q12 to flanking segmental duplications, suggesting that these are also sites of recurrent rearrangement. In common with the 17q21.31 deletion, these breakpoint regions are sites of copy number polymorphism in controls, indicating that these may be inherently unstable genomic regions.     

Mutations in the gene encoding GlyT2 (SLC6A5) define a presynaptic component of human startle disease

Hyperekplexia is a human neurological disorder characterized by an excessive startle response and is typically caused by missense and nonsense mutations in the gene encoding the inhibitory glycine receptor (GlyR) alpha1 subunit (GLRA1). Genetic heterogeneity has been confirmed in rare sporadic cases, with mutations affecting other postsynaptic glycinergic proteins including the GlyR beta subunit (GLRB), gephyrin (GPHN) and RhoGEF collybistin (ARHGEF9). However, many individuals diagnosed with sporadic hyperekplexia do not carry mutations in these genes. Here we show that missense, nonsense and frameshift mutations in SLC6A5 (ref. 8), encoding the presynaptic glycine transporter 2 (GlyT2), also cause hyperekplexia. Individuals with mutations in SLC6A5 present with hypertonia, an exaggerated startle response to tactile or acoustic stimuli, and life-threatening neonatal apnea episodes. SLC6A5 mutations result in defective subcellular GlyT2 localization, decreased glycine uptake or both, with selected mutations affecting predicted glycine and Na+ binding sites.     

Inevitability,contingency, and epistemic humility

This paper offers an epistemological framework for the debate about whether the results of scientific enquiry are inevitable or contingent. I argue in Sections 2 and 3 that inevitabilist stances are doubly guilty of epistemic hubris—a lack of epistemic humility—and that the real question concerns the scope and strength of our contingentism. The latter stages of the paper—Sections 4 and 5—address some epistemological and historiographical worries and sketch some examples of deep contingencies to guide further debate. I conclude by affirming that the concept of epistemic humility can usefully inform critical reflection on the contingency of the sciences and the practice of history of science.     

Genetic variegation of clonal architecture and propagating cells in leukaemia

Little is known of the genetic architecture of cancer at the subclonal and single-cell level or in the cells responsible for cancer clone maintenance and propagation. Here we have examined this issue in childhood acute lymphoblastic leukaemia in which the ETV6-RUNX1 gene fusion is an early or initiating genetic lesion followed by a modest number of recurrent or 'driver' copy number alterations. By multiplexing fluorescence in situ hybridization probes for these mutations, up to eight genetic abnormalities can be detected in single cells, a genetic signature of subclones identified and a composite picture of subclonal architecture and putative ancestral trees assembled. Subclones in acute lymphoblastic leukaemia have variegated genetics and complex, nonlinear or branching evolutionary histories. Copy number alterations are independently and reiteratively acquired in subclones of individual patients, and in no preferential order. Clonal architecture is dynamic and is subject to change in the lead-up to a diagnosis and in relapse. Leukaemia propagating cells, assayed by serial transplantation in NOD/SCID IL2Rγ(null) mice, are also genetically variegated, mirroring subclonal patterns, and vary in competitive regenerative capacity in vivo. These data have implications for cancer genomics and for the targeted therapy of cancer.     

Crucial role for DNA ligase III in mitochondria but not in Xrcc1-dependent repair

Mammalian cells have three ATP-dependent DNA ligases, which are required for DNA replication and repair. Homologues of ligase I (Lig1) and ligase IV (Lig4) are ubiquitous in Eukarya, whereas ligase III (Lig3), which has nuclear and mitochondrial forms, appears to be restricted to vertebrates. Lig3 is implicated in various DNA repair pathways with its partner protein Xrcc1 (ref. 1). Deletion of Lig3 results in early embryonic lethality in mice, as well as apparent cellular lethality, which has precluded definitive characterization of Lig3 function. Here we used pre-emptive complementation to determine the viability requirement for Lig3 in mammalian cells and its requirement in DNA repair. Various forms of Lig3 were introduced stably into mouse embryonic stem (mES) cells containing a conditional allele of Lig3 that could be deleted with Cre recombinase. With this approach, we find that the mitochondrial, but not nuclear, Lig3 is required for cellular viability. Although the catalytic function of Lig3 is required, the zinc finger (ZnF) and BRCA1 carboxy (C)-terminal-related (BRCT) domains of Lig3 are not. Remarkably, the viability requirement for Lig3 can be circumvented by targeting Lig1 to the mitochondria or expressing Chlorella virus DNA ligase, the minimal eukaryal nick-sealing enzyme, or Escherichia coli LigA, an NAD(+)-dependent ligase. Lig3-null cells are not sensitive to several DNA-damaging agents that sensitize Xrcc1-deficient cells. Our results establish a role for Lig3 in mitochondria, but distinguish it from its interacting protein Xrcc1.     

Direct measurement of the quantum wavefunction

The wavefunction is the complex distribution used to completely describe a quantum system, and is central to quantum theory. But despite its fundamental role, it is typically introduced as an abstract element of the theory with no explicit definition. Rather, physicists come to a working understanding of the wavefunction through its use to calculate measurement outcome probabilities by way of the Born rule. At present, the wavefunction is determined through tomographic methods, which estimate the wavefunction most consistent with a diverse collection of measurements. The indirectness of these methods compounds the problem of defining the wavefunction. Here we show that the wavefunction can be measured directly by the sequential measurement of two complementary variables of the system. The crux of our method is that the first measurement is performed in a gentle way through weak measurement, so as not to invalidate the second. The result is that the real and imaginary components of the wavefunction appear directly on our measurement apparatus. We give an experimental example by directly measuring the transverse spatial wavefunction of a single photon, a task not previously realized by any method. We show that the concept is universal, being applicable to other degrees of freedom of the photon, such as polarization or frequency, and to other quantum systems--for example, electron spins, SQUIDs (superconducting quantum interference devices) and trapped ions. Consequently, this method gives the wavefunction a straightforward and general definition in terms of a specific set of experimental operations. We expect it to expand the range of quantum systems that can be characterized and to initiate new avenues in fundamental quantum theory.     

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

Induced pluripotent stem cells (iPSCs) offer immense potential for regenerative medicine and studies of disease and development. Somatic cell reprogramming involves epigenomic reconfiguration, conferring iPSCs with characteristics similar to embryonic stem (ES) cells. However, it remains unknown how complete the reestablishment of ES-cell-like DNA methylation patterns is throughout the genome. Here we report the first whole-genome profiles of DNA methylation at single-base resolution in five human iPSC lines, along with methylomes of ES cells, somatic cells, and differentiated iPSCs and ES cells. iPSCs show significant reprogramming variability, including somatic memory and aberrant reprogramming of DNA methylation. iPSCs share megabase-scale differentially methylated regions proximal to centromeres and telomeres that display incomplete reprogramming of non-CG methylation, and differences in CG methylation and histone modifications. Lastly, differentiation of iPSCs into trophoblast cells revealed that errors in reprogramming CG methylation are transmitted at a high frequency, providing an iPSC reprogramming signature that is maintained after differentiation.