WNT7b mediates macrophage-induced programmed cell death in patterning of the vasculature

Macrophages have a critical role in inflammatory and immune responses through their ability to recognize and engulf apoptotic cells. Here we show that macrophages initiate a cell-death programme in target cells by activating the canonical WNT pathway. We show in mice that macrophage WNT7b is a short-range paracrine signal required for WNT-pathway responses and programmed cell death in the vascular endothelial cells of the temporary hyaloid vessels of the developing eye. These findings indicate that macrophages can use WNT ligands to influence cell-fate decisions--including cell death--in adjacent cells, and raise the possibility that they do so in many different cellular contexts.     

Gene therapy: is IL2RG oncogenic in T-cell development?

The gene IL2RG encodes the gamma-chain of the interleukin-2 receptor and is mutated in patients with X-linked severe combined immune deficiency (X-SCID). Woods et al. report the development of thymus tumours in a mouse model of X-SCID after correction by lentiviral overexpression of IL2RG and claim that these were caused by IL2RG itself. Here we find that retroviral overexpression of IL2RG in human CD34+ cells has no effect on T-cell development, whereas overexpression of the T-cell acute lymphoblastic leukaemia (T-ALL) oncogene LMO2 leads to severe abnormalities. Retroviral expression of IL2RG may therefore not be directly oncogenic--rather, the restoration of normal signalling by the interleukin-7 receptor to X-SCID precursor cells allows progression of T-cell development to stages that are permissive for the pro-leukaemic effects of ectopic LMO2.     

The complete genome of an individual by massively parallel DNA sequencing

The association of genetic variation with disease and drug response, and improvements in nucleic acid technologies, have given great optimism for the impact of 'genomic medicine'. However, the formidable size of the diploid human genome, approximately 6 gigabases, has prevented the routine application of sequencing methods to deciphering complete individual human genomes. To realize the full potential of genomics for human health, this limitation must be overcome. Here we report the DNA sequence of a diploid genome of a single individual, James D. Watson, sequenced to 7.4-fold redundancy in two months using massively parallel sequencing in picolitre-size reaction vessels. This sequence was completed in two months at approximately one-hundredth of the cost of traditional capillary electrophoresis methods. Comparison of the sequence to the reference genome led to the identification of 3.3 million single nucleotide polymorphisms, of which 10,654 cause amino-acid substitution within the coding sequence. In addition, we accurately identified small-scale (2-40,000 base pair (bp)) insertion and deletion polymorphism as well as copy number variation resulting in the large-scale gain and loss of chromosomal segments ranging from 26,000 to 1.5 million base pairs. Overall, these results agree well with recent results of sequencing of a single individual by traditional methods. However, in addition to being faster and significantly less expensive, this sequencing technology avoids the arbitrary loss of genomic sequences inherent in random shotgun sequencing by bacterial cloning because it amplifies DNA in a cell-free system. As a result, we further demonstrate the acquisition of novel human sequence, including novel genes not previously identified by traditional genomic sequencing. This is the first genome sequenced by next-generation technologies. Therefore it is a pilot for the future challenges of 'personalized genome sequencing'.     

Expression, purification and characterization of the soluble CuA domain of cytochrome c oxidase ofParacoccus versutus

The key subunit Ⅱ of cytochrome c oxidase (CcO) contains a soluble binuclear copper center (Cu_A) domain. The Cu_A domain of Paracoccus versutus was cloned, expressed, purified and characterized. The gene encoding the Cu_A domain in pET11d vector was expressed in E. coli BL21 (DE3). The results showed that the Cu_A domain was expressed mostly in inclusion bodies and the Cu_A domain protein synthesized in E. coli cells represents approximately 10 percent of the total cellular proteins. Dissolved in urea, dialyzed and recombined with Cu⁺/Cu²⁺ and purified by the Q-sepharose fast flow anion-exchange column and Sephadex G-75 gel filtration column, the soluble purple-colored protein, which shows a single band in electrophoresis, was obtained. The UV-visible absorption spectrum of Cu_A domain showed that there are intense band at 478 nm and a shoulder peak at 530 nm, and two weak bands at 360 and 806 nm respectively, which can be assigned to the charge transfer and the interactions of obitals of Cu—S and Cu——Cu in the mixed-valence binuclear metal center (Cu₂S₂R₂). The far-UV CD spectrum indicated that this domain is predominantly in β-sheet structure. The fluorescence spectra showed that its maximal excitation wavelength and maximal emission wavelength are at 280 and 345 nm, respectively.     

Constructivism: A ‘Next’ Area of Scientific Development?

Radical Constructivism has been defined as an‘unconventional approach to the problem ofknowledge and knowing’. Its unconventionalityis summarised by its claim that it isimpossible to attribute unique meaning toexperience – as no mind-independent yardstick canbe assumed to exist against which to identifyuniqueness, and hence to produce knowledge andknowing. In other words, it is claimed thatthere is no ‘reality’ that is knowable to allindividual knowers. This claim appearsindefensible by itself, as it does not explainwhy the successes of traditional science appearas such. However, it is defensible in thecontext of numerous failures to achieve uniqueattributions, or of the history of science.Even so, what is missing are concrete methodsand research designs. This often leaves RadicalConstructivism to be critical only, toconcentrate on justifying the impossibility ofsuccess without contributing itself.Where this is the case it reduces scientiststo individuals considered unable to communicatewith others on public (and unique)attributions-who may do so only by borrowingmethods from previous approaches. It is arguedthat a more valuable contribution is possibleif Radical Constructivism is seen as a responseto the challenge defined by frequent failuresof traditional approaches. The latter may beextended such that the extensions converge toRadical Constructivism. Such extensions arebased on reported observations, rather than onexperiences in general, and are to beattributed meanings – uniquely as well asnon-uniquely – by way of a collective. The lattershould allow its ‘actors’ to restrict whatmaintains the collective to what is observableto others, as well as use the collective torestrict their own observations. The study ofcollectives thus allows for the study ofrestrictions or values, and hence for includingsubjective or constructivist experiences beyond(reportable) observations.     

Explaining the Origin of Life is not Enough for a Definition of Life

The comments focus on a presumed circular reasoning in the operator hierarchy and the necessity of understanding life’s origin for defining life. Below it is shown that its layered structure prevents the operator hierarchy from circular definitions. It is argued that the origin of life is an insufficient basis for a definition of life that includes multicellular and neural network organisms.     

The Italian-Hour Nocturnal

The general view is that there is one type of nocturnal, which is universal, first illustrated in a printed book in 1524. Recently, a number of quite differently constructed nocturnals has come to light. Six of these were made at the very beginning of the sixteenth century by Falcono of Bergamo in northern Italy. One of them, with the initials of the inventor, may well be the prototype. Five more are closely similar. Five further nocturnals of the same type have been identified, but they are unsigned, and are not by Falcono. This paper establishes the existence of a hitherto unrecognized Italian workshop, and of a variant type of nocturnal.     

Proteome survey reveals modularity of the yeast cell machinery

Protein complexes are key molecular entities that integrate multiple gene products to perform cellular functions. Here we report the first genome-wide screen for complexes in an organism, budding yeast, using affinity purification and mass spectrometry. Through systematic tagging of open reading frames (ORFs), the majority of complexes were purified several times, suggesting screen saturation. The richness of the data set enabled a de novo characterization of the composition and organization of the cellular machinery. The ensemble of cellular proteins partitions into 491 complexes, of which 257 are novel, that differentially combine with additional attachment proteins or protein modules to enable a diversification of potential functions. Support for this modular organization of the proteome comes from integration with available data on expression, localization, function, evolutionary conservation, protein structure and binary interactions. This study provides the largest collection of physically determined eukaryotic cellular machines so far and a platform for biological data integration and modelling.     

X-linked inheritance of Fanconi anemia complementation group B

Fanconi anemia is an autosomal recessive syndrome characterized by diverse clinical symptoms, hypersensitivity to DNA crosslinking agents, chromosomal instability and susceptibility to cancer. Fanconi anemia has at least 11 complementation groups (A, B, C, D1, D2, E, F, G, I, J, L); the genes mutated in 8 of these have been identified. The gene BRCA2 was suggested to underlie complementation group B, but the evidence is inconclusive. Here we show that the protein defective in individuals with Fanconi anemia belonging to complementation group B is an essential component of the nuclear protein 'core complex' responsible for monoubiquitination of FANCD2, a key event in the DNA-damage response pathway associated with Fanconi anemia and BRCA. Unexpectedly, the gene encoding this protein, FANCB, is localized at Xp22.31 and subject to X-chromosome inactivation. X-linked inheritance has important consequences for genetic counseling of families with Fanconi anemia belonging to complementation group B. Its presence as a single active copy and essentiality for a functional Fanconi anemia-BRCA pathway make FANCB a potentially vulnerable component of the cellular machinery that maintains genomic integrity.     

The complexities of skeletal biology

For a long time, the skeleton was seen as an amorphous tissue of little biological interest. But such a view ignored the large number of genetic and degenerative diseases affecting this organ. Over the past 15 years, molecular and genetic studies have modified our understanding of skeletal biology. By so doing this progress has affected our understanding of diseases and suggested in many instances new therapeutic opportunities.