A new highly penetrant form of obesity due to deletions on chromosome 16p11.2.

Obesity has become a major worldwide challenge to public health, owing to an interaction between the Western 'obesogenic' environment and a strong genetic contribution. Recent extensive genome-wide association studies (GWASs) have identified numerous single nucleotide polymorphisms associated with obesity, but these loci together account for only a small fraction of the known heritable component. Thus, the 'common disease, common variant' hypothesis is increasingly coming under challenge. Here we report a highly penetrant form of obesity, initially observed in 31 subjects who were heterozygous for deletions of at least 593 kilobases at 16p11.2 and whose ascertainment included cognitive deficits. Nineteen similar deletions were identified from GWAS data in 16,053 individuals from eight European cohorts. These deletions were absent from healthy non-obese controls and accounted for 0.7% of our morbid obesity cases (body mass index (BMI) >or= 40 kg m(-2) or BMI standard deviation score >or= 4; P = 6.4 x 10(-8), odds ratio 43.0), demonstrating the potential importance in common disease of rare variants with strong effects. This highlights a promising strategy for identifying missing heritability in obesity and other complex traits: cohorts with extreme phenotypes are likely to be enriched for rare variants, thereby improving power for their discovery. Subsequent analysis of the loci so identified may well reveal additional rare variants that further contribute to the missing heritability, as recently reported for SIM1 (ref. 3). The most productive approach may therefore be to combine the 'power of the extreme' in small, well-phenotyped cohorts, with targeted follow-up in case-control and population cohorts.

Human genes involved in copy number variation: mechanisms of origin, functional effects and implications for disease.

Copy number variants (CNVs) overlap over 7000 genes, many of which are pivotal in biological pathways. The implications of this are profound, with consequences for evolutionary studies, population genetics, gene function and human phenotype, including elucidation of genetic susceptibility to major common diseases, the heritability of which has thus far defied full explanation. Even though this research is still in its infancy, CNVs have already been associated with a number of monogenic, syndromic and complex diseases: the development of high throughput and high resolution techniques for CNV screening is likely to bring further new insights into the contribution of copy number variation to common diseases. Amongst genes overlapped by CNVs, significant enrichments for certain gene ontology categories have been identified, including those related to immune responses and interactions with the environment. Genes in both of these categories are thought to be important in evolutionary adaptation and to be particular targets of natural selection. Thus, a full appreciation of copy number variation may be important for our understanding of human evolution.

The molecular mechanism of the control of excitation energy dissipation in chloroplast membranes. Inhibition of delta pH-dependent quenching of chlorophyll fluorescence by dicyclohexylcarbodiimide.

Non-radiative dissipation of absorbed excitation energy in chloroplast membranes is induced in the presence of the trans-thylakoid proton motive force; this dissipation is measured as high energy state quenching of chlorophyll fluorescence, qE. It has been suggested that this results from a low pH-induced structural alteration in the light harvesting complex of photosystem II, LHCII [(1991) FEBS Letters 292, 1-4]. The effect of the carboxyl-modifying agent, dicyclohexylcarbodiimide (DCCD), on energy dissipation in chloroplast membranes has been investigated. At concentrations below that required to inhibit electron transport, DCCD caused a decrease in the steady state delta pH, completely inhibited qE and also inhibited the low pH-dependent induction of qE. DCCD binding to polypeptides in the 22-28 kDa range correlated with inhibition of qE. It is suggested that DCCD reacts with amino acid residues in LHCII whose protonation is the primary event in the induction of energy dissipation. This LHCII domain may be identical to one forming a proton channel linking the site of PSII-dependent water oxidation to the thylakoid lumen [(1990) Eur. J. Biochem. 193, 731-736].

Increasing rice photosynthesis by manipulation of the acclimation and adaptation to light.

There are three important considerations in assessing the interaction of crop plants with light: (a) how does the plant respond to the light environment both in the short-term (regulation) and in the long-term (acclimation), (b) under what conditions are these responses inadequate, leading to photoinhibition, and (c) are the responses optimally adapted for maximum agricultural yield? Despite a wealth of knowledge about these processes in model plant species, it is impossible to predict how significant they are in influencing the yield of rice. Therefore, in collaboration with IRRI, we have undertaken a study of photoinhibition and photoacclimation of rice under field conditions. The results of this study are presented, along with an assessment of the implications for improvement of rice yield.

A case of peroneal neuropathy-induced footdrop. Correlated and compensatory lower-extremity function.

This article reports on the case of a man with peroneal neuropathy-induced footdrop who was seen at the authors' institution 3 years after open reduction and internal fixation of a proximal fibular fracture and a distal, spiral, oblique tibial fracture of the right leg. A comprehensive gait analysis was conducted. A significant footdrop in gait resulted in a "reverse check mark" center-of-pressure pattern, an increased transverse-plane rotation of the foot, and excessive knee and hip flexion in the sagittal plane. These objective findings documented significant dysfunction within the involved lower extremity; in addition, aberrant biomechanics were observed in structures other than the site of initial injury within both limbs.

Resolution of components of non-photochemical chlorophyll fluorescence quenching in barley leaves.

Non-photochemical chlorophyll fluorescence quenching (qN) in barley leaves has been analysed by monitoring its relaxation in the dark, by applying saturating pulses of light. At least three kinetically distinct phases to qN recovery are observed, which have previously been identified (Quick and Stitt 1989) as being due to high-energy state quenching ('fast'), excitation energy redistribution due to a state transition ('medium') and photoinhibition ('slow'). However, measurements of chlorophyll fluorescence at 77 K from leaf extracts show that state transitions only occur in low light conditions, whereas the 'medium' component of qN is very large in high light. The source of that part of the 'medium' component not accounted for by a state transition is discussed.

Acclimation of Arabidopsis thaliana to the light environment: regulation of chloroplast composition.

The regulation by light of the composition of the photosynthetic apparatus was investigated in Arabidopsis thaliana (L.) Heynh. cv. Landsberg erecta. When grown in high- and low-irradiance white light, wild-type plants and photomorphogenic mutants showed large differences in their maximum photosynthetic rate and chlorophyll a/b ratios; such changes were abolished by growth in red light. Photosystem I (PSI) and PSII levels were measured in wild-type plants grown under a range of light environments; the results indicate that regulation of photosystem stoichiometry involves the specific detection of blue light. Supplementing red growth lights with low levels of blue light led to large increases in PSII content, while further increases in blue irradiance had the opposite effect; this latter response was abolished by the hy4 mutation, which affects certain events controlled by a blue-light receptor. Mutants defective in the phytochrome photoreceptors retained regulation of photosystem stoichiometry. We discuss the results in terms of two separate responses controlled by blue-light receptors: a blue-high-fluence response which controls photosystem stoichiometry; and a blue-low-fluence response necessary for activation of such control. Variation in the irradiance of the red growth light revealed that the blue-high-fluence response is attenuated by red light; this may be evidence that photosystem stoichiometry is controlled not only by photoreceptors, but also by photosynthetic metabolism.

Acclimation of Arabidopsis thaliana to the light environment: changes in photosynthetic function.

Arabidopsis thaliana (L.) Heynh. cv. Landsberg erecta was grown under light regimes of differing spectral qualities, which results in differences in the stoichiometries of the two photosynthetic reaction centres. The acclimative value of these changes was investigated by assessing photosynthetic function in these plants when exposed to two spectrally distinct actinic lights. Plants grown in an environment enriched in far-red light were better able to make efficient use of non-saturating levels of actinic light enriched in long-wavelength red light. Simultaneous measurements of chlorophyll fluorescence and absorption changes at 820 nm indicated that differences between plants grown under alternative light regimes can be ascribed to imbalances in excitation of photosystems I and II (PSI, PSII). Measurements of chlorophyll fluorescence emission and excitation spectra at 77 K provided strong evidence that there was little or no difference in the composition or function of PSI or PSII between the two sets of plants, implying that changes in photosynthetic stoichiometry are primarily responsible for the observed differences in photosynthetic function.

Theoretical assessment of alternative mechanisms for non-photochemical quenching of PS II fluorescence in barley leaves.

The components of non-photochemical chlorophyll fluorescence quenching (qN) in barley leaves have been quantified by a combination of relaxation kinetics analysis and 77 K fluorescence measurements (Walters RG and Horton P 1991). Analysis of the behaviour of chlorophyll fluorescence parameters and oxygen evolution at low light (when only state transitions - measured as qNt - are present) and at high light (when only photoinhibition - measured as qNi - is increasing) showed that the parameter qNt represents quenching processes located in the antenna and that qNi measures quenching processes located in the reaction centre but which operate significantly only when those centres are closed. The theoretical predictions of a variety of models describing possible mechanisms for high-energy-state quenching, measured as the residual quenching, qNe, were then tested against the experimental data for both fluorescence quenching and quantum yield of oxygen evolution. Only one model was found to agree with these data, one in which antennae exist in two states, efficient in either energy transfer or energy dissipation, and in which those photosynthetic units in a dissipative state are unable to exchange energy with non-dissipative units.

Higher plant light-harvesting complexes LHCIIa and LHCIIc are bound by dicyclohexylcarbodiimide during inhibition of energy dissipation.

We have investigated the binding to proteins of the photosynthetic apparatus of the carboxy-modifying agent dicyclohexylcarbodiimide, (cHxN)2C; this inhibits the protective dissipation of excess absorbed light energy (qE) by the light-harvesting apparatus of photosystem II (LHCII), suggesting that carboxyl amino-acid side chains within hydrophobic protein domains may be involved in qE. (cHxN)2(14)C was used to label thylakoids and photosystem II particles, so as to identify proteins which may be involved in the detection of lumen pH during qE induction. Of six thylakoid proteins labelled with (cHxN)2C under conditions where qE is efficiently induced, three are associated with photosystem I, and none with the bulk LHCII. PSII-associated label is bound to three minor components of LHCII, identified as LHCIIa (two species) and LHCIIc, as shown by protein sequencing of tryptic fragments of purified complexes. pH titration of qE formation and protein labelling in coupled thylakoids showed that both qE and labelling of LHCIIa increased at pH 7-8.

REGULATION OF LIGHT HARVESTING IN GREEN PLANTS.

When plants are exposed to light intensities in excess of those that can be utilized in photosynthetic electron transport, nonphotochemical dissipation of excitation energy is induced as a mechanism for photoprotection of photosystem II. The features of this process are reviewed, particularly with respect to the molecular mechanisms involved. It is shown how the dynamic properties of the proteins and pigments of the chlorophyll a/b light-harvesting complexes of photosystem II first enable the level of excitation energy to be sensed via the thylakoid proton gradient and subsequently allow excess energy to be dissipated as heat by formation of a nonphotochemical quencher. The nature of this quencher is discussed, together with a consideration of how the variation in capacity for energy dissipation depends on specific features of the composition of the light-harvesting system. Finally, the prospects for future progress in understanding the regulation of light harvesting are assessed.

Identification of proton-active residues in a higher plant light-harvesting complex.

The thermal dissipation of absorbed light energy by the light-harvesting apparatus of higher plants is important in protecting the photosynthetic machinery from the effects of excess illumination. A major mechanism for such photoprotection, known as trans-thylakoid delta pH-dependent chlorophyll fluorescence quenching (qE), is induced by acidification of the lumen, is correlated with the interconversion of xanthophyll pigments, and is manifested as quenching of chloropyll fluorescence. The mechanistic basis for qE remains unknown. The reagent N, N'-dicyclohexylcarbodiimide (DCCD) specifically inhibits qE and covalently binds to two minor light-harvesting pigment-protein complexes (LHCII), LHCIIa and LHCIIc. It is shown that DCCD treatment of isolated LHCIIc complexes reverses acid-induced chlorophyll fluorescence quenching in an in vitro system. Fingerprinting of [14C]DCCD-labeled LHCIIc demonstrates that there are two DCCD-sensitive amino acid residues on this complex, and these are shown to be glutamate residues, each of which is located near the lumen. In view of the effects of DCCD on the pattern of proton release from photosystem II during photosynthesis, we propose a model for the mechanism of the induction of qE--that these residues from part of a proton pathway, the lumen pH being sensed via its effects on the rate of proton release. One possibility is that the resulting changes in the protonation state of these carboxyl side chains may modulate the structural and energetic organization of LHCII.

Antisense inhibition of the photosynthetic antenna proteins CP29 and CP26: implications for the mechanism of protective energy dissipation.

The specific roles of the chlorophyll a/b binding proteins CP29 and CP26 in light harvesting and energy dissipation within the photosynthetic apparatus have been investigated. Arabidopsis was transformed with antisense constructs against the genes encoding the CP29 or CP26 apoprotein, which gave rise to several transgenic lines with remarkably low amounts of the antisense target proteins. The decrease in the level of CP24 protein in the CP29 antisense lines indicates a physical interaction between these complexes. Analysis of chlorophyll fluorescence showed that removal of the proteins affected photosystem II function, probably as a result of changes in the organization of the light-harvesting antenna. However, whole plant measurements showed that overall photosynthetic rates were similar to those in the wild type. Both antisense lines were capable of the qE type of nonphotochemical fluorescence quenching, although there were minor changes in the capacity for quenching and in its induction kinetics. High-light-induced violaxanthin deepoxidation to zeaxanthin was not affected, although the pool size of these pigments was decreased slightly. We conclude that CP29 and CP26 are unlikely to be sites for nonphotochemical quenching.

Acclimation of Arabidopsis thaliana to the light environment: the existence of separate low light and high light responses.

The capacity for photosynthetic acclimation in Arabidopsis thaliana (L.) Heynh. cv. Landsberg erecta was assessed during growth over a broad range of irradiance. Discontinuities in the response to growth irradiance were revealed for the light- and CO2-saturated rate of photosynthesis (Pmax) and the ratio of chlorophyll a to chlorophyll b (Chl a/b). Three separate phases in the response of Pmax and Chl a/b to growth light were evident, with increases at low and high irradiance ranges and a plateau at intermediate irradiance. By measuring all chlorophyll-containing components of the thylakoid membrane that contribute to Chl a/b we reveal that distinct strategies for growth at low and high irradiance underlie the discontinuous response. These strategies include, in addition to changes in the major light-harvesting complexes of photosystem II (LHCII), large shifts in the amounts of both reaction centres as well as significant changes in the levels of minor LHCII and LHCI components.

A transposon insertion in the Escherichia coli uvrC gene; UvrC protein is absolutely required for the incision step in excision repair.

The formation of single-stranded breaks in DNA following UV irradiation is assessed in uvrC34 mutants. By altering the SOS DNA-repair system, either by additional mutations or by using drugs affecting transcription or translation, it is shown that such single-stranded breaks require one or more DNA-damage-inducible functions. A UV-sensitive strain is characterized as carrying a Tn10 insertion into the uvrC gene. The absence of post-irradiation incision in this strain demonstrates that uvrC function is absolutely required in vivo for the incision stage of excision repair, and suggests that other uvrC mutants are 'leaky'.

Acclimation of Arabidopsis thaliana to the light environment: the role of photoreceptors.

The regulation by light of the composition of the photosynthetic apparatus was investigated in photomorphogenic mutants of Arabidopsis thaliana (L.) Heynh. cv. Landsberg erecta. Leaf chlorophyll, photosynthesis, photosystem II function, and ribulose-1, 5-bisphosphate carboxylase-oxygenase and photosystem II contents were determined for plants grown under high- or low-irradiance growth regimes. Although certain mutant lines had altered chloroplast composition compared to the wild type, all photoreceptor mutants tested were capable of light-dependent changes in chloroplast composition and photosynthetic function, indicating that photoreceptors do not play a central role in the regulation of acclimation at the level of the chloroplast. However, the clear acclimation defect in a det1 signal transduction mutant indicates that photoreceptor-controlled responses either share regulatory components with acclimation, or are important in the expression of components which in turn regulate acclimation. We suggest that the COP/DET/FUS regulatory cluster is a focus for multiple signal transduction pathways, including some of the metabolic signals which form the basis for the acclimatory response.