Strigolactone inhibition of shoot branching

A carotenoid-derived hormonal signal that inhibits shoot branching in plants has long escaped identification. Strigolactones are compounds thought to be derived from carotenoids and are known to trigger the germination of parasitic plant seeds and stimulate symbiotic fungi. Here we present evidence that carotenoid cleavage dioxygenase 8 shoot branching mutants of pea are strigolactone deficient and that strigolactone application restores the wild-type branching phenotype to ccd8 mutants. Moreover, we show that other branching mutants previously characterized as lacking a response to the branching inhibition signal also lack strigolactone response, and are not deficient in strigolactones. These responses are conserved in Arabidopsis. In agreement with the expected properties of the hormonal signal, exogenous strigolactone can be transported in shoots and act at low concentrations. We suggest that endogenous strigolactones or related compounds inhibit shoot branching in plants. Furthermore, ccd8 mutants demonstrate the diverse effects of strigolactones in shoot branching, mycorrhizal symbiosis and parasitic weed interaction.     

The evaluation of measurement uncertainties and its epistemological ramifications

The way metrologists conceive of measurement has undergone a major shift in the last two decades. This shift can in great part be traced to a change in the statistical methods used to deal with the expression of measurement results, and, more particularly, with the calculation of measurement uncertainties. Indeed, as we show, the incapacity of the frequentist approach to the calculus of uncertainty to deal with systematic errors has prompted the replacement of the customary frequentist methods by fully Bayesian procedures. The epistemological ramifications of the Bayesian approach merge with a deep empiricist mood tantamount to an “epistemic turn”: measurement results are analysed in terms of degrees of belief, and central concepts such as error and accuracy are called into question. We challenge the perspective entailed by this epistemic turn: we insist on the centrality of the concepts of error and accuracy by underlining the intentional character of measurement that is intimately linked to the process of correction of experimental data. We further circumvent the difficulties posed by the classical analysis of measurement by stressing the social rather than the epistemic dimension of measurement activities.     

Abscisic acid controls calcium-dependent egress and development in Toxoplasma gondii

Calcium controls a number of critical events, including motility, secretion, cell invasion and egress by apicomplexan parasites. Compared to animal and plant cells, the molecular mechanisms that govern calcium signalling in parasites are poorly understood. Here we show that the production of the phytohormone abscisic acid (ABA) controls calcium signalling within the apicomplexan parasite Toxoplasma gondii, an opportunistic human pathogen. In plants, ABA controls a number of important events, including environmental stress responses, embryo development and seed dormancy. ABA induces production of the second-messenger cyclic ADP ribose (cADPR), which controls release of intracellular calcium stores in plants. cADPR also controls intracellular calcium release in the protozoan parasite T. gondii; however, previous studies have not revealed the molecular basis of this pathway. We found that addition of exogenous ABA induced formation of cADPR in T. gondii, stimulated calcium-dependent protein secretion, and induced parasite egress from the infected host cell in a density-dependent manner. Production of endogenous ABA within the parasite was confirmed by purification (using high-performance liquid chromatography) and analysis (by gas chromatography-mass spectrometry). Selective disruption of ABA synthesis by the inhibitor fluridone delayed egress and induced development of the slow-growing, dormant cyst stage of the parasite. Thus, ABA-mediated calcium signalling controls the decision between lytic and chronic stage growth, a developmental switch that is central in pathogenesis and transmission. The pathway for ABA production was probably acquired with an algal endosymbiont that was retained as a non-photosynthetic plastid known as the apicoplast. The plant-like nature of this pathway may be exploited therapeutically, as shown by the ability of a specific inhibitor of ABA synthesis to prevent toxoplasmosis in the mouse model.     

Integrated analysis of somatic mutations and focal copy-number changes identifies key genes and pathways in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is the most common primary liver malignancy. Here, we performed high-resolution copy-number analysis on 125 HCC tumors and whole-exome sequencing on 24 of these tumors. We identified 135 homozygous deletions and 994 somatic mutations of genes with predicted functional consequences. We found new recurrent alterations in four genes (ARID1A, RPS6KA3, NFE2L2 and IRF2) not previously described in HCC. Functional analyses showed tumor suppressor properties for IRF2, whose inactivation, exclusively found in hepatitis B virus (HBV)-related tumors, led to impaired TP53 function. In contrast, inactivation of chromatin remodelers was frequent and predominant in alcohol-related tumors. Moreover, association of mutations in specific genes (RPS6KA3-AXIN1 and NFE2L2-CTNNB1) suggested that Wnt/β-catenin signaling might cooperate in liver carcinogenesis with both oxidative stress metabolism and Ras/mitogen-activated protein kinase (MAPK) pathways. This study provides insight into the somatic mutational landscape in HCC and identifies interactions between mutations in oncogene and tumor suppressor gene mutations related to specific risk factors.     

Exploration of molecular dynamics during transient sorption of fluids in mesoporous materials

In recent years, considerable progress has been made in the development of novel porous materials with controlled architectures and pore sizes in the mesoporous range. An important feature of these materials is the phenomenon of adsorption hysteresis: for certain ranges of applied pressure, the amount of a molecular species adsorbed by the mesoporous host is higher on desorption than on adsorption, indicating a failure of the system to equilibrate. Although this phenomenon has been known for over a century, the underlying internal dynamics responsible for the hysteresis remain poorly understood. Here we present a combined experimental and theoretical study in which microscopic and macroscopic aspects of the relaxation dynamics associated with hysteresis are quantified by direct measurement and computer simulations of molecular models. Using nuclear magnetic resonance techniques and Vycor porous glass as a model mesoporous system, we have explored the relationship between molecular self-diffusion and global uptake dynamics. For states outside the hysteresis region, the relaxation process is found to be essentially diffusive in character; within the hysteresis region, the dynamics slow down dramatically and, at long times, are dominated by activated rearrangement of the adsorbate density within the host material.     

Birth and adaptive evolution of a hominoid gene that supports high neurotransmitter flux

The enzyme glutamate dehydrogenase (GDH) is important for recycling the chief excitatory neurotransmitter, glutamate, during neurotransmission. Human GDH exists in housekeeping and brain-specific isotypes encoded by the genes GLUD1 and GLUD2, respectively. Here we show that GLUD2 originated by retroposition from GLUD1 in the hominoid ancestor less than 23 million years ago. The amino acid changes responsible for the unique brain-specific properties of the enzyme derived from GLUD2 occurred during a period of positive selection after the duplication event.     

Evolutionary biology: adaptive developmental plasticity in snakes

The morphology of organisms is generally well matched to their environment, presumably because expression of their genes is tailored either at the population or the individual level to suit local conditions: for example, snake populations that persistently encounter large prey may accumulate gene mutations that specify a large head size, or head growth may be increased in individual snakes to meet local demands (adaptive developmental plasticity). Here we test the relative contributions of genetics and environment to the jaw sizes of two tiger snake populations: one that consumes small prey on the mainland, and an island population that relies on larger prey and has a larger jaw size. Although the idea of adaptive plasticity in response to environmental pressures is controversial, we find that both factors influence the difference in jaw size between the two populations, and the influence of developmental plasticity is greater in the island population.