Site-specific incorporation of phosphotyrosine using an expanded genetic code.

Access to phosphoproteins with stoichiometric and site-specific phosphorylation status is key to understanding the role of protein phosphorylation. Here we report an efficient method to generate pure, active phosphotyrosine-containing proteins by genetically encoding a stable phosphotyrosine analog that is convertible to native phosphotyrosine. We demonstrate its general compatibility with proteins of various sizes, phosphotyrosine sites and functions, and reveal a possible role of tyrosine phosphorylation in negative regulation of ubiquitination

Lysine 27 Ubiquitination of the Mitochondrial Transport Protein Miro Is Dependent on Serine 65 of the Parkin Ubiquitin Ligase

Mitochondrial transport plays an important role in matching mitochondrial distribution to localised energy production and calcium buffering requirements. Here we demonstrate that Miro1, an outer mitochondrial membrane (OMM) protein crucial for the regulation of mitochondrial trafficking and distribution, is a substrate of the PINK1/Parkin mitochondrial quality control system in human dopaminergic neuroblastoma cells. Moreover Miro1 turnover on damaged mitochondria is altered in Parkinson's disease (PD) patient derived fibroblasts containing a pathogenic mutation in the PARK2 gene (encoding Parkin). By analysing the kinetics of Miro1 ubiquitination we further demonstrate that mitochondrial damage triggers rapid (within minutes) and persistent K27 type ubiquitination of Miro1 on the OMM, dependent on PINK1 and Parkin. Proteasomal degradation of Miro1 is then seen on a slower timescale, within 2-3 hours of the onset of ubiquitination. We find Miro ubiquitination in dopaminergic neuroblastoma cells is independent of Miro1 phosphorylation at serine 156 (S156), but is dependent on the recently identified serine S65 residue within Parkin that is phosphorylated by PINK1. Interestingly we find that Miro1 can stabilise phospho-mutant versions of Parkin on the OMM, suggesting that Miro is also part of a Parkin receptor complex. Moreover, we demonstrate that S65 in Parkin is critical for regulating Miro levels upon mitochondrial damage in rodent cortical neurons. Our results provide new insights into the ubiquitination-dependent regulation of the Miro-mediated mitochondrial transport machinery by PINK1/Parkin and also suggest that disruption of this regulation may be implicated in PD pathogenesis

RBR ligase–mediated ubiquitin transfer: a tale with many twists and turns

RBR ligases are an enigmatic class of E3 ubiquitin ligases that combine properties of RING and HECT-type E3s and undergo multilevel regulation through autoinhibition, post-translational modifications, multimerization and interaction with binding partners. Here, we summarize recent progress in RBR structures and function, which has uncovered commonalities in the mechanisms by which different family members transfer ubiquitin through a multistep process. However, these studies have also highlighted clear differences in the activity of different family members, suggesting that each RBR ligase has evolved specific properties to fit the biological process it regulates

Differences in tidal breathing between infants with chronic lung diseases and healthy controls

BACKGROUND: The diagnostic value of tidal breathing (TB) measurements in infants is controversially discussed. The aim of this study was to investigate to what extent the breathing pattern of sleeping infants with chronic lung diseases (CLD) differ from healthy controls with the same postconceptional age and to assess the predictive value of TB parameters. METHODS: In the age of 36–42 postconceptional weeks TB measurements were performed in 48 healthy newborns (median age and weight 7d, 3100 g) and 48 infants with CLD (80d, 2465 g)) using the deadspace-free flow-through technique. Once the infants had adapted to the mask and were sleeping quietly and breathing regularly, 20–60 breathing cycles were evaluated. Beside the shape of the tidal breathing flow-volume loop (TBFVL) 18 TB parameters were analyzed using ANOVA with Bonferroni correction. Receiver-operator characteristic (ROC) curves were calculated to investigate the discriminative ability of TB parameters. RESULTS: The incidence of concave expiratory limbs in CLD infants was 31% and significantly higher compared to controls (2%) (p < 0.001). Significant differences between CLD infants and controls were found in 11/18 TB parameters. The largest differences were seen in the mean (SD) inspiratory time 0.45(0.11)s vs. 0.65(0.14)s (p < 0.0001) and respiratory rate (RR) 55.4(14.2)/min vs. 39.2(8.6)/min (p < 0.0001) without statistically significant difference in the discriminative power between both time parameters. Most flow parameters were strongly correlated with RR so that there is no additional diagnostic value. No significant differences were found in the tidal volume and commonly used TB parameters describing the expiratory flow profile. CONCLUSION: The breathing pattern of CLD infants differs significantly from that of healthy controls. Concave TBFVL and an increased RR measured during quiet sleep and under standardized conditions may indicate diminished respiratory functions in CLD infants whereas most of the commonly used TB parameters are poorly predictive

Pollination and Predation Limit Fruit Set in a Shrub, Bourreria succulents (Boraginaceae), after Hurricanes on San Salvador Island, Bahamas 1

Hurricanes have been assumed to reduce the reproduction of plants, either directly by leaf stripping and stress or indirectly by reducing pollinators. I examined the pollination and fruit set of a common shrub, Bourreria succulenta , after hurricanes on San Salvador island, Bahamas. Contrary to the assumption of resource limitation, B. succulenta showed unusually prolific flowering after Hurricane Lili stripped leaves from most of the plants in October 1996. I predicted that the abundant flowering would saturate pollinators and that fruit set would be pollination-limited. Fruit set was strongly pollination-limited by 71 percent. Butterflies are probably the major pollinators and were present at the site, but they rarely visited B. succulenta flowers even though flowers were brimming with nectar. Nectarivorous birds (Bananaquits and Bahama Wbodstars) visit B. succulenta flowers, but their populations were decimated by Hurricane Lili and they rarely visited flowers during this time. Fruit set was also severely predation-limited; a moth caterpillar (Gelechiidae) was extremely abundant and ate buds, flowers, and fruits, causing a further 68 percent reduction in fruit set. Together, pollination limitation and predation limitation reduced fruit set to only 7 percent or less. Predation was also intense in 1999 after Hurricane Floyd and resulted in 11 percent fruit set or less. Whether or not hurricanes were the cause of limited pollinators or abundant predators, the resulting low fruit set could have population effects because hurricanes can provide opportunities for the recruitment of new plants. These results emphasize that understanding plant–animal interactions may be necessary for predicting the effects of hurricanes on plant reproductive success, which may affect subsequent recruitment. Species on small islands like San Salvador (150 km 2 ) with relatively few species may be especially vulnerable to environmental disturbances such as hurricanes.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75721/1/j.1744-7429.2001.tb00184.x.pd

Un élément fini de poutre fissurée application à la dynamique des arbres tournants

International audienceDans ce travail on présente une méthode originale de construction d'un élément fini de poutre affectée de fissurations. La souplesse additionnelle due à la présence des fissures est identifiée à partir de calculs éléments finis tridimensionnels tenant compte des conditions de contact unilatéral entre les lèvres. Cette souplesse est répartie sur toute la longueur de l'élément dont on se propose de construire la matrice de rigidité. La démarche permet un gain considérable en temps de calcul par rapport à la représentation nodale de la section fissurée lors de l'intégration temporelle de systèmes différentiels en dynamique des structures

A Realistic Validation Study of a New Nitrogen Multiple-Breath Washout System

Background For reliable assessment of ventilation inhomogeneity, multiple-breath washout (MBW) systems should be realistically validated. We describe a new lung model for in vitro validation under physiological conditions and the assessment of a new nitrogen (N2)MBW system. Methods The N2MBW setup indirectly measures the N2 fraction (FN2) from main-stream carbon dioxide (CO2) and side-stream oxygen (O2) signals: FN2 = 1−FO2−FCO2−FArgon. For in vitro N2MBW, a double chamber plastic lung model was filled with water, heated to 37°C, and ventilated at various lung volumes, respiratory rates, and FCO2. In vivo N2MBW was undertaken in triplets on two occasions in 30 healthy adults. Primary N2MBW outcome was functional residual capacity (FRC). We assessed in vitro error (√[difference]2) between measured and model FRC (100–4174 mL), and error between tests of in vivo FRC, lung clearance index (LCI), and normalized phase III slope indices (Sacin and Scond). Results The model generated 145 FRCs under BTPS conditions and various breathing patterns. Mean (SD) error was 2.3 (1.7)%. In 500 to 4174 mL FRCs, 121 (98%) of FRCs were within 5%. In 100 to 400 mL FRCs, the error was better than 7%. In vivo FRC error between tests was 10.1 (8.2)%. LCI was the most reproducible ventilation inhomogeneity index. Conclusion The lung model generates lung volumes under the conditions encountered during clinical MBW testing and enables realistic validation of MBW systems. The new N2MBW system reliably measures lung volumes and delivers reproducible LCI values

Determination of the pK(a) of the N-terminal amino group of ubiquitin by NMR

This work was supported by the Medical Research Council (grants U117533887 and grant U117565398 until March 2015) and by the Francis Crick Institute which receives its core funding from Cancer Research UK (FC001142, FC10029), the UK Medical Research Council (FC001142, FC10029), and the Wellcome Trust (FC001142, FC10029)