Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling

Proximity labeling provides a powerful in vivo tool to characterize the proteome of subcellular structures and the interactome of specific proteins. The nematode Caenorhabditis elegans is one of the most intensely studied organisms in biology, offering many advantages for biochemistry. Using the highly active biotin ligase TurboID, we optimize here a proximity labeling protocol for C. elegans. An advantage of TurboID is that biotin''s high affinity for streptavidin means biotin-labeled proteins can be affinity-purified under harsh denaturing conditions. By combining extensive sonication with aggressive denaturation using SDS and urea, we achieved near-complete solubilization of worm proteins. We then used this protocol to characterize the proteomes of the worm gut, muscle, skin, and nervous system. Neurons are among the smallest C. elegans cells. To probe the method''s sensitivity, we expressed TurboID exclusively in the two AFD neurons and showed that the protocol could identify known and previously unknown proteins expressed selectively in AFD. The active zones of synapses are composed of a protein matrix that is difficult to solubilize and purify. To test if our protocol could solubilize active zone proteins, we knocked TurboID into the endogenous elks-1 gene, which encodes a presynaptic active zone protein. We identified many known ELKS-1-interacting active zone proteins, as well as previously uncharacterized synaptic proteins. Versatile vectors and the inherent advantages of using C. elegans, including fast growth and the ability to rapidly make and functionally test knock-ins, make proximity labeling a valuable addition to the armory of this model organism.     

Different determinants of exercise capacity in HFpEF compared to HFrEF

Background

Quality of life is as important as survival in heart failure (HF) patients. Controversies exist with regards to echocardiographic determinants of exercise capacity in HF, particularly in patients with preserved ejection fraction (HFpEF). The aim of this study was to prospectively examine echocardiographic parameters that correlate and predict functional exercise capacity assessed by 6 min walk test (6-MWT) in patients with HFpEF.

Methods

In 111 HF patients (mean age 63?±?10 years, 47% female), an echo-Doppler study and a 6-MWT were performed in the same day. Patients were divided into two groups based on the 6-MWT distance (Group I: ≤ 300 m and Group II: >300 m).

Results

Group I were older (p?=?0.008), had higher prevalence of diabetes (p?=?0.027), higher baseline heart rate (p?=?0.004), larger left atrium - LA (p?=?0.001), longer LV filling time - FT (p?=?0.019), shorter isovolumic relaxation time (p?=?0.037), shorter pulmonary artery acceleration time - PA acceleration time (p?=?0.006), lower left atrial lateral wall myocardial velocity (a’) (p?=?0.018) and lower septal systolic myocardial velocity (s’) (p?=?0.023), compared with Group II.Patients with HF and reduced EF (HFrEF) had lower hemoglobin (p?=?0.007), higher baseline heart rate (p?=?0.005), higher NT-ProBNP (p?=?0.001), larger LA (p?=?0.004), lower septal s’, e’, a’ waves, and septal mitral annular plane systolic excursion (MAPSE), shorter PA acceleration time (p?<?0.001 for all), lower lateral MAPSE, higher E/A & E/e’, and shorter LVFT (p?=?0.001 for all), lower lateral e’ (p?=?0.009), s’ (p?=?0.006), right ventricular e’ and LA emptying fraction (p?=?0.012 for both), compared with HFpEF patients.In multivariate analysis, only LA diameter [2.676 (1.242–5.766), p?=?0.012], and diabetes [0.274 (0.084–0.898), p?=?0.033] independently predicted poor 6-MWT performance in the group as a whole. In HFrEF, age [1.073 (1.012–1.137), p?=?0.018] and LA diameter [3.685 (1.348–10.071), p?=?0.011], but in HFpEF, lateral s’ [0.295 (0.099–0.882), p?=?0.029], and hemoglobin level [0.497 (0.248–0.998), p?=?0.049] independently predicted poor 6-MWT performance.

Conclusions

In HF patients determinants of exercise capacity differ according to severity of overall LV systolic function, with left atrial enlargement in HFrEF and longitudinal systolic shortening in HFpEF as the the main determinants.

     

Enhanced biological phosphate removal by granular sludge in a sequencing batch reactor

A laboratory-scale sequencing batch reactor was started-up with flocculated biomass and operated primarily for enhanced biological phosphate removal. Ten weeks after the start-up, gradual formation of granular sludge was observed. The compact biomass structure allowed halving the settling time, the initial reactor volume, and doubling the influent COD concentration. Continued operation confirmed the possibility of maintaining a stable granular biomass with a sludge volume index less than 40 ml g^–1, while securing a removal efficiency of 95% for carbon, 99.6% for phosphate, and 71% for nitrogen. Microscopic observations revealed a morphological diversity.