Inhibition of extracellular lipase from Streptomyces rimosus with 3,4-dichloroisocoumarin

Kinetic characterization of lipase inhibition was performed by activity measurement and mass spectrometry (MS), for the first time with serine-protease inhibitor 3,4-dichloroisocoumarin (DCI). Inhibition of Streptomyces rimosus extracellular lipase (SrLip), a member of the SGNH superfamily, by means of DCI follows the mechanism of two-step irreversible inhibition. The dissociation constant of the noncovalent E?I complex and first-order rate constant for inactivation were determined by incubation (K_i* = 26.6?±?2.8 µM, k₂ = 12.2?±?0.6 min–1) or progress curve (K_i* = 6.5?±?1.5 µM, k₂ = 0.11?±?0.01 min–1) method. Half-times of reactivation for lipase inhibited with 10-fold molar excess of DCI were determined by activity measurement (t_1/2 = 11.3?±?0.2?h), matrix-assisted laser desorption/ionization (MALDI, t_1/2 = 13.5?±?0.4?h), and electro-spray ionization (ESI, t_1/2 = 12.2?±?0.5?h) MS. The active SrLip concentration was determined by incubating the enzyme with near equimolar concentrations of DCI, followed by activity and MS measurement.     

Identification of endogenous acyl amino acids based on a targeted lipidomics approach

Using a partially purified bovine brain extract, our lab identified three novel endogenous acyl amino acids in mammalian tissues. The presence of numerous amino acids in the body and their ability to form amides with several saturated and unsaturated fatty acids indicated the potential existence of a large number of heretofore unidentified acyl amino acids. Reports of several additional acyl amino acids that activate G-protein coupled receptors (e.g., N-arachidonoyl glycine, N-arachidonoyl serine) and transient receptor potential channels (e.g., N-arachidonoyl dopamine, N-acyl taurines) suggested that some or many novel acyl amino acids could serve as signaling molecules. Here, we used a targeted lipidomics approach including specific enrichment steps, nano-LC/MS/MS, high-throughput screening of the datasets with a potent search algorithm based on fragment ion analysis, and quantification using the multiple reaction monitoring mode in Analyst software to measure the biological levels of acyl amino acids in rat brain. We successfully identified 50 novel endogenous acyl amino acids present at 0.2 to 69 pmol g⁻¹ wet rat brain.     

Structure of the Human TELO2-TTI1-TTI2 Complex

Phosphatidylinositol 3-kinase-related protein kinases (PIKKs) play critical roles in various metabolic pathways related to cell proliferation and survival. The TELO2-TTI1-TTI2 (TTT) complex has been proposed to recognize newly synthesized PIKKs and to deliver them to the R2TP complex (RUVBL1-RUVBL2-RPAP3-PIH1D1) and the heat shock protein 90 chaperone, thereby supporting their folding and assembly. Here, we determined the cryo-EM structure of the TTT complex at an average resolution of 4.2 Å. We describe the full-length structures of TTI1 and TELO2, and a partial structure of TTI2. All three proteins form elongated helical repeat structures. TTI1 provides a platform on which TELO2 and TTI2 bind to its central region and C-terminal end, respectively. The TELO2 C-terminal domain (CTD) is required for the interaction with TTI1 and recruitment of Ataxia-telangiectasia mutated (ATM). The N- and C-terminal segments of TTI1 recognize the FRAP-ATM-TRRAP (FAT) domain and the N-terminal HEAT repeats of ATM, respectively. The TELO2 CTD and TTI1 N- and C-terminal segments are required for cell survival in response to ionizing radiation.     

Effect of density on magnitude of directional selection on seed mass and emergence time in Plantago wrightiana Dcne. (Plantaginaceae)

Although population density is believed to be an important factor influencing evolutionary processes, surprisingly few studies have documented the existence or nature of density-dependent selection. We quantified the effects of density on directional selection on seed mass (the mass of a sown seed) and emergence time in the greenhouse and field for the annual plant Plantago wrightiana. In the greenhouse, we quantified selection on seed mass and emergence time at each of five planting densities (1 m^–2 to 10,000 m^–2) using the relationship between final plant mass and each trait at each density. We observed no significant selection on either seed mass or emergence time when plants were grown alone. At all higher densities, there was significant selection favoring early emergence and large seed mass, but there were no significant differences among the selection gradients determined at densities greater than individually grown plants. In the field, we detected no relationship between the magnitude of selection for early emergence and density. Our results suggest that selection on seed mass and time of emergence is density dependent, but the relationship between density and the magnitude of directional selection on these traits is not continuously increasing. Over broad ranges of density in the greenhouse and in the field, there was no detectable relationship between density and the magnitude of directional selection.     

Effects of nitrogen supply on the anatomy and chemical composition of leaves of four grass species belonging to the genus Poa, as determined by image-processing analysis and pyrolysis–mass spectrometry

Previous experiments have shown that the anatomy and chemical composition of leaves of inherently fast- and slow-growing grass species, grown at non-limiting nitrogen supply, differ systematically. The present experiment was carried out to investigate whether these differences persist when the plants are grown at an intermediate or a very low nitrogen supply. To this end, the inherently fast-growing Poa annua L. and Poa trivialis L., and the inherently slow-growing Poa compressa L. and Poa pratensis (L.) Schreb. were grown hydroponically at three levels of nitrate supply: at optimum (RGR_max) and at relative addition rates of 100 and 50 mmol N (mol N)^?1 d^?1 (RAR₁₀₀ and RAR₅₀), respectively. As expected, at the lowest N supply, the potentially fast-growing species grew at the same rate as the inherently slow-growing ones. Similarly, the differences in leaf area ratio (LAR, leaf area:total dry mass), specific leaf area (SLA, leaf arear:leaf dry mass) and leaf mass ratio (LMR, leaf dry mass:total dry mass) disappeared. Under optimal conditions, the fast-growing species differed from the slow-growing ones in that they had a higher N concentration. There were no significant differences in C concentration. With decreasing N supply, the total N concentration decreased and the differences between the species disappeared. The total C concentration increased for the fast-growing species and decreased for the slow-growing ones, i.e. the small, but insignificant, difference in C concentration between the species at RGR_max increased with decreasing N supply. The chemical composition of the leaves at low N supply, analysed in more detail by pyrolysis–mass spectrometry, showed an increase in the relative amounts of guaiacyl lignin, cellulose and hemicellulose, whereas those of syringyl lignin and protein decreased. The anatomy and morphology of the leaves of the four grass species differing in RGR_max were analysed by image-processing analysis. The proportion of the total volume occupied by mesophyll plus intercellular spaces and epidermis did not correlate with the amount of leaf mass per unit leaf area (specific leaf mass, SLM) at different N supply. The higher SLM at low N supply was caused partly by a high proportion of non-veinal sclerenchymatic cells per cross-section and partly by the smaller volume of epidermal cells. We conclude that the decrease in relative growth rate (and increase in SLM) at decreasing N supply is partly due to chemical and anatomical changes. The differences between the fast- and slow-growing grass species at an optimum nutrient supply diminished when plants were growing at a limiting nitrogen supply.     

Accuracy of body mass estimates of formalin-preserved fish – a review

This paper highlights possible effects of physical and chemical mechanisms of formalin fixation and preservation on biological tissue and reviews the consequent potential inaccuracies on estimates of body mass of small fishes fixed and preserved in formalin. Twenty-six papers including 65 independent experiments with 35 species which examine effects of formalin on body mass estimates on small fishes are included. The effect of the formalin on the specimens depends on the salinity of the water used to dilute the commercial formalin (usually 1:9 formalin: water) before being used to fixate and preserve fish. Mean wet body mass of the specimens from the studies using seawater or fresh water diluted formalin deceases by 13% and increases by 7%, respectively, from before to after being immersed in formalin. The same trend is found with condition factor in the few papers that report this parameter. Body length decreases on average by c. 2% in fixated and preserved fish regardless of whether the formalin is diluted in seawater or fresh water.     

Is GPR146 really the receptor for proinsulin C-peptide?

Proinsulin C-peptide has previously been proposed to interact with a G-protein coupled receptor (GPCR), specifically the orphan receptor GPR146. To investigate the potential of C-peptide in treating complications of diabetes, such as kidney damage, it is necessary to understand its mode of action. We used CHO-K1 cells expressing human GPR146 to study human and murine C-peptide in dynamic mass redistribution and GPCR β-arrestin assays, as well as with fluorescence confocal microscopy. Neither assay revealed any significant intracellular response to C-peptide at concentrations of up to 33 µM. We observed no internalisation of C-peptide by fluorescence microscopy. Our results do not support GPR146 as the receptor for C-peptide, but suggest that further investigations of the mode of action of C-peptide should be undertaken.     

Accurate MS-based Rab10 Phosphorylation Stoichiometry Determination as Readout for LRRK2 Activity in Parkinson's Disease

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Highlights

• •MS-based clinical assay that accurately determines phospho Rab10 occupancy.
• •Stable isotope labeled phosphopeptide injected as a standard with endogenous tryptic phospho Rab peptide for accurate ratio determination.
• •Determination of pRab levels in neutrophils of Parkinson disease patients.
• •Relevance of pRab levels as marker of PD.

     

Rethinking trophic niches: Speed and body mass colimit prey space of mammalian predators

1. Realized trophic niches of predators are often characterized along a one‐dimensional range in predator–prey body mass ratios. This prey range is constrained by an “energy limit” and a “subdue limit” toward small and large prey, respectively. Besides these body mass ratios, maximum speed is an additional key component in most predator–prey interactions.
2. Here, we extend the concept of a one‐dimensional prey range to a two‐dimensional prey space by incorporating a hump‐shaped speed‐body mass relation. This new “speed limit” additionally constrains trophic niches of predators toward fast prey.
3. To test this concept of two‐dimensional prey spaces for different hunting strategies (pursuit, group, and ambush predation), we synthesized data on 63 terrestrial mammalian predator–prey interactions, their body masses, and maximum speeds.
4. We found that pursuit predators hunt smaller and slower prey, whereas group hunters focus on larger but mostly slower prey and ambushers are more flexible. Group hunters and ambushers have evolved different strategies to occupy a similar trophic niche that avoids competition with pursuit predators. Moreover, our concept suggests energetic optima of these hunting strategies along a body mass axis and thereby provides mechanistic explanations for why there are no small group hunters (referred to as “micro‐lions”) or mega‐carnivores (referred to as “mega‐cheetahs”).
5. Our results demonstrate that advancing the concept of prey ranges to prey spaces by adding the new dimension of speed will foster a new and mechanistic understanding of predator trophic niches and improve our predictions of predator–prey interactions, food web structure, and ecosystem functions.

     

The Cap-Snatching SFTSV Endonuclease Domain Is an Antiviral Target

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