Structural basis of tubulin tyrosination by tubulin tyrosine ligase

Tubulin tyrosine ligase (TTL) catalyzes the post-translational retyrosination of detyrosinated α-tubulin. Despite the indispensable role of TTL in cell and organism development, its molecular mechanism of action is poorly understood. By solving crystal structures of TTL in complex with tubulin, we here demonstrate that TTL binds to the α and β subunits of tubulin and recognizes the curved conformation of the dimer. Biochemical and cellular assays revealed that specific tubulin dimer recognition controls the activity of the enzyme, and as a consequence, neuronal development. The TTL–tubulin structure further illustrates how the enzyme binds the functionally crucial C-terminal tail sequence of α-tubulin and how this interaction catalyzes the tyrosination reaction. It also reveals how TTL discriminates between α- and β-tubulin, and between different post-translationally modified forms of α-tubulin. Together, our data suggest that TTL has specifically evolved to recognize and modify tubulin, thus highlighting a fundamental role of the evolutionary conserved tubulin tyrosination cycle in regulating the microtubule cytoskeleton.     

Solitary and repetitive binding motifs for the AP2 complex alpha-appendage in amphiphysin and other accessory proteins

Adaptor protein (AP) complexes bind to transmembrane proteins destined for internalization and to membrane lipids, so linking cargo to the accessory internalization machinery. This machinery interacts with the appendage domains of APs, which have platform and beta-sandwich subdomains, forming the binding surfaces for interacting proteins. Proteins that interact with the subdomains do so via short motifs, usually found in regions of low structural complexity of the interacting proteins. So far, up to four motifs have been identified that bind to and partially compete for at least two sites on each of the appendage domains of the AP2 complex. Motifs in individual accessory proteins, their sequential arrangement into motif domains, and partial competition for binding sites on the appendage domains coordinate the formation of endocytic complexes in a temporal and spatial manner. In this work, we examine the dominant interaction sequence in amphiphysin, a synapse-enriched accessory protein, which generates membrane curvature and recruits the scission protein dynamin to the necks of coated pits, for the platform subdomain of the alpha-appendage. The motif domain of amphiphysin1 contains one copy of each of a DX(F/W) and FXDXF motif. We find that the FXDXF motif is the main determinant for the high affinity interaction with the alpha-adaptin appendage. We describe the optimal sequence of the FXDXF motif using thermodynamic and structural data and show how sequence variation controls the affinities of these motifs for the alpha-appendage.     

Affordable Nutrient Solutions for Improved Food Security as Evidenced by Crop Trials

The continuing depletion of nutrients from agricultural soils in Sub-Saharan African is accompanied by a lack of substantial progress in crop yield improvement. In this paper we investigate yield gaps for corn under two scenarios: a micro-dosing scenario with marginal increases in nitrogen (N) and phosphorus (P) of 10 kg ha⁻¹ and a larger yet still conservative scenario with proposed N and P applications of 80 and 20 kg ha⁻¹ respectively. The yield gaps are calculated from a database of historical FAO crop fertilizer trials at 1358 locations for Sub-Saharan Africa and South America. Our approach allows connecting experimental field scale data with continental policy recommendations. Two critical findings emerged from the analysis. The first is the degree to which P limits increases in corn yields. For example, under a micro-dosing scenario, in Africa, the addition of small amounts of N alone resulted in mean yield increases of 8% while the addition of only P increased mean yields by 26%, with implications for designing better balanced fertilizer distribution schemes. The second finding was the relatively large amount of yield increase possible for a small, yet affordable amount of fertilizer application. Using African and South American fertilizer prices we show that the level of investment needed to achieve these results is considerably less than 1% of Agricultural GDP for both a micro-dosing scenario and for the scenario involving higher yet still conservative fertilizer application rates. In the latter scenario realistic mean yield increases ranged between 28 to 85% in South America and 71 to 190% in Africa (mean plus one standard deviation). External investment in this low technology solution has the potential to kick start development and could complement other interventions such as better crop varieties and improved economic instruments to support farmers.     

Multimarker Proteomic Profiling for the Prediction of Cardiovascular Mortality in Patients with Chronic Heart Failure

Risk stratification of patients with systolic chronic heart failure (HF) is critical to better identify those who may benefit from invasive therapeutic strategies such as cardiac transplantation. Proteomics has been used to provide prognostic information in various diseases. Our aim was to investigate the potential value of plasma proteomic profiling for risk stratification in HF. A proteomic profiling using surface enhanced laser desorption ionization - time of flight - mass spectrometry was performed in a case/control discovery population of 198 patients with systolic HF (left ventricular ejection fraction <45%): 99 patients who died from cardiovascular cause within 3 years and 99 patients alive at 3 years. Proteomic scores predicting cardiovascular death were developed using 3 regression methods: support vector machine, sparse partial least square discriminant analysis, and lasso logistic regression. Forty two ion m/z peaks were differentially intense between cases and controls in the discovery population and were used to develop proteomic scores. In the validation population, score levels were higher in patients who subsequently died within 3 years. Similar areas under the curves (0.66 – 0.68) were observed for the 3 methods. After adjustment on confounders, proteomic scores remained significantly associated with cardiovascular mortality. Use of the proteomic scores allowed a significant improvement in discrimination of HF patients as determined by integrated discrimination improvement and net reclassification improvement indexes. In conclusion, proteomic analysis of plasma proteins may help to improve risk prediction in HF patients.     

Dominance of Geobacteraceae in BTX-degrading enrichments from an iron-reducing aquifer

Microbial community structure was linked to degradation potential in benzene-, toluene- or xylene- (BTX) degrading, iron-reducing enrichments derived from an iron-reducing aquifer polluted with landfill leachate. Enrichments were characterized using 16S rRNA gene-based analysis, targeting of the benzylsuccinate synthase-encoding bssA gene and phospholipid fatty acid (PLFA) profiling in combination with tracking of labelled substrate. 16S rRNA gene analysis indicated the dominance of Geobacteraceae, and one phylotype in particular, in all enrichments inoculated with polluted aquifer material. Upon cultivation, progressively higher degradation rates with a concomitant decrease in species richness occurred in all primary incubations and successive enrichments. Yet, the same Geobacteraceae phylotype remained common and dominant, indicating its involvement in BTX degradation. However, the bssA gene sequences in BTX degrading enrichments differed considerably from those of Geobacter isolates, suggesting that the first steps of toluene, but also benzene and xylene oxidation, are carried out by another member of the enrichments. Therefore, BTX would be synthrophically degraded by a bacterial consortium in which Geobacteraceae utilized intermediate metabolites. PLFA analysis in combination with (13)C-toluene indicated that the enriched Geobacteraceae were assimilating carbon originally present in toluene. Combined with previous studies, this research suggests that Geobacteraceae play a key role in the natural attenuation of each BTX compound in situ.     

Slow infusions of vinblastine in the treatment of adult idiopathic thrombocytopenic purpura: a report on 43 cases

Forty-three adult patients with idiopathic thrombocytopenic purpura (ITP) were treated by slow intravenous infusions of vinblastine. Nineteen had ITP of recent onset (i.e. of less than 6 months duration) and had contraindication to steroids (3 patients), refractoriness to steroids (6 patients) or to steroids and high dose intravenous immunoglobulins (IVIg, 10 patients). Of the 19 patients, 10 achieved complete response (CR), 2 achieved partial response (PR), 2 had minor response (MR) and the remaining 5 patients had no response (NR). Six of the complete responders remained in CR after 12 to 48 months, whereas all other responders relapsed within 3 months, in spite of maintenance therapy. Twenty-four patients had chronic ITP (i.e. of 6 months duration or more) and had showed no or only transient response to steroids and/or splenectomy, and in many of them, to other therapeutic approaches. Four achieved CR, 4 PR, 6 MR and 10 NR. All but 3 responses were shorter than 3 months, in spite of maintenance therapy. Most responses to slow infusions of vinblastine began after the first infusion. Main side effects included leukopenia in 9 patients (but with absolute neutropenia in only one) and peripheral neuropathy in 2 patients. Interval from diagnosis was the only prognostic factor of response to treatment. We conclude that slow infusions of vinblastine may be a useful approach in ITP of recent onset, when contraindication or refractoriness to steroids and/or IVIg exists. In our experience, this treatment has limited benefit in chronic ITP. In addition, it remains to be demonstrated that slow infusions of vinca alkaloids have any superiority over intravenous bolus injections of the same drugs.     

High photosynthetic capacity of Sahelian C3 and C4 plants

Photosynthesis Research - The semi-arid ecosystems of the African Sahel play an important role in the global carbon cycle and are among the most sensitive ecosystems to future environmental...     

The structural biology of the dynamin‐related proteins: New insights into a diverse,multitalented family

Dynamin‐related proteins are multidomain, mechanochemical GTPases that self‐assemble and orchestrate a wide array of cellular processes. Over the past decade, structural insights from X‐ray crystallography and cryo‐electron microscopy have reshaped our mechanistic understanding of these proteins. Here, we provide a historical perspective on these advances that highlights the structural attributes of different dynamin family members and explores how these characteristics affect GTP hydrolysis, conformational coupling and oligomerization. We also discuss a number of lingering challenges remaining in the field that suggest future directions of study.     

Budget Constraints Affect Male Rats’ Choices between Differently Priced Commodities

Demand theory can be applied to analyse how a human or animal consumer changes her selection of commodities within a certain budget in response to changes in price of those commodities. This change in consumption assessed over a range of prices is defined as demand elasticity. Previously, income-compensated and income-uncompensated price changes have been investigated using human and animal consumers, as demand theory predicts different elasticities for both conditions. However, in these studies, demand elasticity was only evaluated over the entirety of choices made from a budget. As compensating budgets changes the number of attainable commodities relative to uncompensated conditions, and thus the number of choices, it remained unclear whether budget compensation has a trivial effect on demand elasticity by simply sampling from a different total number of choices or has a direct effect on consumers’ sequential choice structure. If the budget context independently changes choices between commodities over and above price effects, this should become apparent when demand elasticity is assessed over choice sets of any reasonable size that are matched in choice opportunities between budget conditions. To gain more detailed insight in the sequential choice dynamics underlying differences in demand elasticity between budget conditions, we trained N=8 rat consumers to spend a daily budget by making a number of nosepokes to obtain two liquid commodities under different price regimes, in sessions with and without budget compensation. We confirmed that demand elasticity for both commodities differed between compensated and uncompensated budget conditions, also when the number of choices considered was matched, and showed that these elasticity differences emerge early in the sessions. These differences in demand elasticity were driven by a higher choice rate and an increased reselection bias for the preferred commodity in compensated compared to uncompensated budget conditions, suggesting a budget context effect on relative valuation.