Unveiling Contacts within Macromolecular Assemblies by Solving Minimum Weight Connectivity Inference (MWC) Problems*

Consider a set of oligomers listing the subunits involved in subcomplexes of a macromolecular assembly, obtained e.g. using native mass spectrometry or affinity purification. Given these oligomers, connectivity inference (CI) consists of finding the most plausible contacts between these subunits, and minimum connectivity inference (MCI) is the variant consisting of finding a set of contacts of smallest cardinality. MCI problems avoid speculating on the total number of contacts but yield a subset of all contacts and do not allow exploiting a priori information on the likelihood of individual contacts. In this context, we present two novel algorithms, MILP-W and MILP-W_B. The former solves the minimum weight connectivity inference (MWCI), an optimization problem whose criterion mixes the number of contacts and their likelihood. The latter uses the former in a bootstrap fashion to improve the sensitivity and the specificity of solution sets.Experiments on three systems (yeast exosome, yeast proteasome lid, human eIF3), for which reference contacts are known (crystal structure, cryo electron microscopy, cross-linking), show that our algorithms predict contacts with high specificity and sensitivity, yielding a very significant improvement over previous work, typically a twofold increase in sensitivity.The software accompanying this paper is made available and should prove of ubiquitous interest whenever connectivity inference from oligomers is faced.     

Genotypic and Phenotypic Characterization of P23H Line 1 Rat Model

Rod-cone dystrophy, also known as retinitis pigmentosa (RP), is the most common inherited degenerative photoreceptor disease, for which no therapy is currently available. The P23H rat is one of the most commonly used autosomal dominant RP models. It has been created by incorporation of a mutated mouse rhodopsin (Rho) transgene in the wild-type (WT) Sprague Dawley rat. Detailed genetic characterization of this transgenic animal has however never been fully reported. Here we filled this knowledge gap on P23H Line 1 rat (P23H-1) and provide additional phenotypic information applying non-invasive and state-of-the-art in vivo techniques that are relevant for preclinical therapeutic evaluations. Transgene sequence was analyzed by Sanger sequencing. Using quantitative PCR, transgene copy number was calculated and its expression measured in retinal tissue. Full field electroretinography (ERG) and spectral domain optical coherence tomography (SD-OCT) were performed at 1-, 2-, 3- and 6-months of age. Sanger sequencing revealed that P23H-1 rat carries the mutated mouse genomic Rho sequence from the promoter to the 3’ UTR. Transgene copy numbers were estimated at 9 and 18 copies in the hemizygous and homozygous rats respectively. In 1-month-old hemizygous P23H-1 rats, transgene expression represented 43% of all Rho expressed alleles. ERG showed a progressive rod-cone dysfunction peaking at 6 months-of-age. SD-OCT confirmed a progressive thinning of the photoreceptor cell layer leading to the disappearance of the outer retina by 6 months with additional morphological changes in the inner retinal cell layers in hemizygous P23H-1 rats. These results provide precise genotypic information of the P23H-1 rat with additional phenotypic characterization that will serve basis for therapeutic interventions, especially for those aiming at gene editing.     

Exploring the fate of inhaled monoclonal antibody in the lung parenchyma by microdialysis

Therapeutic antibodies (Abs) are emerging as major drugs to treat respiratory diseases, and inhalation may provide substantial benefits for their delivery. Understanding the behavior of Abs after pulmonary deposition is critical for their development. We investigated the pharmacokinetics of a nebulized Ab by continuous sampling in lung parenchyma using microdialysis in non-human primates. We defined the optimal conditions for microdialysis of Ab and demonstrated that lung microdialysis of Ab is feasible over a period of several days. The concentration-profile indicated a two-phase non-linear elimination and/or distribution of inhaled mAbX. Lung exposition was higher than the systemic one over a period of 33 hours and above MabX affinity for its target. The microdialysis results were supported by an excellent relationship with dosages from lung extracts.     

Current trends in the structure-activity relationships of sialyltransferases

Sialyltransferases (STs) represent an important group of enzymes that transfer N-acetylneuraminic acid (Neu5Ac) from cytidine monophosphate-Neu5Ac to various acceptor substrates. In higher animals, sialylated oligosaccharide structures play crucial roles in many biological processes but also in diseases, notably in microbial infection and cancer. Cell surface sialic acids have also been found in a few microorganisms, mainly pathogenic bacteria, and their presence is often associated with virulence. STs are distributed into five different families in the CAZy database (http://www.cazy.org/). On the basis of crystallographic data available for three ST families and fold recognition analysis for the two other families, STs can be grouped into two structural superfamilies that represent variations of the canonical glycosyltransferase (GT-A and GT-B) folds. These two superfamilies differ in the nature of their active site residues, notably the catalytic base (a histidine or an aspartate residue). The observed structural and functional differences strongly suggest that these two structural superfamilies have evolved independently.     

Effects of a phosphorus amendment and the pH of water used for watering on the mobility and phytoavailability of Cd, Pb and Zn in highly contaminated kitchen garden soils

Studies on two lead and zinc smelters in Northern France (Metaleurop Nord and Umicore) showed that the level of metallic contamination of kitchen garden soils is higher than the agricultural soils located in the same environment. This results most particularly from cropping practices and the addition of various products. Due to the physical and chemical parameters of these soils, the behaviour and transfer of pollutants towards various plants (grass, trees, and vegetables) may be perceptibly different than what is observed on agricultural soils.For a better understanding of pollutant behaviour in kitchen garden topsoils, the Cd, Pb and Zn was fractionated using the SM&T protocol and various extracting solutions (CaCl₂, acetic acid, and citric acid) to evaluate their mobility in two highly contaminated soils chosen in the area affected by the past atmospheric emissions of the two smelters. In addition, agricultural topsoil was sampled in a non-massively contaminated area and was therefore chosen as the control soil.The three soils were amended with a mixture of hydroxyapatite (HA) and diammonium phosphate (DAP). At 6 months, extracting procedures were carried out to evaluate the effects of the amendment on the mobility of Cd, Pb and Zn. This step was then supplemented by an evaluation of the impact of the amendment on the phytoavailability of pollutants, which was determined in plant uptake studies with ryegrass (Lolium perenne L.) by considering only the pollutant concentrations in their shoots. Two experiments were carried out. In the first one, unamended and amended soils and ryegrass were watered with distilled water (pH = 7). In the second one, osmosed water (pH = 5.5) was used to evaluate the effects of the acid water-phosphate amendment system on the mobility and phytoavailability of Cd, Pb and Zn. Six months after the start of the experiments, the selective extractions showed that the effectiveness of the amendment studied depended on the element, the soil and the water's pH. Reductions of metal eluted from the contaminated soils were 1.5-37.9% for Cd, and 9.1-80.9% for Pb. Application of P amendment to the combination of osmosed water was generally the most effective for immobilising Cd and Pb elution. In contrast, the mixture of HA and DAP was ineffective for reducing Zn elution. The plant-fresh biomass yield was significantly (p < 0.05) increased by the combination of P amendment and distilled water, whereas a reduction of biomass was recorded with the combined amendment and osmosed water. Addition of P amendment generally reduced Pb uptake in ryegrass shoots (1-47%), while both Cd and Zn were increased by 17.9-79% and 0.45-100%, respectively.     

Zinc(II) modulates specifically amyloid formation and structure in model peptides

Metal ions such as zinc and copper can have dramatic effects on the aggregation kinetics of and the structures formed by several amyloidogenic peptides/proteins. Depending on the identity of the amyloidogenic peptide/protein and the conditions, Zn(II) and Cu(II) can promote or inhibit fibril formation, and in some cases these metal ions have opposite effects. To better understand this modulation of peptide aggregation by metal ions, the impact of Zn(II) binding to three amyloidogenic peptides (Aβ14-23, Aβ11-23, and Aβ11-28) on the formation and structure of amyloid-type fibrils was investigated. Zn(II) was able to accelerate fibril formation for all three peptides as measured by thioflavin T fluorescence and transmission electron microscopy. The effects of Zn(II) on Aβ11-23 and Aβ11-28 aggregation were very different compared with the effects of Cu(II), showing that these promoting effects were metal-specific. X-ray absorption spectroscopy suggested that the Zn(II) binding to Aβ11-23 and Aβ11-28 is very different from Cu(II) binding, but that the binding is similar in the case of Aβ14-23. A model is proposed in which the different coordination chemistry of Zn(II) compared with Cu(II) explains the metal-specific effect on aggregation and the difference between peptides Aβ14-23 and Aβ11-23/Aβ11-28.     

Ionomics suggests niche differences between sympatric heathers (Ericaceae)

Plant and Soil - The co-existence of large number of competing plant species with the same basic needs is a major question in ecology, particularly when this involves closely related species. We...     

Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline

1. Download high-res image (316KB)
2. Download full-size image