Small angle X-ray scattering-assisted protein structure prediction in CASP13 and emergence of solution structure differences

Small angle X-ray scattering (SAXS) measures comprehensive distance information on a protein's structure, which can constrain and guide computational structure prediction algorithms. Here, we evaluate structure predictions of 11 monomeric and oligomeric proteins for which SAXS data were collected and provided to predictors in the 13th round of the Critical Assessment of protein Structure Prediction (CASP13). The category for SAXS-assisted predictions made gains in certain areas for CASP13 compared to CASP12. Improvements included higher quality data with size exclusion chromatography-SAXS (SEC-SAXS) and better selection of targets and communication of results by CASP organizers. In several cases, we can track improvements in model accuracy with use of SAXS data. For hard multimeric targets where regular folding algorithms were unsuccessful, SAXS data helped predictors to build models better resembling the global shape of the target. For most models, however, no significant improvement in model accuracy at the domain level was registered from use of SAXS data, when rigorously comparing SAXS-assisted models to the best regular server predictions. To promote future progress in this category, we identify successes, challenges, and opportunities for improved strategies in prediction, assessment, and communication of SAXS data to predictors. An important observation is that, for many targets, SAXS data were inconsistent with crystal structures, suggesting that these proteins adopt different conformation(s) in solution. This CASP13 result, if representative of PDB structures and future CASP targets, may have substantive implications for the structure training databases used for machine learning, CASP, and use of prediction models for biology.     

A new approach to divalent thio-azo ligands; Ni(dpesdt)2

The preparation of a new bis(2-pyridylethylsulfanyl)-1,3-dithiole-2-one (1) and the first example of a tetra-azo substituted bisdithiolene transition metal complex, Ni(dpesdt)₂ (2) are reported. This complex crystallizes in two polymorphs, one is triclinic, and the other is monoclinic, P2₁/n space group.     

Xylitol production by <Emphasis Type="Italic">Debaryomyces hansenii</Emphasis> in brewery spent grain dilute-acid hydrolysate: effect of supplementation

A brewery spent-grain hemicellulosic hydrolysate was used for xylitol production by Debaryomyces hansenii. Addition of 6 g yeast extract/l increased the xylitol yield to 0.57 g/g, and productivity to 0.51 g/l h that were, respectively, 1.4 -and 1.8-times higher than the values obtained with non-supplemented hydrolysate. When corn steep liquor was combined with 3 g yeast extract/l, the highest xylitol yield, 0.58 g/g, was obtained with a similar productivity.     

Role of Reactive Oxygen Species in the Initiation of Plant Retrograde Signaling

The interaction between the nucleus and the different organelles is important in the physiology of the plant. Reactive oxygen species (ROS) are a by-product of the oxidation of organic molecules to obtain energy by the need to carry out the electron transfer between the different enzymatic complexes. However, they also have a role in the generation of what is known as retrograde signaling. This signal comes from the different organelles in which the oxidation of molecules or the electron transference is taking place such as mitochondria and chloroplasts. Furthermore, ROS can also induce the release of signals from the apoplast. It seems that these signals plays a role communicating to the nucleus the current status of the different parts of the plant cell to induce a changes in gene expression. In this review, the molecular mechanism of ROS retrograde signaling is described.

     

Fine mapping and candidate gene analysis of a dravet syndrome modifier locus on mouse chromosome 11

Mammalian Genome - Pathogenic variants in SCN1A result in a spectrum of phenotypes ranging from mild febrile seizures to Dravet syndrome, a severe infant-onset epileptic encephalopathy. Individuals...     

One for all and all for one: retention of colour‐unchanged old flowers increases pollinator attraction in a hermaphroditic plant

• Long‐lived flowers increase pollen transfer rates, but these entail high water and carbon maintenance costs. The retention of pollinated and reward‐free old flowers enhances pollinator visitation to young receptive flowers by increasing floral display size. This mechanism is associated with acropetal inflorescences or changes in flower colour and openness, but the retention of unchanging solitary flowers remains overlooked.
• We examined pollination‐dependent variation in floral longevity and determined stigmatic receptivity, pollen viability and pollen removal rates among flower ages in Kielmeyera regalis, a Neotropical savanna shrub. We also evaluated the effects of floral display size on pollinator visitation rates. Lastly, we determined whether old flowers are unvisited and exclusively increase pollinator attraction to young flowers through flower removal experiments.
• Regardless of pollination treatment, flowers lasted fully open with no detectable physical changes for 3 days. Over time, stigmas remained receptive but >95% of pollen was removed. Pollinator visitation significantly increased with floral display size and intermediate percentages (15–30%) of newly opened flowers. Accordingly, the retention of reward‐free and unvisited old flowers increased young flower–pollinator interaction.
• Our results reveal the importance of a prolonged floral longevity in increasing pollinator attraction toward newly opened receptive flowers without changes in flower colour and form. We conclude that the retention of pollinated, reward‐free and unvisited colour‐unchanged old flowers in K. regalis is a strategy that counteracts the water use costs associated with the maintenance of large flowers with increased mate opportunities in a pollen‐limited scenario.

     

Factors associated with the occurrence of Triatoma sordida (Hemiptera: Reduviidae) in rural localities of Central-West Brazil

This study estimates the factors of artificial environments (houses and peridomestic areas) associated with Triatoma sordida occurrence. Manual searches for triatomines were performed in 136 domiciliary units (DUs) in two rural localities of Central-West Brazil. For each DU, 32 structural, 23 biotic and 28 management variables were obtained. Multiple logistic regression analysis was performed in order to identify statistically significant variables associated with occurrence of T. sordida in the study areas. A total of 1,057 specimens (99% in peridomiciles, mainly chicken coops) of T. sordida were collected from 63 DUs (infestation: 47%; density: ~8 specimens/DU; crowding: ~17 specimens/infested DU; colonisation: 81%). Only six (0.6%) out of 945 specimens examined were infected with Trypanosoma cruzi. The final adjusted logistic regression model indicated that the probability of T. sordida occurrence was higher in DU with wooden chicken coops, presence of > 30 animals in wooden corrals, presence of wood piles and presence of food storeroom. The results show the persistence of T. sordida in peridomestic habitats in rural localities of Central-West Brazil. However, the observed low intradomestic colonisation and minimal triatomine infection rates indicate that T. sordida has low potential to sustain high rates of T. cruzi transmission to residents of these localities.