In-Silico Analyses of Nonsynonymous Variants in the BRCA1 Gene

BReast CAncer gene 1 (BRCA1)—a tumor suppressor gene plays an important role in the DNA repair mechanism. Several BRCA1 variants perturb its structure and function, including synonymous and nonsynonymous single nucleotide polymorphisms (SNPs). In the present study, we performed in-silico analyses of nonsynonymous SNPs (nsSNPs) of the BRCA1 gene. In total, 122 nsSNPs were retrieved from the NCBI SNP database and in-silico analyses were performed using computational prediction tools: SIFT, PROVEAN, Mutation Taster, PolyPhen-2, MutPred, and ConSurf. Of these tools, SIFT, PROVEAN, and Mutation Taster predicted 61 out of 122 nsSNPs as “damaging”, based on structural homology analysis. PolyPhen-2 classified 22 nsSNPs as “probably damaging”. These nsSNPs were further analyzed by MutPred to predict basic molecular mechanisms of amino acid alteration. ConSurf analysis predicted eleven conserved amino acid residues with structural and functional consequences. We identified five amino acid residues in the RING finger domain (L22, C39, H41, C44, and C47) and two in the BRCT domain (P1771 and I1707) with the potential to deter the BRCA1 protein function. This study provides insights into the effect of nsSNPs and amino acid substitutions in BRCA1.

     

Predation of potential insect pests in oil palm plantations,rubber tree plantations,and fruit orchards

In human‐modified landscapes, important ecological functions such as predation are negatively affected by anthropogenic activities, including the use of pesticides and habitat degradation. Predation of insect pests is an indicator of healthy ecosystem functioning, which provides important ecosystem services, especially for agricultural systems. In this study, we compare predation attempts from arthropods, mammals, and birds on artificial caterpillars in the understory, between three tropical agricultural land‐use types: oil palm plantations, rubber tree plantations, and fruit orchards. We collected a range of local and landscape‐scale data including undergrowth vegetation structure; elevation; proximity to forest; and canopy cover in order to understand how environmental variables can affect predation. In all three land‐use types, our results showed that arthropods and mammals were important predators of artificial caterpillars and there was little predation by birds. We did not find any effect of the environmental variables on predation. There was an interactive effect between land‐use type and predator type. Predation by mammals was considerably higher in fruit orchards and rubber tree than in oil palm plantations, likely due to their ability to support higher abundances of insectivorous mammals. In order to maintain or enhance natural pest control in these common tropical agricultural land‐use types, management practices that benefit insectivorous animals should be introduced, such as the reduction of pesticides, improvement of understory vegetation, and local and landscape heterogeneity.     

Lewis histo-blood group α1,3/α1,4 fucose residues may both mediate binding to GII.4 noroviruses

Human noroviruses cause recurrent epidemics of gastroenteritis known to be dominated by the clinically important GII.4 genotype which recognizes human Secretor gene-dependent ABH histo-blood group antigens (HBGAs) as attachment factors. There is increasing evidence that GII.4 noroviruses have undergone evolutionary changes to recognize Lewis antigens and non-Secretor saliva. In this study, we have investigated the possibilities of the Lewis α1,3/α1,4 fucoses as mediators of binding of GII.4 noroviruses to Lewis antigens. The study was carried out using molecular dynamics simulations of Lewis type-1 and type-2 chain HBGAs in complex with VA387 P domain dimers in explicit water. Based on the computer simulations, we suggest the possibility of two receptor binding modes for Lewis HBGAs: the "Secretor pose" with the Secretor Fucα1,2 in the binding site and the "Lewis pose" with the Lewis Fucα1,3/α1,4 residues in the binding site. This was further supported by an extensive GlyVicinity analysis of the Protein Data Bank with respect to the occurrence of the Lewis and Secretor poses in complexes of Lewis antigens with lectins and antibodies as well as GII norovirus strains. The Lewis pose can also explain the interactions of GII.4 norovirus strains with Le(x) and SLe(x) structures. Moreover, the present model suggests binding of complex branched polysaccharides, with the Lewis antigens at the nonreducing end, to P domain dimers of GII.4 strains. Our results are relevant for understanding the evolution of norovirus binding specificities and for in silico design of future antiviral therapeutics.     

3D Vertically Aligned and Interconnected Porous Carbon Nanosheets as Sulfur Immobilizers for High Performance Lithium‐Sulfur Batteries

A unique nanostructure of 3D and vertically aligned and interconnected porous carbon nanosheets (3D‐VCNs) is demonstrated by a simple carbonization of agar. The key feature of 3D‐VCNs is that they possess numerous 3D channels with macrovoids and mesopores, leading to high surface area of 1750 m² g^?1, which play an important role in loading large amount of sulfur, while vertically aligned microporous carbon nanosheets act as the multilayered physical barrier against polysulfides anions and prevent their dissolution in the electrolyte due to strong adsorption during cycling process. As a result, the 3D hybrid (3D‐S‐VCNs) infiltered with 68.3 wt% sulfur exhibits a high and stable reversible capacity of 844 mAh g^?1 at the current density of 837 mA g^?1 with excellent Coulombic efficiency ≈100%, capacity retention of ≈80.3% over 300 cycles, and good rate ability (the reversible capacity of 738 mAh g^?1 at the high current density of 3340 mA g^?1). The present work highlights the vital role of the introduction of 3D carbon nanosheets with macrovoids and mesopores in enhancing the performance of LSBs.     

Inhibition of Mushroom Formation and Induction of Glycerol Release—Ecological Strategies of Burkholderia terrae BS001 to Create a Hospitable Niche at the Fungus Lyophyllum sp. Strain Karsten

We investigated the ecological strategies exerted by the soil bacterium Burkholderia terrae BS001 at the hyphae of the soil saprotrophic fungus Lyophyllum sp. strain Karsten. Recently, this bacterium has been reported to form biofilms around, and to comigrate with, growing hyphae of Lyophyllum sp. strain Karsten. In addition, it was found to be able to utilize fungal metabolites. Here, we extend this work to shed some light on the interactions between the bacterial and fungal partner which allow ecological success for the former. In standing liquid microcosms inoculated with Lyophyllum sp. strain Karsten, we detected, upon prolonged incubation, the formation of a mycelial mat at the liquid–air interface. From this mat, primordia were formed after 4–6 weeks, which eventually resulted in mushrooms. However, upon addition of strain BS001 to the bulk liquid, mushroom formation from the fungal mat was clearly inhibited, as evidenced by (1) the formation of significantly lower numbers of primordia and (2) a delay of the onset of primordia formation. Moreover and importantly, the presence of strain BS001 caused the fungus to secrete large amounts of exudates at the mycelial mat, whereas such exudation was absent from control (uninoculated) or Escherichia coli K12- or Variovorax paradoxus BS64-inoculated microcosms. In the exudates, glycerol was the main carbonaceous component, and this compound could be easily utilized by strain BS001. Thus, in different experimental set-ups with the fungal partner, strain BS001 was shown to grow in the fungal exudates on the mat. The two fungal-interactive phenotypes were specific for B. terrae strain BS001, as the other bacteria used in our study, i.e. E. coli K12 and V. paradoxus BS64, did not exhibit any of these phenomena.