Unusual RNA plant virus integration in the soybean genome leads to the production of small RNAs

Horizontal gene transfer (HGT) is known to be a major force in genome evolution. The acquisition of genes from viruses by eukaryotic genomes is a well-studied example of HGT, including rare cases of non-retroviral RNA virus integration. The present study describes the integration of cucumber mosaic virus RNA-1 into soybean genome. After an initial metatranscriptomic analysis of small RNAs derived from soybean, the de novo assembly resulted a 3029-nt contig homologous to RNA-1. The integration of this sequence in the soybean genome was confirmed by DNA deep sequencing. The locus where the integration occurred harbors the full RNA-1 sequence followed by the partial sequence of an endogenous mRNA and another sequence of RNA-1 as an inverted repeat and allowing the formation of a hairpin structure. This region recombined into a retrotransposon located inside an exon of a soybean gene. The nucleotide similarity of the integrated sequence compared to other Cucumber mosaic virus sequences indicates that the integration event occurred recently. We described a rare event of non-retroviral RNA virus integration in soybean that leads to the production of a double-stranded RNA in a similar fashion to virus resistance RNAi plants.

Unfolding studies on soybean agglutinin and concanavalin a tetramers: A comparative account

The unfolding pathway of two very similar tetrameric legume lectins soybean agglutinin (SBA) and Concanavalin A ( ConA) were determined using GdnCl-induced denaturation. Both proteins displayed a reversible two-state unfolding mechanism. The analysis of isothermal denaturation data provided values for conformational stability of the two proteins. It was found that the DeltaG of unfolding of SBA was much higher than ConA at all the temperatures at which the experiments were done. ConA had a T-g 18 degreesC less than SBA. The higher conformational stability of SBA in comparison to ConA is largely due to substantial differences in their degrees of subunit interactions. Ionic interactions at the interface of the two proteins especially at the noncanonical interface seem to play a significant role in the observed stability differences between these two proteins. Furthermore, SBA is a glycoprotein with a GlcNac(2)Man(9) chain attached to Asn-75 of each subunit. The sugar chain in SBA lies at the noncanonical interface of the protein, and it is found to interact with the amino acid residues in the adjacent noncanonical interface. These interactions further stabilize SBA with respect to ConA, which is not glycosylated.

Enzymatic Degradation of Poly(soybean oil-g-methyl methacrylate)

This study discusses grafting of methyl methacrylate units from thepolymeric soybean oil peroxide to produce poly(soybean oil-graft-methyl methacrylate) (PSO-g-PMMA). The degradation of this copolymer in solution was evaluated in the presence of different lipases, viz Candida rugosa (CR), Lipolase 100T (LP), Novozym 435 (N435) and Porcine pancreas (PP), at different temperatures The copolymer degraded by specific chain end scission and the mass fraction of the specific product evolved was determined The degradation was modeled using continuous distribution kinetics to determine the rate coefficients ofmenzymatic chain end scission and deactivation of the enzyme The enzymes, CR. LP and N435 exhibited maximum activity for the degradation of PSO-g-PMMA at 60 degrees C, while PP was most active at 50 degrees C. The thermal degradability of the copolymer, assessed by thermo-gravimetry, indicated that the activation energy of degradation of the copolymer was 154 kJ mol(-1), which was lesser than that of the PMMA homopolymer.

Studies on the tryptophan residues of soybean agglutinin. Involvement in saccharide binding

Modification of tryptophan side chains of soybean agglutinin (SBA) with N-bromosuccinimide results in a loss of the hemagglutinating and carbohydrate binding activities of the protein. One residue/subunit is probably essential for the binding activity. Modification leads to a large decrease in the fluorescene of the protein accompained by a blue shift. Iodide ion quenching of the protein fluorescence shows that saccharide binding results in a decreased accessibility of some of the tryptophan side chains. These results strongly point towards the involvement of tryptophan residues in the active site of SBA.

Copolyesters from Soybean Oil for Use as Resorbable Biomaterials

A family of soybean oil (SO) based biodegradable cross-linked copolyesters sourced from renewable resources was developed for use as resorbable biomaterials. The polyesters were prepared by a melt condensation of epoxidized soybean oil polyol and sebacic acid with citric acid (CA) as a cross-linker. D-Mannitol (M) was added as an additional reactant to improve mechanical properties. Differential scanning calorimetry revealed that the polyester synthesized using only CA as the cross-linker was semicrystalline and elastomeric at physiological temperature. The polymers were hydrophobic in nature. The water wettability, elongation at break and the degradation rate of the polyesters decreased with increase in M content or curing time. Modeling of release kinetics of dyes showed a diffusion controlled mechanism underlies the observed sustained release from these polymers. The polyesters supported attachment and proliferation of human stem cells and were thus cytocompatible. Porous scaffolds induced osteogenic differentiation of the stern cells suggesting that these polymers are well suited for bone tissue engineering. Thus, this family of polyesters offers a low cost and green alternative as biocompatible, bioresobable polymers for potential use as resorbable biomaterials for tissue engineering and controlled release.

Impact of glycosylation on stability, structure and unfolding of soybean agglutinin (SBA): an insight from thermal perturbation molecular dynamics simulations

Glycosylation has been recognized as one of the most prevalent and complex post-translational modifications of proteins involving numerous enzymes and substrates. Its effect on the protein conformational transitions is not clearly understood yet. In this study, we have examined the effect of glycosylation on protein stability using molecular dynamics simulation of legume lectin soybean agglutinin (SBA). Its glycosylated moiety consists of high mannose type N-linked glycan (Man(9)GlcNAc(2)). To unveil the structural perturbations during thermal unfolding of these two forms, we have studied and compared them to the experimental results. From the perspective of dynamics, our simulations revealed that the nonglycosylated monomeric form is less stable than corresponding glycosylated form at normal and elevated temperatures. Moreover, at elevated temperature thermal destabilization is more prominent in solvent exposed loops, turns and ends of distinct beta sheets. SBA maintains it folded structure due to some important saltbridges, hydrogen bonds and hydrophobic interactions within the protein. The reducing terminal GlcNAc residues interact with the protein residues VAL161, PRO182 and SER225 via hydrophobic and via hydrogen bonding with ASN 9 and ASN 75. Our simulations also revealed that single glycosylation (ASN75) has no significant effect on corresponding cis peptide angle orientation. This atomistic description might have important implications for understanding the functionality and stability of Soybean agglutinin.

Digestibility and nutrient utilization of soybean milk concentrate based diets in Oreochromis niloticus

The digestibility and utilisation of two fresh soybean milk concentrate based diets, two stale soybean milk concentrate based diets and two Fishman based diets serving as control, at optimal (30%) and suboptimal (20%) protein levels were evaluated in Oreochromis niloticus. The diets were as follows: Diet I (control) - fishmeal based diet at 30% crude protein, Diet II (control) Fishman based diet at 20% crude protein, Diet III - fresh soybean milk concentrate based diet at 30% crude protein, Diet IV - fresh soybean milk concentrate based diet at 20%, Diet V - stale soybean milk concentrate based diet at 30% crude protein, Diet VI-stale soybean milk concentrate based diet at 20%. Dry matter digestibility differed not significantly with variation in diets (P:0.05). A significant variation was recorded in the protein, lipid and ash digestibility. Proteins were more digestible at optimum than suboptimum level. Ash digestibility was lowest of all the nutrients. Variations in the utilisation of the diets in terms of weight gain, specific growth rate, food conversion ration, protein efficiency ration and apparent net protein utilization were insignificant (P: 0.05). All diets compared favourably with the standard control diet Diet I. This findings suggest the suitability of stale soybean milk concentrate utilisation as protein supplements in the diets of late fry Oreochromis niloticus

Digestibility and nutrient utilisation of soybean bran-based diets in Nile tilapia Oreochromis niloticus

The digestibility and utilisation of two soybean bran-based diets and two fishmeal-based diets serving as control, at optimal (30%) and suboptimal (20%) protein levels were evaluated in Oreochromis niloticus. These were Diet I (Control)-fishmeal based diet at 30% crude protein, Diet II (Control) - fishmeal based diet at 20% crude protein, Diet III - hydrolysed Soybean Bran based diet at 30% crude protein, Diet IV - hydrolysed Soybean Bran based diet at 20%. Dry matter digestibility differed insignificantly with variation in diets (P<0.05). There was significant variation in the protein (p 20.05), lipid and ash digestibility. Protein was more digestible at optimum level than sub-optimum level, while lipid and ash digestibility did not vary with their inclusion levels. Variation in the utilisation of the diets was significant (P<0.05) except for survival. It was observed that the best diet was Diet 1, closely followed by Diet II with highest values of mean final weight, specific growth rate, protein efficiency ratio and the apparent net protein utilisation. The high digestibility values of Diets III and IV suggests their inclusion in fish diet to spare protein for growth

Estimation of growth and financial analysis through the application of Ipil ipil (Leucaena leucocephala) leaf meal as supplements to soybean and fish meal in the diet of juvenile monosex tilapia (Oreochromis niloticus)

Among plant protein ingredients,ipil ipil (Leucaena leucocephala) leafmeal (ILLM) is considered the most nutritive plant protein source after soybean meal in aquatic feeds. That was proven in a 21-day experiment conducted to assess the response of juvenile Monosex Nile tilapia Oreochromis niloticus with four iso-nitrogenous formulated diets: One control diet was formulated based on fishmeal, one on soybean meal and one on rice bran, ipil ipil leafmeal was also included in experimental diets.

Effect of substituting animal protein sources with soybean meal in diets of Oreochromis karongae (Trewavas 1941)

Three diets were formulated using locally available feed ingredients in Malawi to test the effect of replacing animal protein (fish meal, meat and bone meal) with soybean meal (10:0, 5:5, 0:10% of diet) as the protein source on growth and feed conversion of Oreochromis karongae. There were no significant differences in growth rate (GR), specific growth rate (SGR) and feed conversion ratios (FCR) among the three diets. It can be concluded that more expensive and limited animal protein sources can totally be replaced by cheaper soybean in order to get similar growth rates in O. karongae.