Genetic Diversity and Anti-Oxidative Potential of Streptomyces spp. Isolated from Unexplored Niches of Meghalaya, India.

Streptomyces is genetically and functionally diverse genus known to produce a wide array of phenolics and flavonoids with significant biotechnological applications. 52 isolates belonging to 26 species of Streptomyces collected from Meghalaya, India were analyzed for their genetic diversity using BOX-PCR. Significant inter- and intra- generic diversity was observed among the Streptomyces isolates especially those belonging to S. cacaoi, S. lavendulae, S. olivochromogenes, S. aureus, S. flavovirens. During bioactivity screening of the isolates, S. rectiviolaceus MJM72 recorded the highest DPPH activity (77.13 ± 0.91%) whereas S. antimycoticus MSCA162 showed excellent ABTS radical scavenging activity (99.65 ± 0.41%). On the other hand, S. novaecaesareae MJM58 had the highest (756.4 ± 7.38 µg GAE g-1 fresh weight) phenolic content while S. rectiviolaceus MJM72 was recorded with the highest flavonoid content (69.3 ± 0.12 µg QE g-1 fresh weight). As compared to total flavonoid content, total phenolic content had a stronger correlation with antioxidant activities. HPLC analysis of five selected isolates showed presence of gallic acid and pyrocatechol as predominant phenolics. In case of flavonoids, three isolates showed presence of rutin with S. rochei MSCA130 having the highest rutin content (0.95 µg g-1 fresh weight). The results of this study showed high genetic diversity and antioxidant potential among the Streptomyces isolates.

A Semi-Supervised Autoencoder-Based Approach for Protein Function Prediction.

After the development of next-generation sequencing techniques, protein sequences are abundantly available. Determining the functional characteristics of these proteins is costly and time-consuming. The gap between the number of protein sequences and their corresponding functions is continuously increasing. Advanced machine-learning methods have stepped up to fill this gap. In this work, an advanced deep-learning-based approach is proposed for protein function prediction using protein sequences. A set of autoencoders is trained in a semi-supervised manner with protein sequences. Each autoencoder corresponds to a single protein function only. In particular, 932 autoencoders corresponding to 932 biological processes and 585 autoencoders corresponding to 585 molecular functions are trained separately. Reconstruction losses of each protein sample for every autoencoder are used as a feature to classify these sequences into their corresponding functions. The proposed model is tested on test protein samples and achieves promising results. This method can be easily extended to predict any number of functions having an ample amount of supporting protein sequences. All relevant codes, data and trained models are available at https://github.com/richadhanuka/PFP-Autoencoders.

Characterization of the starch synthase under terminal heat stress and its effect on grain quality of wheat.

Terminal heat stress (HS) is a key barrier for wheat grain yield and quality. Various physiochemical and molecular parameters such as photosynthetic rate, expression analysis and activity of starch synthase (SS), total starch, amylose and amylopectin content, total amylolytic activity, and total antioxidant capacity (TAC) were analysed in wheat cvs.HD3059 (thermotolerant) and BT-Schomburgk (thermosusceptible) at grain-filling stage under HS (32 °C and 40 °C, 1 h). The decrease in photosynthetic rate was observed under HS. Expression analysis of the SS gene at transcript level showed downregulation in both the wheat cvs.HD3059 and BT-Schombugk under HS (32 °C and 40 ºC, 1 h) as compared to the control. Although the downregulation of SS gene transcript expression was less in HD3059 than BT-Schombugk. Both the cultivars showed decrease in starch synthase activity and starch content under HS and the overall content was higher in HD3059, compared to BT-Schomburgk. Higher total amylolytic activity and amylose content were observed in BT-Schomburgk. Scanning electron microscopy (SEM) showed un-structured starch granules under HS. Total antioxidant capacity (TAC) was found higher in HD3059 (14.07 mM FeSO4 gm-1 FW) compared to BT-Schomburgk (8.89 mM FeSO4 gm-1 FW) under HS (40 ºC, 1 h). Findings suggest that HS during grain filling stage had more severe impact on the overall physiochemical properties of the wheat grain. Thus the starch bisynthesis pathway associated gene(s) could be exploit to enhance the yield and quality of wheat under heat stress.

Biochemical Defense Response: Characterizing the Plasticity of Source and Sink in Spring Wheat under Terminal Heat Stress.

Wheat is highly prone to terminal heat stress (HS) under late-sown conditions. Delayed- sowing is one of the preferred methods to screen the genotypes for thermotolerance under open field conditions. We investigated the effect of terminal HS on the thermotolerance of four popular genotypes of wheat i.e. WR544, HD2967, HD2932, and HD2285 under field condition. We observed significant variations in the biochemical parameters like protein content, antioxidant activity, proline and total reducing sugar content in leaf, stem, and spike under normal (26 ± 2°C) and terminal HS (36 ± 2°C) conditions. Maximum protein, sugars and proline was observed in HD2967, as compared to other cultivars under terminal HS. Wheat cv. HD2967 showed more adaptability to the terminal HS. Differential protein-profiling in leaves, stem and spike of HD2967 under normal (26 ± 2°C) and terminal HS (36 ± 2°C) showed expression of some unique protein spots. MALDI-TOF/MS analysis showed the DEPs as RuBisCO (Rub), RuBisCO activase (Rca), oxygen evolving enhancer protein (OEEP), hypothetical proteins, etc. Expression analysis of genes associated with photosynthesis (Rub and Rca) and starch biosynthesis pathway (AGPase, SSS and SBE) showed significant variations in the expression under terminal HS. HD2967 showed better performance, as compared to other cultivars under terminal HS. SSS activity observed in HD2967 showed more stability under terminal HS, as compared with other cultivars. Triggering of different biochemical parameters in response to terminal HS was observed to modulate the plasticity of carbon assimilatory pathway. The identified DEPs will enrich the proteomic resources of wheat and will provide a potential biochemical marker for screening wheat germplasm for thermotolerance. The model hypothesized will help the researchers to work in a more focused way to develop terminal heat tolerant wheat without compromising with the quality and quantity of grains.

SSH Analysis of Endosperm Transcripts and Characterization of Heat Stress Regulated Expressed Sequence Tags in Bread Wheat.

Heat stress is one of the major problems in agriculturally important cereal crops, especially wheat. Here, we have constructed a subtracted cDNA library from the endosperm of HS-treated (42°C for 2 h) wheat cv. HD2985 by suppression subtractive hybridization (SSH). We identified ~550 recombinant clones ranging from 200 to 500 bp with an average size of 300 bp. Sanger's sequencing was performed with 205 positive clones to generate the differentially expressed sequence tags (ESTs). Most of the ESTs were observed to be localized on the long arm of chromosome 2A and associated with heat stress tolerance and metabolic pathways. Identified ESTs were BLAST search using Ensemble, TriFLD, and TIGR databases and the predicted CDS were translated and aligned with the protein sequences available in pfam and InterProScan 5 databases to predict the differentially expressed proteins (DEPs). We observed eight different types of post-translational modifications (PTMs) in the DEPs corresponds to the cloned ESTs-147 sites with phosphorylation, 21 sites with sumoylation, 237 with palmitoylation, 96 sites with S-nitrosylation, 3066 calpain cleavage sites, and 103 tyrosine nitration sites, predicted to sense the heat stress and regulate the expression of stress genes. Twelve DEPs were observed to have transmembrane helixes (TMH) in their structure, predicted to play the role of sensors of HS. Quantitative Real-Time PCR of randomly selected ESTs showed very high relative expression of HSP17 under HS; up-regulation was observed more in wheat cv. HD2985 (thermotolerant), as compared to HD2329 (thermosusceptible) during grain-filling. The abundance of transcripts was further validated through northern blot analysis. The ESTs and their corresponding DEPs can be used as molecular marker for screening or targeted precision breeding program. PTMs identified in the DEPs can be used to elucidate the thermotolerance mechanism of wheat-a novel step toward the development of "climate-smart" wheat.