Alternative splicing shapes the transcriptome complexity in blackgram [Vigna mungo (L.) Hepper].

Vigna mungo, a highly consumed crop in the pan-Asian countries, is vulnerable to several biotic and abiotic stresses. Understanding the post-transcriptional gene regulatory cascades, especially alternative splicing (AS), may underpin large-scale genetic improvements to develop stress-resilient varieties. Herein, a transcriptome based approach was undertaken to decipher the genome-wide AS landscape and splicing dynamics in order to establish the intricacies of their functional interactions in various tissues and stresses. RNA sequencing followed by high-throughput computational analyses identified 54,526 AS events involving 15,506 AS genes that generated 57,405 transcripts isoforms. Enrichment analysis revealed their involvement in diverse regulatory functions and demonstrated that transcription factors are splicing-intensive, splice variants of which are expressed differentially across tissues and environmental cues. Increased expression of a splicing regulator NHP2L1/SNU13 was found to co-occur with lower intron retention events. The host transcriptome is significantly impacted by differential isoform expression of 1172 and 765 AS genes that resulted in 1227 (46.8% up and 53.2% downregulated) and 831 (47.5% up and 52.5% downregulated) transcript isoforms under viral pathogenesis and Fe2+ stressed condition, respectively. However, genes experiencing AS operate differently from the differentially expressed genes, suggesting AS is a unique and independent mode of regulatory mechanism. Therefore, it can be inferred that AS mediates a crucial regulatory role across tissues and stressful situations and the results would provide an invaluable resource for future endeavours in V. mungo genomics.

Engineering Catalytically Active Sites by Sculpting Artificial Edges on MoS2 Basal Plane for Dinitrogen Reduction at a Low Overpotential.

Engineering catalytically active sites have been a challenge so far and often relies on optimization of synthesis routes, which can at most provide quantitative enhancement of active facets, however, cannot provide control over choosing orientation, geometry and spatial distribution of the active sites. Artificially sculpting catalytically active sites via laser-etching technique can provide a new prospect in this field and offer a new species of nanocatalyst for achieving superior selectivity and attaining maximum yield via absolute control over defining their location and geometry of every active site at a nanoscale precision. In this work, a controlled protocol of artificial surface engineering is shown by focused laser irradiation on pristine MoS2 flakes, which are confirmed as catalytic sites by electrodeposition of AuNPs. The preferential Au deposited catalytic sites are found to be electrochemically active for nitrogen adsorption and its subsequent reduction due to the S-vacancies rather than Mo-vacancy, as advocated by DFT analysis. The catalytic performance of Au-NR/MoS2 shows a high yield rate of ammonia (11.43 × 10-8  mol s-1 cm-2 ) at a potential as low as -0.1 V versus RHE and a notable Faradaic efficiency of 13.79% during the electrochemical nitrogen reduction in 0.1 m HCl.

Deciphering the role of alternative splicing as modulators of defense response in the MYMIV-Vigna mungo pathosystem.

Alternative splicing (AS) is a crucial regulatory mechanism that impacts transcriptome and proteome complexity under stressful situations. Although its role in abiotic stresses is somewhat understood, our understanding of the mechanistic regulation of pre-messenger RNA splicing in plant-pathogen interaction is meager. To comprehend this unexplored immune reprogramming mechanism, transcriptome profiles of Mungbean Yellow Mosaic India Virus (MYMIV)-resistant and susceptible Vigna mungo genotypes were analyzed for AS genes that may underlie the resistance mechanism. Results revealed a repertoire of AS-isoforms accumulated during pathogenic infestation, with intron retention being the most common AS mechanism. Identification of 688 differential alternatively spliced (DAS) genes in the resistant host elucidates its robust antiviral response, whereas 322 DAS genes were identified in the susceptible host. Enrichment analyses confirmed DAS transcripts pertaining to stress, signaling, and immune system pathways have undergone maximal perturbations. Additionally, a strong regulation of the splicing factors has been observed both at the transcriptional and post-transcriptional levels. qPCR validation of candidate DAS transcripts with induced expression upon MYMIV infection demonstrated a competent immune response in the resistant background. The AS-impacted genes resulted either in partial/complete loss of functional domains or altered sensitivity to micro-RNA-mediated gene silencing. A complex regulatory module, miR7517-ATAF2, has been identified in an aberrantly spliced ATAF2 isoform that exposes an intronic miR7517 binding site, thereby suppressing the negative regulator to enhance the defense reaction. The present study establishes AS as a noncanonical immune reprogramming mechanism that operates in parallel, thereby offering an alternative strategy for developing yellow mosaic-resistant V. mungo cultivars.

Application of ZnO Nanoparticles Encapsulated in Mesoporous Silica on the Abaxial Side of a Solanum lycopersicum Leaf Enhances Zn Uptake and Translocation via the Phloem.

Foliar application of nutrient nanoparticles (NPs) is a promising strategy for improving fertilization efficiency in agriculture. Phloem translocation of NPs from leaves is required for efficient fertilization but is currently considered to be feasible only for NPs smaller than a cell wall pore size exclusion limit of <20 nm. Using mass spectrometry imaging, we provide here the first direct evidence for phloem localization and translocation of a larger (∼70 nm) fertilizer NP comprised of ZnO encapsulated in mesoporous SiO2 (ZnO@MSN) following foliar deposition. The Si content in the phloem tissue of the petiole connected to the dosed leaf was ∼10 times higher than in the xylem tissue, and ∼100 times higher than the phloem tissue of an untreated tomato plant petiole. Direct evidence of NPs in individual phloem cells has only previously been shown for smaller NPs introduced invasively in the plant. Furthermore, we show that uptake and translocation of the NPs can be enhanced by their application on the abaxial (lower) side of the leaf. Applying ZnO@MSN to the abaxial side of a single leaf resulted in a 56% higher uptake of Zn as well as higher translocation to the younger (upper) leaves and to the roots, than dosing the adaxial (top) side of a leaf. The higher abaxial uptake of NPs is in alignment with the higher stomatal density and lower density of mesophyll tissues on that side and has not been demonstrated before.

Idiopathic Pericardial Ossification Causing Chronic Constrictive Pericarditis.

BACKGROUND: Chronic constrictive pericarditis (CCP) is usually caused by the fibroinflammatory reaction of the visceral and parietal pericardium that encase the heart. The cause of CCP is various including tuberculosis, trauma, prior surgery, radiation, and malignancy. MATERIAL AND METHODS: We examined the pericardiectomy specimen of a case of CCP in a 17-year-old boy. RESULTS: The histopathology of the pericardium revealed pericardial ossification bony remodeling and hematopoiesis within the intertrabecular marrow spaces. No granulomatous or neoplastic etiology was identified. CONCLUSION: Idiopathic pericardial ossification can cause CCP in pediatric patients.

14-3-3 proteins protect AMPK-phosphorylated ten-eleven translocation-2 (TET2) from PP2A-mediated dephosphorylation.

Ten-eleven translocation-2 (TET2) is a member of the methylcytosine dioxygenase family of enzymes and has been implicated in cancer and aging because of its role as a global epigenetic modifier. TET2 has a large N-terminal domain and a catalytic C-terminal region. Previous reports have demonstrated that the TET2 catalytic domain remains active independently of the N-terminal domain. As such, the function of the N terminus of this large protein remains poorly characterized. Here, using yeast two-hybrid screening, co-immunoprecipitation, and several biochemical assays, we found that several isoforms of the 14-3-3 family of proteins bind TET2. 14-3-3 proteins bound TET2 when it was phosphorylated at Ser-99. In particular, we observed that AMP-activated protein kinase-mediated phosphorylation at Ser-99 promotes TET2 stability and increases global DNA 5-hydroxymethylcytosine levels. The interaction of 14-3-3 proteins with TET2 protected the Ser-99 phosphorylation, and disruption of this interaction both reduced TET2 phosphorylation and decreased TET2 stability. Furthermore, we noted that protein phosphatase 2A can interact with TET2 and dephosphorylate Ser-99. Collectively, these results provide detailed insights into the role of the TET2 N-terminal domain in TET2 regulation. Moreover, they reveal the dynamic nature of TET2 protein regulation that could have therapeutic implications for disease states resulting from reduced TET2 levels or activity.

Exploring the GRAS gene family in common bean (Phaseolus vulgaris L.): characterization, evolutionary relationships, and expression analyses in response to abiotic stresses.

MAIN CONCLUSION: Genome-wide identification reveals 55 PvuGRAS genes belonging to 16 subfamilies and their gene structures and evolutionary relationships were characterized. Expression analyses highlight their prominence in plant growth, development and abiotic stress responses. GRAS proteins comprise a plant-specific transcription factor family involved in multiple growth regulatory pathways and environmental cues including abiotic/biotic stresses. Despite its crucial importance, characterization of this gene family is still elusive in common bean. A systematic genome-wide scan identified 55 PvuGRAS genes unevenly anchored to the 11 common bean chromosomes. Segmental duplication appeared to be the key driving force behind expansion of this gene family that underwent purifying selection during evolution. Computational investigation unraveled their intronless organization and identified similar motif composition within the same subfamily. Phylogenetic analyses clustered the PvuGRAS proteins into 16 phylogenetic clades and established extensive orthologous relationships with Arabidopsis and rice. Analysis of the upstream promoter region uncovered cis-elements responsive to growth, development, and abiotic stresses that may account for their differential expression. The identified SSRs could serve as putative molecular markers facilitating future breeding programs. 37 PvuGRAS transcripts were post-transcriptionally regulated by different miRNA families, miR171 being the major player preferentially targeting members of the HAM subfamily. Global expression profile based on RNA-seq data indicates a clade specific expression pattern in various tissues and developmental stages. Additionally, nine PvuGRAS genes were chosen for further qPCR analyses under drought, salt, and cold stress suggesting their involvement in acclimation to environmental stimuli. Combined, the present results significantly contribute to the current understanding of the complexity and biological function of the PvuGRAS gene family. The resources generated will provide a solid foundation in future endeavors for genetic improvement in common bean.

Uptake and Translocation of Mesoporous SiO2-Coated ZnO Nanoparticles to Solanum lycopersicum Following Foliar Application.

Nanoparticles composed of ZnO encapsulated in a mesoporous SiO2 shell (nZnO@SiO2) with a primary particle diameter of ∼70 nm were synthesized for delivery of Zn, a micronutrient, by foliar uptake. Compared to the rapid dissolution of bare nZnO (90% Zn dissolution after 4 h) in a model plant media (pH = 5), nZnO@SiO2 released Zn more slowly (40% Zn dissolution after 3 weeks), thus enabling sustained Zn delivery over a longer period. nZnO@SiO2, nZnO, and ZnCl2 were exposed to Solanum lycopersicum by dosing 40 µg of Zn micronutrient (in a 20 µL suspension) on a single leaf. No Zn uptake was observed for the nZnO treatment after 2 days. Comparable amounts of Zn uptake were observed 2 days after ZnCl2 (15.5 ± 2.4 µg Zn) and nZnO@SiO2 (11.4 ± 2.2 µg Zn) dosing. Single particle inductively coupled plasma mass spectrometry revealed that for foliar applied nZnO@SiO2, almost all of the Zn translocated to upper leaves and the stem were in nanoparticulate form. Our results suggest that the SiO2 shell enhances the uptake of ZnO nanoparticles in Solanum lycopersicum. Sustained and controlled micronutrient delivery in plants through foliar application will reduce fertilizer, energy, and water use.

Reversible Pressure-Induced Partial Phase Transition in Few-Layer Black Phosphorus.

The experimental identification of structural transitions in layered black phosphorus (BP) under mechanical stress is essential to extend its application in microelectromechanical (MEMS) devices under harsh conditions. High-pressure Raman spectroscopic analysis of BP flakes suggests a transition pressure at ∼4.2 GPa, where the BP's crystal structure progressively transforms from an orthorhombic to a rhombohedral symmetry (blue phosphorus, bP). The phase transition has been identified by observing a transition from blueshift to redshift of the in-plane characteristic Raman modes (B2g and Ag2) with increasing pressure. Recovery of the vibrational frequencies for all three characteristic Raman modes confirms the reversibility of the structural phase transition. First-principles calculations provide insight into the behavior of the Raman modes of BP under high pressure and reveal the mechanism responsible for the partial phase transition from BP to bP, corresponding to a metastable equilibrium state where both phases coexist.

Modulating capacitive response of MoS2 flake by controlled nanostructuring through focused laser irradiation.

Unlike graphene nanostructures, various physical properties of nanostructured MoS2 have remained unexplored due to the lack of established fabrication routes. Herein, we have reported unique electrostatic properties of MoS2 nanostructures, fabricated in a controlled manner of different geometries on 2D flake by using focused laser irradiation technique. Electrostatic force microscopy has been carried out on MoS2 nanostructures by varying tip bias voltage and lift height. The analysis depicts no contrast flip in phase image of the patterned nanostructure due to the absence of free surface charges. However, prominent change in phase shift at the patterned area is observed. Such contrast changes signify the capacitive interaction between tip and nanostructures at varying tip bias voltage and lift height, irrespective of their shape and size. Such unperturbed capacitive behavior of the MoS2 nanostructures offer modulation of capacitance in periodic array on 2D MoS2 flake for potential application in capacitive devices.

Genome analysis of crude oil degrading Franconibacter pulveris strain DJ34 revealed its genetic basis for hydrocarbon degradation and survival in oil contaminated environment.

Franconibacter pulveris strain DJ34, isolated from Duliajan oil fields, Assam, was characterized in terms of its taxonomic, metabolic and genomic properties. The bacterium showed utilization of diverse petroleum hydrocarbons and electron acceptors, metal resistance, and biosurfactant production. The genome (4,856,096bp) of this strain contained different genes related to the degradation of various petroleum hydrocarbons, metal transport and resistance, dissimilatory nitrate, nitrite and sulfite reduction, chemotaxy, biosurfactant synthesis, etc. Genomic comparison with other Franconibacter spp. revealed higher abundance of genes for cell motility, lipid transport and metabolism, transcription and translation in DJ34 genome. Detailed COG analysis provides deeper insights into the genomic potential of this organism for degradation and survival in oil-contaminated complex habitat. This is the first report on ecophysiology and genomic inventory of Franconibacter sp. inhabiting crude oil rich environment, which might be useful for designing the strategy for bioremediation of oil contaminated environment.

Minimal Unified Resolution to R_{K

It is a challenging task to explain, in terms of a simple and compelling new physics scenario, the intriguing discrepancies between the standard model expectations and the data for the neutral-current observables R_{K} and R_{K^{*}}, as well as the charged-current observables R(D) and R(D^{*}). We show that this can be achieved in an effective theory with only two unknown parameters. In addition, this class of models predicts some interesting signatures in the context of both B decays as well as high-energy collisions.

Molecular insights into RNA-binding properties of Escherichia coli-expressed RNA-dependent RNA polymerase of Antheraea mylitta cytoplasmic polyhedrosis virus.

Antheraea mylitta cytoplasmic polyhedrosis virus (AmCPV) is responsible for morbidity of the Indian non-mulberry silkworm, A. mylitta. AmCPV belongs to the family Reoviridae and has 11 double-stranded (ds) RNA genome segments (S1-S11). Segment 2 (S2) encodes a 123-kDa polypeptide with RNA-dependent RNA polymerase (RdRp) activity. To examine the RNA-binding properties of the viral polymerase, the full-length RdRp and its three domains (N-terminal, polymerase and C-terminal domains) were expressed in Escherichia coli BL21 (DE3) cells with hexahistidine and trigger factor tag fused consecutively at its amino terminus, and the soluble fusion proteins were purified. The purified full-length polymerase specifically bound to the 3' untranslated region (3'-UTR) of a viral plus-sense (+) strand RNA with strong affinity regardless of the salt concentrations, but the isolated polymerase domain of the enzyme exhibited poor RNA-binding ability. Further, the RdRp recognition signals were found to be different from the cis-acting signals that promote minus-sense (-) strand RNA synthesis, because different internal regions of the 3'-UTR of the (+) strand RNA did not effectively compete out the binding of RdRp to the intact 3'-UTR of the (+) strand RNA, but all of these RNA molecules could serve as templates for (-) strand RNA synthesis by the polymerase.

Reconstitution of the RNA-dependent RNA polymerase activity of Antheraea mylitta cypovirus in vitro using separately expressed different functional domains of the enzyme.

Antheraea mylitta cytoplasmic polyhedrosis virus is a segmented dsRNA virus of the family Reoviridae. Segment 2 (S2)-encoded RNA-dependent RNA polymerase (RdRp) helps the virus to propagate its genome in the host cell of the silkworm, Antheraea mylitta. Cloning, expression, purification and functional analysis of individual domains of RdRp have demonstrated that the purified domains interact in vitro. The central polymerase domain (PD) shows nucleotide binding properties, but neither the N-terminal domain (NTD) nor the C-terminal domain (CTD). Isolated PD does not exhibit RdRp activity but this activity can be reconstituted when all three domains are included in the reaction mixture. Molecular dynamics simulation suggests that the isolated PD has increased internal motions in comparison to when it is associated with the NTD and CTD. The motions of the separated PD may lead to the formation of a less accessible RNA template-binding channel and, thus, impair RdRp activity.

Genome segment 4 of Antheraea mylitta cytoplasmic polyhedrosis virus encodes RNA triphosphatase and methyltransferases.

Cloning and sequencing of Antheraea mylitta cytoplasmic polyhedrosis virus (AmCPV) genome segment S4 showed that it consists of 3410 nt with a single ORF of 1110 aa which could encode a protein of ~127 kDa (p127). Bioinformatics analysis showed the presence of a 5' RNA triphosphatase (RTPase) domain (LRDR), a S-adenosyl-l-methionine (SAM)-binding (GxGxG) motif and the KDKE tetrad of 2'-O-methyltransferase (MTase), which suggested that S4 may encode RTPase and MTase. The ORF of S4 was expressed in Escherichia coli as a His-tagged fusion protein and purified by nickel-nitrilotriacetic acid affinity chromatography. Biochemical analysis of recombinant p127 showed its RTPase as well as SAM-dependent guanine N(7)-and ribose 2'-O-MTase activities. A MTase assay using in vitro transcribed AmCPV S2 RNA having a 5' G*pppG end showed that guanine N(7) methylation occurred prior to the ribose 2'-O methylation to yield a m(7)GpppG/m(7)GpppGm RNA cap. Mutagenesis of the SAM-binding (GxGxG) motif (G831A) completely abolished N(7)- and 2'-O-MTase activities, indicating the importance of these residues for capping. From the kinetic analysis, the Km values of N(7)-MTase for SAM and RNA were calculated as 4.41 and 0.39 µM, respectively. These results suggested that AmCPV S4-encoded p127 catalyses RTPase and two cap methylation reactions for capping the 5' end of viral RNA.

Ligand-induced evolution of intrinsic fluorescence and catalytic activity from cobalt ferrite nanoparticles.

To develop CoFe(2)O(4) as magneto-fluorescent nanoparticles (NPs) for biomedical applications, it would be advantageous to identify any intrinsic fluorescence of this important magnetic material by simply adjusting the surface chemistry of the NPs themselves. Herein, we demonstrate that intrinsic multicolor fluorescence, covering the whole visible region, can be induced by facile functionalization of CoFe(2)O(4) NPs with Na-tartrate. Moreover, the functionalized CoFe(2)O(4) NPs also show unprecedented catalytic efficiency in the degradation of both biologically and environmentally harmful dyes, pioneering the potential application of these NPs in therapeutics and wastewater treatment. Detailed investigation through various spectroscopic tools unveils the story behind the emergence of this unique optical property of CoFe(2)O(4) NPs upon functionalization with tartrate ligands. We believe our developed multifunctional CoFe(2)O(4) NPs hold great promise for advanced biomedical and technological applications.

Mutations in the catalytic domain of human matrix metalloproteinase-1 (MMP-1) that allow for regulated activity through the use of Ca2+.

Conditionally active proteins regulated by a physiological parameter represent a potential new class of protein therapeutics. By systematically creating point mutations in the catalytic and linker domains of human MMP-1, we generated a protein library amenable to physiological parameter-based screening. Mutants screened for temperature-sensitive activity had mutations clustered at or near amino acids critical for metal binding. One mutant, GVSK (Gly(159) to Val, Ser(208) to Lys), contains mutations in regions of the catalytic domain involved in calcium and zinc binding. The in vitro activity of GVSK at 37 °C in high Ca(2+) (10 mm) was comparable with MMP-1 (wild type), but in low Ca(2+) (1 mm), there was an over 10-fold loss in activity despite having similar kinetic parameters. Activity decreased over 50% within 15 min and correlated with the degradation of the activated protein, suggesting that GVSK was unstable in low Ca(2+). Varying the concentration of Zn(2+) had no effect on GVSK activity in vitro. As compared with MMP-1, GVSK degraded soluble collagen I at the high but not the low Ca(2+) concentration. In vivo, MMP-1 and GVSK degraded collagen I when perfused in Zucker rat ventral skin and formed higher molecular weight complexes with α2-macroglobulin, an inhibitor of MMPs. In vitro and in vivo complex formation and subsequent enzyme inactivation occurred faster with GVSK, especially at the low Ca(2+) concentration. These data suggest that the activity of the human MMP-1 mutant GVSK can be regulated by Ca(2+) both in vitro and in vivo and may represent a novel approach to engineering matrix-remodeling enzymes for therapeutic applications.

Genome segment 5 of Antheraea mylitta cytoplasmic polyhedrosis virus encodes a bona fide guanylyltransferase.

BACKGROUND: Antheraea mylitta cytoplasmic polyhedrosis virus (AmCPV), a cypovirus of Reoviridae family, infects non mulberry Indian silk worm, Antheraea mylitta, and contains eleven segmented double stranded RNA in its genome (S1-S11). Some of its genome segments (S1-S3, and S6-S11) have been previously characterized but genome segment encoding the viral guanylyltransferase which helps in RNA capping has not been characterized. RESULTS: In this study genome segment 5 (S5) of AmCPV was converted to cDNA, cloned and sequenced. S5 consisted of 2180 nucleotides, with one long ORF of 1818 nucleotides and could encode a protein of 606 amino acids with molecular mass of ~65 kDa (p65). Bioinformatics analysis showed presence of KLRS and HxnH motifs as observed in some other reoviral guanylyltransferase and suggests that S5 may encodes viral guanylyltransferase. The ORF of S5 was expressed in E. coli as 65 kDa his tagged fusion protein, purified through Ni-NTA chromatography and polyclonal antibody was raised. Immunoblot analysis of virion particles with the purified antibody showed specific immunoreactive band and suggests p65 as a viral structural protein. Functional analysis showed that recombinant p65 possesses guanylyltransferase activity, and transfers GMP moiety to the 5' diphosphate (A/G) ended viral RNA after the formation of p65-GMP complex for capping. Kinetic analysis showed K(m) of this enzyme for GTP and RNA was 34.24 uM and 98.35 nM, respectively. Site directed mutagenesis at K21A in KLRS motif, and H93A or H105A in HxnH motif completely abolished the autoguanylylation activity and indicates importance of these residues at these sites. Thermodynamic analysis showed p65-GTP interaction was primarily driven by enthalpy (ΔH = -399.1 ± 4.1 kJ/mol) whereas the p65-RNA interaction by favorable entropy (0.043 ± 0.0049 kJ/ mol). CONCLUSION: Viral capping enzymes play a critical role in the post transcriptional or post replication modification in case of RNA virus. Our results of cloning, sequencing and functional analysis of AmCPV S5 indicates that S5 encoded p65 through its guanylyltransferase activity can transfer guanine residue to the 5' end of viral RNA for capping. Further studies will help to understand complete capping process of cypoviral RNA during viral replication within the viral capsid.

Identification and expression profiling of Vigna mungo microRNAs from leaf small RNA transcriptome by deep sequencing.

MicroRNAs (miRNAs) represent a class of small non-coding RNA molecules that play a crucial role in post-transcriptional gene regulation. Several conserved and species-specific miRNAs have been characterized to date, predominantly from the plant species whose genome is well characterized. However, information on the variability of these regulatory RNAs in economically important but genetically less characterized crop species are limited. Vigna mungo is an important grain legume, which is grown primarily for its protein-rich edible seeds. miRNAs from this species have not been identified to date due to lack of genome sequence information. To identify miRNAs from V. mungo, a small RNA library was constructed from young leaves. High-throughput Illumina sequencing technology and bioinformatic analysis of the small RNA reads led to the identification of 66 miRNA loci represented by 45 conserved miRNAs belonging to 19 families and eight non-conserved miRNAs belonging to seven families. Besides, 13 novel miRNA candidates in V. mungo were also identified. Expression patterns of selected conserved, non-conserved, and novel miRNA candidates have been demonstrated in leaf, stem, and root tissues by quantitative polymerase chain reaction, and potential target genes were predicted for most of the conserved miRNAs. This information offers genomic resources for better understanding of miRNA mediated post-transcriptional gene regulation.