Investigation of two-pore K+ (TPK) channels in Triticum aestivum L. suggests their role in stress response

Two-pore K+ (TPK) channels are voltage-independent and involved in stress response in plants. Herein, we identified 12 TaTPK genes located on nine chromosomes in the Triticum aestivum genome. The majority of TaTPK genes comprised two exons. Each TaTPK channel comprised four transmembrane (TM) helices, N- and C-terminal ion-channel domains, two EF-hand domains and one 14-3-3 binding site. Additionally, highly conserved 'GYGD' motif responsible for K+ ion specificity, was found in between the TMs in both the ion-channel domains. Nine TaTPK channels were predicted to be localised at the plasma membrane, while three were vacuolar. The protein-protein and protein-chemical interactions indicated the coordinated functioning of the TaTPK channels with the other K+ transporters and their possible interaction with the Ca2+-signaling pathway. Expression studies suggested their importance in both vegetative and reproductive tissues development. Significantly modulated expression of various TaTPK genes during heat, drought, combined heat and drought and salt stresses, and after fungal infestation, depicted their function in stress responses. The miRNAs and transcription factors interaction analyses suggested their role in the hormone, light, growth and development-related, and stress-responsive signaling cascades. The current study suggested vital functions of various TaTPK genes, especially in stress response, and would provide an opportunity for their detailed characterization in future studies.

Modulation in gene expression and enzyme activity suggested the roles of monodehydroascorbate reductase in development and stress response in bread wheat

Monodehydroascorbate reductase (MDHAR) is a crucial enzymatic antioxidant of the ascorbate-glutathione pathway involved in reactive oxygen species scavenging. Herein, we identified 15 TaMDHAR genes in bread wheat. Phylogenetic analysis revealed their clustering into three groups, which are also related to the subcellular localization in the peroxisome matrix, peroxisome membrane, and chloroplast. Each TaMDHAR protein consisted of two conserved domains; Pyr_redox and Pyr_redox_2 of the pyridine nucleotide disulfide oxidoreductase family. The occurrence of diverse groups of cis-regulatory elements in the promoter region and their interaction with numerous transcription factors suggest assorted functions of TaMDHARs in growth and development and in light, phytohormones, and stress responses. Expression analysis in various tissues further revealed their importance in vegetative and reproductive development. In addition, the differential gene expression and enhanced enzyme activity during drought, heat, and salt treatments exposed their role in abiotic stress response. Interaction of MDHARs with various antioxidant enzymes and biochemicals related to the ascorbate-glutathione cycle exposed their synchronized functioning. Interaction with auxin indicated the probability of cross-talk between antioxidants and auxin signaling. The miR168a, miR169, miR172 and others interaction with various TaMDHARs further directed their association with developmental processes and stress responses. The current study provides extensive information about the importance of TaMDHARs, moreover, the precise role of each gene needs to be established in future studies.

Melting the wall: plant parasitism entails pectin modification

Phtheirospermum japonicum shows induced expression of PjPME and PjPMEI genes during haustoria development in rice and Arabidopsis with increased PME activity, which leads to the modulated cell wall during parasitism. Moreover, how PME and PMEI proteins interact and balance during haustoria development remains elusive.

CPK12 and Ca2+-mediated hypoxia signaling

Hypoxia triggers reactive oxygen species (ROS)-induced elevation in cytoplasmic calcium (Ca2+) in the plant cells. Calcium-dependent protein kinase 12 (CPK12) acts as a sensor to recognize the Ca2+ signature and is activated by autophosphorylation. Then, the CPK12 moves into the nucleus with the help of phosphatidic acid (PA) and phosphorylates ERF-VII family proteins that activate hypoxia signaling and response. The study provides a novel mechanism of hypoxia signaling in plants. Moreover, the mechanism of hypoxia-specific Ca2+ signature generation remains elusive.

DPY1 as an osmosensor for drought signaling

Drought stress has been extensively studied for its effect on the downstream signaling cascade and stress-responsive gene expression, but understanding the process has remained elusive. Recently, Zhao et al. identified DROOPY LEAF1 (DPY1) as an osmosensor and revealed a novel mechanism of DPY1-STRESS ACTIVATED PROTEIN KINASE6 (SAPK6)-mediated drought stress signaling in higher plants.

TaGPX1-D overexpression provides salinity and osmotic stress tolerance in Arabidopsis

Glutathione peroxidases (GPXs) are known to play an essential role in guarding cells against oxidative stress by catalyzing the reduction of hydrogen peroxide and organic hydroperoxides. The current study aims functional characterization of the TaGPX1-D gene of bread wheat (Triticum aestivum) for salinity and osmotic stress tolerance. To achieve this, we initially performed the spot assays of TaGPX1-D expressing yeast cells. The growth of recombinant TaGPX1-D expressing yeast cells was notably higher than the control cells under stress conditions. Later, we generated transgenic Arabidopsis plants expressing the TaGPX1-D gene and investigated their tolerance to various stress conditions. The transgenic plants exhibited improved tolerance to both salinity and osmotic stresses compared to the wild-type plants. The higher germination rates, increased antioxidant enzymes activities, improved chlorophyll, carotenoid, proline and relative water contents, and reduced hydrogen peroxide and MDA levels in the transgenic lines supported the stress tolerance mechanism. Overall, this study demonstrated the role of TaGPX1-D in abiotic stress tolerance, and it can be used for improving the tolerance of crops to environmental stressors, such as salinity and osmotic stress in future research.

Phytochemistry and biological activity of Erigeron annuus (L.) Pers

Erigeron annuus L. is a flowering herb of North America, Europe, Asia and Russia. This plant is used as folk medicine in China for the cure of indigestion, enteritis, epidemic hepatitis, haematuria and diabetes. Phytochemical studies showed the presence of 170 bioactive compounds like coumarins, flavonoids, terpenoids, polyacetylenic compounds; γ-pyrone derivatives, sterols and various caffeoylquinic acids derived from the essential oil and organic extracts from its various parts such as aerial parts, roots, leaves, stems and flowers. The pharmacological studies demonstrated various extracts and the compounds of E. annuus to exhibit anti-fungal, anti-atherosclerosis, anti-inflammatory, antidiabetic, phytotoxic, cytoprotective, antiobesity and antioxidant activities. This article covers a critical compendious on geographical distribution, botanical description, phytochemistry, ethnomedicinal uses and pharmacological activities of E. annuus. However, further in-depth studies are needed to determine the medical uses of E. annuus and its chemical constituents, pharmacological activities and clinical applications.

Phosphate Deficiency: A Tale from the End of PILNCR2

A deficiency in inorganic phosphate (Pi) induces the expression of miRNA399 and the accumulation of its target Pi transporters (PHT1s) mRNA, which is contrary to the goal of miRNA-mediated gene regulation. Recently, a novel mechanism of RNA/RNA-duplex formation between the transcripts of a Pi deficiency-induced long non-coding RNA (PILNCR2) and PHT1s has been reported, which prevents the binding and cleavage of miRNA399 to PHT1 mRNAs, thereby providing tolerance of Pi-deficient conditions. Moreover, the way in which ribosomes move through the RNA/RNA-duplex for the translation of PHT1 transporter proteins remains elusive.

Expression of TaNCL2-A ameliorates cadmium toxicity by increasing calcium and enzymatic antioxidants activities in arabidopsis

Cadmium (Cd) is a heavy metal that occurs naturally in the environment and is toxic to both animals and plants. The impact of Cd toxicity is shown to be reduced by the exogenous application of calcium (Ca) in crop plants. The sodium/calcium exchanger-like (NCL) protein is involved in Ca enrichment in the cytoplasm by transporting it from the vacuole in the exchange of cytosolic sodium (Na). However, it has not been utilized to ameliorate the Cd toxicity, to date. An elevated expression of TaNCL2-A gene in the root and shoot tissues of bread wheat seedlings, and a higher growth rate of recombinant yeast cells, suggested its role in Cd stress response. The TaNCL2-A expressing transgenic Arabidopsis lines exhibited significant Cd tolerance with increased Ca (∼10-fold) accumulation. The proline content and antioxidant enzymes activities were increased while oxidative stress-related molecules such as H₂O₂ and MDA were reduced in the transgenic lines. In addition, the growth and yield parameters of transgenic lines such as seed germination rate, root length, leaf biomass, leaf area index, rosette diameter, leaf length and width, and silique count, along with various physiological indicators like chlorophyll, carotenoid, and relative water contents were also improved in comparison to the control plants. Further, the transgenic lines exhibited significant salinity and osmotic stress tolerance, as well. Taken together, these results suggested that the TaNCL2-A could mitigate Cd toxicity along with salinity and osmotic stress. This gene may also be utilized for phytoremediation and Cd sequestration in future studies.

Failure of methanol detoxification in pests confers broad spectrum insect resistance in PME overexpressing transgenic cotton

Methanol is noxious to insect pests, but most plants do not make enough of it to shield themselves from encroaching insects. Methanol emission is known to increase in the instance of herbivory. In the current study, we showed that Aspergillus niger pectin methylesterase over-expression increases methanol emission and confers resistance to polyphagous insect pests on transgenic cotton plants by impeding the possible methanol detoxification pathways. Transgenic plants emitted ~11 fold higher methanol displaying insect mortality of 96% and 93% in Helicoverpa armigera and Spodoptera litura, respectively. The larvae were unable to survive and finish their life cycle and the surviving larvae exhibited severe growth retardation. Insects try to detoxify methanol via catalase, carboxylesterase and cytochrome P450 monooxygenase enzymes, amongst which cytochrome P450 plays a major role in oxidizing methanol to formaldehyde and formaldehyde to formic acid, which is broken down into carbon dioxide and water. In our study, catalase and esterase enzymes were found to be upregulated, but cytochrome P450 monooxygenase levels were not much affected. Leaf disc assays and In-planta bioassays also showed 50-60% population reduction in the sap sucking pests, such as Bemisia tabaci and Phenacoccus solenopsis. These findings imply that elevated methanol emissions confer resistance in plants against chewing and sap-sucking pests by tampering the methanol detoxification pathways. Such mechanism will be useful in imparting expansive resistance against pests in plants.

Revisiting the therapeutic potential of gingerols against different pharmacological activities

The rhizomes of ginger have been in use in many forms of traditional and alternative medicines. Besides being employed as condiment and flavoring agent, it is used in the treatment of nausea, osteoarthritis, muscle pain, menstrual pain, chronic indigestion, Alzheimer's disease, and cancer. Ginger rhizome contains volatile oils, phenolic compounds and resins, and characterization studies showed that [6]-gingerol, [6]-shogaol, and [6]-paradol are reported to be the pharmacologically active components. Gingerol is a major chemical constituent found as volatile oil in the rhizomes of ginger. It has several medicinal benefits and used for the treatment of rheumatoid arthritis, nausea, cancer, and diabetes. Many studies have been carried out in various parts of the world to isolate and standardize gingerol for their use as a complementary medicine. The present review summarizes wide range of research studies on gingerol and its pharmacological roles in various metabolic diseases.

A cell-penetrant peptide blocking C9ORF72-repeat RNA nuclear export reduces the neurotoxic effects of dipeptide repeat proteins

Hexanucleotide repeat expansions in C9ORF72 are the most common genetic cause of familial amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Studies have shown that the hexanucleotide expansions cause the noncanonical translation of C9ORF72 transcripts into neurotoxic dipeptide repeat proteins (DPRs) that contribute to neurodegeneration. We show that a cell-penetrant peptide blocked the nuclear export of C9ORF72-repeat transcripts in HEK293T cells by competing with the interaction between SR-rich splicing factor 1 (SRSF1) and nuclear export factor 1 (NXF1). The cell-penetrant peptide also blocked the translation of toxic DPRs in neurons differentiated from induced neural progenitor cells (iNPCs), which were derived from individuals carrying C9ORF72-linked ALS mutations. This peptide also increased survival of iNPC-differentiated C9ORF72-ALS motor neurons cocultured with astrocytes. Oral administration of the cell-penetrant peptide reduced DPR translation and rescued locomotor deficits in a Drosophila model of mutant C9ORF72-mediated ALS/FTD. Intrathecal injection of this peptide into the brains of ALS/FTD mice carrying a C9ORF72 mutation resulted in reduced expression of DPRs in mouse brains. These findings demonstrate that disrupting the production of DPRs in cellular and animal models of ALS/FTD might be a strategy to ameliorate neurodegeneration in these diseases.

In silico analysis to identify novel ceRNA regulatory axes associated with gallbladder cancer

Competitive endogenous RNA (ceRNA) networks are reported to play a crucial role in regulating cancer-associated genes. Identification of novel ceRNA networks in gallbladder cancer (GBC) may improve the understanding of its pathogenesis and might yield useful leads on potential therapeutic targets for GBC. For this, a literature survey was done to identify differentially expressed lncRNAs (DELs), miRNAs (DEMs), mRNAs (DEGs) and proteins (DEPs) in GBC. Ingenuity pathway analysis (IPA) using DEMs, DEGs and DEPs in GBC identified 242 experimentally observed miRNA-mRNA interactions with 183 miRNA targets, of these 9 (CDX2, MTDH, TAGLN, TOP2A, TSPAN8, EZH2, TAGLN2, LMNB1, and PTMA) were reported at both mRNA and protein levels. Pathway analysis of 183 targets revealed p53 signaling among the top pathway. Protein-protein interaction (PPI) analysis of 183 targets using the STRING database and cytoHubba plug-in of Cytoscape software revealed 5 hub molecules, of which 3 of them (TP53, CCND1 and CTNNB1) were associated with the p53 signaling pathway. Further, using Diana tools and Cytoscape software, novel lncRNA-miRNA-mRNA networks regulating the expression of TP53, CCND1, CTNNB1, CDX2, MTDH, TOP2A, TSPAN8, EZH2, TAGLN2, LMNB1, and PTMA were constructed. These regulatory networks may be experimentally validated in GBC and explored for therapeutic applications.

Calcium Channels, OST1 and Stomatal Defence: Current Status and Beyond

Stomatal immunity is regulated by pathogen-associated molecular patterns (PAMPs)- and abscisic acid (ABA)-triggered signalling in different ways. Cytoplasmic Ca²⁺ signature in the guard cells plays a vital function in stomatal immunity, but the mechanism of Ca²⁺ import is unknown. It has been very recently established that the hyperosmolality-gated calcium-permeable channels (OSCAs) and cyclic nucleotide-gated channels (CNGCs) are responsible for the influx of Ca²⁺ in the cytoplasm, which are activated after BIK1-mediated phosphorylation and ABA interaction during PAMPs- and ABA-triggered stomatal immunity in plants, respectively. Further, ABA-triggered OPEN STOMATA1 (OST1) causes the disassembly of microtubules in the guard cells besides activation of S-type anion channels (SLAC1) for the efflux of cytoplasmic anions that leads to stomata closure.

OSCA Genes in Bread Wheat: Molecular Characterization, Expression Profiling, and Interaction Analyses Indicated Their Diverse Roles during Development and Stress Response

The hyperosmolality-gated calcium-permeable channels (OSCA) are pore-forming transmembrane proteins that function as osmosensors during various plant developmental processes and stress responses. In our analysis, through in silico approaches, a total of 42 OSCA genes are identified in the Triticum aestivum genome. A phylogenetic analysis reveals the close clustering of the OSCA proteins of Arabidopsis thaliana, Oryza sativa, and T. aestivum in all the clades, suggesting their origin before the divergence of dicots and monocots. Furthermore, evolutionary analyses suggest the role of segmental and tandem duplication events (Des) and purifying selection pressure in the expansion of the OSCA gene family in T. aestivum. Expression profiling in various tissue developmental stages and under abiotic and biotic stress treatments reveals the probable functioning of OSCA genes in plant development and the stress response in T. aestivum. In addition, protein-protein and protein-chemical interactions reveal that OSCA proteins might play a putative role in Ca²⁺-mediated developmental processes and adaptive responses. The miRNA interaction analysis strengthens the evidence for their functioning in various biological processes and stress-induced signaling cascades. The current study could provide a foundation for the functional characterization of TaOSCA genes in future studies.

A facile synthesis of palladium nanoparticles decorated bismuth oxybromide nanostructures with exceptional photo-antimicrobial activities

Assessing the interaction between microbes and nanocatalysts for finding an inclusive, proactive and deep understanding of nanoparticles-based toxicity is vital for discovering their broad range of applications. Palladium based photocatalysts owing to their unique fundamental characteristics and brilliant physicochemical potential have gained immense interest in environment remediation as disinfection system. In the present study, we report synthesis of a novel palladium nanoparticles decorated bismuth oxybromide (Pd/BiOBr) nanostructures using an energy efficient solution-based method, having excellent photocatalytic antibacterial action. The synthesized nanomaterials was thoroughly characterized using various analytical techniques. The photocatalytic antibacterial efficiency of Pd/BiOBr was evaluated against some common pathogenic strains of Gram-positive and Gram-negative bacteria (Pseudomonas fluorescens, Pseudomonas aeruginosa, Escherichia coli, Aeromonas salmonicida, Salmonella typhimurium, Klebsiella pneumoniae, Bacillus subtilis). In our results Pd/BiOBr showed excellent photocatalytic disinfection efficacy with > 99.9% bacterial inactivation. A very low concentration of Pd/BiOBr (0.5 µg/mL) effectively inhibited the bacterial growth in response to just 2 h of visible light irradiation, while 1 µg/mL of Pd/BiOBr completely killed all the tested bacterial strains proving their magnificent bactericidal potential. The developed materials with exceptional antibacterial broad range efficiency can be used in different photocatalytic disinfection systems including water purification systems, biofilm exclusion and combating differential antibiotic resistance.

Biodegradation of bisphenol A using psychrotolerant bacterial strain Pseudomonas palleroniana GBPI_508

A psychrotolerant bacterial strain of Pseudomonas sp. (P. palleroniana GBPI_508), isolated from the Indian Himalayan region, is studied for analyzing its potential for degrading bisphenol A (BPA). Response surface methodology using Box-Behnken design was used to statistically optimize the environmental factors during BPA degradation and the maximum degradation (97%) was obtained at optimum conditions of mineral salt media pH 9, experimental temperature 25 °C, an inoculum volume of 10% (v/v), and agitation speed 130 rpm at the BPA concentration 270 mg L^-1. The Monod model was used for understanding bacterial degradation kinetics, and 37.5 mg^-1 half saturation coefficient (K_S) and 0.989 regression coefficient (R²) were obtained. Besides, the utmost specific growth rate µmax was witnessed as 0.080 h^-1 with the GBPI_508 during BPA degradation. Metabolic intermediates detected in this study by GC-MS were identified as valeric acid, propionic acid, diglycolic acid, and phenol. The psychrotolerant bacterial strain of Pseudomonas sp. (P. palleroniana GBPI_508), isolated from the Indian Himalayan region has shown good potential for remediation of BPA at variable conditions.

Molecular Characterization, Evolutionary Analysis, and Expression Profiling of BOR Genes in Important Cereals

Boron (B) is an essential micronutrient of plants. Plants grapple with a narrow range of B between its toxicity and deficiency. B homeostasis mechanism is required to rescue plants from such a quagmire. B transporters are specialized proteins involved in the homeostasis of B. In the present study, a total of 29 BOR genes were identified in five major cereals, including three BORs in each Brachypodium distachyon and Sorghum bicolor, four in Oryza sativa, six in Zea mays, and 13 in Triticum aestivum. Multiple sequence alignments, domain structure analyses, and phylogenetic analysis indicated the conserved nature of the BOR protein family. Duplication events and Ka/Ks analysis of TaBORs showed the role of segmental duplication events and purifying selection in the expansion of the BOR family in T. aestivum. Furthermore, in silico expression and co-expression analyses under biotic and abiotic stress conditions depicted their involvement in combating such conditions. Moreover, qRT-PCR of TaBORs in B treatment suggested the roles of BOR genes in B stress management. The present study hints at the conserved nature of BOR proteins and their different aspects. The study will lay down a way for several crop improvement programs.

Exploration of glutathione reductase for abiotic stress response in bread wheat (Triticum aestivum L.)

A total of seven glutathione reductase (GR) genes were identified in Triticum aestivum, which were used for comparative structural characterization, phylogenetic analysis and expression profiling with the GR genes of other cereal plants. The modulated gene expression and enzyme activity revealed the role of GRs in abiotic stress response in T. aestivum. Glutathione reductase (GR) is an enzymatic antioxidant that converts oxidized glutathione (GSSG) into reduced glutathione (GSH) through the ascorbate-glutathione cycle. In this study, a total of seven GR genes forming two homeologous groups were identified in the allohexaploid genome of bread wheat (Triticum aestivum). Besides, we identified three GR genes in each Aegilops tauschii, Brachypodium distachyon, Triticum urartu and Sorghum bicolor, which were used for comparative characterization. Phylogenetic analysis revealed the clustering of GR proteins into two groups; class I and class II, which were predicted to be localized in cytoplasm and chloroplast, respectively. The exon-intron and conserved motif patterns were almost conserved in each group, in which a maximum of 10 and 17 exons were present in chloroplastic and cytoplasmic GRs, respectively. The protein structure analysis confirmed the occurrence of conserved pyridine nucleotide disulfide oxidoreductase (Pyr_redox) and pyridine nucleotide disulfide oxidoreductase dimerization (Pyr_redox_dim) domains in each GR. The active site of GR proteins consisted of two conserved cysteine residues separated by four amino acid residues. Promoter analysis revealed the occurrence of growth and stress-related cis-active elements. Tissue-specific expression profiling suggested the involvement of GRs in both vegetative and reproductive tissue development in various plants. The differential expression of TaGR genes and enhanced GR enzyme activity suggested their roles under drought, heat, salt and arsenic stress. Interaction of GRs with other proteins and chemical compounds of the ascorbate-glutathione cycle revealed their coordinated functioning. The current study will provide a foundation for the validation of the precise role of each GR gene in future studies.

Characterization of APX and APX-R gene family in Brassica juncea and B. rapa for tolerance against abiotic stresses

APX and APX-R gene families were identified and characterized in two important oilseed species of Brassica. Gene expression under abiotic stress conditions, recombinant protein expression, and analysis further divulged their drought, heat, and salt-responsive behavior. Ascorbate peroxidases (APX) are heme-dependent enzymes that rid the cells of H₂O₂ and regulate diverse biological processes. In the present study, we performed APX gene family characterization in two Brassica sp. (B. juncea and B. rapa) as these are commercially important oilseed crops and affected severely by abiotic stresses. We identified 16 BjuAPX and 9 BraAPX genes and 2 APX-R genes each in B. juncea and B. rapa genomes, respectively. Phylogenetic analysis divided the APX genes into five distinct clades, which exhibited conservation in the gene structure, motif organization, and sub-cellular location within the clade. Structural analysis of APX and APX-R proteins revealed the amino acid substitutions in conserved domains of APX-R proteins. The expression profiling of BjuAPX and BraAPX genes showed that 3 BjuAPX, 7BraAPX, and 2 BraAPX-R genes were drought and heat responsive. Notably, BjuAAPX1a, BjuAPX1d, BjuAAPX6, BraAAPX1a, BraAAPX2, and BraAAPX3b showed high expression levels in RT-qPCR. Cis-regulatory elements in APX and APX-R gene promoters supported the differential behavior of these genes. Further, two stress-responsive genes BjuAPX1d and BraAAPX2 were cloned, characterized, and their roles were validated under heat, drought, salt, and cold stress in bacterial expression system. This study for the first time reports the presence of APX activity in dimeric and LMW form of purified BraAAPX2 protein. The study may help pave way for developing abiotic stress-tolerant Brassica crops.

Investigation of Roles of TaTALE Genes during Development and Stress Response in Bread Wheat

The three amino acid loop extension (TALE) genes of the homeobox superfamily are responsible for numerous biological functions in plants. Herein, we identified a total of 72 TaTALE genes in the allohexaploid genome of bread wheat (Triticum aestivum L.) and performed a comprehensive investigation for gene and protein structural properties, phylogeny, expression patterns, and multilevel gene regulations. The identified TaTALE proteins were further classified into two groups, TaBLHs and TaKNOXs, which were tightly clustered into the phylogeny. The negative Ka/Ks ratio of duplicated genes suggested purifying selection pressure with confined functional divergence. Various signature domains and motifs were found conserved in both groups of proteins. The occurrence of diverse cis-regulatory elements and modulated expression during various developmental stages and in the presence of abiotic (heat, drought, salt) and two different fungal stresses suggested their roles in development and stress response, as well. The interaction of TaTALEs with the miRNAs and other development-related homeobox proteins also suggested their roles in growth and development and stress response. The present study revealed several important aspects of TaTALEs that will be useful in further functional validation of these genes in future studies.

Compendium of Plant-Specific CRISPR Vectors and Their Technical Advantages

CRISPR/Cas mediated genome editing is a revolutionary approach for manipulating the plant genome. However, the success of this technology is highly dependent on selection of a specific vector and the other components. A plant-specific CRISPR/Cas vector usually consists of a Cas gene, target-specific gRNA, leader sequence, selectable marker gene, precise promoters, and other accessories. It has always been challenging to select the specific vector for each study due to a lack of comprehensive information on CRISPR vectors in one place. Herein, we have discussed every technical aspect of various important elements that will be highly useful in vector selection and efficient editing of the desired plant genome. Various factors such as the promoter regulating the expression of Cas and gRNA, gRNA size, Cas variants, multicistronic gRNA, and vector backbone, etc. influence transformation and editing frequency. For example, the use of polycistronic tRNA-gRNA, and Csy4-gRNA has been documented to enhance the editing efficiency. Similarly, the selection of an efficient selectable marker is also a very important factor. Information on the availability of numerous variants of Cas endonucleases, such as Cas9, Cas12a, Cas12b, Casɸ, and CasMINI, etc., with diverse recognition specificities further broadens the scope of editing. The development of chimeric proteins such as Cas fused to cytosine or adenosine deaminase domain and modified reverse transcriptase using protein engineering enabled base and prime editing, respectively. In addition, the newly discovered Casɸ and CasMINI would increase the scope of genetic engineering in plants by being smaller Cas variants. All advancements would contribute to the development of various tools required for gene editing, targeted gene insertion, transcriptional activation/suppression, multiplexing, prime editing, base editing, and gene tagging. This review will serve as an encyclopedia for plant-specific CRISPR vectors and will be useful for researchers.

Molecular characterization of N-methyl-d-aspartate receptor from Bemisia tabaci

The N-methyl-d-aspartate receptors (NMDARs) are ionotropic ligand gated channels that are highly permeable to calcium ions. In insects, NMDARs are associated with glutamatergic neurotransmission governing diverse physiological and biological processes like vitellogenesis and ovarian development. Therefore, NMDAR may act as attractive target for insect pest control. In present study, we performed structural and functional characterization of NMDARs in Bemisia tabaci, a highly invasive crop pest and potent virus vector. We identified that NMDAR consists of three subunits each encoded by single gene in whiteflies which are highly conserved among different insect orders. Expression analysis suggests that subunit 1 (BtNR1) and subunit 2 (BtNR2) are the main functional units. External supplementation of NMDAR ligand or BtNRs silencing was lethal to insects, which suggested that NMDAR function is highly balanced in whiteflies.

RNAi-based gene silencing in Phenacoccus solenopsis and its validation by in planta expression of a double-stranded RNA

BACKGROUND

Cotton is a cash crop majorly affected by many hemipteran pests, among them the cotton mealybug, Phenacoccus solenopsis. Cotton mealybug attack has a devastating effect on cotton production and causes huge yield losses.

RESULTS

In this study, 25 potential RNA interference (RNAi) target genes were selected from the iBeetle database and a transcriptome data set for P. solenopsis. To assess the effectiveness of the selected target genes, three methods were utilized to deliver double-stranded (ds)RNA (ingestion, artificial diet bioassay and transient gene silencing). dsRNA molecules at different concentrations were fed to insects and insect mortality was recorded for each target gene. Based on the mortality data, three genes, Krüppel homologue-1, ADP-ATP/Translocase and IDGF-1, were selected for further gene expression studies using a reduced concentration of dsRNA (5 μg/ml). Of the three genes, Krüppel homologue-1 showed significantly downregulated expression (by 70.81% and 84.33%) at two different time points (8 and 14 days). An RNAi silencing construct was designed for Krüppel homologue-1 under control of the double enhancer CamV35S promoter in the plant binary vector. Significant downregulation of gene expression, by 66.69% and 81.80%, was found for Krüppel homologue-1 using transient gene silencing at the same time intervals.

CONCLUSION

This work provides the first evidence for targeting the Krüppel homologue-1 gene in a hemipteran pest, P. solenopsis, using RNAi technology through oral delivery and in planta-based transient gene silencing methods. © 2020 Society of Chemical Industry.

Molecular characterization revealed the role of catalases under abiotic and arsenic stress in bread wheat (Triticum aestivum L.)

Catalases are crucial antioxidant enzymes that reduce the excessive level of H₂O₂ caused by various environmental stresses and metal toxicity and hence protect the plant cells. In this study, a total of ten TaCAT genes, forming three homeologous groups, were identified in the genome of bread wheat (Triticum aestivum L.) and named as per the wheat gene symbolization guidelines. The identified catalases were characterized for various structural and physicochemical features. The proximal active-site (F(D/A)RERIPERVVHAKGASA) and heme-ligand (R(I/V)F(S/A)Y(A/S)DTQ) signature motifs, catalytic residues and peroxisomal targeting peptides were found conserved. Phylogenetic analysis clustered TaCATs into three classes, which showed conserved functional specialization based on their tissue specific expression. Modulated spatio-temporal expression of various TaCAT genes and alteration in total catalase enzyme activity during heat, drought, salt and arsenic (As^III and As^V) treatment suggested their roles in abiotic stress response and arsenic tolerance. Molecular cloning and overexpression of TaCAT3-B gene in Escherichia coli showed tolerance against heat, drought, salt and varied concentrations of As^III and As^V treatments. The results further confirmed their role in stress tolerance and recommended that these genes can be used in future stress management strategies for the development of abiotic and arsenic stress resistant transgenic crops.

Molecular Characterization Revealed the Role of Thaumatin-Like Proteins of Bread Wheat in Stress Response

Thaumatin-like proteins (TLPs) are related to pathogenesis-related-5 (PR-5) family and involved in stress response. Herein, a total of 93 TLP genes were identified in the genome of Triticum aestivum. Further, we identified 26, 27, 39, and 37 TLP genes in the Brachypodium distachyon, Oryza sativa, Sorghum bicolor, and Zea mays genomes for comparative characterization, respectively. They could be grouped into small and long TLPs with conserved thaumatin signature motif. Tightly clustered genes exhibited conserved gene and protein structure. The physicochemical analyses suggested significant differences between small and long TLPs. Evolutionary analyses suggested the role of duplication events and purifying selection in the expansion of the TLP gene family. Expression analyses revealed the possible roles of TLPs in plant development and abiotic and fungal stress response. Recombinant expression of TaTLP2-B in Saccharomyces cerevisiae provided significant tolerance against cold, heat, osmotic, and salt stresses. The results depicted the importance of TLPs in cereal crops that would be highly useful in future crop improvement programs.

Genome-wide characterization and expression and co-expression analysis suggested diverse functions of WOX genes in bread wheat

WUSCHEL-related homeobox (WOX) genes belong to the homeobox superfamily, are plant-specific and play vital functions in the growth and development. Herein, we identified a total of 43 TaWOX genes in the allohexaploid (AABBDD) genome of Triticum aestivum L. These genes were distributed on the various chromosomes of each subgenome (A, B and D). The phylogenetic analysis showed the clustering of TaWOXs into three clades: ancient, intermediate and modern or WUS. The gene and protein structures including exon/intron organization, intron phases, and domain and motif distribution were found to be conserved in each phylogenetic clade. The subcellular localization was predicted as nuclear. The Ka/Ks analyses suggested the purifying selection of paralogous genes. The differential expression profiling of various TaWOXs in numerous tissue developmental stages and different layers of grains suggested their role in growth and development. Moreover, a few genes exhibited modulated expression during abiotic and biotic stress conditions, which revealed their roles in stress response. The occurrence of various cis-acting regulatory elements further confirmed their role in plant development and stress tolerance. The co-expression analyses suggested the interactions of these genes with other genes, involved in various processes including plant development, signalling and stress responses. The present study reported several characteristic features of TaWOXs genes that can be useful for further characterization in future studies.

Genome-wide characterization and expression analysis suggested diverse functions of the mechanosensitive channel of small conductance-like (MSL) genes in cereal crops

Mechanosensitive ion channels are pore-forming transmembrane proteins that allow ions to move down their electrochemical gradient in response to mechanical stimuli. They participate in many plant developmental processes including the maintenance of plastid shape, pollen tube growth, etc. Herein, a total of 11, 10, 6, 30, 9, and 8 MSL genes were identified in Aegilops tauschii, Hordeum vulgare, Sorghum bicolor, Triticum aestivum, Triticum urartu, and Zea mays, respectively. These genes were located on various chromosomes of their respective cereal, while MSLs of T. urartu were found on scaffolds. The phylogenetic analysis, subcellular localization, and sequence homology suggested clustering of MSLs into two classes. These genes consisted of cis-regulatory elements related to growth and development, responsive to light, hormone, and stress. Differential expression of various MSL genes in tissue developmental stages and stress conditions revealed their precise role in development and stress responses. Altered expression during CaCl2 stress suggested their role in Ca2+ homeostasis and signaling. The co-expression analysis suggested their interactions with other genes involved in growth, defense responses etc. A comparative expression profiling of paralogous genes revealed either retention of function or pseudo-functionalization. The present study unfolded various characteristics of MSLs in cereals, which will facilitate their in-depth functional characterization in future studies.

Structural basis of UCUU RNA motif recognition by splicing factor RBM20

The vertebrate splicing factor RBM20 (RNA binding motif protein 20) regulates protein isoforms important for heart development and function, with mutations in the gene linked to cardiomyopathy. Previous studies have identified the four nucleotide RNA motif UCUU as a common element in pre-mRNA targeted by RBM20. Here, we have determined the structure of the RNA Recognition Motif (RRM) domain from mouse RBM20 bound to RNA containing a UCUU sequence. The atomic details show that the RRM domain spans a larger region than initially proposed in order to interact with the complete UCUU motif, with a well-folded C-terminal helix encoded by exon 8 critical for high affinity binding. This helix only forms upon binding RNA with the final uracil, and removing the helix reduces affinity as well as specificity. We therefore find that RBM20 uses a coupled folding-binding mechanism by the C-terminal helix to specifically recognize the UCUU RNA motif.

Molecular characterization of ascorbate peroxidase (APX) and APX-related (APX-R) genes in Triticum aestivum L

Ascorbate peroxidases (APXs) are heme-dependent H₂O₂ scavenging enzymes involved in myriad biological processes. Herein, a total of 21 TaAPX and six TaAPX-R genes were identified from the A, B and D sub-genomes of Triticum aestivum L. The occurrence of three paralogous gene pairs with unequal evolutionary rate suggested functional divergence. The phylogenetic analysis formed four distinct clades having conserved gene and protein architecture, and sub-cellular localization. The tertiary structure analysis revealed the presence of helices and coils and residues involved in ligand binding. Transcriptional profiling of each TaAPX and TaAPX-R gene suggested their specific role during development and stress response. Modulated transcript expression and APX enzyme activity during various stress conditions indicated their role in stress response. Interaction analyses suggested their association with other genes, miRNAs and various legends. The present study reported numerous features of these genes, and may provide a platform for their detailed functional characterization in future studies.

Genome wide characterization of the SERK/SERL gene family in Phalaenopsis equestris, Dendrobium catenatum and Apostasia shenzhenica (Orchidaceae)

Somatic embryogenesis receptor kinases (SERKs) play a significant role in morphogenesis, stress/defense and signal transduction. In the present study, we have identified two SERK and 11 SERK-like (SERL) genes in Phalaenopsis equestris, two SERK and 11 SERL genes in Dendrobium catenatum, and one SERK and eight SERL genes in Apostasia shenzhenica genome. Characterization of the SERK proteins revealed the presence of a signal peptide, a leucine zipper, five leucine-rich repeats (LRRs), a serine proline proline (SPP) motif, a transmembrane region, a kinase domain, and a C-terminus. Most of the SERK/SERL proteins were characterized with similar physicochemical properties. The presence of transmembrane region predicted their membranous localization. Tertiary structure prediction of all the five identified SERK proteins had sequence identity with BAK1 protein of Arabidopsis thaliana. Generally, all the SERK/SERL genes shared similar gene architecture and intron phasing. Gene ontology analysis indicated the role of SERKs in receptor and ATP binding, signal transduction, and protein phosphorylation. Phylogenetic analysis revealed the clustering of SERKs and SERLs in distinct clades. Expression of SERKs in reproductive tissues like floral bud, floral stalk, whole flower and pollen was reported to be higher than their expression in vegetative tissues with an exception of PeSERK1 and DcSERK1 which showed higher expression in leaves and roots, respectively. Likewise, a higher expression of AsSERK1 was observed in tubers. However, lower expression of SERLs was observed in majority of tissues studied irrespective of their vegetative or reproductive origin. This work paves way for future studies involving functional characterization of SERK/SERLs and their potential role in embryogenesis/organogenesis as an aid to regeneration and multiplication of endangered orchids.

Thaumatin-like protein kinases: Molecular characterization and transcriptional profiling in five cereal crops

Thaumatin-like protein kinases (TLPKs) are defense related proteins having antimicrobial property. Herein, we identified two TLPKs in the genome of Brachypodium distachyon and Oryza sativa, four in Hordeum vulgare and Sorghum bicolor, and 16 in Triticum aestivum. All the TLPKs were located at only one chromosome in each plant except T. aestivum, where they were located on chromosome 2 and chromosome 3. Paralogous analysis suggested the occurrence of one duplication event (DE) in each B. distachyon and O. sativa, two in H. vulgare while four DEs in T. aestivum genome during the evolution of TLPKs. The majority of TLPKs were intron less, while a few contains one or two introns. The introns were found in each 0, 1 and 2 phase. Protein structure analysis suggested the occurrence of a thaumatin and a kinase domain with a transmembrane (TM) helix in each TLPK. Further, a thaumatin family signature motif "GX[GF]XCXT[GA]DCX(1,2)GX(2,3)C", a "REDDD" motif and 16 cysteine residues were found conserved in the majority of TLPKs. Expression analysis indicated variable expression of TLPKs in various tissues of different cereal crops. They were high expressing in reproductive tissues in B. distachyon, while in leaves in T. aestivum. Modulated expression of TaTLPKs in the presence of fungal pathogen, and heat, drought and salt stress in T. aestivum suggested their roles in stress response. Co-expression analysis showed interaction of TLPKs with various development and stress related genes. The results indicated diverse roles of TLPKs, which can be utilized for the development of eco-friendly pest resistant crops in future.

Thaumatin-like protein kinases: Molecular characterization and transcriptional profiling in five cereal crops

Thaumatin-like protein kinases (TLPKs) are defense related proteins having antimicrobial property. Herein, we identified two TLPKs in the genome of Brachypodium distachyon and Oryza sativa, four in Hordeum vulgare and Sorghum bicolor, and 16 in Triticum aestivum. All the TLPKs were located at only one chromosome in each plant except T. aestivum, where they were located on chromosome 2 and chromosome 3. Paralogous analysis suggested the occurrence of one duplication event (DE) in each B. distachyon and O. sativa, two in H. vulgare while four DEs in T. aestivum genome during the evolution of TLPKs. The majority of TLPKs were intron less, while a few contains one or two introns. The introns were found in each 0, 1 and 2 phase. Protein structure analysis suggested the occurrence of a thaumatin and a kinase domain with a transmembrane (TM) helix in each TLPK. Further, a thaumatin family signature motif "GX[GF]XCXT[GA]DCX(1,2)GX(2,3)C", a "REDDD" motif and 16 cysteine residues were found conserved in the majority of TLPKs. Expression analysis indicated variable expression of TLPKs in various tissues of different cereal crops. They were high expressing in reproductive tissues in B. distachyon, while in leaves in T. aestivum. Modulated expression of TaTLPKs in the presence of fungal pathogen, and heat, drought and salt stress in T. aestivum suggested their roles in stress response. Co-expression analysis showed interaction of TLPKs with various development and stress related genes. The results indicated diverse roles of TLPKs, which can be utilized for the development of eco-friendly pest resistant crops in future.

Backbone 1H, 13C, and 15N resonance assignments of BoMan26A, a β-mannanase of the glycoside hydrolase family 26 from the human gut bacterium Bacteroides ovatus

Bacteroides ovatus is a member of the human gut microbiota. The importance of this microbial consortium involves the degradation of complex dietary glycans mainly conferred by glycoside hydrolases. In this study we focus on one such catabolic glycoside hydrolase from B. ovatus. The enzyme, termed BoMan26A, is a β-mannanase that takes part in the hydrolytic degradation of galactomannans. The crystal structure of BoMan26A has previously been determined to reveal a TIM-barrel like fold, but the relation between the protein structure and the mode of substrate processing has not yet been studied. Here we report residue-specific assignments for 95% of the 344 backbone amides of BoMan26A. The assignments form the basis for future studies of the relationship between substrate interactions and protein dynamics. In particular, the potential role of loops adjacent to glycan binding sites is of interest for such studies.

Identification, characterization and expression profiling of cation-proton antiporter superfamily in Triticum aestivum L. and functional analysis of TaNHX4-B

The monovalent cation proton antiporter (CPA) superfamily comprises Na⁺/H⁺ exchanger (NHX), K⁺ efflux antiporter (KEA), and cation/H⁺ exchanger (CHX) family proteins, which play vital functions in plants. A total of 107 TaCPA proteins were identified in Triticum aestivum, and phylogenetically classified into 35 TaNHX, 24 TaKEA and 48 TaCHX proteins. These families had representatives derived from all three sub-genomes. TaKEA genes consisted of higher number of exons, followed by TaNHXs and TaCHXs. The occurrence of about 10 transmembrane regions and higher composition of helices and coils support their membrane-bound and hydrophobic nature. Diverse expression in various tissues and modulated expression under stress conditions suggested their role in development and in response to stress. Co-expression analyses revealed their complex interaction networks. Expression of TaNHX4-B.1 and TaNHX4-B.4 facilitated differential abiotic stress tolerance to Escherichia coli. Our study provides comprehensive information about CPA genes, which would be useful in their future functional characterization.

Subjective Elicitation of Dirichlet Hyperparameters Using Past Data: A Study of Ovarian Cancer Patients

Elicitation of prior plays a very important role in Bayesian paradigm especially when dealing with rare disease problems in medical field. The reason being that we do not get enough data to draw valid inferences always. Since the subject of study is human population, one cannot do experiments with their health. The prior distribution supports the final results by some additional information gained from the experts. In any case if an appropriate expert is not available, we can use past data to get information about the prior and its hyperparameters. The present paper provides a technique of elicitation of prior hyperparameters based on a well known multinomial-Dirichlet model. Since the main focus is on medical data problems, the inferences on odds ratios and interaction parameters are also provided. Numerical illustration is based on a real dataset from Israel on patients having ovarian cancer. Although the details have been given in the context of ovarian cancer patients, the development in the paper is equally well applicable for any such disease.

Specific Cholesterol Binding Drives Drastic Structural Alterations in Apolipoprotein A1

Proteins typically adopt a multitude of flexible and rapidly interconverting conformers, many of which are governed by specific protein interaction domains. Whereas disc-shaped oligomeric HDL and its major protein component ApoA1 have been the focus of several investigations, the structural properties of monomeric ApoA1 remain poorly understood. Using tens of independent molecular simulations (>50 μs), we reveal that ApoA1 adopts a compact conformation. Upon the addition of a physiological concentration of cholesterol to ApoA1, the monomeric protein spontaneously formed a circular conformation. Remarkably, these drastic structural perturbations are driven by a specific cholesterol binding site at the C-terminal and a novel cholesterol binding site at the N-terminal. We propose a mechanism whereby ApoA1 opens in a stagewise manner and mutating the N-terminal binding site destroys the open "belt-shaped" topology. Complementary experiments confirm that the structural changes are induced by specific association of cholesterol with ApoA1, not by the nonspecific hydrophobic effect.

Genome-wide identification and characterization of LRR-RLKs reveal functional conservation of the SIF subfamily in cotton (Gossypium hirsutum)

BACKGROUND

As one of the largest subfamilies of the receptor-like protein kinases (RLKs) in plants, Leucine Rich Repeats-RLKs (LRR-RLKs) are involved in many critical biological processes including growth, development and stress responses in addition to various physiological roles. Arabidopsis contains 234 LRR-RLKs, and four members of Stress Induced Factor (SIF) subfamily (AtSIF1-AtSIF4) which are involved in abiotic and biotic stress responses. Herein, we aimed at identification and functional characterization of SIF subfamily in cultivated tetraploid cotton Gossypium hirsutum.

RESULTS

Genome-wide analysis of cotton LRR-RLK gene family identified 543 members and phylogenetic analysis led to the identification of 6 cotton LRR-RLKs with high homology to Arabidopsis SIFs. Of the six SIF homologs, GhSIF1 is highly conserved exhibiting 46-47% of homology with AtSIF subfamily in amino acid sequence. The GhSIF1 was transiently silenced using Virus-Induced Gene Silencing system specifically targeting the 3' Untranslated Region. The transiently silenced cotton seedlings showed enhanced salt tolerance compared to the control plants. Further, the transiently silenced plants showed better growth, lower electrolyte leakage, and higher chlorophyll and biomass contents.

CONCLUSIONS

Overall, 543 LRR-RLK genes were identified using genome-wide analysis in cultivated tetraploid cotton G. hirsutum. The present investigation also demonstrated the conserved salt tolerance function of SIF family member in cotton. The GhSIF1 gene can be knocked out using genome editing technologies to improve salt tolerance in cotton.

Molecular characterization and differential expression suggested diverse functions of P-type II Ca2+ATPases in Triticum aestivum L

Background

Plant P-type II Ca²⁺ATPases are formed by two distinct groups of proteins (ACAs and ECAs) that perform pumping of Ca²⁺ outside the cytoplasm during homeostasis, and play vital functions during development and stress management. In the present study, we have performed identification and characterisation of P-type II Ca²⁺ATPase gene family in an important crop plant Triticum aestivum.

Results

Herein, a total of 33 TaACA and 9 TaECA proteins were identified from the various chromosomes and sub-genomes of Triticum aestivum. Phylogenetic analysis revealed clustering of the homoeologous TaACA and TaECA proteins into 11 and 3 distinct groups that exhibited high sequence homology and comparable structural organization as well. Both TaACA and TaECA group proteins consisted of eight to ten transmembrane regions, and their respective domains and motifs. Prediction of sub-cellular localization was found variable for most of the proteins; moreover, it was consistent with the evolutionarily related proteins from rice and Arabidopsis in certain cases. The occurrence of assorted sets of cis-regulatory elements indicated their diverse functions. The differential expression of various TaACA and TaECA genes during developmental stages suggested their roles in growth and development. The modulated expression during heat, drought, salt and biotic stresses along with the occurrence of various stress specific cis-regulatory elements suggested their association with stress response. Interaction of these genes with numerous development and stress related genes indicated their decisive role in various biological processes and signaling.

Conclusion

T. aestivum genome consisted of a maximum of 42 P-type II Ca²⁺ATPase genes, derived from each A, B and D sub-genome. These genes may play diverse functions during plant growth and development. They may also be involved in signalling during abiotic and biotic stresses. The present study provides a comprehensive insight into the role of P-type II Ca²⁺ATPase genes in T. aestivum. However, the specific function of each gene needs to be established, which could be utilized in future crop improvement programs.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4792-9) contains supplementary material, which is available to authorized users.

De novo characterization of Phenacoccus solenopsis transcriptome and analysis of gene expression profiling during development and hormone biosynthesis

The cotton mealybug Phenacoccus solenopsis is a devastating pest of cotton causing tremendous loss in the yield of crops each year. Widespread physiological and biological studies on P. solenopsis have been carried out, but the lack of genetic information has constrained our understanding of the molecular mechanisms behind its growth and development. To understand and characterize the different developmental stages, RNA-Seq platform was used to execute de-novo transcriptome assembly and differential gene expression profiling for the eggs, first, second, third instar and adult female stages. About 182.67 million reads were assembled into 93,781 unigenes with an average length of 871.4 bp and an N50 length of 1899 bp. These unigenes sequences were annotated and classified by performing NCBI non-redundant (Nr) database, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Clusters of Orthologous Groups (COG), Gene ontology (GO), the Swiss-Prot protein database (Swiss-Prot), and nearest related organism Acyrthosiphon pisum (pea aphid) database. To get more information regarding the process of metamorphosis, we performed a pairwise comparison of four developmental stages and obtained 29,415 differentially expressed genes. Some of the differentially expressed genes were associated with functional protein synthesis, anti-microbial protection, development and hormone biosynthesis. Functional pathway enrichment analysis of differentially expressed genes showed the positive correlation with specific physiological activities of each stage, and these results were confirmed by qRT-PCR experiments. This study gives a valuable genomics resource of P. solenopsis covering all its developmental stages and will promote future studies on biological processes at the molecular level.

Gene architecture and expression analyses provide insights into the role of glutathione peroxidases (GPXs) in bread wheat (Triticum aestivum L.)

Glutathione peroxidases (GPXs) are redox sensor proteins that maintain a steady-state of H₂O₂ in plant cells. They exhibit distinct sub-cellular localization and have diverse functionality in response to different stimuli. In this study, a total of 14 TaGPX genes and three splice variants were identified in the genome of Triticum aestivum and evaluated for various physicochemical properties. The TaGPX genes were scattered on the various chromosomes of the A, B, and D sub-genomes and clustered into five homeologous groups based on high sequence homology. The majority of genes were derived from the B sub-genome and localized on chromosome 2. The intron-exon organization, motif and domain architecture, and phylogenetic analyses revealed the conserved nature of TaGPXs. The occurrence of both development-related and stress-responsive cis-acting elements in the promoter region, the differential expression of these genes during various developmental stages, and the modulation of expression in the presence of biotic and abiotic stresses suggested their diverse role in T. aestivum. The majority of TaGPX genes showed higher expression in various leaf developmental stages. However, TaGPX1-A1 was upregulated in the presence of each abiotic stress treatment. A co-expression analysis revealed the interaction of TaGPXs with numerous development and stress-related genes, which indicated their vital role in numerous biological processes. Our study revealed the opportunities for further characterization of individual TaGPX proteins, which might be useful in designing future crop improvement strategies.

Molecular recognition of flunarizine dihydrochloride and β-cyclodextrin inclusion complex by NMR and computational approaches

Background

Flunarizine dihydrochloride (FLN) is used in the prophylactic treatment of migraine, vertigo, occlusive peripheral vascular disease and epilepsy. Cyclodextrins (CDs) are chiral, truncated cone shaped macrocycles known for their inner hydrophobic and outer hydrophilic site. They form complexes with hydrophobic drug molecules and enhance the solubility and bioavailability of such compounds by enhancing drug permeability through mucosal tissues. NMR spectroscopy and computational docking have been recognized as an important tool for the interaction study of CDs-drug inclusion complexes in solution state.

Results

The structural assignments of FLN and β-CD protons were determined by ¹H NMR and 2D ¹H-¹H COSY NMR spectroscopy. ¹H NMR spectroscopic studies of FLN, β-CD and their mixtures confirmed the formation of β-CD-FLN inclusion complex in solution. ¹H NMR titration data for β-CD-FLN inclusion complex showed 1:1 stoichiometry, an association constant of K_a = 157 M⁻¹ and change in Gibbs free energy of ∆G = − 12.65 kJ mol⁻¹. The binding constant of the β-CD inclusion complex with two nearly similar structures, FLN and cetirizine dihydrochloride, were compared. Two-dimensional ¹H-¹H ROESY spectral data and molecular docking studies showed the modes of penetration of the aromatic rings from the wider rim side into the β-CD cavity. The possible geometrical structures of the β-CD-FLN inclusion complex have been proposed in which aromatic rings protrude close to the narrower rim of the β-CD truncated cone.

Conclusion

NMR spectroscopic studies of FLN, β-CD and FLN:β-CD mixtures confirmed the formation of 1:1 inclusion complex in solution at room temperature. Two-dimensional ¹H-¹H ROESY together with molecular docking study confirmed that the F-substituted aromatic ring of FLN penetrates into β-CD truncated cone and the tail of aromatic rings were proximal to narrower rim of β-CD. The splitting of aromatic signals of FLN in the presence of β-CD suggests chiral differentiation of the guest FLN by β-CD.

Electronic supplementary material

The online version of this article (10.1186/s13065-018-0395-4) contains supplementary material, which is available to authorized users.

Reference genes validation in Phenacoccus solenopsis under various biotic and abiotic stress conditions

Real-time PCR (RT-qPCR) expression analysis is a powerful analytical technique, but for normalization of data requires the use of stable reference genes. However, suitable reference genes are still not known in the case of Phenacoccus solenopsis under variable experimental treatments. The present study focused on the identification of stable housekeeping genes as a reference for analysis under different abiotic and biotic factors in P. solenopsis. We analyzed the relative expression of six commonly used candidate reference genes in different developmental stages, host-feeding assay, temperature treatments and field distribution conditions. Expression stabilities were analyzed by geNorm, NormFinder, and RefFinder. Under developmental and field distribution conditions, β-Tubulin was found to be most stable reference genes followed by rpl32 and α-Tubulin. In the case host feeding treatment conditions, β-Tubulin and α-tubulin identified to be the most stable reference genes, while in temperature stress, a combination of α-Tubulin and rpl32 found to be suitable for normalizing the RT-qPCR data. Further, the above-identified genes were validated using RT-qPCR based gene expression analysis of four objective genes namely, Myoinhibitory peptides (MIPs), Zinc_metalloprotease (Zn_Mp), fatty acid synthase (fas) and alpha-glucosidase. Identified reference genes will facilitate gene expression studies in future under different stress treatments in P. solenopsis.

Structural insights into the inclusion complexes between clomiphene citrate and β-cyclodextrin: The mechanism of preferential isomeric selection

A major challenge in pharmaceuticals for clinical applications is to alter the solubility, stability, and toxicity of drug molecules in living systems. Cyclodextrins (CDs) have the ability to form host-guest inclusion complexes with pharmaceuticals for further development of new drug formulations. The inclusion complex of clomiphene citrate (CL), a poorly water-soluble drug, with native β-cyclodextrin (β-CD) was characterized by a one and two-dimensional nuclear magnetic resonance (NMR) spectroscopic approach and also by molecular docking techniques. Here we report NMR and a computational approach in preferential isomeric selection of CL, which exists in two stereochemical isomers, enclomiphene citrate (ENC; E isomer) and zuclomiphene citrate (ZNC; Z isomer) with β-CD. β-CD cavity protons, namely, H-3' and H-5', experienced shielding in the presence of CL. The aromatic ring protons of the CL molecule were observed to be deshielded in the presence of β-CD. The stoichiometric ratio of the β-CD:CL inclusion complex was observed by NMR and found to be 1:1. The overall binding constant of β-CD:CL inclusion complexes was based on NMR chemical shifts and was calculated to be 50.21 M^-1 . The change in Gibb's free energy (∆G) was calculated to be -9.80 KJ mol^-1 . The orientation and structure of the β-CD:CL inclusion complexes are proposed on the basis of NMR and molecular docking studies. 2D ¹ H-¹ H ROESY confirmed the involvement of all three aromatic rings of CL in the inclusion complexation with β-CD in the solution, confirming the multiple equilibria between β-CD and CL. Molecular docking and 2D ¹ H-¹ H ROESY provide insight into the inclusion complexation of two isomers of CL into the β-CD cavity. A molecular docking technique further provided the different binding affinities of the E and Z isomers of CL with β-CD and confirmed the preference of the Z isomer binding for β-CD:CL inclusion complexes. The study indicates that the formation of a hydrogen bond between -O- of CL and the hydrogen atom of the hydroxyl group of β-CD was the main factor for noncovalent β-CD:CL inclusion complex formation and stabilization in the aqueous phase.

Grb2 carboxyl-terminal SH3 domain can bivalently associate with two ligands, in an SH3 dependent manner

Src homology domain containing leukocyte protein of 65 kDa (SLP65), the growth factor receptor binding protein 2 (Grb2), and the guanine nucleotide exchange factor for the Rho family GTPases (Vav), self associate in unstimulated B cells as components of the preformed B cell receptor transducer module, in an SH3-dependent manner. The complex enables the B cell to promptly respond to BCR aggregation, resulting in signal amplification. It also facilitates Vav translocation to the membrane rafts, for activation. Here we uncover the molecular mechanism by which the complex may be formed in the B cell. The C-terminal SH3 domain (SH3C) of Grb2 bivalently interacts with the atypical non-PxxP proline rich region of SLP65, and the N-terminal SH3 domain (SH3N) of Vav, both the interactions crucial for the proper functioning of the B cell. Most surprisingly, the two ligands bind the same ligand binding site on the surface of Grb2 SH3C. Addition of SLP65 peptide to the Grb2-Vav complex abrogates the interaction completely, displacing Vav. However, the addition of Vav SH3N to the SLP65-Grb2 binary complex, results in a trimeric complex. Extrapolating these results to the in vivo conditions, Grb2 should bind the SLP65 transducer module first, and then Vav should associate.

Binding and thermodynamics of REV peptide-ctDNA interaction

The thermodynamics of DNA-ligand binding is important as it provides useful information to understand the details of binding processes. HIV-1 REV response element (RRE) located in the env coding region of the viral genome is reported to be well conserved across different HIV-1 isolates. In this study, the binding characteristics of Calf thymus DNA (ctDNA) and REV peptide from HIV-1 were investigated using spectroscopic (UV-visible, fluorescence, and circular dichroism (CD)) and isothermal titration calorimetric (ITC) techniques. Thermal stability and ligand binding properties of the ctDNA revealed that native ctDNA had a T_m of 75.5 °C, whereas the ctDNA-REV peptide complex exhibited an incremental shift in the T_m by 8 °C, indicating thermal stability of the complex. CD data indicated increased ellipticity due to large conformational changes in ctDNA molecule upon binding with REV peptide and two binding stoichiometric modes are apparent. The ctDNA experienced condensation due to large conformational changes in the presence of REV peptide and positive B→Ψ transition was observed at higher molar charge ratios. Fluorescence studies performed at several ligand concentrations revealed a gradual decrease in the fluorescence intensity of EtBr-bound ctDNA in response to increasing ligand concentrations. The fluorescence data further confirmed two stoichiometric modes of binding for ctDNA-REV peptide complex as previously observed with CD studies. The binding enthalpies were determined using ITC in the temperature range of 293 K-308 K. The ITC binding isotherm was exothermic at all temperatures examined, with low ΔH values indicating that the ctDNA-REV peptide interaction is driven largely by entropy. The heat capacity change (ΔC_p ) was insignificant, an unusual finding in the area of DNA-peptide interaction studies. The variation in the values obtained for ΔH, ΔS, and ΔG with temperature further suggests that ctDNA-REV peptide interaction is entropically driven. ITC based analysis of salt dependence of binding constant gave a charge value (Z) = +4.01, as determined for the δlnK/δln[Na⁺ ] parameter, suggesting the participation of only 3-4 Arg out of 11 Arg charge from REV peptide. The stoichiometry observed for the complex was three molar charge of REV peptide binding per molar charge of ctDNA. ITC based analysis further confirmed that the binding between ctDNA and REV peptide is governed by electrostatic interaction. Molecular interactions including H-bonding, van der Waals forces, and solvent molecules rearrangement, underlie the binding of REV peptide to ctDNA.

Admitting Deserving Medical Students from Rural and Disadvantaged: Patan Academy of Health Sciences' Approach

BACKGROUND

Patan Academy of Health Sciences (PAHS) aims to produce physicians who would be able and willing to serve in the rural areas. Recognizing the critical importance of student selection strategy, among others, in achieving the program goals, it has adopted an innovative scheme for selecting medical students. This paper describes PAHS medical student selection scheme that favors enrollment of deserving applicants from rural and disadvantaged groups so as to help improve distribution of physicians in rural Nepal.

METHODS

A student admission committee comprising a group of medical educators finalized a three-step student selection scheme linked with scholarships after reviewing relevant literatures and consultative meetings with experts within and outside Nepal. The committee did local validation of Personal Quality Assessment (PQA) that tested cognitive ability and personality traits, Admission OSPE (Objective Structured Performance Examination) that assessed non-cognitive attributes of applicants. It also provided preferential credits to applicants' socio-economic characteristics to favor the enrollment of deserving applicants from rural and disadvantaged groups through Social Inclusion Matrix (SIM). Three different categories of scholarship schemes namely Partial, Collaborative and Full were devised with Partial providing 50% and other two categories each providing 100% coverage of tuition fee.

RESULTS

PAHS student selection scheme succeeded in enrolling more than half of its students from rural areas of Nepal, including about 10% of the students from that of the most backward region of the country. About one third of students were female and about the same were from public and community school. Sixty percent of students receive different categories of scholarships.

CONCLUSIONS

Limited findings indicate the success of the selection scheme in enrolling high proportion of applicants from rural and disadvantageous groups and enable them to pursue study by providing scholarships.

Ca2+/Cation Antiporters (CaCA): Identification, Characterization and Expression Profiling in Bread Wheat (Triticum aestivum L.)

The Ca2+/cation antiporters (CaCA) superfamily proteins play vital function in Ca2+ ion homeostasis, which is an important event during development and defense response. Molecular characterization of these proteins has been performed in certain plants, but they are still not characterized in Triticum aestivum (bread wheat). Herein, we identified 34 TaCaCA superfamily proteins, which were classified into TaCAX, TaCCX, TaNCL, and TaMHX protein families based on their structural organization and evolutionary relation with earlier reported proteins. Since the T. aestivum comprises an allohexaploid genome, TaCaCA genes were derived from each A, B, and D subgenome and homeologous chromosome (HC), except chromosome-group 1. Majority of genes were derived from more than one HCs in each family that were considered as homeologous genes (HGs) due to their high similarity with each other. These HGs showed comparable gene and protein structures in terms of exon/intron organization and domain architecture. Majority of TaCaCA proteins comprised two Na_Ca_ex domains. However, TaNCLs consisted of an additional EF-hand domain with calcium binding motifs. Each TaCaCA protein family consisted of about 10 transmembrane and two α-repeat regions with specifically conserved signature motifs except TaNCL, which had single α-repeat. Variable expression of most of the TaCaCA genes during various developmental stages suggested their specified role in development. However, constitutively high expression of a few genes like TaCAX1-A and TaNCL1-B indicated their role throughout the plant growth and development. The modulated expression of certain genes during biotic (fungal infections) and abiotic stresses (heat, drought, salt) suggested their role in stress response. Majority of TaCCX and TaNCL family genes were found highly affected during various abiotic stresses. However, the role of individual gene needs to be established. The present study unfolded the opportunity for detail functional characterization of TaCaCA proteins and their utilization in future crop improvement programs.