Stress combinations and their interactions in plants database: a one-stop resource on combined stress responses in plants.

We have developed a compendium and interactive platform, named Stress Combinations and their Interactions in Plants Database (SCIPDb; http://www.nipgr.ac.in/scipdb.php), which offers information on morpho-physio-biochemical (phenome) and molecular (transcriptome and metabolome) responses of plants to different stress combinations. SCIPDb is a plant stress informatics hub for data mining on phenome, transcriptome, trait-gene ontology, and data-driven research for advancing mechanistic understanding of combined stress biology. We analyzed global phenome data from 939 studies to delineate the effects of various stress combinations on yield in major crops and found that yield was substantially affected under abiotic-abiotic stresses. Transcriptome datasets from 36 studies hosted in SCIPDb identified novel genes, whose roles have not been earlier established in combined stress. Integretome analysis under combined drought-heat stress pinpointed carbohydrate, amino acid, and energy metabolism pathways as the crucial metabolic, proteomic, and transcriptional components in plant tolerance to combined stress. These examples illustrate the application of SCIPDb in identifying novel genes and pathways involved in combined stress tolerance. Further, we showed the application of this database in identifying novel candidate genes and pathways for combined drought and pathogen stress tolerance. To our knowledge, SCIPDb is the only publicly available platform offering combined stress-specific omics big data visualization tools, such as an interactive scrollbar, stress matrix, radial tree, global distribution map, meta-phenome analysis, search, BLAST, transcript expression pattern table, Manhattan plot, and co-expression network. These tools facilitate a better understanding of the mechanisms underlying plant responses to combined stresses.

When two negatives make a positive: the favorable impact of the combination of abiotic stress and pathogen infection on plants.

Combined abiotic and biotic stresses modify plant defense signaling, leading to either the activation or suppression of defense responses. Although the majority of combined abiotic and biotic stresses reduce plant fitness, certain abiotic stresses reduce the severity of pathogen infection in plants. Remarkably, certain pathogens also improve the tolerance of some plants to a few abiotic stresses. While considerable research focuses on the detrimental impact of combined stresses on plants, the upside of combined stress remains hidden. This review succinctly discusses the interactions between abiotic stresses and pathogen infection that benefit plant fitness. Various factors that govern the positive influence of combined abiotic stress and pathogen infection on plant performance are also discussed. In addition, we provide a brief overview of the role of pathogens, mainly viruses, in improving plant responses to abiotic stresses. We further highlight the critical nodes in defense signaling that guide plant responses during abiotic stress towards enhanced resistance to pathogens. Studies on antagonistic interactions between abiotic and biotic stressors can uncover candidates in host plant defense that may shield plants from combined stresses.

Determining the prevalence of Escherichia coli, Salmonella, and shiga toxin-producing Escherichia coli in manure of dairy lagoons.

AIM: The aim of this study was to determine the prevalence of microbial pathogens in manure of dairy lagoons in California. METHODS AND RESULTS: To determine pathogens in dairy manure stored in anaerobic lagoons of dairy farm, an extensive field study was conducted across California to sample manure from 20 dairy farms. Samples were analyzed to determine the prevalence of indicator Escherichia coli, Shiga toxin producing E. coli (STEC), Salmonella, and E. coli O157: H7. To test the E. coli, STEC, and Salmonella, we used agar culture-based method followed by polymerase chain reaction (PCR) method. In addition, a real- time PCR based method was used to determine the presence of E coli O157: H7. Study demonstrated that the prevalence of Salmonella in manure sample is lower than E. coli. The presence of Salmonella was found in 2.26% of the samples, and both the culture-based and PCR methods yielded comparable outcomes in detecting Salmonella. Moreover, ∼11.30% of the total samples out of the 177 were identified as positive for STEC by qPCR. CONCLUSION: These findings demonstrate that indicator E. coli are abundantly present in anaerobic lagoons. However, the presence of STEC, and Salmonella is substantially low.

Time-Dependent Multireference Coupled-Cluster Method (TDMRCCM) for the Bath-Dynamics in System-Bath Approach to Nonadiabatic Dynamics.

The time-dependent multireference coupled-cluster method (TDMRCCM) fits well in the scheme of the system-bath separation used to study the nonadiabatic dynamics. In TDMRCCM, a projection operator is defined as one that projects the full Hilbert space onto the space spanned by the collection of system degrees of freedom, called the model space. The inverse of this projection operator is a wave operator that acts on the model space and takes its projection back to the full wave function. This wave operator is defined as an exponential of the excitation terms and, hence, can be expanded into a Taylor series, which we have truncated in this work at the second-order of excitations. The attraction of using TDMRCCM for describing the bath dynamics is due to the exponential nature of the ansatz used in the method, which makes it possible for the higher-order excitations to be absorbed by the lower-order terms, even upon truncating the series. This improves the accuracy of the numerical calculations using TDMRCCM as an approximation for the bath-mode dynamics in the system-bath framework for nonadiabatic dynamics. We present the theoretical details of TDMRCCM and the numerical results for implementing this method to study the dynamics in the butatriene cation.

Criteria for the Classification of System and Bath Variables in Nonadiabatic Dynamics: Application to Pyrazine.

The present work deals with the system-bath separation of the vibrational modes involved in a nonadiabatic system. System modes are the strongly interacting modes which dominate the overall dynamics and, hence, need a near-exact treatment. Bath modes have relatively weaker couplings and can be approximately treated. Thus, the exponential bottleneck involved in computations is controlled by the size of the system-subspace. The aim of this work is to put forward a set of criteria that provides clear guidelines for choosing the system degrees of freedom. The extent of wave packet dephasing caused by repeated crossings across the surface of curve-crossing is the basis for distinction between system and bath modes. The mechanisms of the wave packet dephasing and the criteria are discussed in detail. Numerically converged results presented for the 24-mode pyrazine and 3-mode spin-boson model validate the efficiency of these criteria.

Glutathione reductase a unique enzyme: molecular cloning, expression and biochemical characterization from the stress adapted C4 plant, Pennisetum glaucum (L.) R. Br.

The generation of excess reactive oxygen species (ROS) is one of the most common consequences of abiotic stress on plants. Glutathione reductase (GR, E.C. 1.6.4.2) and allied enzymes of the ascorbate-glutathione cycle play a crucial role to maintain the homeostatic redox balance in the cellular environment. GR plays an essential role in upholding the reduced glutathione pool under stress conditions. In the present study, a full-length GR cDNA and corresponding genomic clone was isolated from Pennisetum glaucum (L.) R. Br. The PgGR cDNA, encodes a 497-amino acid peptide with an estimated molecular mass of ~53.5 kDa. The PgGR peptide exhibits 54-89% sequence homology with GR from other plants and is cytoplasmic in nature. The PgGR enzyme was purified to near homogeneity, the recombinant protein being relatively thermostable and displaying activity in a broad range of temperature, pH and substrate concentrations. The PgGR transcript level was differentially regulated by heat, cold, salinity and methyl viologen-induced oxidative stress. The heterologously expressed PgGR protein in E. coli showed an improved protection against metal- and methyl viologen-induced oxidative stress. Our overall finding underscores the role of PgGR gene that responds to multiple abiotic stresses and provides stress tolerance in the experimental model (E. coli) which can be potentially used for the improvement of crops under abiotic stress conditions.

Enhancing C3 photosynthesis: an outlook on feasible interventions for crop improvement.

Despite the declarations and collective measures taken to eradicate hunger at World Food Summits, food security remains one of the biggest issues that we are faced with. The current scenario could worsen due to the alarming increase in world population, further compounded by adverse climatic conditions, such as increase in atmospheric temperature, unforeseen droughts and decreasing soil moisture, which will decrease crop yield even further. Furthermore, the projected increase in yields of C3 crops as a result of increasing atmospheric CO2 concentrations is much less than anticipated. Thus, there is an urgent need to increase crop productivity beyond existing yield potentials to address the challenge of food security. One of the domains of plant biology that promises hope in overcoming this problem is study of C3 photosynthesis. In this review, we have examined the potential bottlenecks of C3 photosynthesis and the strategies undertaken to overcome them. The targets considered for possible intervention include RuBisCO, RuBisCO activase, Calvin-Benson-Bassham cycle enzymes, CO2 and carbohydrate transport, and light reactions among many others. In addition, other areas which promise scope for improvement of C3 photosynthesis, such as mining natural genetic variations, mathematical modelling for identifying new targets, installing efficient carbon fixation and carbon concentrating mechanisms have been touched upon. Briefly, this review intends to shed light on the recent advances in enhancing C3 photosynthesis for crop improvement.

Molecular and biochemical characterization of dehydroascorbate reductase from a stress adapted C4 plant, pearl millet [Pennisetum glaucum (L.) R. Br].

KEY MESSAGE: PgDHAR was isolated from Pennisetum glaucum. PgDHAR responded to abiotic stress and exhibited enzyme activity at broad ranges of temperature, pH and substrate concentrations suggesting its role in stress tolerance. ABSTRACT: Dehydroascorbate reductase (EC 1.8.5.1) is a crucial enzyme actively involved in the recycling of ascorbate redox pool in the cellular environment. In this study, the full-length cDNA coding for DHAR polypeptide and its corresponding gene was isolated from Pennisetum glaucum (PgDHAR). PgDHAR encodes a polypeptide of 213 amino acids with a predicted molecular mass of 23.4 kDa and shares 80-75 % sequence homology with DHAR from other plants. The heterologously expressed recombinant PgDHAR protein exhibited activity in a wide range of substrate concentrations. The recombinant PgDHAR is thermostable and retains its activity over a broad pH range. Furthermore, transcript level of PgDHAR is quantitatively up-regulated in response to temperature. On the whole, PgDHAR alone or in combination with other genes of ascorbate-glutathione cycle can be used for the development of stress tolerant as well as nutritionally improved food crop with enhanced ascorbic acid content.

Unmasking complexities of combined stresses for creating climate-smart crops.

Understanding the complex challenges that plants face from multiple stresses is key to developing climate-ready crops. We highlight the significance of the Stress Combinations and their Interactions in Plants database (SCIPdb) for studying the impact of stress combinations on plants and the importance of aligning thematic research programs to create crops aligned with achieving sustainable development goals.

Application of sphingolipid-based nanocarriers in drug delivery: an overview.

Sphingolipids (SL) are well recognized for their cell signaling through extracellular and intracellular pathways. Based on chemistry different types of SL are biosynthesized in mammalian cells and have specific function in cellular activity. SL has an ampiphilic structure with have hydrophobic body attached to the polar head enables their use as a drug delivery agent in the form of nanocarriers. SL-based liposomes can improve the solubility of lipophilic drugs through host and drug complexes and are more stable than conventional liposomal formulations. Preclinical studies of SL nanocarriers are reported on topical delivery, oral delivery, ocular delivery, chemotherapeutic delivery, cardiovascular delivery and Alzheimer's disease. The commercial challenges and patents related to SL nanoformulations are highlighted in this article.

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Glucagon: Delivery advancements for hypoglycemia management.

As the 100th anniversary of glucagon's discovery approaches, we reflect on the remarkable journey of understanding its pivotal role in glucose regulation. Advancements in glucagon delivery systems for managing hypoglycemia are unfolding with promise, albeit accompanied by formulation and implementation challenges. Recent developments include non-injectable methods like BAQSIMI® (Nasal glucagon) offers a user-friendly option, but stability, bioavailability, and rapid onset remain formulation hurdles. Closed-loop systems, combining glucagon with insulin, aim to automate glucose control, demanding stable and precise formulations compatible with complex algorithms. However, achieving co-delivery harmony and effective dual-hormone responses poses substantial challenges. Ogluo® and Gvoke HypoPen® are auto-injector pens, a ready-to-use solution that can rapidly control hypoglycemia and eliminate the need for mixing powder and liquid. GlucaGen® Hypokit® and Glucagon Emergency Kits are traditional deliveries that possess complexity during administration and are still widely used in clinical practice. In addition to this advancement, we have covered the recent patents and clinical trials of glucagon delivery. The synergy of patent innovation and clinical validation offers a glimpse into the transformative potential of glucagon delivery yet underscores the intricate path toward widespread adoption and improved diabetes care. Finally, this review will help the formulation scientist, clinicians, healthcare providers, and patient to manage hypoglycemia using glucagon.

Comprehensive Analysis of Omicron Subvariants: EG.5 Rise, Vaccination Strategies, and Global Impact.

The emergence of new variants of the SARS-CoV-2 virus during the COVID-19 pandemic has prompted significant developments in the understanding, monitoring, and response to these strains. This comprehensive review focuses on two prominent variants of interest (VoI), XBB. 1.5 (Kraken) and XBB.1.16 ("Arcturus"), along with seven variants under observation (VuM), including EG.5. The World Health Organization (WHO) identified these variants in July 2023, highlighting EG.5's noteworthy rise in prevalence. EG.5, also known as "Eris," has exhibited an increased effective reproductive rate, prompting concerns about its contagiousness and immune evasion capabilities. With an altered spike protein in the Receptor-Binding Domain (RBD), EG.5 shares similarities with XBB.1.5 but surpasses it in prevalence, constituting 20% of COVID-19 cases in the United States by late August. EG.5's subvariant, EG.5.1, poses challenges with mutations like Q52H and F456L, contributing to its ability to bypass neutralizing antibodies. The global distribution of SARS-CoV-2 variants presents a dynamic landscape, with XBB.1.16 and other strains gaining prominence. The advent of the BA.2.86 variant further complicates the scenario, with its notable spread in regions lacking robust viral surveillance. A thorough analysis of mutations reveals the evolving nature of the Omicron variant, with distinct amino acid changes characterizing XBB.1.5, XBB.1.16, and EG.5. The WHO designates EG.5 as a "variant of interest" due to its increased contagiousness and potential immune evasion, emphasizing the need for vigilant monitoring. The risk assessment of EG.5 underscores its rapid development and growing prevalence globally. While booster vaccines targeting XBB.1.5 are in development, antiviral medications like nirmatrelvir/ritonavir (Paxlovid) continue to exhibit efficacy. In the context of the evolving variants, the FDA has granted emergency use authorization for updated COVID-19 vaccines targeting circulating strains, reflecting the adaptability of vaccination strategies to address emerging challenges. This comprehensive overview provides a nuanced understanding of the diverse Omicron subvariants, their global impact, and the ongoing efforts to combat their spread through vaccination and therapeutic interventions.

Chronic illness adjustment scale (CIAS): Development and validation.

OBJECTIVES: The objectives of this study were to (i) develop a self-report instrument to measure adjustment to chronic illness, (ii) evaluate its core structure and (iii) study various psychometric properties in the development of this instrument. METHOD: The entire process of developing and validating the instrument is conducted in different phases: item writing and content validation; exploratory factor analysis (EFA) and confirmatory factor analysis (CFA) to extract dimensions of the instrument; reliability and validity testing. A total of 1095 participants were included in the study. The EFA was run using IBM SPSS 23 and CFA was done by AMOS 21. RESULTS: The Cronbach alpha of the chronic illness adjustment scale was found to be .70. The instrument correlates positively with illness perception and well-being which supports the notion that the chronic illness adjustment scale has satisfactory convergent validity. DISCUSSION: The multifaceted nature of the chronic illness adjustment scale can serve as a global indicator of adjustment to chronic illness, allowing various interventions to flow toward the healthcare arena.

Striatin family proteins: The neglected scaffolds.

The Striatin family of proteins constitutes Striatin, SG2NA, and Zinedin. Members of this family of proteins act as a signaling scaffold due to the presence of multiple protein-protein interaction domains. At least two members of this family, namely Zinedin and SG2NA, have a proven role in cancer cell proliferation. SG2NA, the second member of this family, undergoes alternative splicing and gives rise to several isoforms which are differentially regulated in a tissue-dependent manner. SG2NA evolved earlier than the other two members of the family, and SG2NA undergoes not only alternative splicing but also other posttranscriptional gene regulation. Striatin also undergoes alternative splicing, and as a result, it gives rise to multiple isoforms. It has been shown that this family of proteins plays a significant role in estrogen signaling, neuroprotection, cancer as well as in cell cycle regulation. Members of the striatin family form a complex network of signaling hubs with different kinases and phosphatases, and other signaling proteins named STRIPAK. Here, in the present manuscript, we thoroughly reviewed the findings on striatin family members to elaborate on the overall structural and functional idea of this family of proteins. We also commented on the involvement of these proteins in STRIPAK complexes and their functional relevance.

Cloning and molecular characterization of a gene encoding late embryogenesis abundant protein from Pennisetum glaucum: protection against abiotic stresses.

Late embryogenesis abundant (LEA) protein family is a large protein family that protects other proteins from aggregation due to desiccation or osmotic stresses. A cDNA clone encoding a group 7 late embryogenesis abundant protein, termed PgLEA, was isolated from Pennisetum glaucum by screening a heat stress cDNA library. PgLEA cDNA encodes a 176 amino acid polypeptide with a predicted molecular mass of 19.21 kDa and an estimated isoelectric point of 7.77. PgLEA shares 70-74% sequence identity with other plant homologs. Phylogenetic analysis revealed that PgLEA is evolutionarily close to the LEA 7 group. Recombinant PgLEA protein expressed in Escherichia coli possessed in vitro chaperone activity and protected PgLEA-producing bacteria from damage caused by heat and salinity. Positive correlation existed between differentially up-regulated PgLEA transcript levels and the duration and intensity of different environmental stresses. In silico analysis of the promoter sequence of PgLEA revealed the presence of a distinct set of cis-elements and transcription factor binding sites. Transcript induction data, the presence of several putative stress-responsive transcription factor binding sites in the promoter region of PgLEA, the in vitro chaperone activity of this protein and its protective effect against heat and salt damage in E. coli suggest a role in conferring abiotic stress tolerance in plants.

Recent Advances in Plant Gene Silencing Methods.

With the increasing understanding of fundamentals of gene silencing pathways in plants, various tools and techniques for downregulating the expression of a target gene have been developed across multiple plant species. This chapter provides an insight into the molecular mechanisms of gene silencing and highlights the advancements in various gene silencing approaches. The prominent aspects of different gene silencing methods, their advantages and disadvantages have been discussed. A succinct discussion on the newly emerged microRNA-based technologies like microRNA-induced gene silencing (MIGS) and microRNA-mediated virus-induced gene silencing (MIR-VIGS) are also presented. We have also discussed the gene-editing system like CRISPR-Cas. The prominent bottlenecks in gene silencing methods are the off-target effects and lack of universal applicability. However, the tremendous growth in understanding of this field reflects the potentials for improvements in the currently available approaches and the development of new widely applicable methods for easy, fast, and efficient functional characterization of plant genes.

Cationic microcrystalline cellulose - Montmorillonite composite aerogel for preconcentration of inorganic anions from dairy wastewater.

Development of efficient adsorbents to inorganic anions as a solid phase extraction (SPE) material is highly desirable for chromatographic analysis and pollution control. In this work we developed a new hybrid cationic microcrystalline cellulose aerogel composite. Cationic cetylpyridinium imbedded montmorillonite (CPC-MT) was uniformly entrapped in microcrystalline cellulose (MCC) to enhance anionic adsorption efficiency and mechanical stability. The developed CPC-MT@MCC aerogel was used as an SPE adsorbent for anions from dairy wastewater by coupling with ion-column chromatography. Further quaternized CPC-MT@MCC aerogel (CPC-MT@QMCC) showed unique low density (10.6 mg cm-3), large specific surface area (320 m2 g-1), porosity 70%, 800 mg g-1 nitrate adsorption capacity within 60 min and ease of elution in alkaline solutions. The CPC-MT@QMCC aerogel showed efficient regeneration and reuse performances for up to 10 cycles. More importantly, a dynamic binding efficiency of 710 mg g-1 highlights its excellent performance for practical applications. 96% of nitrate anion from environmental manure wastewater samples were adsorbed with 98.7% recovery. A good linear relationship was obtained in the range of 0.01-10 mg L-1 and the limits of detection was 0.5 mg L-1 using CPC-MT@QMCC aerogel as a preconcentration column. The successful synthesis of such intriguing and economic CPC-MT@QMCC aerogel may provide a promising matrix for high-performance and high efficiency chromatographic media.

Combined Drought and Heat Stress Influences the Root Water Relation and Determine the Dry Root Rot Disease Development Under Field Conditions: A Study Using Contrasting Chickpea Genotypes.

Abiotic stressors such as drought and heat predispose chickpea plants to pathogens of key importance leading to significant crop loss under field conditions. In this study, we have investigated the influence of drought and high temperature on the incidence and severity of dry root rot disease (caused by Macrophomina phaseolina) in chickpea, under extensive on- and off-season field trials and greenhouse conditions. We explored the association between drought tolerance and dry root rot resistance in two chickpea genotypes, ICC 4958 and JG 62, with contrasting resistance to dry root rot. In addition, we extensively analyzed various patho-morphological and root architecture traits altered by combined stresses under field and greenhouse conditions in these genotypes. We further observed the role of edaphic factors in dry root rot incidence under field conditions. Altogether, our results suggest a strong negative correlation between the plant water relations and dry root rot severity in chickpeas, indicating an association between drought tolerance and dry root rot resistance. Additionally, the significant role of heat stress in altering the dynamics of dry root rot and the importance of combinatorial screening of chickpea germplasm for dry root rot resistance, drought, and heat stress have been revealed.

An affinity-based genome walking method to find transgene integration loci in transgenic genome.

Identifying a good transgenic event from the pool of putative transgenics is crucial for further characterization. In transgenic plants, the transgene can integrate in either single or multiple locations by disrupting the endogenes and/or in heterochromatin regions causing the positional effect. Apart from this, to protect the unauthorized use of transgenic plants, the signature of transgene integration for every commercial transgenic event needs to be characterized. Here we show an affinity-based genome walking method, named locus-finding (LF) PCR (polymerase chain reaction), to determine the transgene flanking sequences of rice plants transformed by Agrobacterium tumefaciens. LF PCR includes a primary PCR by a degenerated primer and transfer DNA (T-DNA)-specific primer, a nested PCR, and a method of enriching the desired amplicons by using a biotin-tagged primer that is complementary to the T-DNA. This enrichment technique separates the single strands of desired amplicons from the off-target amplicons, reducing the template complexity by several orders of magnitude. We analyzed eight transgenic rice plants and found the transgene integration loci in three different chromosomes. The characteristic illegitimate recombination of the Agrobacterium sp. was also observed from the sequenced integration loci. We believe that the LF PCR should be an indispensable technique in transgenic analysis.