Browsing by Author "Akanksha Srivastava"

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A qualitative exploration of stressors and coping strategies of transmen during the global crisis
(Sapienza Universita Editrice, 2024) Akanksha Srivastava; Yogesh Kumar Arya; Shobhna Joshi; Tushar Singh
Introduction: The lockdown protocols with various restrictions were put in effect to stop the proliferation of coronavirus. It brought many challenges in the life of the mass community, but the challenges faced by transmen during the lockdown were unique and, in some cases, more challenging due to the high level of marginalization, ignorance, and lack of basic support for them even in normal times. This further led to the poor psychological and physical health of these individuals. The present paper aims to understand the subjective ordeal of transmen, the stressors they faced at the time of lockdown and the coping strategies opted to deal with the stressors. Method: Semi-structured interviews were conducted with 15 transmen of the age range 21 to 30 years residing in India. The interviews were conducted after the end of the pandemic during and after phase 4 of unlock in India when the restriction on movement was removed. The interviews were later analyzed using Thematic analysis. Result: The analysis shows several physical, psychological, and social stressors emerged during the pandemic including emotional and physical violence from unaccepting parents, unavailability of supportive organizations, inaccessibility of medical assistance and hormone treatment, suicidal ideation due to free time, feelings of isolation and use of wrong pronouns all affecting the mental health severely. To deal with these stressors, transmen adopted various strategies that include, cognitive appraisal, emotional support from friends, and self-help thought. Conclusion: These findings are discussed within the Indian context during the pandemic. The findings of the present work will help transmen in suggesting the ways of dealing with the stressors at uncertain times. © Author(s)
Acute cadmium toxicity and post-stress recovery: Insights into coordinated and integrated response/recovery strategies of Anabaena sp. PCC 7120
(Elsevier B.V., 2021) Akanksha Srivastava; Subhankar Biswas; Sandhya Yadav; Sanjiv Kumar; Vaibhav Srivastava; Yogesh Mishra
Cyanobacteria, the first photoautotrophs have remarkable adaptive capabilities against most abiotic stresses, including Cd. A model cyanobacterium, Anabaena sp. PCC 7120 has been commonly used to understand cyanobacterial plasticity under different environmental stresses. However, very few studies have focused on the acute Cd toxicity. In this context, Anabaena was subjected to 100 μM Cd for 48 h (acute Cd stress, ACdS) and then transferred into the fresh medium for post-stress recovery (PSR). We further investigated the dynamics of morpho-ultrastructure, physiology, cytosolic proteome, thylakoidal complexes, chelators, and transporters after ACdS, as well as during early (ER), mid (MR), and late (LR) phases of PSR. The findings revealed that ACdS induced intracellular Cd accumulation and ROS production, altered morpho-ultrastructure, reduced photosynthetic pigments, and affected the structural organization of PSII, which subsequently hindered photosynthetic efficiency. Anabaena responded to ACdS and recovered during PSR by reprogramming the expression pattern of proteins/genes involved in cellular defense and repair; CO2 access, Calvin-Benson cycle, glycolysis, and pentose phosphate pathway; protein biosynthesis, folding, and degradation; regulatory functions; PSI-based cyclic electron flow; Cd chelation; and efflux. These modulations occurred in an integrated and coordinated manner that facilitated Anabaena to detoxify Cd and repair ACdS-induced cellular damage. © 2021 Elsevier B.V.
Artificial intelligence as a smart approach in clinical microbiology laboratory
(Academic Press Inc., 2024) Akanksha Srivastava
Artificial intelligence (AI) is rapidly growing field with potential impact on global health. AI involves an algorithmic rule which have been used to analyse a set of data with an automated system. AI is expeditiously penetrating the field of biotechnology and microbiology with higher impact in clinical laboratories, disease diagnosis and healthcare. In addition, emergence of AI will be highly beneficial for clinical microbiologist, academicians, and researchers. It provides optimal efficiency and quality, with rapid and cost-effective results for disease diagnosis. In this chapter, we elaborate some of the routine diagnosis test occurred in clinical microbiology laboratories. Further, we explore the AI applications in image analysis of microbial staining, bacterial infection, ova and parasite examination, analysis of antimicrobial resistance with whole genome sequencing (WGS) and matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is also enlightened here. © 2024 Elsevier Ltd
Biochemical and proteomic analysis reveals oxidative stress tolerance strategies of Scenedesmus abundans against allelochemicals released by Microcystis aeruginosa
(Elsevier B.V., 2019) Simranjeet Kaur; Akanksha Srivastava; Sanjiv Kumar; Vaibhav Srivastava; Amrik Singh Ahluwalia; Yogesh Mishra
We studied the possible survival strategies of a green alga, Scenedesmus abundans, against allelochemicals secreted by Microcystis aeruginosa. We exposed the monoculture of S. abundans to a cell free-filtrate (allelochemicals)of M. aeruginosa at the start of our experiment and measured the growth behaviour, morphological changes and oxidative stress markers. The results suggest that exposure to allelochemicals induced oxidative stress in S. abundans, which had significantly reduced the growth of green alga with certain morphological changes. However, after seven days, S. abundans found ways to reduce oxidative stress by recovering its morphology and growth close to that of control. To understand possible survival strategies of test alga, we measured biochemical as well as protein level changes in S. abundans. Biochemical response of the green alga clearly showed that as a response to allelochemicals, enzymatic and non-enzymatic antioxidants were induced. Proteomic analysis showed that exposure to allelochemicals induced accumulation of 13 proteins on the 2-DE gel of S. abundans, which falls in three functional categories, i.e., (i)energy metabolism (photosynthesis, carbon fixation and respiration), (ii)ROS scavenging enzymes and molecular chaperones, and (iii)amino acid and protein biosynthesis. After chronic oxidative stress, these proteins presumably retained glycolysis, pentose phosphate pathway and turnover rate of the Calvin-Benson cycle. Moreover, these proteins assisted in the adequate detoxification of ROS and played an important role in the damage removal and repair of oxidized proteins, lipids and nucleic acids. Therefore, our study anticipates that S. abundans embraces biochemical and proteomic reprogramming to thrives against allelochemicals released by M. aeruginosa. © 2019
Bryophytes as Modern Model Plants: An Overview of Their Development, Contributions, and Future Prospects
(Springer, 2023) Sandhya Yadav; Suvajit Basu; Akanksha Srivastava; Subhankar Biswas; Raju Mondal; Vishal Kumar Jha; Sushil Kumar Singh; Yogesh Mishra
Model organisms are commonly employed in research as convenient tools for studying diverse biological processes. Plant research relied on several non-model plants until the Arabidopsis thaliana was developed as powerful model for identifying genes and determining their functions. To study the genetics of unique processes in different species, few other model photosynthetic organisms have recently been established, including Synechocystis sp. PCC 6803, Anabaena sp. PCC 7120, Chlamydomonas reinhardatii, Oryza sativa, Zea mays, Triticum dicoccoides, Populus trichocarpa, and Picea abies. However, when it comes to answering different biological problems, each of the current model plants has its own set of advantages and disadvantages, and many questions about land plant adaptation strategies at the level of morpho-physiology, development, and stress mitigation could not be adequately answered using these models. Furthermore, the high occurrence of embryo lethal mutations rendered studying the molecular basis of 3-dimensional (3-D) growth and gametogenesis unfeasible. Since bryophytes have a low cellular complexity and a dominant haploid gametophytic phase, they could be useful models not only for avoiding the aforementioned drawbacks, but also for functional genomics research and understanding the chronology of land plant evolution. These distinguishing characteristics and the advancement of sequencing technology have led to the development of some bryophytes as modern model plants, including Physcomitrium patens, Marchantia polymorpha, Anthoceros agrestis. Here, we review at how bryophytes became model plants, and how they have been able to answer crucial plant biology-related concerns like stress tolerance and evolutionary developmental (evo-devo) biology that other model plants have not been able to. © 2023, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
Cd-induced cytosolic proteome changes in the cyanobacterium Anabaena sp. PCC7120 are mediated by LexA as one of the regulatory proteins
(Elsevier B.V., 2023) Akanksha Srivastava; Arvind Kumar; Subhankar Biswas; Vaibhav Srivastava; Hema Rajaram; Yogesh Mishra
LexA, a well-characterized transcriptional repressor of SOS genes in heterotrophic bacteria, has been shown to regulate diverse genes in cyanobacteria. An earlier study showed that LexA overexpression in a cyanobacterium, Anabaena sp. PCC7120 reduces its tolerance to Cd stress. This was later shown to be due to modulation of photosynthetic redox poising by LexA under Cd stress. However, due to the global regulatory nature of LexA and the prior prediction of AnLexA-box in a few heavy metal-responsive genes, we speculated that LexA has a broad role in Cd tolerance, with regulation over a variety of Cd stress-responsive genes in addition to photosynthetic genes. Thus, to further expand the knowledge on the regulatory role of LexA in Cd stress tolerance, a cytosolic proteome profiling of Anabaena constitutively overexpressing LexA upon Cd stress was performed. The proteomic study revealed 25 differentially accumulated proteins (DAPs) in response to the combined effect of LexA overexpression and Cd stress, and the other 11 DAPs exclusively in response to either LexA overexpression or Cd stress. The 36 identified proteins were related with a variety of functions, including photosynthesis, C-metabolism, antioxidants, protein turnover, post-transcriptional modifications, and a few unknown and hypothetical proteins. The regulation of LexA on corresponding genes, and six previously reported Cd efflux transporters, was further validated by the presence of AnLexA-boxes, transcript, and/or promoter analyses. In a nutshell, this study identifies the regulation of Anabaena LexA on several Cd stress-responsive genes of various functions, hence expanding the regulatory role of LexA under Cd stress. © 2023 Elsevier B.V.
Comparison and optimization of protein extraction and two-dimensional gel electrophoresis protocols for liverworts
(BioMed Central Ltd., 2020) Sandhya Yadav; Akanksha Srivastava; Subhankar Biswas; Neha Chaurasia; Sushil Kumar Singh; Sanjiv Kumar; Vaibhav Srivastava; Yogesh Mishra
Objective: Liverworts possess historical adaptive strategies for abiotic stresses because they were the first plants that shifted from water to land. Proteomics is a state-of-the-art technique that can capture snapshots of events occurring at the protein level in many organisms. Herein, we highlight the comparison and optimization of an effective protein extraction and precipitation protocol for two-dimensional gel electrophoresis (2-DE) of liverworts. Results: We compared three different protein extraction methods, i.e.,1.5 M Tris-HCl (pH 8.8), 50 mM Tris-HCl (pH 7.5), and polyvinylpolypyrrolidone (PVPP) extraction, followed by three precipitation methods, i.e., 80% ethanol, 80% acetone, and 20% tricholoroacetic acid (TCA)-acetone, in a liverwort Dumortiera hirsuta. Among these methods, 50 mM Tris-HCl (pH 7.5) extraction, followed by 20% TCA-acetone precipitation, appeared to be more suitable for 2-DE. Furthermore, we performed modifications during protein washing, re-solubilization in rehydration buffer and isoelectric focusing (IEF). The modifications provided us better results in terms of protein yield, resolution, spot numbers, and intensities for 2-DE gels of D. hirsuta and other two liverworts, i.e., Marchantia paleacea and Plagiochasma appendiculatum. Furthermore, we randomly selected spots from the 2-DE gel of D. hirsuta and identified using mass spectrometry, which confirms the applicability of this protocol for liverworts proteomics. © 2020 The Author(s).
Cyanobacteria, Lyngbya aestuarii and Aphanothece bullosa as antifungal and antileishmanial drug resources
(Asian Pacific Tropical Biomedicine Press, 2013) Maheep Kumar; Manoj Kumar Tripathi; Akanksha Srivastava; Jalaj Kumar Gour; Rakesh Kumar Singh; Ragini Tilak; Ravi Kumar Asthana
Objective: To investigate two cyanobacteria isolated from different origins i.e. Lyngbya aestuarii (L. aestuarii) from brackish water and Aphanothece bullosa (A. bullosa) from fresh water paddy fields for antifungal and antileishmanila activity taking Candida albicans and Leishmania donovain as targets. Methods: Biomass of L. aestuarii and A. bullosa were harvested after 40 and 60 d respectively and lyophilized twice in methanol (100%) and redissolved in methanol (5%) for bioassay. Antifungal bioassay was done by agar well diffusion method while antileishmanial, by counting cell numbers and flageller motility observation of promastigotes and amastigotes from L. donovani. Fluconazole and 5% methanol were used as control. Results: Both the cyanobacteria were found to be potent source of antifungal activity keeping fluconazole as positive control, however, methanolic crude extract (15 mg/mL) of A. bullosa was found more potent (larger inhibition zone) over that of methanolic crude extract of L. aestuarii. Similarly antileishmanial activity of crude extract (24.0 mg/mL) of A. bullosa was superior over that of methanolic crude extract of L. aestuarii (25.6 mg/mL). Conclusions: Antifungal and antileishmanial drugs are still limited in the market. Screening of microbes possessing antifungal and antileishmanial activity drug is of prime importance. Cyanobacteria are little explored in this context because most of the drugs in human therapy are derived from microorganisms, mainly bacterial, fungal and actinomycetes. Thus in the present study two cyanobacterial strains from different origins showed potent source of antifungal and antileishmanial biomolecules. © 2013 Asian Pacific Tropical Biomedical Magazine.
Cyanobacterial blooms and Cyanotoxins: Occurrence and Detection
(Springer Singapore, 2020) Simranjeet Kaur; Akanksha Srivastava; Amrik S. Ahluwalia; Yogesh Mishr
Enormous increase in anthropogenic activities results in nutrient loading into the environment causing eutrophication of aquatic bodies. The increased eutrophication of freshwater and marine water bodies has intensiﬁed the algal growth which is commonly known as algal blooms. Prokaryotic blue green algae/cyanobacteria are one of the most common bloom causing algae in aquatic ecosystem, commonly known as cyanobacterial harmful algal blooms (CHABs). Some cyanobacteria can produce toxins called as cyanotoxins, which not only hinder recreational use of water bodies but also adversely affect microalgae, invertebrates, ﬁsh, birds, plants, and mammals. The current chapters offer an overview of occurrence of CHABs and their toxins. Further, emphasis has been given on types of cyanotoxins, their measurement and removal from aquatic ecosystem. © Springer Nature Singapore Pte Ltd. 2021
Development of Bryophytes as a New Model System to Understand the Phenomenon of Terrestrialization with Environmental Changes
(Springer Nature, 2019) Sandhya Yadav; Subhankar Biswas; Akanksha Srivastava; Yogesh Mishra
Bryophytes are earliest diverging lineages of the extant land plants with around 25,000 species distributed all over the world. Bryophytes can be further classified into three main classes viz. Liverworts, Hornworts and Mosses that grow on a wide range of habitats. Bryophytes, with high ecological and economic values, occupy a very important position in the evolution of terrestrial plants. During the transition of aquatic to terrestrial habitat (terrestrialization), bryophytes got exposed to global climate changes as well as dehydrating atmosphere of terrestrial habitats that led to the desiccation of plant tissues. In order to tolerate the environmental alterations and to protect themselves from abiotic stresses, bryophytes must have enabled themselves to develop certain adaptive strategies. In order to understand these adaptive strategies at molecular level, attempts have been made to develop certain bryophytes as new model system such as Physcomitrella patens and Marchantia polymorpha. In the current chapter we will addresses how does these model systems have been used to address the uniqueness of bryophytes in terms of their capabilities behind the conquering the land i.e. terrestrialization. © 2019, Springer Nature Singapore Pte Ltd.
Endophytes and their secondary metabolites against human pathogenic MDR microbes
(Elsevier, 2022) Akanksha Srivastava; Richa Raghuwanshi
The antimicrobial agents counter with multidrug resistant (MDR) pathogenic microbes, compounded with the raised number of patients, are of great concern all around the world, which has given impetus to the research on less explored eco-friendly agents such as endophytes which have emerged as a source of novel drugs. Endophytes residing in plants produce natural compounds of therapeutic importance which can find a way in pharmaceutical industry. The endophytic actinomycetes isolated from Panxi plateau and endophytic Streptomyces sp. TQR12-4 isolated from Elite Citrus nobilis fruit shows large spectrum antimicrobial activity inhibiting pathogens like Colletotrichum truncatum, Geotrichum candidum, Fusarium. oxysporum, and F. udum. Endophytic strains of Bacillus sp. isolated from Adhatoda beddomei and Garcinia xanthochymus synthesized silver nanoparticles (AgNPs) have promising antimicrobial potential. With potent drug possibilities, structural varieties of bioactive metabolites such as peptides, alkaloids, isocoumarins, steroids, quinines, terpenoids, phenols, perylene derivatives, and flavonoids have triggered large interest in characterization and isolation of eco-friendly endophytes, challenging the pathogenicity of MDR microbes. Endophytes have impacted our lives in several ways and exploiting them as a novel source of bioactive metabolites against MDR microbes is the priority endeavor of this chapter. © 2023 Elsevier Inc. All rights reserved.
Epidemiological Distribution and Potential Risk Factors of Orientia tsutsugamushi Infection in Eastern Uttar Pradesh, India
(Hamadan University of Medical Sciences, 2021) Alka Shukla; Mayank Gangwar; Akanksha Srivastava; Sonam Rastogi; Deepak Kumar; Digvijay Singh; Rajesh Kumar; Pradyot Prakash; Gopal Nath
Background: Scrub typhus (ST) is a rickettsial infection caused by Orientia tsutsugamushi, which presents with flu like symptoms. This disease has been reported from all over India but with slight variations in its pattern. For decreasing the prevalence, preventing new incidences, and predicting the course of the ST, therefore, it is crucial to gain knowledge and perception of local risk components associated with the disease. The present study aimed to investigate the epidemiological distribution and potential risk factors of O. tsutsugamushi Infection in Eastern Uttar Pradesh (EUP), India. Methods: The serums of 211 samples were collected from the suspected cases along with the detailed information about the participants such as age, location, and place recorded in case history form (CRF). IgM estimation was performed using enzyme-linked immunosorbent assay (ELISA) assay. Results: A total of 58 samples (27.4%) out of 211 ones were found to be positive for IgM antibodies against O. tsutsugamushi bacterium. Furthermore, the results were correlated with epidemiological data such as gender, rural or urban background, pets, and occupation. The results showed that 76.7% of the study participants were from rural areas or had bushes around their houses, 88.3% of them had pets/cattle or frequent encounter with rodents at their houses, and 30.3% of them had no toilet facilities at home. Conclusions: It was concluded that the proximity to pets/cattle, having rodents in closer vicinity, residing in places surrounded by vegetation/farm/bushy areas, and following occupations involving field work increased the chances of getting bitten by mites/chiggers. Overall, Orientia tsutsugamushi prevalence increased in EUP, with respect to clinical features, disease presentation, and laboratory diagnosis can help our community to reduce the mortality caused by this infectious disease. © 2021 The Author(s); Published by Hamadan University of Medical Sciences.
Evolution of Genetically Modified (GM) Crops and The Scared World
(Elsevier, 2020) Subhankar Biswas; Akanksha Srivastava; Sandhya Yadav; Yogesh Mishra
Since antiquity, it was a key desire of human beings to develop new crops with higher nutritional values and good flavors. The classical plant breeding approaches has given many improved varieties of crops to the world but it has its own limitations, such as (1) genetic exchange can be done in the same species (2) while crossing, many traits are transferred along with the trait/s of interest that might have undesirable effects on yield potential. To overcome these limitations there was an emergence of new technology that is genetic engineering which has developed transgenic plants which are popularly known as genetically modified (GM) plants. First genetic engineering mediated transgenic tobacco plant was developed in 1987. After that, there was a boom in the development of GM crops such as “flavr-savr” tomato, Bt-cotton, corn, etc. In the journey of the past 3 decades, GM crops faced several vicissitudes but never stopped its improvement. The case-by-case study has demonstrated that the technique was never the problem but the consequences may be. In this chapter, we have briefly highlighted the necessity, current status and global impact of genetically modified plants. Apart from these, we have also addressed the question that why a large part of the human population is still scared of GM foods?. © 2021 Elsevier Inc. All rights reserved.
Fresh water cyanobacteria Geitlerinema sp. CCC728 and Arthrospira sp. CCC729 as an anticancer drug resource
(Public Library of Science, 2015) Akanksha Srivastava; Ratnakar Tiwari; Vikas Srivastava; Tej Bali Singh; Ravi Kumar Asthana
An increasing number of cancer patients worldwide, especially in third world countries, have raised concern to explore natural drug resources, such as the less explored fresh water filamentous cyanobacteria. Six strains of cyanobacteria (Phormidium sp. CCC727, Geitlerinema sp. CCC728, Arthrospira sp. CCC729, Phormidium sp. CCC731, Phormidium sp. CCC730, and Leptolyngbya sp. CCC732) were isolated (paddy fields and ponds in the Banaras Hindu University, campus) and five strains screened for anticancer potential using human colon adenocarcinoma (HT29) and human kidney adenocarcinoma (A498) cancer cell lines. Geitlerinema sp. CCC728 and Arthrospira sp. CCC729 were the most potent as determined by examination of morphological features and by inhibition of growth by graded concentrations of crude extracts and thin-layer chromatography (TLC) eluates. Cell cycle analysis and multiplex assays using cancer biomarkers also confirmed Geitlerinema sp. CCC728 and Arthrospira sp. CCC729 as cancer drug resources. Apoptotic studies in the cells of A498 (cancer) and MCF-10A (normal human epithelial) exposed to crude extracts and TLC fractions revealed no significant impact on MCF-10A cells emphasizing its importance in the development of anticancer drug. Identification of biomolecules from these extracts are in progress. © 2015 Srivastava et al.
Gamma (γ)-radiation stress response of the cyanobacterium Anabaena sp. PCC7120: Regulatory role of LexA and photophysiological changes
(Elsevier Ireland Ltd, 2023) Akanksha Srivastava; Arvind Kumar; Subhankar Biswas; Rajender Kumar; Vaibhav Srivastava; Hema Rajaram; Yogesh Mishra
High radioresistance of the cyanobacterium, Anabaena sp. PCC7120 has been attributed to efficient DNA repair, protein recycling, and oxidative stress management. However, the regulatory network involved in these batteries of responses remains unexplored. In the present study, the role of a global regulator, LexA in modulating gamma (γ)-radiation stress response of Anabaena was investigated. Comparison of the cytosolic proteome profiles upon γ-radiation in recombinant Anabaena strains, AnpAM (vector-control) and AnlexA+ (LexA-overexpressing), revealed 41 differentially accumulated proteins, corresponding to 29 distinct proteins. LexA was found to be involved in the regulation of 27 of the corresponding genes based on the presence of AnLexA-Box, EMSA, and/or qRT-PCR studies. The majority of the regulated genes were found to be involved in C-assimilation either through photosynthesis or C-catabolism and oxidative stress alleviation. Photosynthesis, measured in terms of PSII photophysiological parameters and thylakoid membrane proteome was found to be affected by γ-radiation in both AnpAM and AnlexA+ cells, with LexA affecting them even under control growth conditions. Thus, LexA functioned as one of the transcriptional regulators involved in modulating γ-radiation stress response in Anabaena. This study could pave the way for a deeper understanding of the regulation of γ-radiation-responsive genes in cyanobacteria at large. © 2022 Elsevier B.V.
Implementation of artificial intelligence (AI) and machine learning (ML) in microbiology
(Academic Press Inc., 2024) Prashant Tripathi; Akanksha Srivastava; Chetan Kumar Dubey; Vaibhav Mishra; Shipra Dwivedi; Amit Kumar Madeshiya
Artificial intelligence (AI) is the ability of a machine to perform a cognitive function that resembles the human brain. In today's world, AI is being largely applied in the field of medical science including clinical microbiology and environmental microbiology. According to a recent report by PwC Middle East, 2% of the total global benefit of AI which is about US$320 billion has been projected by 2030.With the help of AI in the medical field, the way of undertaking emergencies and life-threatening conditions has changed. Its applications include diagnosing patients, end-to-end drug discovery and development, improving communication between physician and patient, transcribing medical documents, such as prescriptions, and remotely treating patients. In this chapter, we discuss, what is AI and machine learning and how it is being implemented in the field of clinical microbiology, and environmental microbiology as well as where we need improvement. © 2024 Elsevier Ltd
In silico analysis and expression profiling of S-domain receptor-like kinases (SD-RLKs) under different abiotic stresses in Arabidopsis thaliana
(BioMed Central Ltd, 2021) Raju Mondal; Subhankar Biswas; Akanksha Srivastava; Suvajit Basu; Maitri Trivedi; Sunil Kumar Singh; Yogesh Mishra
Background: S-domain receptor-like kinases (SD-RLKs) are an important and multi-gene subfamily of plant receptor-like/pelle kinases (RLKs), which are known to play a significant role in the development and immune responses of Arabidopsis thaliana. The conserved cysteine residues in the extracellular domain of SD-RLKs make them interesting candidates for sensing reactive oxygen species (ROS), assisting oxidative stress mitigation and associated signaling pathways during abiotic stresses. However, how closely SD-RLKs are interrelated to abiotic stress mitigation and signaling remains unknown in A. thaliana. Results: This study was initiated by examining the chromosomal localization, phylogeny, sequence and differential expression analyses of 37 SD-RLK genes using publicly accessible microarray datasets under cold, osmotic stress, genotoxic stress, drought, salt, UV-B, heat and wounding. Out of 37 SD-RLKs, 12 genes displayed differential expression patterns in both the root and the shoot tissues. Promoter structure analysis suggested that these 12 SD-RLK genes harbour several potential cis-regulatory elements (CREs), which are involved in regulating multiple abiotic stress responses. Based on these observations, we investigated the expression patterns of 12 selected SD-RLKs under ozone, wounding, oxidative (methyl viologen), UV-B, cold, and light stress at different time points using semi-qRT-PCR. Of these 12 SD-SRKs, the genes At1g61360, At1g61460, At1g61380, and At4g27300 emerged as potential candidates that maintain their expression in most of the stress treatments till exposure for 12 h. Expression patterns of these four genes were further verified under similar stress treatments using qRT-PCR. The expression analysis indicated that the gene At1g61360, At1g61380, and At1g61460 were mostly up-regulated, whereas the expression of At4g27300 either up- or down-regulated in these conditions. Conclusions: To summarize, the computational analysis and differential transcript accumulation of SD-RLKs under various abiotic stresses suggested their association with abiotic stress tolerance and related signaling in A. thaliana. We believe that a further detailed study will decipher the specific role of these representative SD-RLKs in abiotic stress mitigation vis-a-vis signaling pathways in A. thaliana. © 2021, The Author(s).
In silico characterization and structural modeling of a homeobox protein MSX1 from Homo sapiens
(Elsevier Ltd, 2021) Sneha Singh; Subhankar Biswas; Akanksha Srivastava; Yogesh Mishra; Thakur Prasad Chaturvedi
Introduction: MSX1 protein, a homeobox transcriptional regulator plays a significant role in various developmental processes of the mammalian system such as limb-pattern formation, craniofacial development, in particular, odontogenesis, and tumor growth inhibition. Several studies have been performed on MSX1 at the genomic and transcriptomic levels. However, there is a lack of information on its structural and conformational aspects. Objective: For better understanding of the molecular mechanism of MSX1, the present study aims to conduct a detailed in-silico analysis of this protein in terms of its physicochemical properties, secondary and tertiary structure predictions, interacting partners, and phylogenetic relationship with other orthologs. Methods: The sequence of the MSX1 protein from Homo sapiens was retrieved in the FASTA format from the National Center for Biotechnology Information (NCBI). The standard bioinformatic tools were further used to characterize and model the structure of this protein. Results: The in-silico characterization of MSX1 revealed that it is a basic, non-polar, and thermostable globular protein mainly localized in the nucleus. This protein is extremely rigid due to the presence of high proline content. The phylogenetic and synteny analysis revealed that the gene is highly conserved at the level of the amino acid sequences, but underwent several modifications at the genomic level in the course of evolution possibly to attain the diverse function. Major part of this protein is a random coil, making it suitable for interaction with other proteins. Subcellular localization and protein-protein interaction suggested that the protein may act as a secretory protein and play a crucial role in regulating several developmental processes. Docking analysis suggested that the MSX1 protein may interact with other proteins and form complexes to carry out its function. Conclusion: The structural characterization of this protein will help to better understand its molecular mechanism of action. In addition, the predicted 3-D model would act as a base for further understanding of the protein's other functional potential. © 2020 The Author(s)
In silico characterization, molecular phylogeny, and expression profiling of genes encoding legume lectin-like proteins under various abiotic stresses in Arabidopsis thaliana
(BioMed Central Ltd, 2022) Subhankar Biswas; Raju Mondal; Akanksha Srivastava; Maitri Trivedi; Sunil Kumar Singh; Yogesh Mishra
Background: Lectin receptor-like kinases (Lec-RLKs), a subfamily of RLKs, have been demonstrated to play an important role in signal transduction from cell wall to the plasma membrane during biotic stresses. Lec-RLKs include legume lectin-like proteins (LLPs), an important group of apoplastic proteins that are expressed in regenerating cell walls and play a role in immune-related responses. However, it is unclear whether LLPs have a function in abiotic stress mitigation and related signaling pathways. Therefore, in this study, we examined the possible role of LLPs in Arabidopsis thaliana (AtLLPs) under various abiotic stresses. Results: The study was initiated by analyzing the chromosomal localization, gene structure, protein motif, peptide sequence, phylogeny, evolutionary divergence, and sub-cellular localization of AtLLPs. Furthermore, the expression profiling of these AtLLPs was performed using publicly accessible microarray datasets under various abiotic stresses, which indicated that all AtLLPs were differently expressed in both root and shoot tissues in response to abiotic stresses. The cis-regulatory elements (CREs) analysis in 500 bp promoter sequences of AtLLPs suggested the presence of multiple important CREs implicated for regulating abiotic stress responses, which was further supported by expressional correlation analysis between AtLLPs and their CREs cognate transcription factors (TFs). qRT-PCR analysis of these AtLLPs after 2, 6, and 12 h of cold, high light, oxidative (MV), UV-B, wound, and ozone stress revealed that all AtLLPs displayed differential expression patterns in most of the tested stresses, supporting their roles in abiotic stress response and signaling again. Out of these AtLLPs, AT1g53070 and AT5g03350 appeared to be important players. Furthermore, the mutant line of AT5g03350 exhibited higher levels of ROS than wild type plants till 12 h of exposure to high light, MV, UV-B, and wound, whereas its overexpression line exhibited comparatively lower levels of ROS, indicating a positive role of this gene in abiotic stress response in A. thaliana. Conclusions: This study provides basic insights in the involvement of two important representative AtLLPs, AT1g53070 and AT5g03350, in abiotic stress response. However, further research is needed to determine the specific molecular mechanism of these AtLLPs in abiotic stress mitigation and related signaling pathways in A. thaliana. © 2022, The Author(s).
Landscape of natural product diversity in land-plants as source for anticancer molecules
(Elsevier Science Ltd., 2020) Akanksha Srivastava; Richa Raghuwanshi
The land plants are an ancient lineage that has been constantly used in folk medicines by almost every human civilization. Several phyto-constituents with therapeutic potential have been studied for antibacterial, antifungal, antiviral, antioxidative, antiinflamatory, and anticancerous efficacy. Natural products and phytochemicals obtained from microbes and plants growing in marine and terrestrial environment have served as a major source in anticancer drug development. The search for novel drug continues in the goals of cancer therapy due to the resistance developed against chemotherapeutic drugs and their side effects. Exploring the diverse plant kingdom for their therapeutic value has been for ages and the emerging new technologies have paved new hopes in this area. This chapter aims an overview on the phytochemicals derived from the diverse plant kingdom that have therapeutic properties and are potent anticancer agents. © 2021 Elsevier Inc. All rights reserved.