Role of calcium nutrition in plant Physiology: Advances in research and insights into acidic soil conditions - A comprehensive review.

Plant mineral nutrition has immense significance for crop productivity and human well-being. Soil acidity plays a major role in determining the nutrient availability that influences plant growth. The importance of calcium (Ca) in biological processes, such as signaling, metabolism, and cell growth, underlines its critical role in plant growth and development. This review focuses on soil acidification, a gradual process resulting from cation leaching, fertilizer utilization, and drainage issues. Soil acidification significantly hampers global crop production by modifying nutrient accessibility. In acidic soils, essential nutrients, such as nitrogen (N), phosphorus (P), potassium (K), magnesium (Mg), and Ca become less accessible, establishing a correlation between soil pH and plant nutrition. Cutting-edge Ca nutrition technologies, including nanotechnology, genetic engineering, and genome sequencing, offer the potential to deliver Ca and reduce the reliance on conventional soluble fertilizers. These fertilizers not only contribute to environmental contamination but also impose economic burdens on farmers. Nanotechnology can enhance nutrient uptake, and Ca nanoparticles improve nutrient absorption and release. Genetic engineering enables the cultivation of acid-tolerant crop varieties by manipulating Ca-related genes. High-throughput technologies such as next-generation sequencing and microarrays aid in identifying the microbial structures, functions, and biosynthetic pathways involved in managing plant nutritional stress. The ultimate goal is to shed light on the importance of Ca, problems associated with soil acidity, and potential of emerging technologies to enhance crop production while minimizing the environmental impact and economic burden on farmers.

USP28 promotes tumorigenesis and cisplatin resistance by deubiquitinating MAST1 protein in cancer cells.

Cisplatin is a chemotherapy drug that causes a plethora of DNA lesions and inhibits DNA transcription and replication, resulting in the induction of apoptosis in cancer cells. However, over time, patients develop resistance to cisplatin due to repeated treatment and thus the treatment efficacy is limited. Therefore, identifying an alternative therapeutic strategy combining cisplatin treatment along with targeting factors that drive cisplatin resistance is needed. CRISPR/Cas9 system-based genome-wide screening for the deubiquitinating enzyme (DUB) subfamily identified USP28 as a potential DUB that governs cisplatin resistance. USP28 regulates the protein level of microtubule-associated serine/threonine kinase 1 (MAST1), a common kinase whose expression is elevated in several cisplatin-resistant cancer cells. The expression level and protein turnover of MAST1 is a major factor driving cisplatin resistance in many cancer types. Here we report that the USP28 interacts and extends the half-life of MAST1 protein by its deubiquitinating activity. The expression pattern of USP28 and MAST1 showed a positive correlation across a panel of tested cancer cell lines and human clinical tissues. Additionally, CRISPR/Cas9-mediated gene knockout of USP28 in A549 and NCI-H1299 cells blocked MAST1-driven cisplatin resistance, resulting in suppressed cell proliferation, colony formation ability, migration and invasion in vitro. Finally, loss of USP28 destabilized MAST1 protein and attenuated tumor growth by sensitizing cells to cisplatin treatment in mouse xenograft model. We envision that targeting the USP28-MAST1 axis along with cisplatin treatment might be an alternative therapeutic strategy to overcome cisplatin resistance in cancer patients.

Production and characterization of polyhydroxyalkanoates by Halomonas alkaliantarctica utilizing dairy waste as feedstock.

Currently, the global demand for polyhydroxyalkanoates (PHAs) is significantly increasing. PHAs are produced by several bacteria that are an alternative source of synthetic polymers derived from petrochemical refineries. This study established a simple and more feasible process of PHA production by Halomonas alkaliantarctica using dairy waste as the only carbon source. The data confirmed that the analyzed halophile could metabolize cheese whey (CW) and cheese whey mother liquor (CWML) into biopolyesters. The highest yield of PHAs was 0.42 g/L in the cultivation supplemented with CWML. Furthermore, it was proved that PHA structure depended on the type of by-product from cheese manufacturing, its concentration, and the culture time. The results revealed that H. alkaliantarctica could produce P(3HB-co-3HV) copolymer in the cultivations with CW at 48 h and 72 h without adding of any precursors. Based on the data obtained from physicochemical and thermal analyses, the extracted copolymer was reported to have properties suitable for various applications. Overall, this study described a promising approach for valorizing of dairy waste as a future strategy of industrial waste management to produce high value microbial biopolymers.

Arabinose as an overlooked sugar for microbial bioproduction of chemical building blocks.

The circular economy is anticipated to bring a disruptive transformation in manufacturing technologies. Robust and industrial scalable microbial strains that can simultaneously assimilate and valorize multiple carbon substrates are highly desirable, as waste bioresources contain substantial amounts of renewable and fermentable carbon, which is diverse. Lignocellulosic biomass (LCB) is identified as an inexhaustible and alternative resource to reduce global dependence on oil. Glucose, xylose, and arabinose are the major monomeric sugars in LCB. However, primary research has focused on the use of glucose. On the other hand, the valorization of pentose sugars, xylose, and arabinose, has been mainly overlooked, despite possible assimilation by vast microbial communities. The present review highlights the research efforts that have explicitly proven the suitability of arabinose as the starting feedstock for producing various chemical building blocks via biological routes. It begins by analyzing the availability of various arabinose-rich biorenewable sources that can serve as potential feedstocks for biorefineries. The subsequent section outlines the current understanding of arabinose metabolism, biochemical routes prevalent in prokaryotic and eukaryotic systems, and possible products that can be derived from this sugar. Further, currently, exemplar products from arabinose, including arabitol, 2,3-butanediol, 1,2,3-butanetriol, ethanol, lactic acid, and xylitol are discussed, which have been produced by native and non-native microbial strains using metabolic engineering and genome editing tools. The final section deals with the challenges and obstacles associated with arabinose-based production, followed by concluding remarks and prospects.

Microalgal lutein: Advancements in production, extraction, market potential, and applications.

Lutein, a bioactive xanthophyll, has recently attracted significant attention for numerous health benefits, e.g., protection of eye health, macular degeneration, and acute and chronic syndromes etc. Microalgae have emerged as the best platform for high-value lutein production with high productivity, lutein content, and scale-up potential. Algal lutein possesses numerous bioactivities, hence widely used in pharmaceuticals, nutraceuticals, aquaculture, cosmetics, etc. This review highlights advances in upstream lutein production enhancement and feasible downstream extraction and cell disruption techniques for a large-scale lutein biorefinery. Besides bioprocess-related advances, possible solutions for existing production challenges in microalgae-based lutein biorefinery, market potential, and emerging commercial scopes of lutein and its potential health applications are also discussed. The key enzymes involved in the lutein biosynthesizing Methyl-Erythritol-phosphate (MEP) pathway have been briefly described. This review provides a comprehensive updates on lutein research advancements covering scalable upstream and downstream production strategies and potential applications for researchers and industrialists.

ßTrCP1 promotes SLC35F2 protein ubiquitination and inhibits cancer progression in HeLa cells.

The solute carrier family 35 F2 (SLC35F2) belongs to membrane-bound carrier proteins that are associated with multiple cancers. The main factor that determines cancer progression is the expression level of SLC35F2. Thus, identifying the E3 ligase that controls SLC35F2 protein abundance in cancer cells is critical. Here, we identified ßTrCP1 interacting with and reducing the SLC35F2 protein level. ßTrCP1 signals SLC35F2 protein ubiquitination and reduces SLC35F2 protein half-life. The mRNA expression pattern between ßTrCP1 and SLC35F2 across a panel of cancer cell lines showed a negative correlation. Additionally, the depletion of ßTrCP1 accumulated SLC35F2 protein and promoted SLC35F2-mediated cell growth, migration, invasion, and colony formation ability in HeLa cells. Overall, we demonstrate that ßTrCP1 acts as a tumor suppressor by controlling SLC35F2 protein abundance in cancer cells. The depletion of ßTrCP1 promotes SLC35F2-mediated carcinogenesis. Thus, we envision that ßTrCP1 may be a potential target for cancer therapeutics.

Exploring the potential of phage and their applications.

Antibiotic resistant microorganisms are significantly increasing due to horizontal gene transfer, mutation and overdose of antibiotics leading to serious health conditions globally. Several multidrug resistant microorganisms have shown resistance to even the last line of antibiotics making it very difficult to treat them. Besides using antibiotics, an alternative approach to treat such resistant bacterial pathogens through the use of bacteriophage (phage) was used in the early 1900s which however declined and vanished after the discovery of antibiotics. In recent times, phage has emerged and gained interest as an alternative approach to antibiotics to treat MDR pathogens. Phage can self-replicate by utilizing cellular machinery of bacterial host by following lytic and lysogenic life cycles and therefore suitable for rapid regeneration. Application of phage for detection of bacterial pathogens, elimination of bacteria, agents for controlling food spoilage, treating human disease and several others entitles phage as a futuristic antibacterial armamentarium.

Fate of pesticides in agricultural runoff treatment systems: Occurrence, impacts and technological progress.

The levels of pesticides in air, water, and soil are gradually increasing due to its inappropriate management. In particular, agricultural runoff inflicts the damages on the ecosystem and human health at massive scale. Present study summarizes 70 studies in which investigations on removal or treatment of pesticides/insecticides/herbicides are reported. A bibliometric analysis was also done to understand the recent research trends through the analysis of 2218 publications. The specific objectives of this study are as follows: i) to inventorize the characteristics details of agriculture runoff and analyzing the occurrence and impacts of pesticides, ii) analyzing the role and interaction of pesticides in different environmental segments, iii) investigating the fate of pesticides in agriculture runoff treatment systems, iv) summarizing the experiences and findings of most commonly technology deployed for pesticides remediation in agriculture runoff including target pesticide(s), specifications, configuration of technological intervention. Among the reported technologies for pesticide treatment in agriculture runoff, constructed wetland was at the top followed by algal or photobioreactor. Among various advanced oxidation processes, photo Fenton method is mainly used for pesticides remediation such as triazine, methyl parathion, fenuron and diuron. Algal bioreactors are extensively used for a wide range of pesticides treatment including 2,4-Dichlorophenoxyacetic acid, 2-methyl-4-chlorophenoxyacetic acid, alachlor, diuron, chlorpyrifos, endosulfan, and imidacloprid; especially at lower hydraulic retention time of 2-6 h. This study highlights that hybrid approaches can offers potential opportunities for effective removal of pesticides in a more viable manner.

Phage for drug delivery vehicles.

Viruses being the natural carriers of gene have been widely used as drug delivery systems. However, the commonly used eukaryotic viruses such as adenoviruses, retroviruses, and lentiviruses, besides efficiently targeting the cells, can also stimulate immunological response or disrupt tumour suppressor genes leading to cancer. Consequently, there has been an increase interest in the scientific fraternity towards exploring other alternatives, which are safer and equally efficient for drug delivery. Bacteriophages, in this context have been at the forefront as an efficient, reliable, and safer choice. Novel phage dependent technologies led the foundation of peptide libraries and provides way to recognising abilities and targeting of specific ligands. Hybridisation of phage with inorganic complexes could be an appropriate strategy for the construction of carrying bioinorganic carriers. In this chapter, we have tried to cover major advances in the phage species that can be used as drug delivery vehicles.

Biochar production and its environmental applications: Recent developments and machine learning insights.

Biochar production through thermochemical processing is a sustainable biomass conversion and waste management approach. However, commercializing biochar faces challenges requiring further research and development to maximize its potential for addressing environmental concerns and promoting sustainable resource management. This comprehensive review presents the state-of-the-art in biochar production, emphasizing quantitative yield and qualitative properties with varying feedstocks. It discusses the technology readiness level and commercialization status of different production strategies, highlighting their environmental and economic impacts. The review focuses on integrating machine learning algorithms for process control and optimization in biochar production, improving efficiency. Additionally, it explores biochar's environmental applications, including soil amendment, carbon sequestration, and wastewater treatment, showcasing recent advancements and case studies. Advances in biochar technologies and their environmental benefits in various sectors are discussed herein.

USP19 Negatively Regulates p53 and Promotes Cervical Cancer Progression.

p53 is a tumor suppressor gene activated in response to cellular stressors that inhibits cell cycle progression and induces pro-apoptotic signaling. The protein level of p53 is well balanced by the action of several E3 ligases and deubiquitinating enzymes (DUBs). Several DUBs have been reported to negatively regulate and promote p53 degradation in tumors. In this study, we identified USP19 as a negative regulator of p53 protein level. We demonstrate a direct interaction between USP19 and p53 by pull down assay. The overexpression of USP19 promoted ubiquitination of p53 and reduced its protein half-life. We also demonstrate that CRISPR/Cas9-mediated knockout of USP19 in cervical cancer cells elevates p53 protein levels, resulting in reduced colony formation, cell migration, and cell invasion. Overall, our results indicate that USP19 negatively regulates p53 protein levels in cervical cancer progression.

Advanced approaches for resource recovery from wastewater and activated sludge: A review.

Due to resource scarcity, current industrial systems are switching from waste treatment, such as wastewater treatment and biomass, to resource recovery (RR). Biofuels, manure, pesticides, organic acids, and other bioproducts with a great market value can be produced from wastewater and activated sludge (AS). This will not only help in the transition from a linear economy to a circular economy, but also contribute to sustainable development. However, the cost of recovering resources from wastewater and AS to produce value-added products is quite high as compared to conventional treatment methods. In addition, most antioxidant technologies remain at the laboratory scale that have not yet reached the level at industrial scale. In order to promote the innovation of resource recovery technology, the various methods of treating wastewater and AS to produce biofuels, nutrients and energy are reviewed, including biochemistry, thermochemistry and chemical stabilization. The limitations of wastewater and AS treatment methods are prospected from biochemical characteristics, economic and environmental factors. The biofuels derived from third generation feedstocks, such as wastewater are more sustainable. Microalgal biomass are being used to produce biodiesel, bioethanol, biohydrogen, biogas, biooils, bioplastics, biofertilizers, biochar and biopesticides. New technologies and policies can promote a circular economy based on biological materials.

Halomonas gemina sp. nov. and Halomonas llamarensis sp. nov., two siderophore-producing organisms isolated from high-altitude salars of the Atacama Desert.

Introduction: This study aimed to identify and characterize novel siderophore-producing organisms capable of secreting high quantities of the iron-binding compounds. In the course of this, two not yet reported halophilic strains designated ATCHAT and ATCH28T were isolated from hypersaline, alkaline surface waters of Salar de Llamará and Laguna Lejía, respectively. The alkaline environment limits iron bioavailability, suggesting that native organisms produce abundant siderophores to sequester iron. Methods: Both strains were characterized by polyphasic approach. Comparative analysis of the 16S rRNA gene sequences revealed their affiliation with the genus Halomonas. ATCHAT showed close similarity to Halomonas salicampi and Halomonas vilamensis, while ATCH28T was related closest to Halomonas ventosae and Halomonas salina. The ability of both strains to secrete siderophores was initially assessed using the chromeazurol S (CAS) liquid assay and subsequently further investigated through genomic analysis and NMR. Furthermore, the effect of various media components on the siderophore secretion by strain ATCH28T was explored. Results: The CAS assay confirmed the ability of both strains to produce iron-binding compounds. Genomic analysis of strain ATCHAT revealed the presence of a not yet reported NRPS-dependant gene cluster responsible for the secretion of siderophore. However, as only small amounts of siderophore were secreted, further investigations did not lie within the scope of this study. Via NMR and genomic analysis, strain ATCH28T has been determined to produce desferrioxamine E (DFOE). Although this siderophore is common in various terrestrial microorganisms, it has not yet been reported to occur within Halomonas, making strain ATCH28T the first member of the genus to produce a non-amphiphilic siderophore. By means of media optimization, the produced quantity of DFOE could be increased to more than 1000 µM. Discussion: Phenotypic and genotypic characteristics clearly differentiated both strains from other members of the genus Halomonas. Average nucleotide identity (ANI) values and DNA-DNA relatedness indicated that the strains represented two novel species. Therefore, both species should be added as new representatives of the genus Halomonas, for which the designations Halomonas llamarensis sp. nov. (type strain ATCHAT = DSM 114476 = LMG 32709) and Halomonas gemina sp. nov. (type strain ATCH28T = DSM 114418 = LMG 32708) are proposed.

Applications of bioinformatics in epigenetics.

Epigenetic modifications such as DNA methylation, post-translational chromatin modifications and non-coding RNA-mediated mechanisms are responsible for epigenetic inheritance. Change in gene expression due to these epigenetic modifications are responsible for new traits in different organisms leading to various diseases including cancer, diabetic kidney disease (DKD), diabetic nephropathy (DN) and renal fibrosis. Bioinformatics is an effective approach for epigenomic profiling. These epigenomic data can be analyzed by a large number of bioinformatics tools and software. Many databases are available online, which comprises huge amount of information regarding these modifications. Recent methodologies include many sequencing and analytical techniques to extrapolate different types of epigenetic data. This data can be used to design drugs against diseases linked to epigenetic modifications. This chapter briefly highlights different epigenetics databases (MethDB, REBASE, Pubmeth, MethPrimerDB, Histone Database, ChromDB, MeInfoText database, EpimiR, Methylome DB, and dbHiMo), and tools (compEpiTools, CpGProD, MethBlAST, EpiExplorer, and BiQ analyzer), which are being utilized to retrieve the data and mechanistically analysis of epigenetics modifications.

CRISPR-dCas9 system for epigenetic editing towards therapeutic applications.

In the past few decades, epigenetics has emerged as an important area of study to enable a better understanding of gene expression and its regulation. Due to epigenetics, stable phenotypic changes have been possible without alterations in DNA sequences. Epigenetic changes may occur due to DNA methylation, acetylation, phosphorylation and other such mechanisms which alter the level of gene expression without making any difference to DNA sequences. In this chapter, CRISPR-dCas9 used to bring about epigenome modifications for regulating gene expression towards a therapeutic approaches for treating human diseases have been discussed.

Phage engineering and phage-assisted CRISPR-Cas delivery to combat multidrug-resistant pathogens.

Antibiotic resistance ranks among the top threats to humanity. Due to the frequent use of antibiotics, society is facing a high prevalence of multidrug resistant pathogens, which have managed to evolve mechanisms that help them evade the last line of therapeutics. An alternative to antibiotics could involve the use of bacteriophages (phages), which are the natural predators of bacterial cells. In earlier times, phages were implemented as therapeutic agents for a century but were mainly replaced with antibiotics, and considering the menace of antimicrobial resistance, it might again become of interest due to the increasing threat of antibiotic resistance among pathogens. The current understanding of phage biology and clustered regularly interspaced short palindromic repeats (CRISPR) assisted phage genome engineering techniques have facilitated to generate phage variants with unique therapeutic values. In this review, we briefly explain strategies to engineer bacteriophages. Next, we highlight the literature supporting CRISPR-Cas9-assisted phage engineering for effective and more specific targeting of bacterial pathogens. Lastly, we discuss techniques that either help to increase the fitness, specificity, or lytic ability of bacteriophages to control an infection.

Endocytosis of GABA receptor: Signaling in nervous system.

GABA (ᵞ-aminobutyric acid), is the principal neurotransmitter known for its inhibitory role in chemical synapses. Being localized primarily in the central nervous system (CNS) it maintains a balance between excitatory (regulated by another neurotransmitter, glutamate) and inhibitory impulses. GABA acts by binding to their specific receptors GABAA and GABAB when released into the post-synaptic nerve terminal. Both of these receptors are responsible for fast and slow inhibition of neurotransmission, respectively. GABAA is a ligand-gated ionopore receptor which opens the Cl- ion channel and decreases the resting potential of the membrane resulting into inhibition of the synapse. On the other hand, GABAB is a metabotropic receptor which increases the K+ ion levels preventing Ca+ ion release inhibiting the release of other neurotransmitters into the presynaptic membrane. The internalization and trafficking of these receptors is also conducted through distinct pathways and mechanism, discussed in detail in the chapter. Without the desired levels of GABA in the body, the psychological and neurological states of brain get hard to maintain. Various neurodegenerative diseases/disorders have been associated to low levels of GABA, such as anxiety, mood disorders, fear, schizophrenia, hungtington's chorea, seizures, epilepsy, etc. The allosteric sites present on GABA receptors have been proved to be potent drug targets to pacify the pathological states of these brain related disorders to an extent. Further in depth studies focussing on the subtypes of GABA receptors and their comprehensive mechanism are required to explore new drug targets and therapeutic avenues for effectual management of GABA related neurological diseases.