The distal-proximal relationships among the human moonlighting proteins: Evolutionary hotspots and Darwinian checkpoints.

Moonlighting proteins, known for their ability to perform multiple, often unrelated functions within a single polypeptide chain, challenge the traditional "one gene, one protein, one function" paradigm. As organisms evolved, their genomes remained relatively stable in size, but the introduction of post-translational modifications and sub-strategies like protein promiscuity and intrinsic disorder enabled multifunctionality. Enzymes, in particular, exemplify this phenomenon, engaging in unrelated processes alongside their primary catalytic roles. This study employs a systematic, quantitative informatics approach to shed light on human moonlighting protein sequences. Phylogenetic analyses of human moonlighting proteins are presented, elucidating the distal-proximal relationships among these proteins based on sequence-derived quantitative features. The findings unveil the captivating world of human moonlighting proteins, urging further investigations in the emerging field of moonlighting proteomics, with the potential for significant contributions to our understanding of multifunctional proteins and their roles in diverse cellular processes and diseases.

Antibiofilm activity of mesoporous silica nanoparticles against the biofilm associated infections.

In pharmaceutical industries, various chemical carriers are present which are used for drug delivery to the correct target sites. The most popular and upcoming drug delivery carriers are mesoporous silica nanoparticles (MSN). The main reason for its popularity is its ability to be specific and optimize the drug delivery process in a controlled manner. Nowadays, MSNs are widely used to eradicate various microbial infections, especially the ones related to biofilms. Biofilms are sessile groups of cells that live by forming a consortium and exhibit antibacterial resistance (AMR). They exhibit AMR by extracellular polymeric substances (EPS) and various quorum sensing (QS) signaling molecules. Usually, bacterial and fungal cells are capable of forming biofilms. These biofilms are pathogenic. In the majority of the cases, biofilms cause nosocomial diseases. This review will focus on the antibiofilm activities of MSN, its mechanism of target-specific drug delivery, and its ability to disrupt the bacterial biofilms inhibiting the infection. The review will also discuss various mechanisms for the delivery of pharmaceutical molecules by the MSNs to inhibit the bacterial biofilms, and lastly, we will talk about the different types of MSNs and their antibiofilm activities.

Role of mesoporous silica nanoparticles in combating mercury-induced stress in Vigna radiata (mung bean) and Bacillus coagulans (soil bacteria).

The last few decades have witnessed a dramatic progress of human civilization via industrialization, which, in turn, is associated with a surge in pollution of the environment. Heavy metals being one of the most hazardous pollutants have posed a serious threat to life sustaining ecosystem. Among the various remediation techniques, presently, the use of nanoparticles as adsorbents and chelator of heavy metal ions has emerged being practical and cost effective. Mesoporous silica nanoparticles, due to its unique structural attributes, have found application in adsorption of heavy metals in solutions. This study encompasses elucidation of the role of mesoporous silica nanoparticles MCM 41 and MCM 48 in mitigating stress caused by toxic dose of heavy metal Hg2+ (25 ppm) on growing seedlings of Vigna radiata and probiotic soil bacteria Bacillus coagulans. The results revealed that application of the nanoparticles at specific concentration can stimulate an increase in growth of plantlets, decrease in the yield reactive oxygen species like superoxide anion and hydrogen peroxide, reduction of lipid peroxidation, increase in antioxidant enzyme activity in Vigna radiata, and enhancement of growth of Bacillus coagulans as compared to that of Hg2+ alone. Moreover, it was found that MCM 41 was effective at higher dosages compared to MCM 48, which indicates the structure to function relationship.

Effectiveness of metal and metal oxide nanoparticles against bacterial biofilms: Perspectives and limitations.

In the last few years, there has been a necessary demand in the pharmaceutical industries for finding a treatment against biofilms formed by different bacterial species. We are aware of the fact that classical processes, which are already there for the removal of bacterial biofilms gives a very low efficiency and consequently antimicrobial resistance makes it even worse. To cope up with the cited problems, scientists from the past few years are inclining toward various types of nanoparticle based treatment procedures as a pharmaceutical agent against bacterial biofilms. Nanoparticles are known for their extremely efficient antimicrobial properties. The current review gives a description of different types of metal oxide nanoparticles and their antibiofilm properties. It also shows a comparative analysis of the nanoparticles and depicts the efficiency rates of biofilm degradation in each of them. It explains the mechanism of the nanoparticles through which the disintegration of bacterial biofilm is carried out. Lastly, the review throws light upon the limitations of different nanoparticles, their safety issues, the mutagenicity, genotoxicity concerns, and toxicity hazards caused by them.

A brief study on the role of cerium oxide nanoparticles in growth and alleviation of mercury-induced stress in Vigna radiata and soil bacteria Bacillus coagulans.

Cerium oxide nanoparticles have so far been investigated for their role as an antioxidant in pathologies involving inflammation and high oxidative stress. However, its role as a plant and bacterial growth modulator and heavy metal stress reliever has been overlooked to date. Heavy metal contamination poses a major threat to mankind and the life-sustaining ecosystem. This study emphasizes the role of cerium oxide produced by the combustion method in promoting growth in Vigna radiata and Bacillus coagulans in the presence of mercury. The results show that cerium oxide nanoparticles significantly reduce the production of reactive oxygen species, hydrogen peroxide, and product of lipid peroxidation malondialdehyde in plants grown in the presence of 50 ppm mercury, thereby reducing oxidative stress. Nanoceria also increases plant growth with respect to those growing solely in mercury. Nanoceria alone does not significantly affect the growth of Vigna radiata as well as Bacillus coagulans and Escherichia coli, thereby proving its non-hazardous nature. It also significantly increases the growth of Bacillus coagulans at 25 ppm and 50 ppm of mercury. This study throws light upon the biologically non-hazardous nature of this particle by revealing how it promotes the growth of two soil bacteria Bacillus coagulans and E.coli at various dosages. The results of this study pave the way for the use of cerium oxide nanoparticles in plants and various other organisms to combat abiotic stress.

Definition of agronomic circular economy metrics and use for assessment for a nanofertilizer case study.

Circular economy has become global priority, and fertigation make large contribution. Modern circular methodologies base their definitions, besides on waste minimisation and recovery, on the product usage U and lifetime L. We have modified a commonly used equation for the mass circularity indicator (MCI) to permit MCI determination for agricultural cultivation. We defined U as intensity for diverse investigated parameters of plant growth and L as the bioavailability period. In this way, we compute circularity metrics for the plantgrowth performance when exposed to three nanofertilizers and one biostimulant, as compared to no-use of micronutrients (control 1), and micronutrients supplied via conventional fertilizers (control 2). We determined an MCI of 0.839 for best nanofertilizer performance (1.000 denotes full circularity), while the MCI of conventional fertilizer was 0.364. Normalised to control 1, U was determined as 1.196, 1.121 and 1.149 for manganese, copper and iron-based nanofertilizers, respectively, while U was 1.709, 1.432, 1.424 and 1.259 for manganese, copper, iron nanofertilizers and gold biostimulant when normalised to control 2, respectively. Based on the learning of the plant growth experiments, a tailored process design is proposed for the use of nanoparticles with pre-conditioning, post-processing and recycling steps. A life cycle assessment shows that the additional use of pumps for this process design does not increase energy costs, while preserving environmental advantages related to the lower water usage of the nanofertilizers. Moreover, the impact of the losses of conventional fertilisers by missing absorption of plant roots, which is presumed to be lower for the nanofertilizers.

Possible functional proximity of various organisms based on the bioinformatics analysis of their taste receptors.

Taste is one of the essential senses in providing the organism a faithful representation of the external world. Taste perception is responsible for basic food and drink appraisal and bestows the organism with valuable discriminatory power. Umami and sweet are "good" tastes that promote consumption of nutritive food, whereas bitter and sour are "bad" tastes that alert the organism to toxins and low pH, promoting rejection of foods containing harmful substances. Not every animal has the same sense of taste as humans. Variation in the taste receptor genes contributes to inter and intra organism differences of taste (sweet/bitter) sensation and preferences. Therefore a deeper understanding was needed to comprehend taste perception by various vertebrates and accordingly elucidate a possible proximity among them. In this study, a total 20 Type-1 (sweet) and 189 Type-2 (bitter) taste receptor complete-amino acid sequences were taken from the 20 vertebrate organisms (18 mammalian, 1 Aves, and 1 amphibian). Among 10 primates, 8 including humans were very close based on genomics of taste receptors and rodent organisms viz. the rat and mouse were away from them. This investigation throws light on the similitude and dissimilitude of perception of sweet and bitter taste among 20 different organisms, steered by quantitative analysis of their genomic data. Furthermore, it enlightened that ligand binding affinity of sweet/bitter taste molecules in the taste receptors of any proximal pair of organisms would be similar.

A comparative study on the modulatory role of mesoporous silica nanoparticles MCM 41 and MCM 48 on growth and metabolism of dicot Vigna radiata.

With the advent of nanoscience, nanotechnology and their applications in various fields, mesoporous silica nanoparticles have gained popularity due to their stability, biocompatibility, unique honeycomb-like structures - ordered and random by nature, large surface to volume ratio, porosity, active surfaces, high loading capacity, ease of interactions with solvent, solute and suspended particles. These multitudes of intrinsic properties have motivated us towards an interdisciplinary detailed study on applications of mesoporous silica with an intention in increasing efficacy of productivity, growth if any, in plant life. This study aims at finding modus operandi of the structural uniqueness and eccentricity of various types of mesoporous silica in maneuvering their own functionality as a potential regulator for growth of seedlings of model plant Vigna radiata. We undertook characterization of surface, morphology, epitome of porosity for MCM 41 and MCM 48 using various experimental techniques followed by application of the same to growing seedlings at various dosages. It turned out that mesoporous silica nanoparticles, inarguably have higher efficacy in promoting plant growth, reducing stress, and enhancing basic metabolic rates at optimum dosage. Optimal operation point was determined at effective dosages for MCM 41 and MCM 48 those are being much lower than that of conventional silica nanoparticles. This optimum dosage is attributed to the structures of the nanoparticles used and implied further that higher pore volume, higher surface to volume ratio in case of MCM 41 at higher dosage lead to better adsorption of ions and functionality in contrast to that of MCM 48.

Structural insights from water-ferredoxin interaction in mesophilic algae and halophilic archaea.

We analyzed the water-ferredoxin interaction in mesophilic (moderate temperature) algae (PDB ID: 1AWD) and halophilic (salt-tolerant) archaea (PDB ID: 1DOI) using POWAIND version 2.0 (a protein-water interactions calculation program). It is found that the shell water (SW) is 2.5 fold greater in halophilic ferredoxin than mesophilic ferredoxin. Water-ferredoxin interactions in the core and cavity are the signature of stability. The normalized frequency of such interactions is less in halophilic relative to mesophilic ferredoxin and the halophilic signature for stability by such interactions is negligible. However, the surface dominated with such interactions seems to be important for ferredoxin and oxido-reductase recognition.

Insights from the salt bridge analysis of malate dehydrogenase from H. salinarum and E.coli.

Halophilic proteins have greater abundance of acidic over basic residues in sequence. In structure, the surface is decorated by negative charges, with lower content of Lysine. Using sequence BLOCKs and 3D model of malate dehydrogenase from halophilic archaea (Halobacterium salinarum; hsMDH) and X-ray structure from mesophilic bacteria (E. coli; ecMDH), we show that not only acidic and basic residues have higher mean relative abundance (MRA) and thus, impart higher polarity to the sequences, but also show their presence in the surface of the structure of hsMDH relative to its mesophilic counterpart. These observations may indicate that both the acidic and the basic residues have a concerted role in the stability of hsMDH. Analysis on salt bridges from hsMDH and ecMDH show that in the former, salt bridges are highly intricate, newly engineered and global in nature. Although, these salt bridges are abundant in hsMDH, in the active site the design remains unperturbed. In high salt where hydrophobic force is weak, these salt bridges seem to play a major role in the haloadaptation of the tertiary structure of hsMDH. This is the first report of such an observation.

Stability of buried and networked salt-bridges (BNSB)in thermophilic proteins.

Thermophilic proteins function at high temperature, unlike mesophilic proteins. Thermo-stability of these proteins is due to the unique buried and networked salt-bridge (BNSB). However, it is known that the desolvation cost of BNSB is too high compared to other favorable energy terms. Nonetheless, it is known that stability is provided generally by hydrophobic isosteres without the need for BNSB. We show in this analysis that the BNSB is the optimal evolutionary design of salt-bridge to offset desolvation cost efficiently. Hence, thermophilic proteins with a high level of BNSB provide thermo-stability.

Analysis of salt-bridges in prolyl oligopeptidase from Pyrococcus furiosus and Homo sapiens.

Hyper thermophilic archaea not only tolerate high temperature but also operate its biochemical machineries, normally under these conditions. However, the structural signatures in proteins that answer for the hyper thermo-stability relative to its mesophilic homologue remains poorly understood. We present comparative analyses of sequences, structures and salt-bridges of prolyl-oligopeptidase from Pyrococcus furiosus (pfPOP - PDB ID: 5T88) and human (huPOP - PDB ID: 3DDU). A similar level of hydrophobic and hydrophilic residues in pfPOP and huPOP is observed. A low level of interactions between shell-waters and atom-types in pfPOP indicated hyper thermophilic features are negligible. Salt-bridge-forming-residues (sbfrs) are high in pfPOP's core and surface (pfPOP). Increased sbfrs largely indicate specific-electrostatic is important for thermo stability in pfPOP. Four classes of sbfrs are found namely positionally non-conservative (PNCS), conservative (PCS), unchanged (PU) and interchanged (PIC) type of substitutions. PNCS-sbfrs constitutes 28% and it is associated with the topology of pfPOP at high temperature. PCS helps to increase the salt-bridge population. It is also found that PU maintains similar salt-bridges at the active site and other binding sites while PIC abolishes mesophilic patterns.

Fluorescence enhancement via aggregation effect due to microenvironmental alterations in human hemoglobin protein in presence of carbon quantum dots (CQD): Comparative spectroscopic approach.

CQDs have emerged with outstanding properties as a star member of carbon nanomaterial family and in order to reveal its wide-range of application in biological microenvironment the interactions between human hemoglobin (HHb) and CQD and also with ethylenediamine-functionalized CQD (NCQD) are assessed using several techniques. Firstly, UV-vis absorption spectra of HHb reveal hyperchromic effect in the region of absorbance of tryptophan and tyrosine residues and also hypochromicity of Soret band in presence of CQD and NCQD. Interestingly, steady-state fluorescence spectroscopy reveal distinct fluorescence enhancement of HHb with significant red shift thereby indicating exposures of tryptophan and tyrosine residues to a more hydrophilic environment. However synchronous fluorescence spectra reveal that the microenvironment of tryptophan and tyrosine residues is altered in opposite manner, i.e. exposure of tryptophan residues to a more hydrophilic environment and the tyrosine residues to a more hydrophobic environment. Moreover the fluorescence enhancement is observed to be accompanied by increase in average fluorescence-lifetime and decrease in steady-state anisotropy thus signifying a decrease in restriction of rotational motion. Furthermore tryptophan residues within HHb appear to interact more with CQD compared to NCQD. Thermodynamic parameters as revealed by Isothermal Titration Calorimetry (ITC) demonstrate that electrostatic, hydrogen bonding and hydrophobic interactions are the predominant modes of interactions in presence of CQD. Whereas hydrophobic and hydrogen bonding interactions are the major interacting forces in presence of NCQD with five-site sequential binding as best-fit model in both the cases. Such interactions also appear to be associated with an increase in aggregation of HHb as evident from the measurements by atomic force microscopy (AFM) and dynamic light scattering (DLS) study. Although FT-IR spectra display alteration of amide I band, but the overall secondary structure of HHb seems to be nearly retained even in presence of CQDs, as evident in the CD spectra. These observations thus highlight the potential biomedical application of CQDs in biological microenvironment of human especially as drug-delivery system. Also bimolecular interaction of HHb as a model protein with other nanoparticles at the nano bio-interface has been outlined.

Nanohexaconazole: synthesis, characterisation and efficacy of a novel fungicidal nanodispersion.

Here, the authors describe a simple method to formulate the nanodispersion of hexaconazole (hexa); henceforth, referred to as nanohexaconazole (N-hexa) that is water soluble and effective against several species of Aspergillus. Size and shape of the prepared nanocomposite was determined with high-resolution transmission electron microscopy and field-emission scanning electron microscopy. Nanohexaconazole structure was further confirmed by Fourier-transform infrared spectroscopy and gas chromatography-mass spectrometry. The antifungal efficacy of nanohexaconazole (N-hexa) was studied in vitro, compared with micronised hexaconazole (M-hexa) at different doses (5 ppm, 10 ppm and control) against two food pathogenic fungi: Aspergillus niger (MTCC 282, MTCC 2196 and BDS 113) and Aspergillus fumigatus through poisoned food technique. A dose-dependent significant growth inhibition was observed in nanohexaconazole (N-hexa) treated fungal sample compared with that of micronised hexaconazole (M-hexa). Micrographic studies for the morphological analysis of control and nanohexaconazole (N-hexa) treated fungal samples were done, exhibited an alternation in fungal morphology. Results showed that nanohexaconazole (N-hexa) is more efficacious than commercially available micronised hexaconazole (M-hexa). In future nanohexaconazole (N-hexa) could be a possible candidate for modern medical science and also reduce damage to the environment from injudicious use of pesticides.

Effect of Nanohexaconazole on Nitrogen Fixing Blue Green Algae and Bacteria.

Nanohexaconazole is a highly efficient fungicide against Rhizoctonia solani. Nanoparticles are alleged to adversely affect the non-target organisms. In order to evaluate such concern, the present study was carried out to investigate the effect of nanohexaconazole and its commercial formulation on sensitive nitrogen fixing blue green algae (BGA) and bacteria. Various activities of algae and bacteria namely growth, N-fixation, N-assimilation, Indole acetic acid (IAA) production and phosphate solubilization were differently affected in the presence of hexaconazole. Although, there was stimulatory to slightly inhibitory effect on the growth measurable parameters of the organisms studied at the recommended dose of nanohexaconazole, but its higher dose was inhibitory to all these microorganisms. On the other hand, the recommended as well as higher dose of commercial hexaconazole showed much severe inhibition of growth and metabolic activity of these organisms as compared to the nano preparation. The uses of nanohexazconazole instead of hexaconazole as a fungicide will not only help to control various fungal pathogens but also sustain the growth and activity of these beneficial microorganisms for sustaining soil fertility and productivity.

Development and Quality Control of Nanohexaconazole as an Effective Fungicide and Its Biosafety Studies on Soil Nitifiers.

The study was aimed to develop a nano form of an existing fungicide for improving plant protection and reducing crop losses caused by fungal pathogens. The protocol for the preparation and estimation of nanohexaconazole was developed. Technically pure hexaconazole was converted into its nanoform using polyethyleneglycol-400 (PEG) as the surface stabilizing agent. Nanohexaconazole was characterized using Scanning Electron Microscopy (SEM) and Dynamic Light Scattering (DLS) studies. The average particle size of nanohexaconazole was about 100 nm. An analytical method was also developed for quality control of the nanofungicide by GLC fitted with flame ionization detector. Its limit of detection was 2.5 ppm. Fungicidal potential of nanohexaconazole was better in comparison to that of conventional hexaconazole. Hydrolytic and thermal stability studies confirmed its stability at par with the conventional formulation of fungicide. Impact of nanohexaconazole on soil nitrifiers was tested in vitro and there were no significant adverse effect in their numbers observed as compared to conventional registered formulation, proving the safety of the nanofungicide.

Simple synthesis of biocompatible biotinylated porous hexagonal ZnO nanodisc for targeted doxorubicin delivery against breast cancer cell: In vitro and in vivo cytotoxic potential.

Targeted drug delivery with porous materials features great promise as improved therapeutic potential for treatment of various diseases. In the present study we have attempted a microwave synthesis of porous hexagonal nanodisc of zinc oxide (PZHD) for the first time and its subsequent targeted delivery to breast cancer cells, MCF7. PZHD has been fabricated suitably with 3-aminopropyltriethoxysilane to impart additional stability and surface amines to anchor site directing ligand NHS-biotin. Biotinylated scaffold showed targeted delivery of anticancer drug doxorubicin and pH triggered release to MCF 7 cells with preferential distribution on specified domain. A detailed in vitro cytotoxicity study was associated with it to evaluate the mode of action of Dox loaded PZHD on MCF-7 cells by means of cell cycle analysis, apoptosis assays, Western blot and immuno-fluorescence image analysis. The efficacy of the Dox loaded PZHD was further validated from our in vivo tumor regression studies. Finally, the whole study has been supported by in vitro and in vivo bio-safety studies which also signified its biocompatibility with real time applications. To the best of our knowledge this is the first effort to use biotinylated PZHD for targeted delivery of doxorubicin within MCF 7 cells with a detailed study of its mechanistic application. This study might thus hold future prospects for therapeutic intervention for treatment of cancer.

Copper nanoparticle (CuNP) nanochain arrays with a reduced toxicity response: a biophysical and biochemical outlook on Vigna radiata.

Copper deficiency or toxicity in agricultural soil circumscribes a plant's growth and physiology, hampering photochemical and biochemical networks within the system. So far, copper sulfate (CS) has been used widely despite its toxic effect. To get around this long-standing problem, copper nanoparticles (CuNPs) have been synthesized, characterized, and tested on mung bean plants along with commercially available salt CS, to observe morphological abnormalities enforced if any. CuNPs enhanced photosynthetic activity by modulating fluorescence emission, photophosphorylation, electron transport chain (ETC), and carbon assimilatory pathway under controlled laboratory conditions, as revealed from biochemical and biophysical studies on treated isolated mung bean chloroplast. CuNPs at the recommended dose worked better than CS in plants in terms of basic morphology, pigment contents, and antioxidative activities. CuNPs showed elevated nitrogen assimilation compared to CS. At higher doses CS was found to be toxic to the plant system, whereas CuNP did not impart any toxicity to the system including morphological and/or physiological alterations. This newly synthesized polymer-encapsulated CuNPs can be utilized as nutritional amendment to balance the nutritional disparity enforced by copper imbalance.

Microwave synthesis of ZnO@mSiO2 for detailed antifungal mode of action study: understanding the insights into oxidative stress.

A simple chemical method has been devised for deliberate incorporation of zinc oxide nanoparticles (ZNPs) within mesoporous nanosilica (mSiO2) matrix to yield zinc oxide nanoparticles embedded in mesoporous nanosilica (ZnO@mSiO2). ZnO@mSiO2 inhibited the growth of four strains of fungi in a dose dependant manner. A series of biochemical assays revealed generation of oxidative stress from ZnO@mSiO2 for such biocidal response. We proposed transient superoxide and its subsequent conversion to H2O2 played a pivotal role behind such biocidal response as revealed from our systematic evaluation. This resulted morphological alteration of fungi through increase in number of facets, in correlation we found up-regulation in oxidative stress related genes. Bioavailability within the fungal sample was confirmed from microscopic, spectroscopic, biophysical techniques. Protein carbonylation of fungal species was the chemical outcome of such above mentioned stress and quantified by high performance liquid chromatography (HPLC) via subsequent hydrazone derivatization. Several in vitro and in vivo evaluations revealed the biocompatibility of ZnO@mSiO2. Altogether this report claims a new biocidal agent with a detailed mode of action focusing on the origin and quantification of oxidative stress through biophysical and biochemical techniques for the first time for real time applications.

The effect of nanoparticles on plankton dynamics: a mathematical model.

A simple modification of the Rosenzweig-MacArthur predator (zooplankton)-prey (phytoplankton) model with the interference of the predators by adding the effect of nanoparticles is proposed and analyzed. It is assumed that the effect of these particles has a potential to reduce the maximum physiological per-capita growth rate of the prey. The dynamics of nanoparticles is assumed to follow a simple Lotka-Volterra uptake term. Our study suggests that nanoparticle induce growth suppression of phytoplankton population can destabilize the system which leads to limit cycle oscillation. We also observe that if the contact rate of nanoparticles and phytoplankton increases, then the equilibrium densities of phytoplankton as well as zooplankton decrease. Furthermore, we observe that the depletion/removal of nanoparticles from the aquatic system plays a crucial role for the stable coexistence of both populations. Our investigation with various types of functional response suggests that Beddington functional response is the most appropriate representation of the interaction of phytoplankton-nanoparticles in comparison to other widely used functional responses.