A green and economic approach to synthesize magnetic Lagenaria siceraria biochar (γ-Fe2O3-LSB) for methylene blue removal from aqueous solution.

In the printing and textile industries, methylene blue (a cationic azo dye) is commonly used. MB is a well-known carcinogen, and another major issue is its high content in industrial discharge. There are numerous removal methodologies that have been employed to remove it from industrial discharge; however, these current modalities have one or more limitations. In this research, a novel magnetized biochar (γ-Fe2O3-LSB) was synthesized using Lagenaria siceraria peels which were further magnetized via the co-precipitation method. The synthesized γ-Fe2O3-LSB was characterized using FTIR, X-ray diffraction, Raman, SEM-EDX, BET, and vibrating sample magnetometry (VSM) for the analysis of magnetic properties. γ-Fe2O3-LSB showed a reversible type IV isotherm, which is a primary characteristic of mesoporous materials. γ-Fe2O3-LSB had a specific surface area (SBET = 135.30 m2/g) which is greater than that of LSB (SBET = 11.54 m2/g). γ-Fe2O3-LSB exhibits a saturation magnetization value (Ms) of 3.72 emu/g which shows its superparamagnetic nature. The batch adsorption process was performed to analyze the adsorptive removal of MB dye using γ-Fe2O3-LSB. The adsorption efficiency of γ-Fe2O3-LSB for MB was analyzed by varying parameters like the initial concentration of adsorbate (MB), γ-Fe2O3-LSB dose, pH effect, contact time, and temperature. Adsorption isotherm, kinetic, and thermodynamics were also studied after optimizing the protocol. The non-linear Langmuir model fitted the best to explain the adsorption isotherm mechanism and resulting adsorption capacity ( q e =54.55 mg/g). The thermodynamics study showed the spontaneous and endothermic nature, and pseudo-second-order rate kinetics was followed during the adsorption process. Regeneration study showed that γ-Fe2O3-LSB can be used up to four cycles. In laboratory setup, the cost of γ-Fe2O3-LSB synthesis comes out to be 162.75 INR/kg which is low as compared to commercially available adsorbents. The results obtained suggest that magnetic Lagenaria siceraria biochar, which is economical and efficient, can be used as a potential biochar material for industrial applications in the treatment of wastewater.

Copper(II) nanodots stabilized on Cassia fistula galactomannan: preparation and catalytic application towards fast solvent-free Biginelli reactions.

New Cu(II) nanodots have been developed using biopolymeric polysaccharide galactomannan. The nanocatalyst Cu(II)NDs@CFG has been developed through a one-step clean and sustainable reaction of Cassia fistula galactomannan and CuSO4·5H2O in an aqueous medium. The catalyst Cu(II)NDs@CFG is well characterized by FT-IR, FE-SEM, EDS, ICP-MS, HR-TEM, XPS, XRD, TGA and BET analysis. This is the first example of preparing copper nanodots by using polysaccharide galactomannan as a supporting template to form copper nanodots in water. Moreover, the copper nanodots act as a potential nanocatalyst for multicomponent Biginelli reactions. A simple, one pot, efficient and environmentally benign synthesis of 3,4-dihydropyrimidin-2(1H)-ones/thiones has been achieved with wide variety of aldehydes, ß-dicarbonyl compounds and urea or thiourea indicating the good tolerance of the catalyst towards various functionalities. The presented work has several merits in terms of economy which include easy operation, complete avoidance of toxic organic solvents and expensive catalysts, simple work-up, less reaction time, and excellent yields.

Isolation, Characterization, and Expression Analysis of NAC Transcription Factor from Andrographis paniculata (Burm. f.) Nees and Their Role in Andrographolide Production.

Andrographis paniculata (Burm. f.) Nees is an important medicinal plant known for its bioactive compound andrographolide. NAC transcription factors (NAM, ATAF1/2, and CUC2) play a crucial role in secondary metabolite production, stress responses, and plant development through hormonal signaling. In this study, a putative partial transcript of three NAC family genes (ApNAC83, ApNAC21 22 and ApNAC02) was used to isolate full length genes using RACE. Bioinformatics analyses such as protein structure prediction, cis-acting regulatory elements, and gene ontology analysis were performed. Based on in silico predictions, the diterpenoid profiling of the plant's leaves (five-week-old) and the real-time PCR-based expression analysis of isolated NAC genes under abscisic acid (ABA) treatment were performed. Additionally, the expression analysis of isolated NAC genes under MeJA treatment and transient expression in Nicotiana tabacum was performed. Full-length sequences of three members of the NAC transcription factor family, ApNAC83 (1102 bp), ApNAC21 22 (996 bp), and ApNAC02 (1011 bp), were isolated and subjected to the promoter and gene ontology analysis, which indicated their role in transcriptional regulation, DNA binding, ABA-activated signaling, and stress management. It was observed that ABA treatment leads to a higher accumulation of andrographolide and 14-deoxyandrographolide content, along with the upregulation of ApNAC02 (9.6-fold) and the downregulation of ApNAC83 and ApNAC21 22 in the leaves. With methyl jasmonate treatment, ApNAC21 22 expression decreased, while ApNAC02 increased (1.9-fold), with no significant change being observed in ApNAC83. The transient expression of the isolated NAC genes in a heterologous system (Nicotiana benthamiana) demonstrated their functional transcriptional activity, leading to the upregulation of the NtHMGR gene, which is related to the terpene pathway in tobacco. The expression analysis and heterologous expression of ApNAC21 22 and ApNAC02 indicated their role in andrographolide biosynthesis.

CRISPR/Cas system: A revolutionary tool for crop improvement.

World's population is elevating at an alarming rate thus, the rising demands of producing crops with better adaptability to biotic and abiotic stresses, superior nutritional as well as morphological qualities, and generation of high-yielding varieties have led to encourage the development of new plant breeding technologies. The availability and easy accessibility of genome sequences for a number of crop plants as well as the development of various genome editing technologies such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) has opened up possibilities to develop new varieties of crop plants with superior desirable traits. However, these approaches has limitation of being more expensive as well as having complex steps and time-consuming. The CRISPR/Cas genome editing system has been intensively studied for allowing versatile target-specific modifications of crop genome that fruitfully aid in the generation of novel varieties. It is an advanced and promising technology with the potential to meet hunger needs and contribute to food production for the ever-growing human population. This review summarizes the usage of novel CRISPR/Cas genome editing tool for targeted crop improvement in stress resistance, yield, quality and nutritional traits in the desired crop plants.

Biosynthesis and characterization of Ocimum sanctum green silver nanoparticles and unravelling their enhanced anti-filarial activity through a HRAMS proteomics approach.

The available anti-filarial medications are largely ineffective against adult filarial worms. Also, these drugs have several drawbacks such as toxicity and development of resistance owing to long-term usage. Green nanomedicine may offer better solutions for Lymphatic Filariasis treatment due to its tiny size, biocompatibility, and better penetration at considerably lower costs with higher therapeutic efficacy. In the present study, Ocimum sanctum silver nanoparticles (OSAgNPs) were bio-synthesized and their anti-filarial efficacy was evaluated against adult filarial parasites. The green nanoparticles were characterized by UV-VIS spectroscopy, XRD, FTIR, SEM, and TEM analysis. The OSAgNPs significantly affected the motility and viability of adult Setaria cervi parasites after 4 h of incubation at concentrations higher than 0.5 µg ml-1. Proteomics analysis by high resolution accurate mass spectrometry revealed that 213 proteins were differentially expressed following OSAgNP treatment. Mostly these DEPs belonged to the many biochemical and molecular pathways of parasites such as muscle proteins, antioxidant proteins, heat shock proteins, signal recognition proteins, and energy metabolism-related proteins. Undoubtedly, this study will open new avenues for the development of novel anti-filarial drugs based on green nanoparticles.

SwrA-mediated Multimerization of DegU and an Upstream Activation Sequence Enhance Flagellar Gene Expression in Bacillus subtilis.

The earliest genes in bacterial flagellar assembly are activated by narrowly-conserved proteins called master regulators that often act as heteromeric complexes. A complex of SwrA and the response-regulator transcription factor DegU is thought to form the master flagellar regulator in Bacillus subtilis but how the two proteins co-operate to activate gene expression is poorly-understood. Here we find using ChIP-Seq that SwrA interacts with a subset of DegU binding sites in the chromosome and does so in a DegU-dependent manner. Using this information, we identify a DegU-specific inverted repeat DNA sequence in the Pflache promoter region and show that SwrA synergizes with DegU phosphorylation to increase binding affinity. We further demonstrate that the SwrA/DegU footprint extends from the DegU binding site towards the promoter, likely through SwrA-induced DegU multimerization. The location of the DegU inverted repeat was critical and moving the binding site closer to the promoter impaired transcription by disrupting a previously-unrecognized upstream activation sequence (UAS). Thus, the SwrA-DegU heteromeric complex likely enables both remote binding and interaction between the activator and RNA polymerase. Small co-activator proteins like SwrA may allow selective activation of subsets of genes where activator multimerization is needed. Why some promoters require activator multimerization and some require UAS sequences is unknown.

Adsorption characteristics of magnetized biochar derived from Citrus limetta peels.

Agro-industrial waste is an alarming issue that needs to be addressed. Waste valorization is an effective technique to deal with such effectively. Synthesis of biochar from fruit waste is one of the emerging approaches for adsorption, energy storage, air purification, catalysis, and biogas production trending these days. Magnetized Citrus limetta biochar (MCLB) was synthesized from Citrus limetta peels and was magnetized using iron oxide. Magnetization of biochar increases its functionalities as well as makes its separation easy. The removal of Methylene Blue (MB) dye from an aqueous solution is achieved through the use of MCLB. Methylene Blue is a prominent and widely used cationic-azo dye in the textile and printing industries. The accumulation of MB in wastewater is the major problem as MB is reported as a carcinogenic agent. The removal of MB dye with MCLB was analyzed by adsorption studies, wherein the effect of factors influencing adsorption such as initial concentration of MB dye, MCLB dosage, the effect of pH, contact time, and adsorption isotherms were studied. Characterization of MCLB was carried out using various techniques, such as FTIR, VSM, XRD, SEM, RAMAN, and Zeta potential. The adsorption isotherm mechanism was well explained with the non-linear Langmuir isotherm model resulting in a good adsorption capacity (qe = 41.57 mg/g) of MCLB when MB (co = 60 mg/L, pH ~ 6.8, T = 273K). The thermodynamics analysis revealed that MB's spontaneous and endothermic adsorption onto the MCLB surface followed pseudo-second-order kinetics. The results obtained from this study suggest that the magnetized biochar derived from Citrus limetta peels has a wide range of potential applications in the treatment of dyeing wastewater.

SwrA extends DegU over an UP element to activate flagellar gene expression in Bacillus subtilis.

SwrA activates flagellar gene expression in Bacillus subtilis to increase the frequency of motile cells in liquid and elevate flagellar density to enable swarming over solid surfaces. Here we use ChIP-seq to show that SwrA interacts with many sites on the chromosome in a manner that depends on the response regulator DegU. We identify a DegU-specific inverted repeat DNA sequence and show that SwrA synergizes with phosphorylation to increase DegU DNA binding affinity. We further show that SwrA increases the size of the DegU footprint expanding the region bound by DegU towards the promoter. The location of the DegU inverted repeat was critical and moving the binding site closer to the promoter impaired transcription more that could be explained by deactivation. We conclude that SwrA/DegU forms a heteromeric complex that enables both remote binding and interaction between the activator and RNA polymerase in the context of an interceding UP element. We speculate that multimeric activators that resolve cis-element spatial conflicts are common in bacteria and likely act on flagellar biosynthesis loci and other long operons of other multi-subunit complexes. IMPORTANCE: In Bacteria, the sigma subunit of RNA polymerase recognizes specific DNA sequences called promoters that determine where gene transcription begins. Some promoters also have sequences immediately upstream called an UP element that is bound by the alpha subunit of RNA polymerase and is often necessary for transcription. Finally, promoters may be activated by transcription factors that bind DNA specific sequences and help recruit RNA polymerase to weak promoter elements. Here we show that the promoter for the 32 gene long flagellar operon in Bacillus subtilis requires an UP element and is activated by a heteromeric transcription factor of DegU and SwrA. Our evidence suggests that SwrA oligomerizes DegU over the DNA to allow RNA polymerase to interact with DegU and the UP element simultaneously. Heteromeric activator complexes are known but poorly-understood in bacteria and we speculate they may be needed to resolve spatial conflicts in the DNA sequence.

Effect of tryptophan mutation on the structure of LOV1 domain of phototropin1 protein of Ostreococcus tauri: A combined molecular dynamics simulation and biophysical approach.

BACKGROUND: Light, oxygen and voltage (LOV) proteins detect blue light by formation of a covalent 'photoadduct' between the flavin chromophore and the neighboring conserved cysteine residue. LOV proteins devoid of this conserved photoactive cysteine are unable to form this 'photoadduct' upon light illumination, but they can still elicit functional response via the formation of neutral flavin radical. Recently, tryptophan residue has been shown to be the primary electron donors to the flavin excited state. METHODS: Photoactive cysteine (Cys42) and tryptophan (Trp68) residues in the LOV1 domain of phototropin1 of Ostreococcus tauri (OtLOV1) was mutated to alanine and threonine respectively. Effect of these mutations have been studied using molecular dynamics simulation and spectroscopic techniques. RESULTS: Molecular dynamics simulation indicated that W68T did not affect the structure of OtLOV1 protein, but C42A leads to some structural changes. An increase in the fluorescence lifetime and quantum yield values was observed for the Trp68 mutant. CONCLUSIONS: An increase in the fluorescence lifetime and quantum yield of Trp68 mutant compared to the wild type protein suggests that Trp68 residue participates in quenching of the flavin excited state followed by photoexcitation. GENERAL SIGNIFICANCE: Enhanced photo-physical properties of Trp68 OtLOV1 mutant might enable its use for the optogenetic and microscopic applications.

Temporal muscle thickness as an independent prognostic marker in glioblastoma patients-a systematic review and meta-analysis.

Glioblastoma is the most common primary malignant brain tumor in the adult population. It causes the patient to incur a great deal of malady. Even with the advances in management and the Stupp protocol in place, the prognosis remains grim. There are various parameters to evaluate patients' performance status and frailty pre-operatively, but these are mostly subjective and thus suffer from inter-observer variability. Assessment of sarcopenia serves as an objective parameter to assess the patient's performance status pre-operatively. Temporalis muscle thickness serves as a surrogate to assess sarcopenia in patients with glioblastoma. We conducted a literature review and meta-analysis to determine the prognostic implications of temporalis muscle thickness in 3283 patients with primary glioblastoma. The pooled overall survival hazard's ratio of thick versus thin TMT was 0.54. The pooled progression-free survival hazard's ratio of thick versus thin TMT was 0.38. Thus, the main finding of this study is that thicker temporal muscle is associated with better OS and PFS as compared to thinner temporal muscle. We thus conclude that TMT is a viable surrogate for predicting sarcopenia and survival in primary glioblastoma. TMT measurement is extremely easy and can be incorporated as a part of the routine neurosurgical workflow in these patients. Survival prediction will help inform treatment decisions in glioblastoma patients having poor prognosis, at the initial diagnosis itself.

Deciphering the anti-filarial potential of bioactive compounds from Ocimum sanctum: a combined experimental and computational study.

CONTEXT: The anthelminthic effect of Ocimum species (Lamiaceae) has been reported, however, its anti-filarial effect has not been explored to date. OBJECTIVE: This study evaluates the effect of Ocimum sanctum L. (OS) against lymphatic filarial parasites. MATERIAL AND METHODS: The ethanol extract of OS (EOS) leaves was tested for anti-filarial activity against Setaria cervi. Equal size and number (n = 10) of adult female S. cervi worms were incubated in 125, 250 or 375 µg/mL EOS extract for 6 h at 37 °C. The OS bioactive components were identified by UPLC-ESI-MS/MS and subjected to docking and molecular dynamics (MD) simulation against filarial antioxidant proteins. RESULTS: The EOS significantly inhibited the motility of adult female S. cervi after 6 h of incubation. The motility was found to be reduced by 53.7% in 375 µg/mL and 43.8% in 250 µg/mL EOS after 6 h of treatment. The UPLC-ESI-MS/MS analysis of ethanol extract of O. sanctum revealed the presence of 13 bioactive compounds. The docking analysis showed eight OS bioactive compounds to have high binding affinity (> 4.8 kcal/mol) towards antioxidant proteins of filarial parasites. Additionally, MD simulation studies showed significant impact of (RMSD ≤ 10 Å) chlorogenic acid, luteolin and ursolic acid on filarial antioxidant enzymes/proteins. To our knowledge, this is the first report of the anti-filarial activity of Ocimum sanctum. DISCUSSION AND CONCLUSIONS: The effect of EOS and OS bioactive components on human filarial parasites can be further evaluated for the development of new anti-filarial formulations.

Identification of promising nutraceuticals against filarial immune-modulatory proteins: insights from in silico and ex vivo studies.

Lymphatic filariasis is a neglected tropical disease affecting over 863 million people in 47 countries of the world. The anti-filarial drugs, diethylcarbamazine, albendazole, and ivermectin, are effective only at the larval stages and have proven completely ineffective as adulticides. Besides this, a long-term use of these drugs is associated with several side effects including drug toxicity. Nutraceuticals have emerged as better alternatives for long term treatments due to their safety and lesser side effects. In the present work, we have used drug docking analysis and molecular dynamics simulation approaches to explore the effect of anti-inflammatory nutraceuticals against the immune-modulatory proteins of filarial worms. The filarial proteins enolase, ES-62 precursor, serpin, and cystatin, which are highly efficient in host immune modulation were targeted with more than 50 nutraceuticals. In the in silico study nutraceuticals such as naringin, ß-carotene, and emodin showed higher binding efficacy and lower dissociation constant as compared to anti-filarial drugs. Molecular dynamics simulation results showed that immune-modulatory proteins formed highly stable complexes with naringin, ß-carotene, and emodin over the entire MD simulation run. The nutraceutical emodin formed the most stable system in silico and hence its effect was investigated on adult filarial parasites under ex vivo conditions too. Emodin significantly affected the motility, viability, ROS production, and genomic DNA fragmentation of filarial parasites. Further in vivo and in vitro studies will help in understanding the mechanism of action of emodin at the molecular level and would help in the development of more effective anti-filarial drugs.

Lymphatic filarial serum proteome profiling for identification and characterization of diagnostic biomarkers.

Lymphatic Filariasis (LF) affects more than 863 million people in tropical and subtropical areas of the world, causing high morbidity and long illnesses leading to social exclusion and loss of wages. A combination of drugs Ivermectin, Diethylcarbamazine citrate and Albendazole is recommended by WHO to accelerate the Global Programme to Eliminate Lymphatic Filariasis (GPELF). To assess the outcome of GPELF, to re-evaluate and to formulate further strategies there is an imperative need for high quality diagnostic markers. This study was undertaken to identify Lymphatic Filarial biomarkers which can detect LF infections in asymptomatic cases and would also serve as indicators for differentiating among different clinical stages of the disease. A combination of Fourier-transform infrared spectroscopy (FT-IR), MMP zymography, SDS-PAGE, classical 2DE along with MALDI-TOF/MS was done to identify LF biomarkers from serum samples of different stages of LF patients. FT-IR spectroscopy coupled with univariate and multivariate analysis of LF serum samples, revealed significant differences in peak intensity at 3300, 2950, 1645, 1540 and 1448 cm-1 (p<0.05). The proteomics analysis results showed that various proteins were differentially expressed (p<0.05), including C-reactive protein, α-1-antitrypsin, heterogeneous nuclear ribonucleoprotein D like, apolipoproteins A-I and A-IV in different LF clinical stages. Functional pathway analysis suggested the involvement of differentially expressed proteins in vital physiological pathways like acute phase response, hemostasis, complement and coagulation cascades. Furthermore, the differentiation between different stages of LF cases and biomarkers identified in this study clearly demonstrates the potential of the human serum profiling approach for LF detection. To our knowledge, this is the first report of comparative human serum profiling in different categories of LF patients.

Current trends in non-dairy based synbiotics.

Probiotics provide many beneficial effects to the human body. Traditionally, food products used to deliver bacterial cells are fermented dairy products, among which yogurt is the most common. However, many people suffer from lactose intolerance and indigestion, who need nutrients from non-dairy products without using animal proteins. Thus, there is a need to develop synbiotics based on non-dairy food matrices. This paper reviews the potential and emerging candidates of pre and probiotic groups. The criteria for qualifying bacteria as probiotics and nutrients as prebiotics are discussed. One of the promising prebiotics explored in the recent past is the dietary fibers in the peels of potato, apples, and other fruits. This paper summarizes methods for the preparation of dietary fiber-based non-dairy synbiotics such as microencapsulation, freeze-drying, and spray drying. The standard testing protocols of synbiotics including the in vitro trials are presented. Synbiotics not only favor the survival of probiotics in the gastric conditions of the human gut but also exhibit antimicrobial activity, which confirms their ability to protect the human body from infection. Many fiber-based non-dairy synbiotic products are available in the market and these are also highlighted. The challenges faced by non-dairy-based synbiotics which open up new research opportunities and market demand are also identified.

Active modulation of surfactant-driven flow instabilities by swarming bacteria.

Models based on surfactant-driven instabilities have been employed to describe pattern formation by swarming bacteria. However, by definition, such models cannot account for the effect of bacterial sensing and decision making. Here we present a more complete model for bacterial pattern formation which accounts for these effects by coupling active bacterial motility to the passive fluid dynamics. We experimentally identify behaviors which cannot be captured by previous models based on passive population dispersal and show that a more accurate description is provided by our model. It is seen that the coupling of bacterial motility to the fluid dynamics significantly alters the phase space of surfactant-driven pattern formation. We also show that our formalism is applicable across bacterial species.

Facile green synthesis of silicon nanoparticles from Equisetum arvense for fluorescence based detection of Fe(iii) ions.

Fluorescent silicon nanoparticles (SiNPs) might be one of the excellent candidates for use as optical markers in biological profiling and diagnostic applications. To exploit this perspective, they ought to be essentially synthesized from any green precursor rich in silicon. Stable dispersibility in water along with prolonged luminescence under different conditions is also desired. Moreover, one of the main challenges is to produce such optically (photoluminescence) stable and water-dispersible SiNPs. In our present work, we have reported the synthesis of a highly stable silicon nanoparticle aqueous suspension via a single-step microwave-assisted facile green route. Our as-prepared SiNPs exhibit inherent stable dispersibility, strong fluorescence, and photo-stable behavior. The experimental results demonstrate that the synthesized SiNPs are highly suitable for the detection of Fe(iii) ions. This optical sensing study opens a new avenue for use of SiNPs as a valuable optical probe in chemosensory applications. Our results provide a single-step methodology for the synthesis of highly stable SiNPs from a biological precursor, which can be used as a promising tool for various chemical and biological applications.

Context-Specific Requirement of Forty-Four Two-Component Loci in Pseudomonas aeruginosa Swarming.

Swarming in Pseudomonas aeruginosa is a coordinated movement of bacteria over semisolid surfaces (0.5%-0.7% agar). On soft agar, P. aeruginosa exhibits a dendritic swarm pattern, with multiple levels of branching. However, the swarm patterns typically vary depending upon the experimental design. In the present study, we show that the pattern characteristics of P. aeruginosa swarm are highly environment dependent. We define several quantifiable, macroscale features of the swarm to study the plasticity of the swarm, observed across different nutrient formulations. Furthermore, through a targeted screen of 113 two-component system (TCS) loci of the P. aeruginosa strain PA14, we show that forty-four TCS genes regulate swarming in PA14 in a contextual fashion. However, only four TCS genes-fleR, fleS, gacS, and PA14_59770-were found essential for swarming. Notably, many swarming-defective TCS mutants were found highly efficient in biofilm formation, indicating opposing roles for many TCS loci.