Marvels of Bacilli in soil amendment for plant-growth promotion toward sustainable development having futuristic socio-economic implications.

Microorganisms are integral components of ecosystems, exerting profound impacts on various facets of human life. The recent United Nations General Assembly (UNGA) Science Summit emphasized the critical importance of comprehending the microbial world to address global challenges, aligning with the United Nations Sustainable Development Goals (SDGs). In agriculture, microbes are pivotal contributors to food production, sustainable energy, and environmental bioremediation. However, decades of agricultural intensification have boosted crop yields at the expense of soil health and microbial diversity, jeopardizing global food security. To address this issue, a study in West Bengal, India, explored the potential of a novel multi-strain consortium of plant growth promoting (PGP) Bacillus spp. for soil bioaugmentation. These strains were sourced from the soil's native microbial flora, offering a sustainable approach. In this work, a composite inoculum of Bacillus zhangzhouensis MMAM, Bacillus cereus MMAM3), and Bacillus subtilis MMAM2 were introduced into an over-exploited agricultural soil and implications on the improvement of vegetative growth and yield related traits of Gylcine max (L) Meril. plants were evaluated, growing them as model plant, in pot trial condition. The study's findings demonstrated significant improvements in plant growth and soil microbial diversity when using the bacterial consortium in conjunction with vermicompost. Metagenomic analyses revealed increased abundance of many functional genera and metabolic pathways in consortium-inoculated soil, indicating enhanced soil biological health. This innovative bioaugmentation strategy to upgrade the over-used agricultural soil through introduction of residual PGP bacterial members as consortia, presents a promising path forward for sustainable agriculture. The rejuvenated patches of over-used land can be used by the small and marginal farmers for cultivation of resilient crops like soybean. Recognizing the significance of multi-strain PGP bacterial consortia as potential bioinoculants, such technology can bolster food security, enhance agricultural productivity, and mitigate the adverse effects of past agricultural activities.

Genome-wide analysis of glutamate receptor gene family in allopolyploid Brassica napus and its diploid progenitors.

Ionotropic glutamate receptors are ligand-gated nonselective cation channels that mediate neurotransmission in the central nervous system of animals. Plants possess homologous proteins called glutamate receptor-like channels (GLRs) which are involved in vital physiological processes including seed germination, long-distance signaling, chemotaxis, Ca2+ signaling etc. Till now, a comprehensive genome-wide analysis of the GLR gene family members in different economically important species of Brassica is missing. Considering the origin of allotetraploid Brassica napus from the hybridization between the diploid Brassica oleracea and Brassica rapa, we have identified 11, 27 and 65 GLR genes in B. oleracea, B. rapa and B. napus, respectively showing an expansion of this gene family in B. napus. Chromosomal locations revealed several tandemly duplicated GLR genes in all the three species. Moreover, the gene family expanded in B. napus after allopolyploidization. The phylogenetic analysis showed that the 103 GLRs are classified into three main groups. The exon-intron structures of these genes are not very conserved and showed wide variation in intron numbers. However, protein sequences are much conserved as shown by the presence of ten short amino acid sequence motifs. Predicted cis-acting elements in 1 kb promoters of GLR genes are mainly involved in light, stress and hormone responses. RNA-seq analysis showed that in B. oleracea and B. rapa, some GLRs are more tissue specific than others. In B. napus, some GLRs are downregulated under cold stress, while others are upregulated. In summary, this bioinformatic study of the GLR gene family of the three Brassica species provides evidence for the expansion of this gene family in B. napus and also provided useful information for in-depth studies of their biological functions in Brassica.

Differentiation of Salivary Gland and Salivary Gland Tumor Tissue via Raman Imaging Combined with Multivariate Data Analysis.

Salivary gland tumors (SGTs) are a relevant, highly diverse subgroup of head and neck tumors whose entity determination can be difficult. Confocal Raman imaging in combination with multivariate data analysis may possibly support their correct classification. For the analysis of the translational potential of Raman imaging in SGT determination, a multi-stage evaluation process is necessary. By measuring a sample set of Warthin tumor, pleomorphic adenoma and non-tumor salivary gland tissue, Raman data were obtained and a thorough Raman band analysis was performed. This evaluation revealed highly overlapping Raman patterns with only minor spectral differences. Consequently, a principal component analysis (PCA) was calculated and further combined with a discriminant analysis (DA) to enable the best possible distinction. The PCA-DA model was characterized by accuracy, sensitivity, selectivity and precision values above 90% and validated by predicting model-unknown Raman spectra, of which 93% were classified correctly. Thus, we state our PCA-DA to be suitable for parotid tumor and non-salivary salivary gland tissue discrimination and prediction. For evaluation of the translational potential, further validation steps are necessary.

Gradient SERS Substrates with Multiple Resonances for Analyte Screening: Fabrication and SERS Applications.

Surface-enhanced Raman spectroscopy (SERS) provides a strong enhancement to an inherently weak Raman signal, which strongly depends on the material, design, and fabrication of the substrate. Here, we present a facile method of fabricating a non-uniform SERS substrate based on an annealed thin gold (Au) film that offers multiple resonances and gap sizes within the same sample. It is not only chemically stable, but also shows reproducible trends in terms of geometry and plasmonic response. Scanning electron microscopy (SEM) reveals particle-like and island-like morphology with different gap sizes at different lateral positions of the substrate. Extinction spectra show that the plasmonic resonance of the nanoparticles/metal islands can be continuously tuned across the substrate. We observed that for the analytes 1,2-bis(4-pyridyl) ethylene (BPE) and methylene blue (MB), the maximum SERS enhancement is achieved at different lateral positions, and the shape of the extinction spectra allows for the correlation of SERS enhancement with surface morphology. Such non-uniform SERS substrates with multiple nanoparticle sizes, shapes, and interparticle distances can be used for fast screening of analytes due to the lateral variation of the resonances within the same sample.

Interplay between gene expression and gene architecture as a consequence of gene and genome duplications: evidence from metabolic genes of Arabidopsis thaliana.

Gene and genome duplications have been widespread during the evolution of flowering plant which resulted in the increment of biological complexity as well as creation of plasticity of a genome helping the species to adapt to changing environments. Duplicated genes with higher evolutionary rates can act as a mechanism of generating novel functions in secondary metabolism. In this study, we explored duplication as a potential factor governing the expression heterogeneity and gene architecture of Primary Metabolic Genes (PMGs) and Secondary Metabolic Genes (SMGs) of Arabidopsis thaliana. It is remarkable that different types of duplication processes controlled gene expression and tissue specificity differently in PMGs and SMGs. A complex relationship exists between gene architecture and expression patterns of primary and secondary metabolic genes. Our study reflects, expression heterogeneity and gene structure variation of primary and secondary metabolism in Arabidopsis thaliana are partly results of duplication events of different origins. Our study suggests that duplication has differential effect on PMGs and SMGs regarding expression pattern by controlling gene structure, epigenetic modifications, multifunctionality and subcellular compartmentalization. This study provides an insight into the evolution of metabolism in plants in the light of gene and genome scale duplication. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-022-01188-2.

Determination and Monitoring of Quality Parameters: A Detailed Study of Optical Elements of a Lens-Based Raman Spectrometer.

A lens-based Raman spectrometer is characterized by studying the optical elements in the optical path and we study the measure of aberration-diffraction effects. This is achieved by measuring the spectral resolution (SR) thus encompassing almost all optical elements of a spectrometer that are mostly responsible for such effects. An equation for SR is used to determine the quality factor Q which measures aberration/diffraction effects occurring in a spectrometer. We show how the quality factor changes with different spectrometer parameters such as grating groove density, the wavelength of excitation, pinhole width, charge-coupled device (CCD) pixel density, etc. This work provides an insight into the quality of a spectrometer and helps to monitor the performance of the spectrometer over a certain period. Commercially available spectrometers or home-built spectrometers are prone to misalignment in optical elements and can benefit from this work that allows maintaining the overall quality of the setup. Performing such experiments over a period helps to minimize the aberration/diffraction effects occurring as a result of time and maintaining the quality of measurements.

Neoadjuvant chemotherapy in technically unresectable head and neck cancers: a retrospective audit.

Background: The data regarding the use of neoadjuvant chemotherapy in technically unresectable head and neck cancer (HNC) is limited and real-world studies are needed to look for the efficacy and toxicities of this approach. Patients and methods: This is a retrospective study conducted in the Medical Oncology department of our hospital. All technically unresectable HNC patients who underwent neoadjuvant chemotherapy between May 2018 and May 2020 were included in this analysis. Patients received three-drug regimen docetaxel, cisplatin and 5-fluorouracil (DCF) regimen, two-drug regimens included docetaxel + cisplatin, paclitaxel + carboplatin both weekly and 3-weekly. The resectability assessment was done clinically and radiologically after completing three neoadjuvant cycles. Overall survival was calculated from the first day of chemotherapy to the date of last follow-up or date of death. Results: A total of 119 patients received neoadjuvant chemotherapy during the specified time. Response assessment showed partial response in 41.9% of patients with three-drug regimens and 37.5% of patients with other regimens. Out of 119 patients, 56 (47%) patients were offered radical intent therapy. Resectability was achieved in 32.3% of three-drug regimen patients and 26.1% of other patients. Surgery was feasible in 33 (27.7%) patients, and postoperative radiotherapy and concurrent chemotherapy were done in 30 patients (25.2%), and surgery with only postoperative radiotherapy was done in 3 patients (2.5%). Radical chemoradiotherapy was done in 23 patients (19.3%). The estimated median survival for patients who could undergo surgery was 18 months [95% confidence interval (CI), 14.9-21.0], and nonsurgical patients were 9 months (95% CI, 7.3-10.6) (p = 0.0001). Conclusion: Our study shows that neoadjuvant chemotherapy in technically unresectable HNC patients can make the disease resectable in around one-third of the patients. The patients who could undergo surgery after neoadjuvant chemotherapy had significantly improved survival as compared to those who could not.

Anisotropic and Amphiphilic Mesoporous Core-Shell Silica Microparticles Provide Chemically Selective Environments for Simultaneous Delivery of Curcumin and Quercetin.

Porous silica materials are often used for drug delivery. However, systems for simultaneous delivery of multiple drugs are scarce. Here we show that anisotropic and amphiphilic dumbbell core-shell silica microparticles with chemically selective environments can entrap and release two drugs simultaneously. The dumbbells consist of a large dense lobe and a smaller hollow hemisphere. Electron microscopy images show that the shells of both parts have mesoporous channels. In a simple etching process, the properly adjusted stirring speed and the application of ammonium fluoride as etching agent determine the shape and the surface anisotropy of the particles. The surface of the dense lobe and the small hemisphere differ in their zeta potentials consistent with differences in dye and drug entrapment. Confocal Raman microscopy and spectroscopy show that the two polyphenols curcumin (Cur) and quercetin (QT) accumulate in different compartments of the particles. The overall drug entrapment efficiency of Cur plus QT is high for the amphiphilic particles but differs widely between Cur and QT compared to controls of core-shell silica microspheres and uniformly charged dumbbell microparticles. Furthermore, Cur and QT loaded microparticles show different cancer cell inhibitory activities. The highest activity is detected for the dual drug loaded amphiphilic microparticles in comparison to the controls. In the long term, amphiphilic particles may open up new strategies for drug delivery.

Chemical Imaging of Single Anisotropic Polystyrene/Poly (Methacrylate) Microspheres with Complex Hierarchical Architecture.

Monodisperse polystyrene spheres are functional materials with interesting properties, such as high cohesion strength, strong adsorptivity, and surface reactivity. They have shown a high application value in biomedicine, information engineering, chromatographic fillers, supercapacitor electrode materials, and other fields. To fully understand and tailor particle synthesis, the methods for characterization of their complex 3D morphological features need to be further explored. Here we present a chemical imaging study based on three-dimensional confocal Raman microscopy (3D-CRM), scanning electron microscopy (SEM), focused ion beam (FIB), diffuse reflectance infrared Fourier transform (DRIFT), and nuclear magnetic resonance (NMR) spectroscopy for individual porous swollen polystyrene/poly (glycidyl methacrylate-co-ethylene di-methacrylate) particles. Polystyrene particles were synthesized with different co-existing chemical entities, which could be identified and assigned to distinct regions of the same particle. The porosity was studied by a combination of SEM and FIB. Images of milled particles indicated a comparable porosity on the surface and in the bulk. The combination of standard analytical techniques such as DRIFT and NMR spectroscopies yielded new insights into the inner structure and chemical composition of these particles. This knowledge supports the further development of particle synthesis and the design of new strategies to prepare particles with complex hierarchical architectures.

Systematic Investigation of Polyurethane Biomaterial Surface Roughness on Human Immune Responses in vitro.

It has been widely shown that biomaterial surface topography can modulate host immune response, but a fundamental understanding of how different topographies contribute to pro-inflammatory or anti-inflammatory responses is still lacking. To investigate the impact of surface topography on immune response, we undertook a systematic approach by analyzing immune response to eight grades of medical grade polyurethane of increasing surface roughness in three in vitro models of the human immune system. Polyurethane specimens were produced with defined roughness values by injection molding according to the VDI 3400 industrial standard. Specimens ranged from 0.1 µm to 18 µm in average roughness (Ra), which was confirmed by confocal scanning microscopy. Immunological responses were assessed with THP-1-derived macrophages, human peripheral blood mononuclear cells (PBMCs), and whole blood following culture on polyurethane specimens. As shown by the release of pro-inflammatory and anti-inflammatory cytokines in all three models, a mild immune response to polyurethane was observed, however, this was not associated with the degree of surface roughness. Likewise, the cell morphology (cell spreading, circularity, and elongation) in THP-1-derived macrophages and the expression of CD molecules in the PBMC model on T cells (HLA-DR and CD16), NK cells (HLA-DR), and monocytes (HLA-DR, CD16, CD86, and CD163) showed no influence of surface roughness. In summary, this study shows that modifying surface roughness in the micrometer range on polyurethane has no impact on the pro-inflammatory immune response. Therefore, we propose that such modifications do not affect the immunocompatibility of polyurethane, thereby supporting the notion of polyurethane as a biocompatible material.

Flexible plasmonic graphene oxide/heterostructures for dual-channel detection.

Graphene oxide (GO) films are deposited on flexible Kapton substrates and selectively modified to conductive reduced graphene oxide (rGO) electrodes using laser patterning. Based on this, we design, fabricate, and test a flexible sensor integrating laser-reduced GO with silver plasmonic nanostructures. The fabricated device results in dual transduction channels: for electrochemical and plasmonic nanostructure-based surface-enhanced Raman spectroscopy (SERS) detection. The spectroscopic analysis verifying the formation of rGO and the modification by silver nanostructures is performed by Raman, energy dispersive X-ray (EDX), and X-ray photoelectron spectroscopy (XPS). The morphological investigation is followed by optical and scanning electron microscopy imaging. In addition to pristine silver nanostructures, the Raman spectroscopy results show the formation of species such as Ag2O, Ag2CO3, and Ag2SOx. A dual-channel sensor device based on electrochemical and plasmonic detection is fabricated as a demonstration of our Ag-rGO flexible concept architecture. The dual-channel device performance is successfully demonstrated in the electrochemical and SERS detection of 4-nitrobenzenethiol (4-NBT) using the same device. Our results show that without Ag nanostructures the sensitivity in the electrochemical and optical channels is not sufficient to detect 4-NBT. The performance and stability of the silver modified device are also verified. This work demonstrates an inexpensive, highly efficient, and greener way that is compatible with solution-processing technology for the production of flexible GO-based electrochemical and SERS detection devices integrated with plasmonic nanostructures.

The role of a plasmonic substrate on the enhancement and spatial resolution of tip-enhanced Raman scattering.

Since the first report in the early 2000s, there have been several experimental configurations that have demonstrated enhancement and spatial resolution of tip-enhanced Raman spectroscopy (TERS). The combination of a plasmonic substrate and a metallic tip is one suitable approach to achieve even higher enhancement and lateral resolution. In this contribution, we demonstrate TERS on a monolayer of MoS2 on an array of Au nanodisks. The Au nanodisks were prepared by electron beam writing. Thereafter, MoS2 was transferred onto the plasmonic substrate via the exfoliation technique. We witness an unprecedented enhancement and spatial resolution in the experiments. In the TERS image a ring-like shape is observed that matches the edges of the nanodisks. TERS enhancement at the edges is about 170 times stronger than at the center of the nanodisks. For a better understanding of the experimental results, finite element method (FEM) simulations were employed to simulate the TERS image of the MoS2/plasmonic heterostructure. Our calculations show a higher electric field concentration at the edges that exponentially decays to the center. Therefore, it reproduces the ring-like shape of the experimental image. Moreover, the calculations suggest a TERS enhancement of 135 at the edges compared to the center, which is in very good agreement with the experimental data. According to our calculations, the spatial resolution is also increased at the edges. For comparison, FEM simulations of a tip-flat metal substrate system (conventional gap-mode TERS) were carried out. The calculations confirmed a 110 times stronger enhancement at the edges of the nanodisks than that of conventional gap-mode TERS and explained the experimental maps. Our results provide not only a deeper understanding of the TERS mechanism of this heterostructure, but can also help in realizing highly efficient TERS experiments using similar systems.

Probing interlayer excitons in a vertical van der Waals p-n junction using a scanning probe microscopy technique.

Two dimensional (2D) semiconductors feature exceptional optoelectronic properties controlled by strong confinement in one dimension. In this contribution, we studied interlayer excitons in a vertical p-n junction made of bilayer n-type MoS2 and few layers of p-type GaSe using current sensing atomic force microscopy (CSAFM). The p-n interface is prepared by mechanical exfoliation onto highly ordered pyrolytic graphite (HOPG). Thus the heterostructure creates an ideal layered system with HOPG serving as the bottom contact for the electrical characterization. Home-built Au tips are used as the top contact in CSAFM mode. During the basic diode characterization, the p-n interface shows strong rectification behavior with a rectification ratio of 104 at ±1 V. The I-V characteristics reveal pronounced photovoltaic effects with a fill factor of 0.55 by an excitation below the band gap. This phenomenon can be explained by the dissociation of interlayer excitons at the interface. The possibility of the interlayer exciton formation is indicated by density functional theory (DFT) calculations on this heterostructure: the valence band of GaSe and the conduction band of MoS2 contribute to an interface-specific state at an energy of about 1.5 eV. The proof of excitonic transitions to that state is provided by photoluminescence measurements at the p-n interface. Finally, photocurrent mapping at the interface under an excitation wavelength of 785 nm provides evidence of efficient extraction of such excitons. Our results demonstrate a pathway towards a 2D device for future optoelectronics and light harvesting assisted by interlayer excitons in a van der Waals (vdW) heterostructure.

The role of introns in the conservation of the metabolic genes of Arabidopsis thaliana.

In Arabidopsis thaliana, primary metabolic genes (PMGs) are more evolutionarily conserved and intron-rich than secondary metabolic genes. We observed that PMGs are more primitive and pan-taxonomically persistent as compared to secondary (SMGs) and non-metabolic genes (NMGs). This difference in primitiveness and persistence is primarily correlated with intron number and is independent of gene expression level. We propose a twofold explanation behind higher intron enrichment in PMGs. Firstly, introns might increase protein versatility amongst PMGs through alternative splicing, providing selective advantage of PMGs and making them more persistent across diverse plant taxa. Also, multifunctional PMGs may acquire functional domains by increasing the intronic burden. Additionally, single nucleotide polymorphisms (SNPs) accumulate at a higher rate in introns as compared to exons. Moreover, a strong negative correlation between cumulative exonic SNPs density and intron number indicates that introns may protect the exonic regions against the deleterious effect of these mutations, making them more conserved.

Computational analysis of the glutamate receptor gene family of Arabidopsis thaliana.

Ionotropic glutamate receptors (iGluRs) function as glutamate-activated ion channels in rapid synaptic transmission in animals. Arabidopsis thaliana possess 20 glutamate receptor-like genes (AtGLRs) in its genome which are involved in many functions including light signal transduction and calcium homeostasis. However, little is known about the physico-chemical, functional and structural properties of AtGLRs. In this study, glutamate receptor-like genes of A. thaliana have been studied in silico. Exon-intron structures revealed common origin of majority of these genes. The presence of several phosphorylation and myristoilation sites indicate the involvement of AtGLRs in various signaling processes. Gene ontology analysis showed the participation of AtGLRs in various biological processes including different stress responses. In two genes namely AT2G17260 and AT4G35290, presence of RAV1-A binding site motif in the promoter coupled with results from gene ontology annotation indicate their role in stomatal movement through abscisic acid signaling. Expression analysis showed differential expression of several tandemly arranged genes which indicates neo or sub-functionalization. Two genes namely AT5G48400 and AT5G48410 showed significantly more expression in response to Botrytis cinerea infection. Five of these genes have shown G-protein-coupled γ-aminobutyric acid (GABA) receptor activity indicating a possible interaction between AtGLRs and GABA. Structurally, all of them were similar while differences were found regarding electrostatic surfaces as well as surface hydrophobicity. Results of this study provide a comprehensive reference regarding AtGLRs for further analysis regarding the structure, function, and evolution of the glutamate receptors in plants.

Evolutionary Rate Heterogeneity of Primary and Secondary Metabolic Pathway Genes in Arabidopsis thaliana.

Primary metabolism is essential to plants for growth and development, and secondary metabolism helps plants to interact with the environment. Many plant metabolites are industrially important. These metabolites are produced by plants through complex metabolic pathways. Lack of knowledge about these pathways is hindering the successful breeding practices for these metabolites. For a better knowledge of the metabolism in plants as a whole, evolutionary rate variation of primary and secondary metabolic pathway genes is a prerequisite. In this study, evolutionary rate variation of primary and secondary metabolic pathway genes has been analyzed in the model plant Arabidopsis thaliana. Primary metabolic pathway genes were found to be more conserved than secondary metabolic pathway genes. Several factors such as gene structure, expression level, tissue specificity, multifunctionality, and domain number are the key factors behind this evolutionary rate variation. This study will help to better understand the evolutionary dynamics of plant metabolism.

[Computational analysis of a cys-loop ligand gated ion channel from the green alga Chlamydomonas reinhardtii].

Plants possess several neurotransmitters with well-known physiological roles. Currently only receptors for glutamate were reported to be found in plants, while receptors for acetylcholine, serotonin and GABA have not yet been reported. In animals, these neurotransmitters act via one class of ligand binding ion channels called Cys-loop receptors which play a major role in fast synaptic transmission. They show the presence of two domains namely Neurotransmitter-gated ion-channel ligand-binding domain (Pfam: PF02931) and Neurotransmitter-gated transmembrane domain (Pfam: PF02932). Cys-loop receptors are also known in prokaryotes. No cys-loop receptor has been characterized from plants yet. In this study, the Ensembl plants database was searched for proteins with these two domains in the sequenced plant genomes, what resulted in only one protein (LIC1) from the alga Chlamydomonas reinhardtii. BLAST and profile HMM searches against the pdb structure database showed that this protein is related to animal and prokaryotic cys-loop receptors, although the cysteine residues characteristic of the cys-loop are absent. Physico-chemical and sequence analysis indicate that LIC1 is an anionic receptor. A model of this protein was generated using homology modeling based on a nicotinic acetylcholine receptor of Torpedo marmorata. The characteristic extracellular domain (ECD) and transmembrane domain (TMD) are well structured but the intercellular region is poorly formed. This is the first report on a detailed characterization of a cys-loop receptor from the plant kingdom.

A computerized spectrophotometric instrumental system to determine the "vertical velocity" of sperm cells: a novel concept.

BACKGROUND: The presently available cell motility-analyzers measure primarily the "horizontal" velocity and there is no instrument available for "vertical" velocity measurement. This development was based on the turbidimetric method of sperm motility analysis. METHODS: Sperm was layered at the bottom of the cuvette containing buffer solution and exposed to the spectrophotometric light path at different heights to track the vertically moving sperms. The vertical movement was materialized with the development of an electromechanical up-down movement devise for the cuvette accomplished with the help of a cuvette holder-stepper motor-computer assembly. The entire system was controlled by the necessary motion control, data acquisition, and data processing software developed for cuvette movement and data analysis. RESULTS: Using goat sperm as the model a unique computer-based spectrophotometric system has been developed for the first time to determine the average "vertical" velocity of motile cells. CONCLUSIONS: Undertaking upward movement against gravity is much tougher as compared with horizontal movement. Consequently average vertical velocity is expected to be a much better identifying parameter for assessing semen and other motile cell quality. The novel instrumental system developed by us has thus the potential for immense application in human infertility clinics, animal-breeding centres, centres for conservation of endangered species, and also for research work on vertical velocity of spermatozoa and other motile cells, such as bacteria, protozoa, etc.