Genetic diversity and population structure analyses and genome-wide association studies of photoperiod sensitivity in cotton (Gossypium hirsutum L.).

KEY MESSAGE: Genetic diversity and population structure analyses showed progressively narrowed diversity in US Upland cotton compared to land races. GWAS identified genomic regions and candidate genes for photoperiod sensitivity in cotton. Six hundred fifty-seven accessions that included elite cotton germplasm (DIV panel), lines of a public cotton breeding program (FB panel), and tropical landrace accessions (TLA panel) of Gossypium hirsutum L. were genotyped with cottonSNP63K array and phenotyped for photoperiod sensitivity under long day-length conditions. The genetic diversity analysis using 26,952 polymorphic SNPs indicated a progressively narrowed diversity from the landraces (0.230) to the DIV panel accessions (0.195) and FB panel (0.116). Structure analysis in the US germplasm identified seven subpopulations representing all four major regions of the US cotton belt. Three subpopulations were identified within the landrace accessions. The highest fixation index (FST) of 0.65 was found between landrace accessions of Guatemala and the Plains-type cultivars from Southwest cotton region while the lowest FST values were between the germplasms of Mid-South and Southeastern regions. Genome wide association studies (GWAS) of photoperiod response using 600 phenotyped accessions identified 14 marker trait associations spread across eight Upland cotton chromosomes. Six of these marker trait associations, on four chromosomes (A10, D04, D05, and D06), showed significant epistatic interactions. Targeted genomic analysis identified regions with 19 candidate genes including Transcription factor Vascular Plant One-Zinc Finger 1 (VOZ1) and Protein Photoperiod-Independent Early Flowering 1 (PIE1) genes. Genetic diversity and genome wide analyses of photoperiod sensitivity in diverse cotton germplasms will enable the use of genomic tools to systematically utilize the tropical germplasm and its beneficial alleles for broadening the genetic base in Upland cotton.

Phenolic Biotransformations in Wheatgrass Juice after Primary and Secondary Fermentation.

Fermented wheatgrass juice was prepared using a two-stage fermentation process by employing Saccharomyces cerevisiae and recombinant Pediococcus acidilactici BD16 (alaD+). During fermentation, a reddish-brown hue appeared in wheatgrass juice due to production of different types of red pigments. The fermented wheatgrass juice has considerably higher content of anthocyanins, total phenols and beta-carotenes as compared to unfermented wheatgrass juice. It has low ethanol content, which might be ascribed to the presence of certain phytolignans in wheatgrass juice. Several yeast-mediated phenolic transformations (such as bioconversion of coumaric acid, hydroxybenzoic acid, hydroxycinnamic acid and quinic acid into respective derivatives; glycosylation and prenylation of flavonoids; glycosylation of lignans; sulphonation of phenols; synthesis of carotenoids, diarylnonanoids, flavanones, stilbenes, steroids, quinolones, di- and tri-terpenoids and tannin) were identified in fermented wheatgrass juice using an untargeted liquid chromatography (LC)-mass spectrometry (MS)-matrix-assisted laser desorption/ionization (MALDI)-time-of-flight (TOF)/time-of-flight (TOF) technique. The recombinant P. acidilactici BD16 (alaD+) also supported flavonoid and lignin glycosylation; benzoic acid, hydroxycoumaric acid and quinic acid derivatization; and synthesis of anthraquinones, sterols and triterpenes with therapeutic benefits. The information presented in this manuscript may be utilized to elucidate the importance of Saccharomyces cerevisiae and P. acidilactici BD16 (alaD+) mediated phenolic biotransformations in developing functional food supplements such as fermented wheatgrass juice.

Novel Wearable Optical Sensors for Vital Health Monitoring Systems-A Review.

Wearable sensors are pioneering devices to monitor health issues that allow the constant monitoring of physical and biological parameters. The immunity towards electromagnetic interference, miniaturization, detection of nano-volumes, integration with fiber, high sensitivity, low cost, usable in harsh environments and corrosion-resistant have made optical wearable sensor an emerging sensing technology in the recent year. This review presents the progress made in the development of novel wearable optical sensors for vital health monitoring systems. The details of different substrates, sensing platforms, and biofluids used for the detection of target molecules are discussed in detail. Wearable technologies could increase the quality of health monitoring systems at a nominal cost and enable continuous and early disease diagnosis. Various optical sensing principles, including surface-enhanced Raman scattering, colorimetric, fluorescence, plasmonic, photoplethysmography, and interferometric-based sensors, are discussed in detail for health monitoring applications. The performance of optical wearable sensors utilizing two-dimensional materials is also discussed. Future challenges associated with the development of optical wearable sensors for point-of-care applications and clinical diagnosis have been thoroughly discussed.

Current status of pesticide effects on environment, human health and it's eco-friendly management as bioremediation: A comprehensive review.

Pesticides are either natural or chemically synthesized compounds that are used to control a variety of pests. These chemical compounds are used in a variety of sectors like food, forestry, agriculture and aquaculture. Pesticides shows their toxicity into the living systems. The World Health Organization (WHO) categorizes them based on their detrimental effects, emphasizing the relevance of public health. The usage can be minimized to a least level by using them sparingly with a complete grasp of their categorization, which is beneficial to both human health and the environment. In this review, we have discussed pesticides with respect to their global scenarios, such as worldwide distribution and environmental impacts. Major literature focused on potential uses of pesticides, classification according to their properties and toxicity and their adverse effect on natural system (soil and aquatic), water, plants (growth, metabolism, genotypic and phenotypic changes and impact on plants defense system), human health (genetic alteration, cancer, allergies, and asthma), and preserve food products. We have also described eco-friendly management strategies for pesticides as a green solution, including bacterial degradation, myco-remediation, phytoremediation, and microalgae-based bioremediation. The microbes, using catabolic enzymes for degradation of pesticides and clean-up from the environment. This review shows the importance of finding potent microbes, novel genes, and biotechnological applications for pesticide waste management to create a sustainable environment.

An In Silico Investigation to Explore Anti-Cancer Potential of Foeniculum vulgare Mill. Phytoconstituents for the Management of Human Breast Cancer.

Breast cancer is one of the most prevalent cancers in the world. Traditionally, medicinal plants have been used to cure various types of diseases and disorders. Based on a literature survey, the current study was undertaken to explore the anticancer potential of Foeniculum vulgare Mill. phytoconstituents against breast cancer target protein (PDB ID: 6CHZ) by the molecular docking technique. Molecular docking was done using Autodock/vina software. Toxicity was predicted by the Protox II server and drug likeness was predicted by Molinspiration. 100 ns MD simulation of the best protein-ligand complexes were done using the Amber 18 tool. The present molecular docking investigation has revealed that among the 40 selected phytoconstituents of F. vulgare, α-pinene and D-limonene showed best binding energy (-6 and -5.9 kcal/mol respectively) with the breast cancer target. α-Pinene and D-limonene followed all the parameters of toxicity, and 100 ns MD simulations of α-pinene and D-limonene complexes with 6CHZ were found to be stable. α-Pinene and D-limonene can be used as new therapeutic agents to cure breast cancer.

Metallosurfactant based synthetic liposomes as a substitute for phospholipids to safely store curcumin.

Curcumin has shown remarkable therapeutic utilization for various medical conditions. Still, its limited chemical stability and rapid hydrolysis capped its applications to a certain extent. Approaches have been made in the past to surpass these shortcomings by encapsulating the drug in surfactant-based micelles or liposomes and so far, natural surfactants have been used to do this bidding. Through this report, we are presenting curcumin entrapped inside synthetic metal-based liposomal assembly (metallosomes) based on hybrid-surfactants known as metallosurfactants (MS). Three metallosomes i.e. metallosomes (a), (b), and (c) were synthesized with increasing cholesterol (Chl) ratio w.r.t MS (MS:Chl 1:0, 1:0.5, and 1:1). Firstly, the membrane properties of the metallosomes were studied in the absence of the drug. The studies confirmed the direct influence of Chl concentration on the membrane properties and the metallosomes were found to be more hydrophobic, rigid, homogenous, stable, and less fluid with Chl incorporation. These studies were proven beneficial when drug-loaded metallosomes were studied and metallosomes (c), with the highest Chl content, emerged as the maximum drug loader due to their most hydrophobic nature. However, the drug was released at the slowest rate for this metallosomal system due to its less fluid and more rigid nature. On the other hand, these metallosomes were more efficient for shielding entrapped drug from acidic and alkaline environs as lesser drug degradation was observed in the experiments compared to the free curcumin. These metallosomes also exhibited efficient interactional behavior with bacterial (MRSA) DNA.

Phytoconstituents of traditional Himalayan Herbs as potential inhibitors of Human Papillomavirus (HPV-18) for cervical cancer treatment: An In silico Approach.

Human papillomavirus (HPV) induced cervical cancer is becoming a major cause of mortality in women. The present research aimed to identify the natural inhibitors of HPV-18 E1 protein (1R9W) from Himalayan herbs with lesser toxicity and higher potency. In this study, one hundred nineteen phytoconstituents of twenty important traditional medicinal plants of Northwest Himalayas were selected for molecular docking with the target protein 1R9W of HPV-18 E1 Molecular docking was performed by AutoDock vina software. ADME/T screening of the bioactive phytoconstituents was done by SwissADME, admetSAR, and Protox II. A couple of best protein-ligand complexes were selected for 100 ns MD simulation. Molecular docking results revealed that among all the selected phytoconstituents only thirty-five phytoconstituents showed the binding affinity similar or more than the standard anti-cancer drugs viz. imiquimod (-6.1 kJ/mol) and podofilox (-6.9 kJ/mol). Among all the selected thirty-five phytoconstituents, eriodictyol-7-glucuronide, stigmasterol, clicoemodin and thalirugidine showed the best interactions with a docking score of -9.1, -8.7, -8.4, and -8.4 kJ/mol. Based on the ADME screening, only two phytoconstituents namely stigmasterol and clicoemodin selected as the best inhibitor of HPV protein. MD simulation study also revealed that stigmasterol and clicoemodin were stable inside the binding pocket of 1R9W, Stigmasterol and clicoemodin can be used as a potential investigational drug to cure HPV infections.

Design and applications of metallo-vesicular structures using inorganic-organic hybrids.

In advanced biomedical diagnosis, various supramolecular assemblies based on inorganic-organic hybrids have found great interest as functional materials. These assemblies describe a new field of metallovesicles where the introduction of metal ions enables the chemical manipulation of assemblies in terms of their structural stability, redox activity, and pH stability. Additionally, they mimic the elaborative architecture of natural liposomal assemblies and exhibit hierarchical morphologies, and promise novel functions. With the constant developments in this field, various supramolecular assemblies such as MCsomes, Polymersomes, and Metallosomes, etc. came into existence. These hybrid assemblies have been utilized for several applications such as drug delivery, MRI contrasting, DNA delivery, and catalytic activity. The key advantage of these assemblies is their ability to deliver therapeutics to specific locations due to their biomimetic properties and release their contents at the desired time. Hence, they provide a valuable platform for the treatment of a variety of diseases. Through the present article, we intend to provide insights into the latest developments made in this field. This modularity underscores the tremendous promise of supramolecular assemblies as an emerging interdisciplinary research branch at the interface of chemistry and biological sciences.

Biomedical applications of L-alanine produced by Pediococcus acidilactici BD16 (alaD+).

L-alanine possesses extensive physiological functionality and tremendous pharmacological significance, therefore could be considered as potential ingredient for food, pharmaceutical, and personal care products. However, therapeutic properties of L-alanine still need to be addressed in detail to further strengthen its utilization as a viable ingredient for developing natural therapeutics with minimum side effects. Thus, the present study was aimed to explore the anticipated therapeutic potential of L-alanine, produced microbially using a lactic acid bacterial strain Pediococcus acidilactici BD16 (alaD+) expressing L-alanine dehydrogenase enzyme. The anticipated therapeutic potential of L-alanine was assessed in terms of anti-proliferative, anti-bacterial, and anti-urolithiatic properties. Anti-bacterial assays revealed that L-alanine successfully inhibited growth and in vitro proliferation of important human pathogens including Enterococcus faecalis, Escherichia coli, Klebsiella pneumonia, Staphylococcus aureus, Streptococcus mutans, and Vibrio cholerae in a concentration-dependent manner. Current investigation has also revealed its significant anti-proliferative potential against human lung adenocarcinoma (A549; IC50 7.32 µM) and mammary gland adenocarcinoma (MCF-7; IC50 8.81 µM) cells. The anti-urolithiatic potential of L-alanine was augmented over three different phases, viz., nucleation inhibition, aggregation inhibition, and oxalate depletion. Further, an in vitro cell culture-based kidney stone dissolution model using HEK293-T cells was also established to further strengthen its anti-urolithiatic potential. This is probably the first in vitro cell culture-based model which experimentally validates the immense therapeutic efficacy of L-alanine in treating urolithiasis disease. KEY POINTS: • Assessment of therapeutic potential of L-alanine produced by LAB. • L-alanine exhibited significant anti-proliferative and anti-bacterial activities. • L-alanine as potential anti-urolithiatic agent.

Recent advancements in optical biosensors for cancer detection.

Optical biosensors are rapid, real-time, and portable, have a low detection limit and a high sensitivity, and have a great potential for diagnosing various types of cancer. Optical biosensors can detect cancer in a few million malignant cells, in comparison to conventional diagnosis techniques that use 1 billion cells in tumor tissue with a diameter of 7 nm-10 nm. Current cancer detection methods are also costly, inconvenient, complex, time consuming, and require technical specialists. This review focuses on recent advances in optical biosensors for early detection of cancer. It is primarily concerned with advancements in the design of various biosensors using resonance, scattering, chemiluminescence, luminescence, interference, fluorescence, absorbance or reflectance, and various fiber types. The development of various two-dimensional materials with optical properties such as biocompatibility, field enhancement, and a higher surface-to-volume ratio, as well as advancements in microfabrication technologies, have accelerated the development of optical sensors for early detection of cancer and other diseases. Surface enhanced Raman spectroscopy technology has the potential to detect a single molecule with high specificity, and terahertz waves are a recently explored technology for cancer detection. Due to the low electromagnetic interference, small size, multiplexing, and remote sensing capabilities of optical fiber-based platforms, they may be a driving force behind the rapid development of biosensors. The advantages and disadvantages of existing and future optical biosensor designs for cancer detection are discussed in detail. Additionally, a prospect for future advancements in the development of optical biosensors for point-of-care and clinical applications is highlighted.

Production of Functional Buttermilk and Soymilk Using Pediococcus acidilactici BD16 (alaD+).

Functional foods or drinks prepared using lactic acid bacteria (LAB) have recently gained considerable attention because they can offer additional nutritional and health benefits. The present study aimed to develop functional drinks by the fermentation of buttermilk and soymilk preparations using the Pediococcus acidilactici BD16 (alaD+) strain expressing the L-alanine dehydrogenase enzyme. LAB fermentation was carried out for 24 h and its impact on the physicochemical and quality attributes of the fermented drinks was evaluated. Levels of total antioxidants, phenolics, flavonoids, and especially L-alanine enhanced significantly after LAB fermentation. Further, GC-MS-based metabolomic fingerprinting was performed to identify the presence of bioactive metabolites such as 1,2-benzenedicarboxylic acid, 1-dodecene, 2-aminononadecane, 3-octadecene, 4-octen-3-one, acetic acid, azanonane, benzaldehyde, benzoic acid, chloroacetic acid, colchicine, heptadecanenitrile, hexadecanal, quercetin, and triacontane, which could be accountable for the improvement of organoleptic attributes and health benefits of the drinks. Meanwhile, the levels of certain undesirable metabolites such as 1-pentadecene, 2-bromopropionic acid, 8-heptadecene, formic acid, and propionic acid, which impart bitterness, rancidity, and unpleasant odor to the fermented drinks, were reduced considerably after LAB fermentation. This study is probably the first of its kind that highlights the application of P. acidilactici BD16 (alaD+) as a starter culture candidate for the production of functional buttermilk and soymilk.

Metabolic Engineering of Pediococcus acidilactici BD16 for Heterologous Expression of Synthetic alaD Gene Cassette and L-Alanine Production in the Recombinant Strain Using Fed-Batch Fermentation.

Metabolic engineering substantially aims at the development of more efficient, robust and industrially competitive microbial strains for the potential applications in food, fermentation and pharmaceutical industries. An efficient lab scale bioprocess was developed for high level fermentative production of L-alanine using metabolically engineered Pediococcus acidilactici BD16 (alaD+). Computational biology tools assisted the designing of a synthetic alaD gene cassette, which was further cloned in shuttle vector pLES003 and expressed using an auto-inducible P289 promoter. Further, L-alanine production in the recombinant P. acidilactici BD16 (alaD+) strain was carried out using fed-batch fermentation under oxygen depression conditions, which significantly enhanced L-alanine levels. The recombinant strain expressing the synthetic alaD gene produced 229.12 g/L of L-alanine after 42 h of fed-batch fermentation, which is the second highest microbial L-alanine titer reported so far. After extraction and crystallization, 95% crystal L-alanine (217.54 g/L) was recovered from the culture broth with an enantiomeric purity of 97%. The developed bioprocess using recombinant P. acidilactici BD16 (alaD+) is suggested as the best alternative to chemical-based commercial synthesis of L-alanine for potential industrial applications.

Metagenomic analysis exploring taxonomic and functional diversity of bacterial communities of a Himalayan urban fresh water lake.

Freshwater lakes present an ecological border between humans and a variety of host organisms. The present study was designed to evaluate the microbiota composition and distribution in Dal Lake at Srinagar, India. The non-chimeric sequence reads were classified taxonomically into 49 phyla, 114 classes, 185 orders, 244 families and 384 genera. Proteobacteria was found to be the most abundant bacterial phylum in all the four samples. The highest number of observed species was found to be 3097 in sample taken from least populated area during summer (LPS) whereas the summer sample from highly populated area (HPS) was found most diverse among all as indicated by taxonomic diversity analysis. The QIIME output files were used for PICRUSt analysis to assign functional attributes. The samples exhibited a significant difference in their microbial community composition and structure. Comparative analysis of functional pathways indicated that the anthropogenic activities in populated areas and higher summer temperature, both decrease functional potential of the Lake microbiota. This is probably the first study to demonstrate the comparative taxonomic diversity and functional composition of an urban freshwater lake amid its highly populated and least populated areas during two extreme seasons (winter and summer).

Anticancer Effects of Extracts from Three Different Chokeberry Species.

Colon cancer risk appears to be lowered by consumption of a diet rich in fruits and vegetables. Chokeberries are rich in phytochemicals that may act as potent anticancer agents. Phytochemicals that are particularly abundant in chokeberries include anthocyanins and phenolic acids. In this study, we compared the growth inhibitory activity of three chokeberry extracts in HT-29 human colon cancer cells. The three extracts tested were derived from Aronia arbutifolia (red), Aronia prunifolia (purple), and Aronia melanocarpa (black). Cells were incubated with either red, purple, or black chokeberry extracts and cell viability was quantified using the thiazolyl blue tetrazolium bromide (MTT) assay. The black chokeberry extract had the greatest effect in reducing cell proliferation. The extracts were also characterized for total phenols (Folin-Ciocalteu assay), total antioxidant activity (oxygen radical absorbance capacity assay), and levels of bioactive phenolic acids (high-performance liquid chromatography). The growth inhibitory activities of the extracts correlated well with total phenolic content, antioxidant activity, and levels of caffeic and chlorogenic acids. The black chokeberry extract had the greatest level of total phenols, antioxidant activity, and individual phenolic acids. This research suggests that the phenolic profile of foods such as chokeberries can help determine their cancer cell growth inhibitory activity.

Response surface optimization of cellulase production from Aneurinibacillus aneurinilyticus BKT-9: An isolate of urban Himalayan freshwater.

Due to their vast industrial potential, cellulases have been regarded as the potential biocatalysts by both the academicians and the industrial research groups. In the present study, culturable bacterial strains of Himalayan Urban freshwater lake were investigated for cellulose degrading activities. Initially, a total of 140 bacterial strains were isolated and only 45 isolates were found to possess cellulose degrading property. On the basis of preliminary screening involving cellulase activity assay on CMC agar (with clear zone of hydrolysis) and biosafety assessment testing, only single isolate named as BKT-9 was selected for the cellulase production studies. Strain BKT-9 was characterized at the molecular level using rRNA gene sequencing and its sequence homology analysis revealed its identity as Aneurinibacillus aneurinilyticus. Further, various physico-chemical parameters and culture conditions were optimized using one factor approach to enhance cellulase production levels in the strain BKT-9. Subsequently, RSM based statistical optimization led to formulation of cellulase production medium, wherein the bacterial strain exhibited ~60 folds increase in enzyme activity as compared to un-optimized culture medium. Further studies are being suggested to scale up cellulase production in A. aneurinilyticus strain BKT-9 so that it can be utilized for biomass saccharification at an industrial level.

Correction to: Construction of a shuttle expression vector for lactic acid bacteria.

An amendment to this paper has been published and can be accessed via the original article.

Tailoring cellular metabolism in lactic acid bacteria through metabolic engineering.

Metabolic engineering combines approaches of synthetic and systems biology for tailoring the existing and creating novel biosynthetic metabolic pathways in the desired industrial microorganisms for production of biofuels, bio-materials and environmental applications. Lactic acid bacteria (LAB) are gaining attention worldwide due to their extensive utilization in food, fermentation and pharmaceutical industries owing to their GRAS status. Well-elucidated genetics and regulatory control of central metabolism make them potential candidates for the production of industrially valuable metabolites. With the recent advancements in metabolic engineering strategies, genetic manipulation and tailoring of cellular metabolism is being successfully carried out in various LAB strains as they are providing highly efficient and industrially competitive robust expression systems. Thus, this review presents a concise overview of metabolic engineering strategies available for the comprehensive tailoring of lactic acid bacterial strains for large-scale production of industrially important metabolites.

Construction of a shuttle expression vector for lactic acid bacteria.

BACKGROUND: Lactic acid bacteria (LAB) are a diverse group of Gram-positive bacteria, which are widely distributed in various diverse natural habitats. These are used in a variety of industrial food fermentations and carry numerous traits with utmost relevance to the food industry. Genetic engineering has emerged as an effective means to improve and enhance the potential of commercially important bacterial strains. However, the biosafety of recombinant systems is an important concern during the implementation of such technologies on an industrial scale. In order to overcome this issue, cloning and expression systems have been developed preferably from fully characterized and annotated LAB plasmids encoding genes with known functions. RESULTS: The developed shuttle vector pPBT-GFP contains two theta-type replicons with a copy number of 4.4 and 2.8 in Pediococcus acidilactici MTCC 5101 and Lactobacillus brevis MTCC 1750, respectively. Antimicrobial "pediocin" produced by P. acidilactici MTCC 5101 and green fluorescent protein (GFP) of Aequorea victoria were successfully expressed as selectable markers. Heterologous bile salt hydrolase (BSH) from Lactobacillus fermentum NCDO 394 has been efficiently expressed in the host strains showing high specific activity of 126.12 ± 10.62 in P. acidilactici MTCC 5101 and 95.43 ± 4.26 in the case of L. brevis MTCC 1750, towards glycine-conjugated bile salts preferably as compared to taurine-conjugated salts. CONCLUSION: The present article details the development of a LAB/LAB shuttle expression vector pPBT-GFP, capable of replication in LAB hosts, P. acidilactici MTCC 5101, and L. brevis MTCC 1750. Pediocin and GFP have been used as selectable markers with the efficient production of heterologous extracellular bile salt hydrolase. Thus, the constructed vector pPBT-GFP, with its ability to replicate in multiple hosts, low copy number, and stability in host cells, may serve as an ideal tool for improving LAB strains of commercial value using genetic engineering.