REVIEW | doi:10.20944/preprints202011.0637.v1
Subject: Chemistry And Materials Science, Nanotechnology Keywords: Bioremediation; Nanomaterials; Biosynthetic; Sustainable; Ecofriendly
Online: 25 November 2020 (12:14:51 CET)
Nanoparticles are widely used in the agricultural sector because of their distinctive properties. Studies have shown the influence of nanoparticles on plant growth and production. Nanoparticles act as effective carriers in the delivery of agrochemicals to plants. They provide site targeted delivery of nutrients and thus, prevents wastage of nutrients applied for plant growth and productivity. Bioremediation of pollutants is an emerging technology that provides bio-nano materials for the protection of agriculture from pollution. The aim of this review is to present and focus on the latest techniques used for the reduction of environmental pollution and improved agricultural production. This review speculates about the biosynthesis of nanomaterials from different sources like plants, fungi, and bacteria along with chemical and organic synthesis from carbon, silver, and gold. The role of nanoscience in detecting plant diseases and the removal of heavy metals. Application of Nanoscience in storing, production, processing, and transport of agricultural materials. It is also emphasized that Nanoscience may transform agriculture through the innovation of new techniques like Precision farming, improvement of plants to engross nutrients, targeted use of inputs, detection and control of diseases and withstand environmental pressures. Further, efforts have been made in describing that nanoparticles may act as a better substitute for agricultural plant growth and nutrition improvement by lowering the content of pollutants and pre-detection of diseases in plants. The biosynthetic route of nanomaterial synthesis could emerge as a better and safer option for environmental pollution reduction. Thus, nanoscience may increase agricultural production to feed a huge population in near future.
CONCEPT PAPER | doi:10.20944/preprints202011.0250.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: antibiotic discovery; STEM education; biosynthetic gene cluster; molecular networking; multi-omics
Online: 6 November 2020 (16:50:46 CET)
The world faces two seemingly unrelated challenges—a shortfall in the STEM workforce and increasing antibiotic resistance among bacterial pathogens. We address these two challenges with Tiny Earth, an undergraduate research course that excites students about science and creates a pipeline for antibiotic discovery.
ARTICLE | doi:10.20944/preprints202310.1564.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Biosynthetic Gene Clusters; Natural Language Processing; Machine Learning; Hybrids PKS-NRPS; SMOTE
Online: 25 October 2023 (11:36:13 CEST)
Biosynthetic gene clusters are specific genomic regions in microorganisms, like bacteria and fungi, responsible for producing bioactive compounds. Identifying these clusters is complex due to their diverse nature. This research presents a comprehensive approach to effective BGC identification. The study focuses on five classes of Natural Products: PKS , NRPS, RiPP, Terpenes, and Hybrid PKS-NRPS. Data was gathered from the MiBIG database in GBK format. Protein sequences from each file were extracted, and sequences under the same BGC ID were combined. Physicochemical properties were calculated, and sequence embeddings were generated using NLP techniques like CountVec, TFIDF, and Word2Vec specific to each NP class. An integrated feature matrix was created by merging physicochemical properties and generated embeddings. This matrix was used for training and testing of nine ML models such SVM, RF and many more. The study explored data balancing techniques with and without SMOTE and employed Grid Search for parameter optimization. This led to six datasets and 54 models. The LR model, using TFIDF with SMOTE, emerged as the most effective, achieving an accuracy of 0.96, AUC of 0.9912, and other strong metrics. This method enhances BGC identification for drug development, offering a broader understanding of their applications in medicine and biotechnology.
ARTICLE | doi:10.20944/preprints202208.0133.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Abscisic acid biosynthetic genes; aquaporins; Biofilm forming bacteria; growth traits; oxidative injury; Tomato
Online: 8 August 2022 (05:48:17 CEST)
Use of rhizosphere microorganisms provides an alternative or supplement to conventional plant breeding to improve water deficit tolerance of tomato plants. Experiment was carried out to explore the effect of two microbial species, AMF (Rhizophagus irregularis) and Bacillus subtilis, in single and co-application, on growth, colonization, and molecular aspects of tomato plants under drought stress. Co-inoculated plants showed less reduction in growth traits, photosynthetic pigments, colonization rate, and increased compatible solutes like proline which help in sustaining relative water content than non-inoculated plants. Inoculation considerably enhanced proline dehydrogenase activity, and significantly reduced both Δ1-pyrroline-5-carboxylate reductase Δ1-pyrroline-5-carboxylate synthetase activity causing lower proline accumulation in inoculated plants under drought stress. Co-inoculated plants showed obvious upregulation of antioxidant system, thus facilitating amelioration of oxidative stress through exclusion of reactive oxygen species. No inoculation under drought stress upregulated abscisic acid related genes expression but have no effect in plants inoculated either sole or mixed inoculation. Expression of aquaporin genes was upregulated in plants co-inoculated and with AMF alone under normal condition. However the expression of aquaporin genes were decreased or unaffected in plants inoculated with Bacillus subtilis but increased in non-inoculated plants. Co-applied AMF and bacillus subtilis substantially increase drought tolerance by upregulating proline metabolism, antioxidant enzymes and aquaporin genes. Therefore our results suggest that co-inoculation mediated drought tolerance is linked with increased proline accumulation, enhanced antioxidant enzyme activities and differential regulation of ABA biosynthetic and aquaporin genes, which is vital for osmotic adjustment of host plant.
ARTICLE | doi:10.20944/preprints202002.0388.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Biosynthetic gene clusters; Eurotium rubrum; halophilic; marine genomics; nonribosomal peptide synthetase; T1pks; Terpene
Online: 26 February 2020 (10:58:18 CET)
Eurotium rubrum is a halophilic marine ascomycete, which can bear the hypersalinities of the Red Sea and proliferate, while most living entities cannot bear this condition. Recently, a 26.2 Mb assembled genome of this fungus had become available. Marine fungi are fascinating organisms capable of harboring several biosynthetic gene clusters (BGCs), which enables them to produce several natural compounds with antibiotic and anticancerous properties. Understanding the BGCs are critically important for the development of biotechnological applications and the discovery of future drugs. There is no knowledge available on the BGCs of this halophilic marine ascomycete. Herein, we set out to explore and characterize BGCs and the corresponding genes from E. rubrum using bioinformatic methods. We deciphered 36 BGCs in the genome of E. rubrum. These 36 BGCs can be grouped into four non-ribosomal peptide synthetase (NRPS) clusters, eight NRPS-like (NRPSL) BGCs, eight type I polyketide synthase (T1PKS), 11 terpene BGCs including one β-lactone cluster, four hybrid BGCs, and two siderophore BGCs. This study is an example of marine genomics application into potential future drug-like compound discovery.
ARTICLE | doi:10.20944/preprints202304.1259.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: rice false smut; quantitative loop-mediated isothermal amplification (q-LAMP); detection; ustiloxins biosynthetic gene
Online: 30 April 2023 (04:40:34 CEST)
Rice false smut caused by Ustilaginoidea virens is one of the most devastating diseases on rice worldwide, which results in serious reduction of rice quality and yield. As an airborne fungal disease, early diagnosis of rice false smut, monitoring the epidemics and distribution of its pathogens, is particularly important to management the infection. In this study, a quantitative loop-mediated isothermal amplification (q-LAMP) method for the U. virens detection and quantifying was developed. This method has higher sensitivity and efficiency compared to quantitative real-time PCR (q-PCR) method. The species-specific primer sets UV-2 used was design based on the unique sequence of U. virens ustiloxins biosynthetic gene (NCBI accession number: BR001221.1). The q-LAMP assay was able to detect a concentration of 6.4 spores/mL at an optimal reaction temperature of 63.4℃ within 60 min. Moreover, the q-LAMP assay can even achieve accurate quantitative detection when there were only 9 spores on the tape. A linearized equation for the standard curve, y =-0.2866x + 13.829 (x is the amplification time, the spore number = 100.65y), was established for detection and quantifying of U. virens. In field detection applications, this q-LAMP method is more accurate and faster than traditional observation method. Collectively, this study has established a powerful and simple monitoring tool for U. virens, which provide valuable technical supports for forecast and management of rice false smut, and theoretical basis for precise fungicide application.
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: natural products; biosynthetic gene clusters; synthetic biology; genome mining strategies; modification strategies; design-build-test-learn (DBTL) cycle
Online: 8 October 2021 (09:10:02 CEST)
A wide variety of bacteria, fungi and plants can produce bioactive secondary metabolites, which are often referred to as natural products. With the rapid development of DNA sequencing technology and bioinformatics, a large number of putative biosynthetic gene clusters have been reported. However, only a few natural products can be detected when isolated species are grown under conventional laboratory conditions, as most biosynthetic gene clusters are not expressed or are expressed at extremely low levels at these conditions. With the rapid development of synthetic biology, advanced genome mining and modification strategies have been reported, and they provide new opportunities for discovery of natural products. This review discusses advances in recent years that can accelerate the design, build, test, and learn (DBTL) cycle of natural product discovery, and prospects trends and key challenges for future research directions.
ARTICLE | doi:10.20944/preprints201912.0399.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: natural product; actinobacteria; quorum sensing inhibition (QSI); biosynthetic gene clusters (BGCs); global natural product social networking (GNPS); cyclic dipeptides (2,5-diketopiperazines, DKPs); LC-HRMS
Online: 31 December 2019 (02:59:59 CET)
Streptomyces, being one of the most promising genera due to its ability to synthesize a variety of bioactive secondary metabolites of pharmaceutical interest, here studied in relation to its genomic and metabolomic potential. Coinciding with the increase in sequenced data, mining of bacterial genomes for biosynthetic gene clusters (BGCs) has become a routine component of natural product discovery. Herein, we describe the isolation and characterization of a Streptomyces tendae VITAKN with quorum sensing inhibitory activity (QSI) that was isolated from southern coastal parts of India. The nearly complete genome consists of 8,621,231bp with a GC content of 72.2%. Utilizing the BiG-SCAPE-CORASON platform, a sequence similarity network predicted from this strain was evaluated through sequence similarity analysis with the MIBiG database and existing 3,365 BGCs predicted by antiSMASH analysis of publicly available complete Streptomyces genomes. Crude extract analyzed on LC-HRMS/MS and Global Natural Product Social Molecular Networking (GNPS) online workflow using dereplication resulted in the identification of cyclic dipeptides (2,5-diketopiperazines, DKPs) in the extract, which are known to possess QSI activity. Our results highlight the potential use of genomic mining coupled with LC-HRMS/MS and bionformatic tools (GNPS) as a potent approach for metabolome studies in discovering novel QSI lead compounds. This study also provides the biosynthetic diversity of these BGCs and an assessment of the predicted chemical space yet to be discovered.
ARTICLE | doi:10.20944/preprints201702.0022.v1
Subject: Physical Sciences, Optics And Photonics Keywords: Cupriavidus necator; E. coli; bofermentors; biosensors; growth phase; biosynthetic pathways; P(3HB); PHB: polyhydroxybutyrate,; spectrofluorometry; SERS: Surface Enhanced Raman Spectroscopy; turbidity as optical density (OD)
Online: 8 February 2017 (09:31:07 CET)
Polyhydroxyalcanoates (PHAs) are biodegradable polymers synthesized in cytoplasmic granules in bacteria, such as Cupriavidus necator (Ralstonia eutropha), Alcaligenes latus, Pseudomonas spp., Comamonas spp. and other species. PHAs accumulation occurs in response to stress conditions, i.e. under high carbon and low nitrogen (24:1 ratio). PHA can be synthesized using recombinant microorganisms (provided with the operon phbA/phbB/phbC), escaping the constrains of nutrient request, except addition of high amount of sugar (glucose, lactose, fructose). In this study; E. coli was genetically modified for PHB production in biofermentors. The production of PHA at industrial scale requires a continuous supplementation of fermentable sugars to support the availability of nutrients and to assess the level of the exponential growth phase; since sugars are required either for bacterial growth either for PHA synthesis and energy storage. The biofermentors need to be run in automated system. Sensors are used at many points in fermentators; in the evaluation of parameters: consumption of sugars; cell density; quantification of PHB synthesis. The need of operational control during the fermentation has prompted us to application of three measurements; one unit linked to a Nanodrop to evaluate OD; one linked to a reaction chamber to measure sugars consumed by enzyme based fluorescence detection; and one for bacteria Nile Blue staining and fluorescence intensity reads. The growth of bacteria on three different plant by-products was monitored and PHB production in four days using a banana by-product feed was optimised. These detectors will make possible to exploit the full potential of bioreactors optimizing the time of use and maximizing the number of bacteria synthesizing PHA.