scholarly journals Current analytical technologies and bioinformatic resources for plant metabolomics data

2021 ◽  
Author(s):  
Chigateri M. Vinay ◽  
Sanjay Kannath Udayamanoharan ◽  
Navya Prabhu Basrur ◽  
Bobby Paul ◽  
Padmalatha S. Rai
Keyword(s):  
Inorganic Compounds ◽  
Biological Data ◽  
Biological Information ◽  
Metabolomics Data ◽  
Primary And Secondary Metabolites ◽  
Chemical Structures ◽  
Plant Metabolomics ◽  
Wide Range ◽  
Analytical Tools

AbstractPlant metabolome as the downstream product in the biological information of flow starting from genomics is highly complex, and dynamically produces a wide range of primary and secondary metabolites, including ionic inorganic compounds, hydrophilic carbohydrates, amino acids, organic compounds, and compounds associated with hydrophobic lipids. The complex metabolites present in biological samples bring challenges to analytical tools for separating and characterization of the metabolites. Analytical tools such as nuclear magnetic resonance (NMR) and mass spectrometry have recently facilitated the separation, characterization, and quantification of diverse chemical structures. The massive amount of data generated from these analytical tools need to be handled using fast and accurate bioinformatics tools and databases. In this review, we focused on plant metabolomics data acquisition using various analytical tools and freely available workflows from raw data to meaningful biological data to help biologists and chemists to move at the same pace as computational biologists.

scholarly journals Mass spectrometry as a quantitative tool in plant metabolomics

2016 ◽  
Vol 374 (2079) ◽  
pp. 20150370 ◽  
Author(s):  
Tiago F. Jorge ◽  
Ana T. Mata ◽  
Carla António
Keyword(s):  
Mass Spectrometry ◽  
Chemical Species ◽  
Chemical Properties ◽  
Research Field ◽  
Plant Metabolomics ◽  
Wide Range ◽  
Metabolite Pool ◽  
Development And Validation ◽  
Analytical Tools ◽  
Quantitative Tool

Metabolomics is a research field used to acquire comprehensive information on the composition of a metabolite pool to provide a functional screen of the cellular state. Studies of the plant metabolome include the analysis of a wide range of chemical species with very diverse physico-chemical properties, and therefore powerful analytical tools are required for the separation, characterization and quantification of this vast compound diversity present in plant matrices. In this review, challenges in the use of mass spectrometry (MS) as a quantitative tool in plant metabolomics experiments are discussed, and important criteria for the development and validation of MS-based analytical methods provided. This article is part of the themed issue ‘Quantitative mass spectrometry’.

scholarly journals Recent advances in melanin-like nanomaterials in biomedical applications: a mini review

2019 ◽  
Vol 23 (1) ◽  
Author(s):  
Jihyo Park ◽  
Haeram Moon ◽  
Seonki Hong
Keyword(s):  
Biomedical Applications ◽  
Near Infrared ◽  
Inflammatory Diseases ◽  
Photoacoustic Imaging ◽  
Radical Scavenging ◽  
Main Body ◽  
Photothermal Conversion ◽  
Chemical Structures ◽  
Wide Range ◽  
Analytical Tools

Abstract Background Melanins are a group of biopigments in microorganisms that generate a wide range of colorants. Due to their multifunctionality, including ultraviolet protection, radical scavenging, and photothermal conversion, in addition to their intrinsic biocompatibility, natural melanins and synthetic melanin-like nanomaterials have been suggested as novel nano-bio platforms in biomedical applications. Main body Recent approaches in the synthesis of melanin-like nanomaterials and their biomedical applications have briefly been reviewed. Melanin-like nanomaterials have been suggested as endogenous chromophores for photoacoustic imaging and radical scavengers for the treatment of inflammatory diseases. The photothermal conversion ability of these materials under near-infrared irradiation allows hyperthermia-mediated cancer treatments, and their intrinsic fluorescence can be an indicator in biosensing applications. Furthermore, catechol-rich melanin and melanin-like nanomaterials possess a versatile affinity for various functional organic and inorganic additives, allowing the design of multifunctional hybrid nanomaterials that expand their range of applications in bioimaging, therapy, theranostics, and biosensing. Conclusion Melanin-like natural and synthetic nanomaterials have emerged; however, the under-elucidated chemical structures of these materials are still a major obstacle to the construction of novel nanomaterials through bottom-up approaches and tuning the material properties at the molecular level. Further advancements in melanin-based medical applications can be achieved with the incorporation of next-generation chemical and molecular analytical tools.

Ethnobotany, Phytochemistry and Traditional Uses of Curcuma spp. and Pharmacological Profile of Two Important Species (C. longa and C. zedoaria): A Review

2019 ◽  
Vol 25 (8) ◽  
pp. 871-935 ◽  
Author(s):  
Zahra Ayati ◽  
Mahin Ramezani ◽  
Mohammad Sadegh Amiri ◽  
Ali Tafazoli Moghadam ◽  
Hoda Rahimi ◽  
...  
Keyword(s):  
Phenolic Compounds ◽  
Animal Studies ◽  
Inorganic Compounds ◽  
Modern Medicine ◽  
Important Species ◽  
Chemical Structures ◽  
Wide Range ◽  
Anti Inflammatory

Ethnopharmacological relevance: The genus Curcuma, which is the most important source of curcumin, has been widely used in different traditional medicines. Various species of Curcuma have long been used for several purposes such as healing wounds, liver disorders, jaundice and also as a blood purifier. Aim of the study: This review focused on the ethnopharmacological uses and phytochemical aspects of Curcuma. Additionally, in this study, the different properties of two species of Curcuma in Islamic Traditional Medicine (ITM), C. longa and C. zedoaria, as well as their pharmacological aspects in modern medicine are reviewed. Materials and methods: ITM literatures were searched to find Curcuma’s applications. Also, electronic databases including PubMed and Scopus were searched to obtain studies giving any in vitro, in vivo or human evidence of the efficacy of C. longa and C. zedoaria in the treatment of different diseases. ChemOffice software was used to find chemical structures. Results: The analysis showed that ethno-medical uses of Curcuma have been recorded for centuries. Approximately, 427 chemical compounds have been isolated and identified from Curcuma spp. This genus is rich in flavonoids, tannins, anthocyanin, phenolic compounds, oil, organic acids and inorganic compounds. Curcumin is one of the main active ingredients in Curcuma which has strong anti-inflammatory and antioxidant effects. Besides, pharmacological studies have indicated wide range of Curcuma’s activities, such as hepato-protective, antifungal, antihypertensive and neuroprotective. Conclusions: In this study, we reviewed various studies conducted on ethno-medicinal, ITM properties and photochemistry of Curcuma spp. Also, pharmacological activities of two species, C. longa and C. zedoaria are summarized. Pre-clinical investigations have demonstrated some of the traditional aspects of Curcuma, such as wound healing, anti-arthritic, anti-tumor and liver protective activities. These could be related to antioxidant and anti-inflammatory properties of Curcuma which might be due to high amounts of phenolic compounds. Curcuma is mentioned to have neural tonic properties in ITM which have been confirmed by some animal studies. Considering various preclinical studies on C. longa and C. zedoaria and their active ingredient, curcumin, randomized controlled trials are warranted to confirm their promise as a clinically effective hepato and neuro-protective agents.

scholarly journals Integração de parâmetros geomorfológicos e biológicos no desenvolvimento do Índice Integrado de Sensibilidade do Litoral (IISL) (Integration of geomorphological and biological parameters to develop a Coastal Integrated Sensitivity Index (CISI))

2019 ◽  
Vol 12 (4) ◽  
pp. 1509 ◽  
Author(s):  
Chayonn Marinho ◽  
João Luiz Nicolodi
Keyword(s):  
Oil Spills ◽  
Oil Industry ◽  
Biological Data ◽  
Biological Information ◽  
Sensitivity Index ◽  
Substrate Type ◽  
South Of Brazil ◽  
Pelotas Basin ◽  
Integrated Sensitivity

No contexto da indústria petrolífera e suas relações com os ecossistemas enquadram-se os instrumentos de políticas públicas, desenvolvidos a fim de prevenir e minimizar os efeitos de acidentes com óleo e derivados, como as Cartas de Sensibilidade Ambiental ao Derramamento de Óleo (Cartas SAO). Dentre as principais informações contidas nas Cartas SAO está o Índice de Sensibilidade do Litoral (ISL). Este índice mede a sensibilidade dos diferentes ambientes costeiros ao contato com óleo de acordo com as características geomorfológicas da região: exposição às forçantes hidrodinâmicas, tipo de substrato e declividade do litoral. Nesse estudo foi desenvolvida uma metodologia específica que integrou dados geomorfológicos e biológicos no desenvolvimento de um Índice Integrado de Sensibilidade do Litoral (IISL). Tal metodologia desenvolveu previamente dois índices distintos, o Índice Geomorfológico de Sensibilidade (IG) e o Índice Biológico de Sensibilidade (IB), os quais tiveram suas variáveis bem definidas permitindo a integração para desenvolvimento do IISL. Três regiões da Bacia de Pelotas, sul do Brasil, foram escolhidas para a aplicação dessa metodologia. Os resultados indicaram alteração nos valores de sensibilidade ao óleo em seis trechos de linha de costa analisados, apurando o mapeamento destas áreas. Assim, o presente estudo buscou apresentar elementos que venham subsidiar o aprimoramento metodológico de mapeamento de sensibilidade ao óleo no país, contribuindo na gestão de incidentes e no gerenciamento costeiro.   A B S T R A C TIn the context of oil industry and its relations with ecosystems the instruments of public policy are framed, which are developed to prevent and minimize the effects accidents involving oil and its derivatives, such as the Environmental Sensibility to Oil (ESO charts). The main information in the ESO charts is the Coastal Integrated Sensitivity Index (CISI), which measures the sensitivity of different coastal environments to contact with oil according to geomorphological characteristics, such as exposure to hydrodynamic forces, substrate type and coastal slope. The concept of sensibility used for the characterization of the coastline does not include in its methodological scope biological information, therefore, a new specific methodology was developed, which integrated geomorphological and biological data to develop a Coastal Integrated Sensitivity Index (CISI). This methodology previously developed two different indexes, the Geomorphological Sensitivity Index (GSI) and Biological Sensitivity Index (BSI), which had their well-defined variables allowing the integration of CISI. Three regions of the Pelotas Basin, south of Brazil, were chosen to test this methodology. The results indicated a change in sensibility values in six coastline segments analyzed, improving the mapping of these áreas. This way, the present study effectively contributed to upgrade the methodology for mapping the sensibility to oil spills, also contributing on the management of accidents involving oil and on coastal management.Keyword: Oil spill, ESO charts, coastal sensitivity, biological and geomorphological data.

Integration of Multi-omics Data Using Probabilistic Graph Models and External Knowledge

2021 ◽  
Vol 16 ◽  
Author(s):  
Bridget A. Tripp ◽  
Hasan H. Otu
Keyword(s):  
Information Integration ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Biological Data ◽  
Biological Information ◽  
Functional Networks ◽  
Omics Data ◽  
Metabolomics Data ◽  
External Knowledge ◽  
Omics Integration

Background: High-throughput sequencing technologies have revolutionized the ability to perform systems-level biology and elucidate molecular mechanisms of disease through the comprehensive characterization of different layers of biological information. Integration of these heterogeneous layers can provide insight into the underlying biology but is challenged by modeling complex interactions. Objective: We introduce OBaNK: omics integration using Bayesian networks and external knowledge, an algorithm to model interactions between heterogeneous high-dimensional biological data to elucidate complex functional clusters and emergent relationships associated with an observed phenotype. Method: Using Bayesian network learning, we modeled the statistical dependencies and interactions between lipidomics, proteomics, and metabolomics data. The strength of a learned interaction between molecules was altered based on external knowledge. Results : Networks learned from synthetic datasets based on real pathways achieved an average area under the curve score of ~0.85, an improvement of ~0.23 from baseline methods. When applied to real multi-omics data collected during pregnancy, five distinct functional networks of heterogeneous biological data were identified, and the results were compared to other multi-omics integration approaches. Conclusion: OBaNK successfully improved the accuracy of learning interaction networks from data integrating external knowledge, identified heterogeneous functional networks from real data, and suggested potential novel interactions associated with the phenotype. These findings can guide future hypothesis generation. OBaNK source code is available at https://github.com/bridgettripp/OBaNK.git, and a graphical user interface is available at http://otulab.unl.edu/OBaNK.

Fault Tolerant Reliable Protocol (FTRP) Performance Evaluation in Wireless Sensor Networks: An Extensitive Study

2019 ◽  
pp. 1-36
Keyword(s):  
Wireless Sensor Networks ◽  
Fault Tolerance ◽  
Sensor Networks ◽  
Fault Tolerant ◽  
Cluster Head ◽  
Biological Data ◽  
Wireless Sensor ◽  
Delivery Ratio ◽  
Good Performer ◽  
Wide Range

Fault Tolerant Reliable Protocol (FTRP) is proposed as a novel routing protocol designed for Wireless Sensor Networks (WSNs). FTRP offers fault tolerance reliability for packet exchange and support for dynamic network changes. The key concept used is the use of node logical clustering. The protocol delegates the routing ownership to the cluster heads where fault tolerance functionality is implemented. FTRP utilizes cluster head nodes along with cluster head groups to store packets in transient. In addition, FTRP utilizes broadcast, which reduces the message overhead as compared to classical flooding mechanisms. FTRP manipulates Time to Live values for the various routing messages to control message broadcast. FTRP utilizes jitter in messages transmission to reduce the effect of synchronized node states, which in turn reduces collisions. FTRP performance has been extensively through simulations against Ad-hoc On-demand Distance Vector (AODV) and Optimized Link State (OLSR) routing protocols. Packet Delivery Ratio (PDR), Aggregate Throughput and End-to-End delay (E-2-E) had been used as performance metrics. In terms of PDR and aggregate throughput, it is found that FTRP is an excellent performer in all mobility scenarios whether the network is sparse or dense. In stationary scenarios, FTRP performed well in sparse network; however, in dense network FTRP’s performance had degraded yet in an acceptable range. This degradation is attributed to synchronized nodes states. Reliably delivering a message comes to a cost, as in terms of E-2-E. results show that FTRP is considered a good performer in all mobility scenarios where the network is sparse. In sparse stationary scenario, FTRP is considered good performer, however in dense stationary scenarios FTRP’s E-2-E is not acceptable. There are times when receiving a network message is more important than other costs such as energy or delay. That makes FTRP suitable for wide range of WSNs applications, such as military applications by monitoring soldiers’ biological data and supplies while in battlefield and battle damage assessment. FTRP can also be used in health applications in addition to wide range of geo-fencing, environmental monitoring, resource monitoring, production lines monitoring, agriculture and animals tracking. FTRP should be avoided in dense stationary deployments such as, but not limited to, scenarios where high application response is critical and life endangering such as biohazards detection or within intensive care units.

Therapeutic Properties of Several Chemical Compounds from Salvia officinalis L. in Alzheimer’s Disease

2020 ◽  
Vol 21 ◽  
Author(s):  
Georgiana Uță ◽  
Denisa Ștefania Manolescu ◽  
Speranța Avram
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Side Effects ◽  
Chemical Compounds ◽  
Natural Compounds ◽  
Salvia Officinalis ◽  
Chemical Structures ◽  
In Silico Studies ◽  
Wide Range ◽  
Salvia Officinalis L

Background.: Currently, the pharmacological management in Alzheimer's disease is based on several chemical structures, represented by acetylcholinesterase and N-methyl-D-aspartate (NMDA) receptor ligands, with still unclear molecular mechanisms, but severe side effects. For this reason, a challenge for Alzheimer's disease treatment remains to identify new drugs with reduced side effects. Recently, the natural compounds, in particular certain chemical compounds identified in the essential oil of peppermint, sage, grapes, sea buckthorn, have increased interest as possible therapeutics. Objectives.: In this paper, we have summarized data from the recent literature, on several chemical compounds extracted from Salvia officinalis L., with therapeutic potential in Alzheimer's disease. Methods.: In addition to the wide range of experimental methods performed in vivo and in vitro, also we presented some in silico studies of medicinal compounds. Results. Through this mini-review, we present the latest information regarding the therapeutic characteristics of natural compounds isolated from Salvia officinalis L. in Alzheimer's disease. Conclusion.: Thus, based on the information presented, we can say that phytotherapy is a reliable therapeutic method in a neurodegenerative disease.

Polymer Chemistry

2004 ◽  
Keyword(s):  
Conducting Polymers ◽  
Liquid Crystalline ◽  
Polymer Chemistry ◽  
Chain Growth ◽  
Crystalline Polymers ◽  
Wide Range ◽  
Cyclic Oligomers ◽  
Step Growth

Polymer Chemistry: A Practical Approach in Chemistry has been designed for both chemists working in and new to the area of polymer synthesis. It contains detailed instructions for preparation of a wide-range of polymers by a wide variety of different techniques, and describes how this synthetic methodology can be applied to the development of new materials. It includes details of well-established techniques, e.g. chain-growth or step-growth processes together with more up-to-date examples using methods such as atom-transfer radical polymerization. Less well-known procedures are also included, e.g. electrochemical synthesis of conducting polymers and the preparation of liquid crystalline elastomers with highly ordered structures. Other topics covered include general polymerization methodology, controlled/"living" polymerization methods, the formation of cyclic oligomers during step-growth polymerization, the synthesis of conducting polymers based on heterocyclic compounds, dendrimers, the preparation of imprinted polymers and liquid crystalline polymers. The main bulk of the text is preceded by an introductory chapter detailing some of the techniques available to the scientist for the characterization of polymers, both in terms of their chemical composition and in terms of their properties as materials. The book is intended not only for the specialist in polymer chemistry, but also for the organic chemist with little experience who requires a practical introduction to the field.

scholarly journals Organelle Genetics in Plants

2021 ◽  
Vol 22 (4) ◽  
pp. 2104
Author(s):  
Pedro Robles ◽  
Víctor Quesada
Keyword(s):  
Rna Editing ◽  
Posttranscriptional Regulation ◽  
Genome Engineering ◽  
Plant Mitochondria ◽  
Plastid Dna ◽  
Chloroplast Genomes ◽  
Wide Range ◽  
Organelle Genetics ◽  
Selection Of

Eleven published articles (4 reviews, 7 research papers) are collected in the Special Issue entitled “Organelle Genetics in Plants.” This selection of papers covers a wide range of topics related to chloroplasts and plant mitochondria research: (i) organellar gene expression (OGE) and, more specifically, chloroplast RNA editing in soybean, mitochondria RNA editing, and intron splicing in soybean during nodulation, as well as the study of the roles of transcriptional and posttranscriptional regulation of OGE in plant adaptation to environmental stress; (ii) analysis of the nuclear integrants of mitochondrial DNA (NUMTs) or plastid DNA (NUPTs); (iii) sequencing and characterization of mitochondrial and chloroplast genomes; (iv) recent advances in plastid genome engineering. Here we summarize the main findings of these works, which represent the latest research on the genetics, genomics, and biotechnology of chloroplasts and mitochondria.

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