Pub Date : 2016-07-02DOI: 10.1080/21553769.2016.1193826
J. Zaglul
ABSTRACT Institutions of higher education have an important role in preparing the professionals that society needs to confront the challenges of the twenty-first century. A transformation of traditional higher education models must occur to ensure the relevance and impact of university education for the individual and society. This can be achieved by taking a student-centered approach that encourages questions and criticisms and provides students with opportunities to discover knowledge through experience. Additionally, the doors of the university must remain open to students of diverse backgrounds to ensure that the benefits of advanced education permeate society. For the past 25 years, EARTH University – a private, not for profit, international university located in Costa Rica – has implemented an innovative educational model to accomplish its unique mission ‘to form leaders with ethical values to contribute to sustainable development and to construct a prosperous and just society’. The EARTH model focuses on four formative areas: scientific and technical knowledge, social and environmental awareness, ethics and values, and entrepreneurship. More than 2000 professionals from over 30 countries in the Americas, the Caribbean, Africa, Asia, and Europe are graduates of the EARTH model with proven results. This article presents the EARTH case as a model for study.
{"title":"EARTH University educational model: perspective on agricultural educational models for the twenty-first century","authors":"J. Zaglul","doi":"10.1080/21553769.2016.1193826","DOIUrl":"https://doi.org/10.1080/21553769.2016.1193826","url":null,"abstract":"ABSTRACT Institutions of higher education have an important role in preparing the professionals that society needs to confront the challenges of the twenty-first century. A transformation of traditional higher education models must occur to ensure the relevance and impact of university education for the individual and society. This can be achieved by taking a student-centered approach that encourages questions and criticisms and provides students with opportunities to discover knowledge through experience. Additionally, the doors of the university must remain open to students of diverse backgrounds to ensure that the benefits of advanced education permeate society. For the past 25 years, EARTH University – a private, not for profit, international university located in Costa Rica – has implemented an innovative educational model to accomplish its unique mission ‘to form leaders with ethical values to contribute to sustainable development and to construct a prosperous and just society’. The EARTH model focuses on four formative areas: scientific and technical knowledge, social and environmental awareness, ethics and values, and entrepreneurship. More than 2000 professionals from over 30 countries in the Americas, the Caribbean, Africa, Asia, and Europe are graduates of the EARTH model with proven results. This article presents the EARTH case as a model for study.","PeriodicalId":12756,"journal":{"name":"Frontiers in Life Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21553769.2016.1193826","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60090742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-07-02DOI: 10.1080/21553769.2016.1204957
Saba S Gill, M. Mehmood, N. Ahmad, M. Ibrahim, U. Rashid, Shafaqat Ali, I. Nehdi
ABSTRACT The present study was focussed on selection of fast-growing microalgae with higher lipid content using cheaper growth media, aimed to reduce the cost of algal biomass production. Samples were collected from 40 different sites from fresh and wastewater bodies. Based on morphological differences, two microalgae (SSG and SA) from wastewater and three (OP, DFM and JRC) from fresh water habitat were selected for further characterization. The specific growth rates (g Day −1 L−1) of the OP, DFM, JRC, SA and SSG were found to be 0.614, 0.638, 0.734, 1.06 and 1.02, respectively, whereas the doubling time (Td) was shown to be as 39.30, 36.48, 22.08, 12.24 and 12.98 h, respectively, when cultured without controlled temperature and CO2 supply, in a locally designed photobioreactor. All five microalgae shown considerable growth at a range of pH 6.0–9.0 with a peak activity within pH range 7.5–8.5. The OP, DFM and JRC contained 27%, whereas SSG and SA shown 39% lipid content. The phylogenetic analyses based on the 18S rRNA gene sequence have shown that studied microalgal strains may be novel species.
{"title":"Strain selection, growth productivity and biomass characterization of novel microalgae isolated from fresh and wastewaters of upper Punjab, Pakistan","authors":"Saba S Gill, M. Mehmood, N. Ahmad, M. Ibrahim, U. Rashid, Shafaqat Ali, I. Nehdi","doi":"10.1080/21553769.2016.1204957","DOIUrl":"https://doi.org/10.1080/21553769.2016.1204957","url":null,"abstract":"ABSTRACT The present study was focussed on selection of fast-growing microalgae with higher lipid content using cheaper growth media, aimed to reduce the cost of algal biomass production. Samples were collected from 40 different sites from fresh and wastewater bodies. Based on morphological differences, two microalgae (SSG and SA) from wastewater and three (OP, DFM and JRC) from fresh water habitat were selected for further characterization. The specific growth rates (g Day −1 L−1) of the OP, DFM, JRC, SA and SSG were found to be 0.614, 0.638, 0.734, 1.06 and 1.02, respectively, whereas the doubling time (Td) was shown to be as 39.30, 36.48, 22.08, 12.24 and 12.98 h, respectively, when cultured without controlled temperature and CO2 supply, in a locally designed photobioreactor. All five microalgae shown considerable growth at a range of pH 6.0–9.0 with a peak activity within pH range 7.5–8.5. The OP, DFM and JRC contained 27%, whereas SSG and SA shown 39% lipid content. The phylogenetic analyses based on the 18S rRNA gene sequence have shown that studied microalgal strains may be novel species.","PeriodicalId":12756,"journal":{"name":"Frontiers in Life Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21553769.2016.1204957","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60090914","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-07-02DOI: 10.1080/21553769.2016.1207569
C. Remya, K. V. Dileep, E. J. Variayr, C. Sadasivan
ABSTRACT In Indian traditional practice of medicines, numerous plants have been used against various neurodegenerative disorders like Alzheimer's disease (AD). Withania somnifera (Ashwagandha in Sanskrit) is one of the medicinal plants exhibiting broad spectrum activity against various diseases. Due to its ability to improve cognitive functions, aswagandha extracts are used in various memory supplements. In the present study, the pharmacological activity of various bioactive compounds of aswagandha has been studied with respect to AD. The blood brain barrier penetrability and central nervous system (CNS) activity of these bioactive compounds were predicted using in silico tools. The predicted pharmacological properties and structure activity relationship focuses that the compounds such as anaferine, anahygrine, cuscohygrine and isopelletierine can be CNS active and neuronal nicotinic acetylcholine receptor (nAChR) agonists. In order to investigate the structure activity relationship results, molecular modeling studies has been carried out with promising ligands against nAChR. It is a known fact that the agonists of nAChRs are capable to improve communication between neurons and hence these compounds may be useful as lead compounds for the development of drugs against neurodegenerative disorders. This study also indirectly focuses how ayurvedic formulations (those containing aswagandha) are effective against neurodegenerative disorders.
{"title":"An in silico guided identification of nAChR agonists from Withania somnifera","authors":"C. Remya, K. V. Dileep, E. J. Variayr, C. Sadasivan","doi":"10.1080/21553769.2016.1207569","DOIUrl":"https://doi.org/10.1080/21553769.2016.1207569","url":null,"abstract":"ABSTRACT In Indian traditional practice of medicines, numerous plants have been used against various neurodegenerative disorders like Alzheimer's disease (AD). Withania somnifera (Ashwagandha in Sanskrit) is one of the medicinal plants exhibiting broad spectrum activity against various diseases. Due to its ability to improve cognitive functions, aswagandha extracts are used in various memory supplements. In the present study, the pharmacological activity of various bioactive compounds of aswagandha has been studied with respect to AD. The blood brain barrier penetrability and central nervous system (CNS) activity of these bioactive compounds were predicted using in silico tools. The predicted pharmacological properties and structure activity relationship focuses that the compounds such as anaferine, anahygrine, cuscohygrine and isopelletierine can be CNS active and neuronal nicotinic acetylcholine receptor (nAChR) agonists. In order to investigate the structure activity relationship results, molecular modeling studies has been carried out with promising ligands against nAChR. It is a known fact that the agonists of nAChRs are capable to improve communication between neurons and hence these compounds may be useful as lead compounds for the development of drugs against neurodegenerative disorders. This study also indirectly focuses how ayurvedic formulations (those containing aswagandha) are effective against neurodegenerative disorders.","PeriodicalId":12756,"journal":{"name":"Frontiers in Life Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21553769.2016.1207569","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60090919","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-07-02DOI: 10.1080/21553769.2016.1209133
N. Hwalla, Sibelle El Labban, Rachel A. Bahn
ABSTRACT This review argues that nutrition is an integral component of food security, and should be embedded within all four of its dimensions – availability, access, utilization, and stability. The review highlights current food insecurity in the Middle East and North Africa (MENA) region, as exacerbated by the triple burden of malnutrition, where undernutrition, micronutrient deficiencies, and overweight/obesity coexist. Previous efforts to address food security in MENA have focused on food availability, overlooking the other three dimensions and leaving nutrition considerations aside. Meanwhile, the literature has recognized the need to highlight nutrition as fundamental, and opted for the term ‘food and nutrition security’. To achieve food and nutrition security in MENA, a nutrition lens must be applied across all four dimensions – from assessment, to policy and programming, to capacity building. For example, MENA countries can adopt policies and programs including well-structured food subsidies, dietary guidelines, public awareness, and education campaigns to increase availability and accessibility of nutritious and safe foods, and stimulate consumer demand for those. To accomplish this, MENA needs to build stakeholders' capacity and equip them to address the challenges that are hindering the achievement of food and nutrition security now and into the future.
{"title":"Nutrition security is an integral component of food security","authors":"N. Hwalla, Sibelle El Labban, Rachel A. Bahn","doi":"10.1080/21553769.2016.1209133","DOIUrl":"https://doi.org/10.1080/21553769.2016.1209133","url":null,"abstract":"ABSTRACT This review argues that nutrition is an integral component of food security, and should be embedded within all four of its dimensions – availability, access, utilization, and stability. The review highlights current food insecurity in the Middle East and North Africa (MENA) region, as exacerbated by the triple burden of malnutrition, where undernutrition, micronutrient deficiencies, and overweight/obesity coexist. Previous efforts to address food security in MENA have focused on food availability, overlooking the other three dimensions and leaving nutrition considerations aside. Meanwhile, the literature has recognized the need to highlight nutrition as fundamental, and opted for the term ‘food and nutrition security’. To achieve food and nutrition security in MENA, a nutrition lens must be applied across all four dimensions – from assessment, to policy and programming, to capacity building. For example, MENA countries can adopt policies and programs including well-structured food subsidies, dietary guidelines, public awareness, and education campaigns to increase availability and accessibility of nutritious and safe foods, and stimulate consumer demand for those. To accomplish this, MENA needs to build stakeholders' capacity and equip them to address the challenges that are hindering the achievement of food and nutrition security now and into the future.","PeriodicalId":12756,"journal":{"name":"Frontiers in Life Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21553769.2016.1209133","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60091175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-07-02DOI: 10.1080/21553769.2016.1209134
M. Kavitha
ABSTRACT Cold active lipases (CLPs) are gaining importance nowadays as they are increasingly used in fine chemical synthesis, bioremediation, food processing and as detergent additive. These enzymes exhibit high catalytic activity at low temperatures and flexibility to act at low water medium. Since they are active at low temperatures consume less energy and also stabilize fragile compounds in the reaction medium. CLPs are commonly obtained from psychrophilic microorganisms which thrive in cold habitats. Compared to mesophilic and thermophilic lipases, only a few CLPs were studied and industrially exploited so far. CLPs (C. antarctica lipase-A and C. antarctica lipase-B) from Candida antarctica isolated from Antarctic region are the well studied and industrially employed, and many are being followed up. This review updates the CLPs reported recently and the industrial applications of CLPs.
{"title":"Cold active lipases – an update","authors":"M. Kavitha","doi":"10.1080/21553769.2016.1209134","DOIUrl":"https://doi.org/10.1080/21553769.2016.1209134","url":null,"abstract":"ABSTRACT Cold active lipases (CLPs) are gaining importance nowadays as they are increasingly used in fine chemical synthesis, bioremediation, food processing and as detergent additive. These enzymes exhibit high catalytic activity at low temperatures and flexibility to act at low water medium. Since they are active at low temperatures consume less energy and also stabilize fragile compounds in the reaction medium. CLPs are commonly obtained from psychrophilic microorganisms which thrive in cold habitats. Compared to mesophilic and thermophilic lipases, only a few CLPs were studied and industrially exploited so far. CLPs (C. antarctica lipase-A and C. antarctica lipase-B) from Candida antarctica isolated from Antarctic region are the well studied and industrially employed, and many are being followed up. This review updates the CLPs reported recently and the industrial applications of CLPs.","PeriodicalId":12756,"journal":{"name":"Frontiers in Life Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21553769.2016.1209134","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60091250","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-06-15DOI: 10.1080/21553769.2016.1193827
V. М. Sellitto, G. Curto, E. Dallavalle, A. Ciancio, M. Colagiero, Laura Pietrantonio, G. Bireescu, V. Stoleru, M. Storari
ABSTRACT EU legislation restricted many chemicals for root-knot nematodes (Meloidogyne spp., RKNs) control. Alternative ways of plant protection were hence investigated, based on the use of microbial formulations exploiting plant parasites antagonism. RKNs are severe and widespread pests causing extensive damage to crops in greenhouse and field. Several antagonistic microorganisms are suitable for biocontrol, including the nematophagous hyphomycete Pochonia chlamydosporia that parasitizes eggs to acquire additional nourishment and face competition with other soil microorganisms. A commercial product (POCHAR) was developed by Microspore based on P. chlamydosporia with other microbial inocula that can be applied through irrigation. The aim of this study was to test POCHAR’s efficacy against RKNs on potato and its promotion effect on tomato in two field trials. Moreover, the research included trials to evaluate the best method for open-field application in crops not managed through drip irrigation, opening up the possibility to treat large areas without major technological needs. RKNs control with POCHAR represented a viable alternative to chemicals. In conclusion, the organic approach developed through the bioformulated product highlighted effective RKNs management, with a potential to sustain both plant nutrition and the related root protection needs.
{"title":"Effect of Pochonia chlamydosporia-based formulates on the regulation of root-knot nematodes and plant growth response","authors":"V. М. Sellitto, G. Curto, E. Dallavalle, A. Ciancio, M. Colagiero, Laura Pietrantonio, G. Bireescu, V. Stoleru, M. Storari","doi":"10.1080/21553769.2016.1193827","DOIUrl":"https://doi.org/10.1080/21553769.2016.1193827","url":null,"abstract":"ABSTRACT EU legislation restricted many chemicals for root-knot nematodes (Meloidogyne spp., RKNs) control. Alternative ways of plant protection were hence investigated, based on the use of microbial formulations exploiting plant parasites antagonism. RKNs are severe and widespread pests causing extensive damage to crops in greenhouse and field. Several antagonistic microorganisms are suitable for biocontrol, including the nematophagous hyphomycete Pochonia chlamydosporia that parasitizes eggs to acquire additional nourishment and face competition with other soil microorganisms. A commercial product (POCHAR) was developed by Microspore based on P. chlamydosporia with other microbial inocula that can be applied through irrigation. The aim of this study was to test POCHAR’s efficacy against RKNs on potato and its promotion effect on tomato in two field trials. Moreover, the research included trials to evaluate the best method for open-field application in crops not managed through drip irrigation, opening up the possibility to treat large areas without major technological needs. RKNs control with POCHAR represented a viable alternative to chemicals. In conclusion, the organic approach developed through the bioformulated product highlighted effective RKNs management, with a potential to sustain both plant nutrition and the related root protection needs.","PeriodicalId":12756,"journal":{"name":"Frontiers in Life Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21553769.2016.1193827","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60090748","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-06-13DOI: 10.1080/21553769.2016.1193828
Gilbert Medawar, G. Srour, D. El Azzi
ABSTRACT Iron is an essential micro-element for plant growth. In the calcareous soils of Lebanon, immobilization of iron can lead to chlorosis and reduce the yields of agricultural production. Iron fertilization is therefore crucial to ensure good plant growth. The objective of this work was to compare the efficiency of the iron chelate HBED-Fe to that of EDDHA-Fe, on tomato (Solanum lycopersicum L.) and cucumber crops (Cucumis sativus L.). Five modules were studied in two separate greenhouses: one control, one module with fertilization by EDDHA-Fe and three modules with different applications of HBED-Fe. Chlorophyll and Fe contents in leaves were analyzed at different stages of the plants' cycle. Cucumber crops treated with HBED-Fe showed 19.2% higher chlorophyll content than the ones treated with EDDHA-Fe. Tomato crops presented 11.2% higher chlorophyll content when treated with HBED-Fe. For cucumbers, HBED-Fe should be applied in three applications separated by 25 days. For tomatoes, HBED-Fe should be applied in two applications separated by a month. The use of the HBED9% iron chelate was proved to be more effective than that of EDDHA6% because more efficiency was achieved with 40% less application rate. Multiple applications were also more effective than single applications.
{"title":"Comparison of chlorophyll content in greenhouse tomato and cucumber leaves after HBED-Fe and EDDHA-Fe applications","authors":"Gilbert Medawar, G. Srour, D. El Azzi","doi":"10.1080/21553769.2016.1193828","DOIUrl":"https://doi.org/10.1080/21553769.2016.1193828","url":null,"abstract":"ABSTRACT Iron is an essential micro-element for plant growth. In the calcareous soils of Lebanon, immobilization of iron can lead to chlorosis and reduce the yields of agricultural production. Iron fertilization is therefore crucial to ensure good plant growth. The objective of this work was to compare the efficiency of the iron chelate HBED-Fe to that of EDDHA-Fe, on tomato (Solanum lycopersicum L.) and cucumber crops (Cucumis sativus L.). Five modules were studied in two separate greenhouses: one control, one module with fertilization by EDDHA-Fe and three modules with different applications of HBED-Fe. Chlorophyll and Fe contents in leaves were analyzed at different stages of the plants' cycle. Cucumber crops treated with HBED-Fe showed 19.2% higher chlorophyll content than the ones treated with EDDHA-Fe. Tomato crops presented 11.2% higher chlorophyll content when treated with HBED-Fe. For cucumbers, HBED-Fe should be applied in three applications separated by 25 days. For tomatoes, HBED-Fe should be applied in two applications separated by a month. The use of the HBED9% iron chelate was proved to be more effective than that of EDDHA6% because more efficiency was achieved with 40% less application rate. Multiple applications were also more effective than single applications.","PeriodicalId":12756,"journal":{"name":"Frontiers in Life Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21553769.2016.1193828","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60090789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-05-05DOI: 10.1080/21553769.2016.1174958
J. Tian, B. C. Bryksa, R. Yada
ABSTRACT By mid-century, the world population will surpass 9 billion people, meaning higher demand for available food, water, arable land and environmental impacts. Food safety issues, nutrition deficiencies, postharvest losses, regulation inconsistencies and consumer attitudes are all striking challenges which must be met in maintaining food security and sustainability. Possible solutions include advancements in food processing technologies, nanotechnology, innovative food formulations and the use of genomic approaches manifested in examples such as alternative protein sources, insect flour, nutrigenomics, 3D food printing, biomimicry, food engineering and merging technology. International organizations like the International Union of Food Science and Technology also play important roles in securing the world’s food supplies by providing expertise through their respective country memberships. The present review addresses the food science and technology roles in meeting current challenges and investigates possible solutions to feed the world in the near future.
{"title":"Feeding the world into the future – food and nutrition security: the role of food science and technology†","authors":"J. Tian, B. C. Bryksa, R. Yada","doi":"10.1080/21553769.2016.1174958","DOIUrl":"https://doi.org/10.1080/21553769.2016.1174958","url":null,"abstract":"ABSTRACT By mid-century, the world population will surpass 9 billion people, meaning higher demand for available food, water, arable land and environmental impacts. Food safety issues, nutrition deficiencies, postharvest losses, regulation inconsistencies and consumer attitudes are all striking challenges which must be met in maintaining food security and sustainability. Possible solutions include advancements in food processing technologies, nanotechnology, innovative food formulations and the use of genomic approaches manifested in examples such as alternative protein sources, insect flour, nutrigenomics, 3D food printing, biomimicry, food engineering and merging technology. International organizations like the International Union of Food Science and Technology also play important roles in securing the world’s food supplies by providing expertise through their respective country memberships. The present review addresses the food science and technology roles in meeting current challenges and investigates possible solutions to feed the world in the near future.","PeriodicalId":12756,"journal":{"name":"Frontiers in Life Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21553769.2016.1174958","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60090649","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-04-02DOI: 10.1080/21553769.2016.1178180
R. Tripathi, Pawan Sharma, P. Chakraborty, P. Varadwaj
ABSTRACT Next-generation sequencing (NGS) technology has led to an unrivaled explosion in the amount of genomic data and this escalation has collaterally raised the challenges of sharing, archiving, integrating and analyzing these data. The scale and efficiency of NGS have posed a challenge for analysis of these vast genomic data, gene interactions, annotations and expression studies. However, this limitation of NGS can be safely overcome by tools and algorithms using big data framework. Based on this framework, here we have reviewed the current state of knowledge of big data algorithms for NGS to reveal hidden patterns in sequencing, analysis and annotation, and so on. The APACHE-based Hadoop framework gives an on-interest and adaptable environment for substantial scale data analysis. It has several components for partitioning of large-scale data onto clusters of commodity hardware, in a fault-tolerant manner. Packages like MapReduce, Cloudburst, Crossbow, Myrna, Eoulsan, DistMap, Seal and Contrail perform various NGS applications, such as adapter trimming, quality checking, read mapping, de novo assembly, quantification, expression analysis, variant analysis, and annotation. This review paper deals with the current applications of the Hadoop technology with their usage and limitations in perspective of NGS.
{"title":"Next-generation sequencing revolution through big data analytics","authors":"R. Tripathi, Pawan Sharma, P. Chakraborty, P. Varadwaj","doi":"10.1080/21553769.2016.1178180","DOIUrl":"https://doi.org/10.1080/21553769.2016.1178180","url":null,"abstract":"ABSTRACT Next-generation sequencing (NGS) technology has led to an unrivaled explosion in the amount of genomic data and this escalation has collaterally raised the challenges of sharing, archiving, integrating and analyzing these data. The scale and efficiency of NGS have posed a challenge for analysis of these vast genomic data, gene interactions, annotations and expression studies. However, this limitation of NGS can be safely overcome by tools and algorithms using big data framework. Based on this framework, here we have reviewed the current state of knowledge of big data algorithms for NGS to reveal hidden patterns in sequencing, analysis and annotation, and so on. The APACHE-based Hadoop framework gives an on-interest and adaptable environment for substantial scale data analysis. It has several components for partitioning of large-scale data onto clusters of commodity hardware, in a fault-tolerant manner. Packages like MapReduce, Cloudburst, Crossbow, Myrna, Eoulsan, DistMap, Seal and Contrail perform various NGS applications, such as adapter trimming, quality checking, read mapping, de novo assembly, quantification, expression analysis, variant analysis, and annotation. This review paper deals with the current applications of the Hadoop technology with their usage and limitations in perspective of NGS.","PeriodicalId":12756,"journal":{"name":"Frontiers in Life Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21553769.2016.1178180","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60090733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-04-02DOI: 10.1080/21553769.2016.1162753
Trishala K. Parmar, Dr. Deepak Rawtani, Y. K. Agrawal
ABSTRACT Bioindicators are living organisms such as plants, planktons, animals, and microbes, which are utilized to screen the health of the natural ecosystem in the environment. They are used for assessing environmental health and biogeographic changes taking place in the environment. Each organic entity inside a biological system provides an indication regarding the health of its surroundings such as plankton responding rapidly to changes taking place in the surrounding environment and serving as an important biomarker for assessing the quality of water as well as an indicator of water pollution. Even the health of aquatic flora is best reflected by plankton, which acts as an early warning signal. In this review we have tried to explain the concept behind Bioindicators and plankton, with particular emphasis on their potential to be used as Bioindicators for water quality assessment and outcomes relating to this.
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