Screening for genomic sequence variants in genes of predictive and prognostic significance is an integral part of precision medicine. Next-generation sequencing (NGS) technologies are progressively ...becoming platforms of choice to facilitate this, owing to their massively parallel sequencing capability, which can be used to simultaneously screen multiple markers in multiple samples for a variety of variants (single nucleotide and multi nucleotide variants, insertions and deletions, gene copy number variations, and fusions). A crucial step in the workflow of targeted NGS is the enrichment of the genomic regions of interest to be sequenced, against the whole genomic background. This ensures that the NGS effort is focused to predominantly screen target regions of interest with minimal off-target sequencing, making it more accurate and economical. Polymerase chain reaction-based (PCR, or amplicon-based) and hybridization capture-based methodologies are the two prominent approaches employed for target enrichment. This review summarizes the basic principles of target enrichment utilized by these methods, their multiple variations that have evolved over time, automation approaches, overall comparison of their advantages and drawbacks, and commercially available choices for these methodologies.
With global population explosion, the available water resources are slowly being polluted due to the excessive human interference. To encounter this, it is the need of this hour to find out ...sustainable pollution remediating technologies to meet the stringent discharge standards for domestic as well as industrial wastewaters. In addition, those techniques should have the capabilities for effective implementation even in developing countries. Based on the available literatures, one such technique, named vermifilter, has been identified which takes care of almost all the sustainable and economical criteria for its effective implementation even in developing countries. The aim of this meta-analysis is to provide a comprehensive review on assessment mechanisms involved, factors affecting the process and performance of vermifiltration under different scenarios. The present review envisages the current state of the knowledge regarding physical, chemical and biological aspects related to the treatment mechanisms and effective functioning of earthworms. This review has also proposed several suggestive plans on its application at any proposed site.
•The review exhaustively outlines the mechanisms involved in vermifiltration.•Factors affecting vermifiltration have been identified and discussed critically.•Application of vermifiltration for industrial wastewater has also been advocated.•It also discusses properties and application of harvested compost from vermifilter.•Growth and reproduction of earthworms in the vermifilter has also been discussed.
The study was conducted with an aim to optimize the parameters involved in removing organics from brewery effluents using a newly developed horizontal subsurface flow vermifilter. It was also aimed ...at understanding the impact of hydraulic retention time (HRT) on the vermifiltration of brewery wastewater. With the help of Box-Behnken design (BBD) and response surface methodology, optimization of the COD removal from the vermifiltration was carried out. The parameters chosen for the optimization were hydraulic loading rate (HLR), organics strength and earthworm densities (EWDs). The model obtained from the response surface methodology (RSM) analysis was a quadratic polynomial model with R2 value of 0.99. The optimal conditions for achieving maximum chemical oxygen demand (COD) removal were at influent COD concentration of 3542.22 mg/L, EWD of 9661.33 earthworms/m3 and HLR of 1.84 m3/m2·d. At the optimum conditions, COD removal of 94.99% was obtained against the predicted value of 95.85%. Verification of the model on real brewery wastewater also showed minimal error against the predicted COD removal. The COD, total nitrogen (TN) and total phosphorous (TP) removal at the HRT of 10.66 h were found to be 73.88%, 18.13% and 39.04%, respectively. Whereas, The COD, TN and TP removals at the HRT of 26.66 h were 96.24, 21.57 and 43.3%, respectively.
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•A RSM based BBD model was utilized to optimize the COD removal from vermifilters.•At the optimized conditions, highest COD removal efficiency of 94.99% was obtained.•The parameters affecting COD removal from vermifilters were identified.•The impact of HRT on vermifiltration is found to be significant.
With the scarcity of fresh water and rise in pollution load in the aquatic ecosystem over the globe, the domestic and industrial effluents need to be reused after suitable treatment. In an attempt to ...do so, soil biofilters have been identified as a treatment alternative that is suitable for application in developing countries. However, rapid development of clogging in the soil biofilters limits its applicability as an effective technology. This paper aims to understand the occurrence of clogging due to biofilms formation in and over the bedding of soil media. To address this, the organic loading rates (OLRs) were varied in the range of 2.25–11.25kgCOD/m3·day to create different degree of clogging. Earthworms were inoculated into the soil bedding at the earthworm densities (EWDs) of 0, 5000 and 10,000earthworms/m3 to study the effect of earthworms introduction on clogging. The degree of clogging was measured using clogging coefficient (CC), hydraulic conductivity and head loss. The study highlights the impact of earthworms on the removal performance and clogging of soil biofilter. For all earthworm densities, head loss and clogging coefficient increased and hydraulic conductivity decreased linearly with organic loading rate. Introduction of earthworms versus no earthworms resulted in lower head loss and clogging coefficient and higher hydraulic conductivity for all organic loading rates, while increasing EWD from 5000 to 10,000 had only marginal effects on all parameters. The study reveals that high organic loading rate activates higher number of microbial sites, in turn causing higher degree of clogging. However, the introduction of earthworms reduces the clogging rate significantly along with enhanced treatment performance. The outcome of this study indicates that incorporation of earthworms into the soil biofilter can reduce the degree of bio-clogging and might provide a highly sustainable, low cost and efficient treatment system for the developing countries.
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•Clogging increases with the increase in organic strength of the influent.•Earthworms decrease the rate of clogging in soil biofilter.•Earthworms maintain requisite dissolved oxygen in soil biofilter.•Hydraulic permeability increases with the introduction of earthworms.•Earthworm's introduction into biofilter reduces nutrient contents in the effluent.
The application of next-generation sequencing (NGS) to characterize cancer genomes has resulted in the discovery of numerous genetic markers. Consequently, the number of markers that warrant routine ...screening in molecular diagnostic laboratories, often from limited tumor material, has increased. This increased demand has been difficult to manage by traditional low- and/or medium-throughput sequencing platforms. Massively parallel sequencing capabilities of NGS provide a much-needed alternative for mutation screening in multiple genes with a single low investment of DNA. However, implementation of NGS technologies, most of which are for research use only (RUO), in a diagnostic laboratory, needs extensive validation in order to establish Clinical Laboratory Improvement Amendments (CLIA) and College of American Pathologists (CAP)-compliant performance characteristics. Here, we have reviewed approaches for validation of NGS technology for routine screening of tumors. We discuss the criteria for selecting gene markers to include in the NGS panel and the deciding factors for selecting target capture approaches and sequencing platforms. We also discuss challenges in result reporting, storage and retrieval of the voluminous sequencing data and the future potential of clinical NGS.
Application of next-generation sequencing (NGS) technology to routine clinical practice has enabled characterization of personalized cancer genomes to identify patients likely to have a response to ...targeted therapy. The proper selection of tumor sample for downstream NGS based mutational analysis is critical to generate accurate results and to guide therapeutic intervention. However, multiple pre-analytic factors come into play in determining the success of NGS testing. In this review, we discuss pre-analytic requirements for AmpliSeq PCR-based sequencing using Ion Torrent Personal Genome Machine (PGM) (Life Technologies), a NGS sequencing platform that is often used by clinical laboratories for sequencing solid tumors because of its low input DNA requirement from formalin fixed and paraffin embedded tissue. The success of NGS mutational analysis is affected not only by the input DNA quantity but also by several other factors, including the specimen type, the DNA quality, and the tumor cellularity. Here, we review tissue requirements for solid tumor NGS based mutational analysis, including procedure types, tissue types, tumor volume and fraction, decalcification, and treatment effects.
In the present research, an experiment was conducted with the objective of optimization of the role of earthworms in alleviating the bioclogging of a horizontal subsurface flow vermifilter (HSSFVF), ...caused due to the application of organics rich brewery wastewater. In this experiment, for the optimization of bioclogging of the vermifilters, the Box-Behnken Design (BBD) and response surface methodology (RSM) were involved. Hydraulic loading rate (HLR), influent COD and earthworm density (EWD) are the variables against which the bioclogging of the HSSFVF has been optimized. EWD of 9475 earthworms/m3, HLR of 1.84 m3/m2-d and influent COD of 3701 mg/L have been observed as the optimized values for the minimum bioclogging in the vermifiltration of brewery wastewater. At this optimum boundary conditions, the reduction in hydraulic conductivity was obtained as 1.49%, against the predicted value of 1.67% based upon the BBD model. The verification of the model against real brewery wastewater yielded insignificant error and thus very strongly portrays the suitability of the derived BBD model. The study indicates that the bioclogging from the vermifilters can be minimized, if the variables are optimized using the response surface methodology.
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•Optimization of bioclogging of vermifilters was done using a RSM based BBD model.•The earthworm inoculation in the soil biofilter can delay the clogging.•The variables influencing the bioclogging of vermifilters were recognised.•The mechanism behind bioclogging and role of earthworms were highlighted.•A significant influence of EWD and HLR on bioclogging was observed.
PurposeOver the years, the fruit and vegetable supply chain has encountered several challenges. From the harvesting stage until it reaches the consumer, a significant portion of fruits and vegetables ...gets wasted in the supply chain. As a result, the present study attempts to identify and analyze the growth barriers in the fresh produce supply chain (FPSC) in the Indian context.Design/methodology/approachAn integrated grey theory and DEMATEL based approach is used to analyze growth barriers in the FPSC. The growth barriers were analyzed and sorted based on their influence and importance relations.FindingsThe results emphasize that the most critical growth barriers in the FPSC that should be addressed to ensure food waste reduction are as follows: Lack of cold chain facilities (B2), lack of transportation or logistic facilities (B1), lack of collaboration and information sharing between supply chain partners (B3), lack of proper quality and safety protocols (B15), a lack of processing and packaging facilities (B14), and poor productivity and efficiency (B13). Results are also verified by conducting a sensitivity analysis.Practical implicationsThe results are highly useful for policymakers to exploit growth barriers within the FPSC that require more attention. The obtained results show that the managers and policymakers need to utilize more funds to develop the cold chain facilities and logistics facilities to develop the FPSC. By improving the cold chain facilities, it is possible to improve the quality of food, make the food safe for human consumption, reduce waste, and increase the efficiency and productivity of the supply chain. Also, this study may encourage policymakers and industrial managers to adopt the most influential SCM practices for food waste reduction.Originality/valueMany researchers have attempted to analyze the causes of food waste and growth barriers in the FPSC using various decision-making methods. Still, no attempts are made to explore the causal relations among various growth barriers in FPSC through the integrated Grey-DEMATEL technique. Also, we devise policy implications in the light of the new farm bills or the Indian agricultural acts of 2020. Lack of cold chain facilities (B2) was found to be the critical driving barrier in the FPSC, as it influences multiple barriers. Also, there is a dire need for cold chain facilities and transportation systems to enhance productivity and efficiency.
Next-generation sequencing (NGS) technologies have come of age as preferred technologies for screening of genomic variants of pathologic and therapeutic potential. Because of their capability for ...high-throughput and massively parallel sequencing, they can screen for a variety of genomic changes in multiple samples simultaneously. This has made them platforms of choice for clinical testing of solid tumors and hematological malignancies. Consequently, they are increasingly replacing conventional technologies, such as Sanger sequencing and pyrosequencing, expression arrays, real-time PCR, and fluorescence in situ hybridization methods, for routine molecular testing of tumors. However, one limitation of routinely used NGS technologies is the inability to detect low-level genomic variants with high accuracy. This can be attributed to the frequent occurrence of low-level sequencing errors and artifacts in NGS workflow that need specialized approaches to be identified and eliminated. This review focuses on the origins and nature of these artifacts and recent improvements in the NGS technologies to overcome them to facilitate accurate high-sensitive detection of low-level mutations. Potential applications of high-sensitive NGS in oncology and comparisons with non-NGS technologies of similar capabilities are also summarized.
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