Next-generation sequencing (NGS) platforms: An exciting era of genome sequence analysis

© Springer Nature Singapore Pte Ltd. 2019. DNA referred to as blueprint of life codes for the diversity and function of all the living organisms. Determining DNA sequences of the living organisms not only gives an overview of their genetic makeup, but also provides information about their function. Nonetheless it was not easy to determine the genome sequencing of all the diversity around us especially with the technologies available before 2010. Therefore, determining the sequence of humans and some other organisms only was prioritized. Pioneering methods for DNA sequencing given discovered by Maxam and Gilbert, and Sanger although were very powerful and popular but were not high throughput and economic. Therefore, it was necessary to develop new economic and high-throughput methods that can sequence the biodiversity consequently providing better insights of their possible function. New methods were developed and commercialized by Roche Life Sciences, Thermo Fisher Scientific, Illumina, and Applied Biosystems. These methods generally referred to as next-generation sequencing methods have revolutionized the DNA sequencing. Many sequencing platforms employing NGS have been developed including pyrosequencing, Ion Torrent technology, Illumina/Solexa platform, and SOLiD (Sequencing by Oligonucleotide Ligation and Detection). Further optimization has led to innovative third and fourth-generation platforms as single molecule real-time (SMRT) sequencing by PacBio, nanopore sequencing, etc. As a consequence there is a sharp increase in the number of genomes being published and other genome-based studies since 2012. This has made it easy even to imagine of sequencing the genomes of individuals. Furthermore, scientists are now looking for third-generation sequencers that may be significantly different from the sequencers that are currently available

Indigenously produced biochar retains fertility in sandy soil through unique microbial diversity sustenance: a step toward the circular economy

IntroductionAgricultural productivity in the arid hot desert climate of UAE is limited by the unavailability of water, high temperature, and salt stresses. Growing enough food under abiotic stresses and decreasing reliance on imports in an era of global warming are a challenge. Biochar with high water and nutrient retention capacity and acid neutralization activity is an attractive soil conditioner. This study investigates the microbial community in the arid soil of Dubai under shade house conditions irrigated with saline water and the shift in the microbial community, following 1 year of amendment with indigenously prepared biochar from date palm waste.MethodsAmplicon sequencing was used to elucidate changes in bacterial, archaeal, and fungal community structures in response to long-term biochar amendment. Samples were collected from quinoa fields receiving standard NPK doses and from fields receiving 20 and 30 tons ha−1 of biochar, in addition to NPK for 1 year. Water holding capacity, pH, electrical conductivity, calcium, magnesium, chloride, potassium, sodium, phosphorus, total carbon, organic matter, and total nitrogen in the soil from biochar-treated and untreated controls were determined.Results and discussionThe results show that soil amendment with biochar helps retain archaeal and bacterial diversity. Analysis of differentially abundant bacterial and fungal genera indicates enrichment of plant growth-promoting microorganisms. Interestingly, many of the abundant genera are known to tolerate salt stress, and some observed genera were of marine origin. Biochar application improved the mineral status and organic matter content of the soil. Various physicochemical properties of soil receiving 30 tons ha−1 of biochar improved significantly over the control soil. This study strongly suggests that biochar helps retain soil fertility through the enrichment of plant growth-promoting microorganisms

Deep learning approach for discovery of in silico drugs for combating COVID-19

Early diagnosis of pandemic diseases such as COVID-19 can prove beneficial in dealing with difficult situations and helping radiologists and other experts manage staffing more effectively. The application of deep learning techniques for genetics, microscopy, and drug discovery has created a global impact. It can enhance and speed up the process of medical research and development of vaccines, which is required for pandemics such as COVID-19. However, current drugs such as remdesivir and clinical trials of other chemical compounds have not shown many impressive results. Therefore, it can take more time to provide effective treatment or drugs. In this paper, a deep learning approach based on logistic regression, SVM, Random Forest, and QSAR modeling is suggested. QSAR modeling is done to find the drug targets with protein interaction along with the calculation of binding affinities. Then deep learning models were used for training the molecular descriptor dataset for the robust discovery of drugs and feature extraction for combating COVID-19. Results have shown more significant binding affinities (greater than -18) for many molecules that can be used to block the multiplication of SARS-CoV-2, responsible for COVID-19. [Abstract copyright: Copyright © 2021 Nishant Jha et al.

Protective Effect of Solanum nigrum

The prophylactic or curative antioxidant efficacy of crude extract and the active constituent of S. nigrum leaves were evaluated in modulating inherent antioxidant system altered due to immobilization stress in rat brain tissues, in terms of measurement of glutathione (GSH), lipid peroxidation (thiobarbituric acid reactive substances, TBARS), and free radical scavenging enzymes activities. Rats were treated with single dose of crude extract of S. nigrum prior to and after 6 h of immobilization stress exposure. Exposure to immobilization stress resulted in a decrease in the brain levels of glutathione, SOD, GST, and catalase, with an increase in thiobarbituric acid reactive substances (TBARS) levels. Treatment of S. nigrum extract and its active constituents to both pre- and poststressed rats resulted in significant modulation in the above mentioned parameters towards their control values with a relative dominance by the latter. Brain is vulnerable to stress induced prooxidant insult due to high levels of fat content. Thus, as a safe herbal medication the S. nigrum leaves extract or its isolated constituents can be used as nutritional supplement for scavenging free radicals generated in the brain due to physical or psychological stress or any neuronal diseases per se

Ecological and kinetic studies of solid-phase denitrification using biodegradable plastics for nitrogen removal from wastewater

豊橋技術科学大

Strategies to Counter Zinc Deficiency, Current Status and Future Directions

Zinc deficiency in humans is caused by a range of problems associated from soil to plants and to human beings. Coordinated efforts of the international community, especially policymakers, agricultural and plant scientists, dieticians, physicians and others, are required to address a variety of issues responsible for global hidden hunger of micronutrient deficiency. Among some of the most important approaches are zinc biofortification of the cereal crops using zinc biofertilizers and the development of zinc-efficient crops. The use of zinc biofertilizers is one of the most effective, sustainable and economic ways to improve the zinc status of the soil to grow zinc-dense cereals. Zinc-dense cereals developed through biofortification should be made available to populations that are mainly dependent on cereal-based diet. Dieticians and scientists should make efforts to encourage diversification of diet and to use zinc supplements to meet the requirement. One study suggests that including fishes in the diet can help to overcome micronutrient deficiency globally. People should also be convinced to shun food beliefs and taboos to combat micronutrient deficiency. Strategies to improve zinc absorption in humans should also be developed. Notably, wheat with reduced phytate content in the grains was developed with an aim to maximize zinc absorption in the intestine. Awareness programmes in areas suffering the most from zinc deficiency should be carried out among all stakeholders. Despite the suggestions from FAO and WHO, global efforts to combat zinc deficiency matching those for combating HIV, etc., are not in place

Members of the Family Comamonadaceae as Primary Poly(3-Hydroxybutyrate-co-3-Hydroxyvalerate)-Degrading Denitrifiers in Activated Sludge as Revealed by a Polyphasic Approach

The distribution and phylogenetic affiliations of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV)-degrading denitrifying bacteria in activated sludge were studied by a polyphasic approach including culture-independent biomarker and molecular analyses as well as cultivation methods. A total of 23 strains of PHBV-degrading denitrifiers were isolated from activated sludges from different sewage treatment plants. 16S ribosomal DNA (rDNA) sequence comparisons showed that 20 of the isolates were identified as members of the family Comamonadaceae, a major group of β-Proteobacteria. When the sludges from different plants were acclimated with PHBV under denitrifying conditions in laboratory scale reactors, the nitrate removal rate increased linearly during the first 4 weeks and reached 20 mg NO(3)(−)-N h(−1) g of dry sludge(−1) at the steady state. The bacterial-community change in the laboratory scale sludges during the acclimation was monitored by rRNA-targeted fluorescence in situ hybridization and quinone profiling. Both approaches showed that the population of β-Proteobacteria in the laboratory sludges increased sharply during acclimation regardless of their origins. 16S rDNA clone libraries were constructed from two different acclimated sludges, and a total of 37 clones from the libraries were phylogenetically analyzed. Most of the 16S rDNA clones were grouped with members of the family Comamonadaceae. The results of our polyphasic approach indicate that β-Proteobacteria, especially members of the family Comamonadaceae, are primary PHBV-degrading denitrifiers in activated sludge. Our data provide useful information for the development of a new nitrogen removal system with solid biopolymer as an electron donor

Sub-lethal doses of widespread nanoparticles promote antifungal activity in Pseudomonas protegens CHA0

Nanoparticles are widely used as antimicrobial compounds. At sub-lethal concentrations, they may also stress microbes, potentially inducing antibiosis. Here we assess whether nanoparticles can serve as an enhancer of antibiosis in beneficial microbes. Several host-associated bacteria can suppress pathogens, providing therefore a first line of defense against diseases. In the present study, we assessed whether nanoparticles stimulate the antifungal activity of Pseudomonas protegens CHA0, a model plant-associated bacterium, against the ascomycete yeast Candida albicans. We synthesized and characterized four of the most common nanoparticles, namely Ag, SiO2, TiO2 and ZnO, with an average size of 25, 11, 25 and 35 nm, respectively. The dose-dependent effect of these nanoparticles on the growth of Pseudomonas protegens CHA0 was assessed. Ag, SiO2, TiO2 and ZnO nanoparticles inhibited the growth of Pseudomonas protegens by 100, 22, 15 and 15%, respectively at a concentration of 250 μg/mL. We then selected sub-lethal dose (500 ng/mL) and assessed whether the same nanoparticles stimulated the production of antifungal compounds inhibiting C. albicans. Incubating the bacteria in the presence of nanoparticles led to a four-fold increase in antifungal activity. We finally show that nanoparticles induce the expression of the prn operon, responsible for the production of antifungal compound pyrrolnitrin, within hours after nanoparticle exposure. This study shows that nanoparticle application may be a valuable tool to stimulate the antifungal activity of fluorescent pseudomonads, potentially assisting the development of future sustainable disease control strategies

Pharmacological Inhibition of Class III Alcohol Dehydrogenase 5: Turning Remote Ischemic Conditioning Effective in a Diabetic Stroke Model

The restoration of cerebral blood flow (CBF) to achieve brain tissue oxygenation (PbtO2) is the primary treatment for ischemic stroke, a significant cause of adult mortality and disability worldwide. Nitric oxide (NO) and its bioactive s-nitrosylated (SNO) reservoirs, such as s-nitrosoglutathione (GSNO), induce hypoxic vasodilation to enhance CBF during ischemia. The endogenous pool of SNOs/GSNO is enhanced via the activation of endothelial NO synthase (eNOS/NOS3) and by the suppression of class III alcohol dehydrogenase 5 (ADH5), also known as GSNO reductase (GSNOR). Remote ischemic conditioning (RIC), which augments NOS3 activity and SNO, is an emerging therapy in acute stroke. However, RIC has so far shown neutral effects in stroke clinical trials. As the majority of stroke patients are presented with endothelial dysfunctions and comorbidities, we tested the hypothesis that NOS3 dysfunction and diabetes will abolish the protective effects of RIC therapy in stroke, and the prior inhibition of GSNOR will turn RIC protective. Our data demonstrate that RIC during thrombotic stroke failed to enhance the CBF and the benefits of thrombolysis in NOS3 mutant (NOS3+/−) mice, a genetic model of NOS3 dysfunction. Interestingly, thrombotic stroke in diabetic mice enhanced the activity of GSNOR as early as 3 h post-stroke without decreasing the plasma nitrite (NO2−). In thrombotic stroke, neither a pharmacological inhibitor of GSNOR (GRI) nor RIC therapy alone was protective in diabetic mice. However, prior treatment with GRI followed by RIC enhanced the CBF and improved recovery. In a reperfused stroke model, the GRI–RIC combination therapy in diabetic mice augmented PbtO2, a translatory signature of successful microvascular reflow. In addition, RIC therapy unexpectedly increased the inflammatory markers at 6 h post-stroke in diabetic stroke that were downregulated in combination with GRI while improving the outcomes. Thus, we conclude that preexisting NOS3 dysfunctions due to comorbidities may neutralize the benefits of RIC in stroke, which can be turned protective in combination with GRI. Our findings may support the future clinical trial of RIC in comorbid stroke. Further studies are warranted to test and develop SNO reservoirs as the blood-associated biomarker to monitor the response and efficacy of RIC therapy in stroke