The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Production of bioplastic through food waste valorization.

https://digital.csic.es/bitstream/10261/157556/1/Postprint_2017_JEnvManagement_V205_P215.pdf

Challenges of scaling-up PHA production from waste streams. A review

The abundance of organic solid waste throughout the world has become a common issue that needs complete management at every level. Also, the scarcity of fuel and the competition between food and substance as an alternative to a petroleum-based product has become a major problem that needs to be properly handled. An urge to find renewable substances for sustainable development results in a strategy to valorize organic solid waste using solid state fermentation (SSF) and to manage the issue of solid wastes in a green approach. This paper reviews management of solid wastes using SSF, with regard to its current application, advantages and challenges, downstream processing in SSF, economic viewpoint, and future perspectives.

/pdf/solid-state-fermentation-as-a-novel-paradigm-for-organic-39nj6ni9vx.pdf

Solid-State Fermentation as a Novel Paradigm for Organic Waste Valorization: A Review

Lipase Inhibitors for Obesity: A Review.

Optimization and characterization of PHA from isolate Pannonibacter phragmitetus ERC8 using glycerol waste.

The bacterial strain producing thermostable, alklophilic alpha-amylase was identified as Bacillus amyloliquefaciens KCP2 using 16S rDNA gene sequencing data (NCBI Accession No: KF112071). Medium components were optimized through the statistical approach for the synthesis of alpha-amylase by the organism under solid-state fermentation using wheat bran as the substrate. The medium components influencing the enzyme production were identified using a two-level fractional factorial Plackett–Burman design. Among the various variables screened, starch, ammonium sulphate and calcium chloride were found to be most significant medium components. The optimum levels of these significant parameters were determined employing the response surface Central Composite design which significantly increased the enzyme production with the supplementation of starch 0.01 g, ammonium sulphate 0.2 g and 5 mM calcium chloride in the production medium. Temperature and pH stability of the alpha-amylase suggested its wide application in the food and pharmaceutical industries.

/pdf/a-statistical-approach-for-the-production-of-thermostable-41vfmj317i.pdf

A statistical approach for the production of thermostable and alklophilic alpha-amylase from Bacillus amyloliquefaciens KCP2 under solid-state fermentation

A halotolerant fungal isolate Aspergillus tubingensis GR1 was isolated from the man-made solar saltern located at Khambhat, Gujarat, India, and identified using 28S rDNA partial genome sequencing. This isolate was studied for β-galactosidase production under solid state fermentation using wheat bran and deproteinized acid cheese whey. The influence of various agro-industrial wastes, nitrogen source and other growth conditions on β-galactosidase production was investigated using ‘one-factor-at-a-time’ approach. Among various variables screened along with wheat bran and deproteinized acid cheese whey as major growth substrate, corn steep liquor and MgSO4 were found to be most significant. The optimum concentrations of these significant parameters were determined employing the response surface central composite design, revealing corn steep liquor concentration (2 mL) and magnesium sulphate (50 mg) per 5 g of wheat bran and 20 mL of deproteinized acid cheese whey for highest enzyme production (15,936 U/gds). These results suggest the feasibility of industrial large-scale production of β-galactosidase known to be valuable in whey hydrolysis and removal of galactosyl residue from polysaccharide.

/pdf/utilization-of-agro-industrial-waste-for-b-galactosidase-3iqo5cm47s.pdf

Utilization of agro-industrial waste for β-galactosidase production under solid state fermentation using halotolerant Aspergillus tubingensis GR1 isolate

Pigments produced by Monascus spp. can be used as food grade biocolorant and are preferred over the synthetic variants which elicit various adverse effects. Monascus purpureus MTCC 410 has been investigated in the present study for red pigment production employing submerged fermentation. The medium components influencing the pigment production were identified using Plackett–Burman design. Among various variables screened, glucose, tryptone and pH were found to be highly significant. The optimum concentrations of these significant parameters were determined employing the response surface central composite design. Glucose (28 g/L), tryptone (1 g/L) and pH 8.0 showed highest pigment production.

An enhancement of red pigment production by submerged culture of Monascus purpureus MTCC 410 employing statistical methodology

Demand of amylase in industrial sector is increasing day by day. Kitchen waste can be used for amylase production as it is generated on a daily basis and if not disposed of properly, creates various environmental problems. Bacillus amyloliquefaciens KCP2 is studied for amylase production using kitchen waste as low cost substrate under solid state fermentation. Dried kitchen waste has been used for amylase production with optimization of various physical parameters in a mineral salt medium. Maximum amylase production was obtained at 37 °C, pH 8 having 1:3 moisture ratio and 30% (v/w) inoculum after 72 h of fermentation. Amylase was partially purified by ammonium sulphate precipitation followed by dialysis with 1.2 fold purification. Partially purified enzyme showed 65 °C and 8 as optimized temperature and pH, respectively. Saccharification of 10% kitchen waste using 10 U/g enzyme showed 80% saccharification efficiency at 60 °C after 6 h.

Vimal S. Prajapati

Papers

Optimization and characterization of PHA from isolate Pannonibacter phragmitetus ERC8 using glycerol waste.

A statistical approach for the production of thermostable and alklophilic alpha-amylase from Bacillus amyloliquefaciens KCP2 under solid-state fermentation

Utilization of agro-industrial waste for β-galactosidase production under solid state fermentation using halotolerant Aspergillus tubingensis GR1 isolate

An enhancement of red pigment production by submerged culture of Monascus purpureus MTCC 410 employing statistical methodology

Kitchen waste for economical amylase production using Bacillus amyloliquefaciens KCP2