Microbial community analysis in anaerobic palm oil mill effluent (pome) waste...eSAT Journals
Microorganisms play a key role in wastewater bio-treatment processes and understanding the microbial community structure is of great importance to improve treatment performance. Denaturing gradient gel electrophoresis (DGGE) was used to monitor succession of the microbial community and thus predominant bands were sequenced to reveal the microbial community composition inside palm oil mill effluent (POME) wastewater.DNA bands from DGGE gels were excised with a sterile blade and placed in 1.5 ml eppendorf tube containing 50 μl deionized water (ddH2O). Tubes were incubated overnight at 4C to elute the DNA. Eluted DNA was purified using QIAquick gel extraction kits (QIAGEN, Inc., Valencia, CA) and was frozen and thawed three times.Microbial DNA successfully excised and purified from DGGE was amplified using polymerase chain reaction (PCR).Five micro liters of the supernatant were used as a template to re-amplify the DNA using 16s rDNA primers,341f (with no GC-clamp) (5'- cct-acg-gga-ggc-agc-ag-3') and reverse(r) primers 907r (5'-ccc-cgt-caa-ttc-att-tga-gtt-t-3'). Amplification was repeated referring to the steps in ‘PCR amplification of 16s rDNA’. PCR products from agarose gels were cut and purified using QIAquick Gel Extraction Kit (QIAGEN, Inc., Valencia, CA), which were similar to the purification steps after recovery of DNA from DGGE, and sequenced in both directions with the same primers (with no GC-clamp) as used in PCR. Moreover, start-up is an important step in establishing proper community structure in all kinds of biological treatment processes. In anaerobic POME wastewater, 6 sequences of Firmicutes, 5 sequence of Proteobacterium and 2 sequences of Bacteroidetes were found through denaturing gradient gel electrophoresis (DGGE) results. Sequence closely related to Rummeliibacillus suwonensis strain G20 was detected grows at band BE10, BE11, BE12, BE15, BE16, BE17 and BE18. Meanwhile BE25 and BE26 were found at band after treatment process done.Rummeliibacillus suwonensis is an aerobic, Gram-positive, rod shaped, round-spore-forming bacteria which were isolated from aerobic condition. Keywords: Palm oil mill effluent (POME), anaerobic POME, Denaturing gradient gel electrophoresis (DGGE), and microbial community.
Summary of BioSeek's work for the EPA's ToxCast (TM) program. BioSeek has been a contractor since 2007 for the EPA, using the company's human cell-based BioMAP(R) systems platform.
Overview of patenting activity in Syn Bio, patentable subject matter, requirements for patentability and infringement issues for innovations in that field.
Introduction to Synthetic Genome
SYNTHETIC GENOMICS Study of Invitro chemical synthesis of genetic material i.e., DNA in the form of oligonucleotides, genes, or genomes with Computational techniques for its design. SYNTHETIC GENOME Artificially synthesised genome (invitro)
Microbial community analysis in anaerobic palm oil mill effluent (pome) waste...eSAT Journals
Microorganisms play a key role in wastewater bio-treatment processes and understanding the microbial community structure is of great importance to improve treatment performance. Denaturing gradient gel electrophoresis (DGGE) was used to monitor succession of the microbial community and thus predominant bands were sequenced to reveal the microbial community composition inside palm oil mill effluent (POME) wastewater.DNA bands from DGGE gels were excised with a sterile blade and placed in 1.5 ml eppendorf tube containing 50 μl deionized water (ddH2O). Tubes were incubated overnight at 4C to elute the DNA. Eluted DNA was purified using QIAquick gel extraction kits (QIAGEN, Inc., Valencia, CA) and was frozen and thawed three times.Microbial DNA successfully excised and purified from DGGE was amplified using polymerase chain reaction (PCR).Five micro liters of the supernatant were used as a template to re-amplify the DNA using 16s rDNA primers,341f (with no GC-clamp) (5'- cct-acg-gga-ggc-agc-ag-3') and reverse(r) primers 907r (5'-ccc-cgt-caa-ttc-att-tga-gtt-t-3'). Amplification was repeated referring to the steps in ‘PCR amplification of 16s rDNA’. PCR products from agarose gels were cut and purified using QIAquick Gel Extraction Kit (QIAGEN, Inc., Valencia, CA), which were similar to the purification steps after recovery of DNA from DGGE, and sequenced in both directions with the same primers (with no GC-clamp) as used in PCR. Moreover, start-up is an important step in establishing proper community structure in all kinds of biological treatment processes. In anaerobic POME wastewater, 6 sequences of Firmicutes, 5 sequence of Proteobacterium and 2 sequences of Bacteroidetes were found through denaturing gradient gel electrophoresis (DGGE) results. Sequence closely related to Rummeliibacillus suwonensis strain G20 was detected grows at band BE10, BE11, BE12, BE15, BE16, BE17 and BE18. Meanwhile BE25 and BE26 were found at band after treatment process done.Rummeliibacillus suwonensis is an aerobic, Gram-positive, rod shaped, round-spore-forming bacteria which were isolated from aerobic condition. Keywords: Palm oil mill effluent (POME), anaerobic POME, Denaturing gradient gel electrophoresis (DGGE), and microbial community.
Summary of BioSeek's work for the EPA's ToxCast (TM) program. BioSeek has been a contractor since 2007 for the EPA, using the company's human cell-based BioMAP(R) systems platform.
Overview of patenting activity in Syn Bio, patentable subject matter, requirements for patentability and infringement issues for innovations in that field.
Introduction to Synthetic Genome
SYNTHETIC GENOMICS Study of Invitro chemical synthesis of genetic material i.e., DNA in the form of oligonucleotides, genes, or genomes with Computational techniques for its design. SYNTHETIC GENOME Artificially synthesised genome (invitro)
James J. Collins
Howard Hughes Medical Institute
Dept of Biomedical Engineering & Center of Synthetic Biology
Boston University
Wyss Institute for Biologically Inspired Engineering
Harvard University
Problem formulation considerations for externally applied dsRNA-based product...OECD Environment
10-12 April 2019: The OECD Conference on RNAi based pesticides provided an overview on the current status and future possibilities for the regulation of externally applied dsRNA-based products that are proposed for use as pesticides. The event facilitated exchanges between policy makers, academia, industry on their implications in health, environment, and regulation.
OBC | Synthetic biology announcing the coming technological revolutionOut of The Box Seminar
Roman Jerala, National Institute of Chemistry, Ljubljana, Slovenia
Synthetic biology announcing the coming technological revolution
http://obc2012.outofthebox.si/
Synthetic biology is an interdisciplinary branch of biology and engineering. The subject combines disciplines from within these domains, such as biotechnology, genetic engineering, molecular biology, molecular engineering, systems biology, biophysics, electrical engineering, computer engineering, control engineering and evolutionary biology. Synthetic biology applies these disciplines to build artificial biological systems for research, engineering, and medical applications
K-mers in metagenomics
K-mers play a critical role in the exploration of metagenomic data. They have been widely used to assign taxonomic attributions to the short genomic fragments characteristic of shotgun (metagenomic) sequencing. These approaches provide an assembly-free method for profiling microbial communities, and have helped elucidate the factors driving microbial community composition across biogeochemical gradients. Advances in sequencing technology are now making it cost-effective to sequence microbial communities at sufficient depths to allow for the assembly of high-quality contigs. This has made it possible to adopt k-mer based approaches to enable reliable binning of contigs originating from a single microbial population within a community. In this session, I will present both an overview of how k-mers can be used to assign taxonomic attributions to short metagenomic reads, and discuss how these approaches have advanced to a point where population genomes can be recovered en masse from even complex microbial communities.
abstract
Extracts of the medicinal plant Palicourea rigida Kunth, popularly known as douradinha, are
widely used for treating urinary tract disorders. Unfortunately, nowadays this is one of the
species endemic to Brazilian Cerrado that is at greatest risk of extinction.
The aim of the this work was to use AFLP molecular markers to determine the genetic
structure and diversity of eight natural populations of P. rigida and to associate their genetic
characteristics with loganin production in order to obtain provide relevant information
to promote programs for the conservation of this valuable medicinal plant.
A total of 120 polymorphic bands were scored and higher proportion of genetic diversity
was found in inter-populations (64%) rather than in intra-populations (36%). Fst value was
found to be significantly greater than zero (0.3601), demonstrating the complex genetic
structure of P. rigida populations. Accessions collected from Cristalina, GO, showed higher
percentage of polymorphic loci (65.5%) and the highest genetic diversity. Analysis of
Molecular variance (AMOVA) demonstrated 63.9% of intra-population genetic variation.
The lowest genetic variability was detected among accessions from the population found
in Sacramento, MG. No spatial standard was observed for P. rigida population, suggesting a
partially isolated island model. It was observed a minor but significant positive correlation
(r ¼ 0.22) between chemical and genetic matrices. The association between chemical and
genetic data indicated that environmental factors promoted the loganin production in
populations growing in Luziânia, GO, and therefore accessions from those populations
should be considered as prime material for initiating the conservation process of P. rigida.
2013 Elsevier Ltd. All rights reserved.
Studies on the Production of Rhamnolipids by Pseudomonas Putida IJORCS
Rhamnolipid as a potent natural biosurfactant has a wide range of potential applications, including enhanced oil recovery, biodegradation, and bioremediation. Observation of tensio-active indicated that biosurfactants were produced by the newly isolated and promising strain Pseudomonas putida. The biosurfactants were identified as rhamnolipids, the amphiphilic surface-active glycolipids usually secreted by Pseudomonas sp. In addition, the ability to generate rhamnolipids by placement of the right microbes might help overcome rhamnolipid adsorption during flow through reservoir rocks and the resultant degradation that would decrease the rhamnolipid concentrations. Their production was observed when the strain was grown on soluble substrates, such as glucose or on poorly soluble substrates. Maximum value 1.13 mg/ ml was occurred on the second day. Production of biosurfactants depends on the nutrient media. The surface tension was decreased with increasing time and growth.
James J. Collins
Howard Hughes Medical Institute
Dept of Biomedical Engineering & Center of Synthetic Biology
Boston University
Wyss Institute for Biologically Inspired Engineering
Harvard University
Problem formulation considerations for externally applied dsRNA-based product...OECD Environment
10-12 April 2019: The OECD Conference on RNAi based pesticides provided an overview on the current status and future possibilities for the regulation of externally applied dsRNA-based products that are proposed for use as pesticides. The event facilitated exchanges between policy makers, academia, industry on their implications in health, environment, and regulation.
OBC | Synthetic biology announcing the coming technological revolutionOut of The Box Seminar
Roman Jerala, National Institute of Chemistry, Ljubljana, Slovenia
Synthetic biology announcing the coming technological revolution
http://obc2012.outofthebox.si/
Synthetic biology is an interdisciplinary branch of biology and engineering. The subject combines disciplines from within these domains, such as biotechnology, genetic engineering, molecular biology, molecular engineering, systems biology, biophysics, electrical engineering, computer engineering, control engineering and evolutionary biology. Synthetic biology applies these disciplines to build artificial biological systems for research, engineering, and medical applications
K-mers in metagenomics
K-mers play a critical role in the exploration of metagenomic data. They have been widely used to assign taxonomic attributions to the short genomic fragments characteristic of shotgun (metagenomic) sequencing. These approaches provide an assembly-free method for profiling microbial communities, and have helped elucidate the factors driving microbial community composition across biogeochemical gradients. Advances in sequencing technology are now making it cost-effective to sequence microbial communities at sufficient depths to allow for the assembly of high-quality contigs. This has made it possible to adopt k-mer based approaches to enable reliable binning of contigs originating from a single microbial population within a community. In this session, I will present both an overview of how k-mers can be used to assign taxonomic attributions to short metagenomic reads, and discuss how these approaches have advanced to a point where population genomes can be recovered en masse from even complex microbial communities.
abstract
Extracts of the medicinal plant Palicourea rigida Kunth, popularly known as douradinha, are
widely used for treating urinary tract disorders. Unfortunately, nowadays this is one of the
species endemic to Brazilian Cerrado that is at greatest risk of extinction.
The aim of the this work was to use AFLP molecular markers to determine the genetic
structure and diversity of eight natural populations of P. rigida and to associate their genetic
characteristics with loganin production in order to obtain provide relevant information
to promote programs for the conservation of this valuable medicinal plant.
A total of 120 polymorphic bands were scored and higher proportion of genetic diversity
was found in inter-populations (64%) rather than in intra-populations (36%). Fst value was
found to be significantly greater than zero (0.3601), demonstrating the complex genetic
structure of P. rigida populations. Accessions collected from Cristalina, GO, showed higher
percentage of polymorphic loci (65.5%) and the highest genetic diversity. Analysis of
Molecular variance (AMOVA) demonstrated 63.9% of intra-population genetic variation.
The lowest genetic variability was detected among accessions from the population found
in Sacramento, MG. No spatial standard was observed for P. rigida population, suggesting a
partially isolated island model. It was observed a minor but significant positive correlation
(r ¼ 0.22) between chemical and genetic matrices. The association between chemical and
genetic data indicated that environmental factors promoted the loganin production in
populations growing in Luziânia, GO, and therefore accessions from those populations
should be considered as prime material for initiating the conservation process of P. rigida.
2013 Elsevier Ltd. All rights reserved.
Studies on the Production of Rhamnolipids by Pseudomonas Putida IJORCS
Rhamnolipid as a potent natural biosurfactant has a wide range of potential applications, including enhanced oil recovery, biodegradation, and bioremediation. Observation of tensio-active indicated that biosurfactants were produced by the newly isolated and promising strain Pseudomonas putida. The biosurfactants were identified as rhamnolipids, the amphiphilic surface-active glycolipids usually secreted by Pseudomonas sp. In addition, the ability to generate rhamnolipids by placement of the right microbes might help overcome rhamnolipid adsorption during flow through reservoir rocks and the resultant degradation that would decrease the rhamnolipid concentrations. Their production was observed when the strain was grown on soluble substrates, such as glucose or on poorly soluble substrates. Maximum value 1.13 mg/ ml was occurred on the second day. Production of biosurfactants depends on the nutrient media. The surface tension was decreased with increasing time and growth.
DOI: 10.21276/ijlssr.2016.2.4.4
ABSTRACT- Microorganisms are the important factors in the degradation of the toxic substances in our environment.
Petrol and diesel oil is one of the complex mixtures which cannot be easily degraded. The Bacillus cereus was involved in
the degradation of oil during which the complex toxic substances were detoxified by the production of biosurfactants. In
our study we have identified that the biosurfactant producing Bacillus cereus have a high potential for hydrocarbon
degradation. The Bacillus cereus was isolated from hydrocarbon contaminated soil and identified based on morphology
and biochemical test according to the Bergey’s manual of systematic bacteriology. The maximum hydrocarbon degrading
biosurfactant producing Bacillus cereus was obtained by qualitative and quantitative methods. In optimization studies, the
best results observed for Bacillus cereus were, Olive oil as the suitable carbon source, Sodium nitrate as the best Nitrogen
source and Optimum pH is 7 and Optimum temperature is 37°C. The ability of these isolates to degrade hydrocarbons and
survive in the oil contaminated soil is attributed to the development of resistance by mutation on the plasmid. It is also
clearly evident that the specific gene was responsible for the production of biosurfactant and the degradation process.
According to the results from the present study the Bacillus cereus has high potential for hydrocarbon degradation and can
be used especially for Microbial Enhanced Oil Recovery and bioremediation of hydrocarbons in near future.
Key-words- Bacillus cereus, Biosurfactant, Hydrocarbon, Biodegradation, Plasmid DNA
Digital Futures Knowledge Networks Bbc R&D At Mmu Create Group LaunchBBC
Digital Futures: Knowledge Networks for Creative Industries. This is a presentation given to the CREATE group at Manchester Metropolitan University. The theme was to explore the potential for a Greater Manchester network of research in education, technology and digital cultures. The presentation showcases work by colleagues across BBC from R&D, Innovation Culture, Learning Innovation and Bitesize.
Summer training (civil engineering)-Ramp constructionVivek_13
Good and short presentation for BACK BENCHERS.
Presentation on ramp construction in hospitals.
Also, discuss the comparison between stairs and ramp.
Design consideration of ramp construction.
Some photographs are available to clarify the topic.
Presentation of Cristina M. M. Machado for the Workshop on Hydrolysis Route for Cellulosic Ethanol from Sugarcane.
Apresentação de Cristina M. M. Machado realizada no "Workshop on Hydrolysis Route for Cellulosic Ethanol from Sugarcane"
Date / Data : February 10 - 11th 2009/
10 e 11 de fevereiro de 2009
Place / Local: Unicamp, Campinas, Brazil
Event Website / Website do evento: http://www.bioetanol.org.br/workshop1
ER Publication,
IJETR, IJMCTR,
Journals,
International Journals,
High Impact Journals,
Monthly Journal,
Good quality Journals,
Research,
Research Papers,
Research Article,
Free Journals, Open access Journals,
erpublication.org,
Engineering Journal,
Science Journals,
Isolation, Screening, and Characterization of Biosurfactant-Producing Microor...BRNSS Publication Hub
Introduction: Biosurfactants are amphiphatic in nature and are surface-active compounds produced by microorganisms. These molecules reduce interfacial surface tension between aqueous solutions and hydrocarbon mixtures. Unfortunately, oil spills and industrial discharges from petroleum-related industries have been identified as the major pollution sources. The hydrophobicity and low aqueous solubility of petroleum pollutant limit the biodegradation process. The features that make biosurfactants as an alternative to commercially synthesized surfactants are its low toxicity, higher biodegradability and, hence, greater environmental compatibility, better foaming properties, and stable activity at extreme pH, temperature, and salinity. Objective: Therefore, in this study, hydrocarbon-degrading bacteria were screened from petroleum-contaminated soil, characterized and optimization of the physical and nutrient parameters were done to enhance the production of biosurfactants. Results: Petroleum-contaminated soil was collected from different petrol pumps in Pune and screening was done on minimal salt medium media containing palm oil as carbon source using hemolytic activity, emulsification index, drop-collapse test, and oil displacement method. The most promising strain was isolated and identified using Bergey’s Manual of Determinative Biology and 16s rRNA sequencing and was found to be Staphylococcus epidermidis. The optimization of various parameters, namely temperature, pH, carbon, and nitrogen sources on growth, and biosurfactant production was studied. The highest biosurfactant production was obtained when MSS media contains sucrose (carbon source) and urea (nitrogen source) at pH 10 and temperature 55°C. The Fourier transform-infrared (FT-IR) analysis of purified biosurfactant indicated the presence of lipopeptide biosurfactant when compared with reference FT-IR spectra.
Science and technology of manipulating and improving microbial strains, in order to enhance their metabolic capacities for biotechnological applications, are referred to as strain improvement.
13. GTI pioneered the development of two-phase anaerobic digestion of biomass to make methane. The reactor pictured here is at the Woodridge, IL wastewater treatment plant.
14.
15.
16. Microbial Corrosion A faster, more accurate, and less expensive method to detect microorganisms associated with corrosion was developed from concept through commercialization .
Three main areas of current and past research Biorefining of Petroleum = Upgrading of petroleum quality using microbes Expression systems using unconventional hosts = unconventional meaning not E. coli, Different host are required in applications of biotechnology to the energy industry. MIC = Little is known about the microorganisms that survive in the harsh environment of an internal natural gas pipeline and can be causative agents of corrosion.
I gave you an overview of some of the projects that I research and manage. I wanted briefly to describe other interactions at GTI that go into developing these projects and commercialization of any technologies that result.