Dr Raman Vaidyanathan
Department of Chemical and Biological Engineering
Senior Lecturer in Chemical Engineering
Course Director MSc (Eng) Biological and Bioprocess Engineering
Course Director MSc (Eng) Biochemical Engineering with Industrial Management
+44 114 222 7526
Full contact details
Department of Chemical and Biological Engineering
Room G60
Sir Robert Hadfield Building
Mappin Street
Sheffield
S1 3JD
- Profile
-
I joined the Department as a lecturer in 2007. I'm a chemical graduate with a Masters degree in Biotechnology (both from India) and completed my PhD in 2001 from the University of Strathclyde in Glasgow, where I investigated the application of near infrared spectroscopy to monitor industrially relevant bioprocesses involving filamentous microorganisms. This was work done in collaboration with Eli Lilly.
I have over five years of pre-doctoral industrial experience applying biotechnological solutions to environmental engineering problems.
Before joining Sheffield I was a research associate at the University of Manchester, where I investigated a) the application of secondary ion mass spectrometry with buckminsterfullerene (C60) cluster ions as primary ion sources to characterize biological surfaces, and b) laser desorption ionization mass spectrometry for metabolomic applications.
I also spent my post-doctoral years investigating the application of soft ionization mass spectrometry to characterize biological systems, at Aberystwyth in Wales.
- Research interests
-
Algae Biotechnology
Systems and synthetic biology
Bioprocess Engineering
Bioenergy
Bioinformatics and use of machine learning
Metabolomics and Proteomics
Mass spectrometric imaging
- Publications
-
Books
- Metabolome Analyses:. Springer.
Journal articles
- Nitrate and phosphate uptake dynamics in two halotolerant strains of Chlorella vulgaris is differentially influenced by carbon, nitrogen and phosphorus supply. Chemical Engineering Journal, 458, 141433-141433.
- Response to nutrient variation on lipid productivity in green microalgae captured using second derivative FTIR and Raman spectroscopy. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 270.
- Towards a Phaeodactylum tricornutum biorefinery in an outdoor UK environment. Bioresource Technology.
- Interactions between polyethylene and polypropylene microplastics and Spirulina sp. microalgae in aquatic systems. Heliyon, 7(8), e07676-e07676.
- Enabling large-scale production of algal oil in continuous output mode. iScience, 102743-102743.
- Co-culturing microbial consortia: approaches for applications in biomanufacturing and bioprocessing. Critical Reviews in Biotechnology. View this article in WRRO
- The transition away from chemical flocculants: Commercially viable harvesting of Phaeodactylum tricornutum. Separation and Purification Technology, 255.
- Diatoms for carbon sequestration and bio-based manufacturing. Biology, 9(8).
- Influence of gas management on biochemical conversion of CO2 by microalgae for biofuel production. Applied Energy, 261. View this article in WRRO
- Phaeodactylum tricornutum : a diatom cell factory. Trends in Biotechnology. View this article in WRRO
- Biomolecular transitions and lipid accumulation in green microalgae monitored by FTIR and Raman analysis. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 224. View this article in WRRO
- Effects of cryopreservation on viability and functional stability of an industrially relevant alga. Scientific Reports, 9. View this article in WRRO
- Quenching for microalgal metabolomics: a case study on the unicellular eukaryotic green alga chlamydomonas reinhardtii. Metabolites, 8(4). View this article in WRRO
- The Effect of High-Intensity Ultraviolet Light to Elicit Microalgal Cell Lysis and Enhance Lipid Extraction.. Metabolites, 8(4). View this article in WRRO
- Effect of ammonium and high light intensity on the accumulation of lipids in Nannochloropsis oceanica (CCAP 849/10) and Phaeodactylum tricornutum (CCAP 1055/1). Biotechnology for Biofuels, 11(1), 60-60. View this article in WRRO
- Microalgae: a robust “green bio-bridge” between energy and environment. Critical Reviews in Biotechnology. View this article in WRRO
- Microbial consortia: a critical look at microalgae co-cultures for enhanced biomanufacturing. Critical Reviews in Biotechnology, 38(5), 690-703. View this article in WRRO
- Influence of washing and quenching in profiling the metabolome of adherent mammalian cells: a case study with the metastatic breast cancer cell line MDA-MB-231. Analyst, 142(11), 2038-2049. View this article in WRRO
- Towards quantitative mass spectrometry based metabolomics in microbial and mammalian systems. Philosophical transactions of the Royal Society of London. Series A: Mathematical and physical sciences, 374. View this article in WRRO
- Proteome response of Phaeodactylum tricornutum, during lipid accumulation induced by nitrogen depletion. Algal Research, 18, 213-224. View this article in WRRO
- The Search for a Lipid Trigger: The Effect of Salt Stress on the Lipid Profile of the Model Microalgal Species Chlamydomonas reinhardtii for Biofuels Production. Current Biotechnology, 5(4), 305-313. View this article in WRRO
- Dissolved inorganic carbon speciation in aquatic environments and its application to monitor algal carbon uptake. Science of The Total Environment, 541, 1282-1295.
- Cell line dependence of metabolite leakage in metabolome analyses of adherent normal and cancer cell lines. Metabolomics, 11(6), 1743-1755. View this article in WRRO
- Influence of nutrient status on the accumulation of biomass and lipid in Nannochloropsis salina and Dunaliella salina. Energy Conversion and Management, 106, 61-72. View this article in WRRO
- An efficient TOF-SIMS image analysis with spatial correlation and alternating non-negativity-constrained least squares. Bioinformatics, 31(5), 753-760.
- Simultaneous assay of pigments, carbohydrates, proteins and lipids in microalgae.. Anal Chim Acta, 776, 31-40.
- HILIC- and SCX-based quantitative proteomics of Chlamydomonas reinhardtii during nitrogen starvation induced lipid and carbohydrate accumulation.. J Proteome Res, 11(12), 5959-5971.
- A solvation-based screening approach for metabolite arrays.. Analyst, 137(10), 2350-2356.
- A simple, reproducible and sensitive spectrophotometric method to estimate microalgal lipids. Analytica Chimica Acta, 724, 67-72.
- A selective metabolite array for the detection of phosphometabolites. Analytica Chimica Acta.
- A simple, reproducible and sensitive spectrophotometric method to estimate microalgal lipids. Analytica Chimica Acta.
- Towards proteomics-on-chip: the role of the surface.. Mol Biosyst, 7(1), 101-115.
- Explanatory multivariate analysis of ToF-SIMS spectra for the discrimination of bacterial isolates.. Analyst, 134(11), 2352-2360.
- Which is more important in bioimaging SIMS experiments-The sample preparation or the nature of the projectile? General Discussion. APPLIED SURFACE SCIENCE, 255(4), 1305-1306.
- A.M. Dopico (ed): Methods in Membrane Lipids. Molecular Biotechnology, 40(2), 214-215.
- Subsurface biomolecular imaging of Streptomyces coelicolor using secondary ion mass spectrometry.. Anal Chem, 80(6), 1942-1951.
- TOF-SIMS 3D biomolecular imaging of Xenopus laevis oocytes using buckminsterfullerene (C60) primary ions.. Anal Chem, 79(6), 2199-2206.
- Proteome and metabolome analyses for monitoring food quality and authenticity, 29-48.
- Quantitative detection of metabolites using matrix-assisted laser desorption/ionization mass spectrometry with 9-aminoacridine as the matrix.. Rapid Commun Mass Spectrom, 21(13), 2072-2078.
- Laser desorption/ionization mass spectrometry on porous silicon for metabolome analyses: influence of surface oxidation.. Rapid Commun Mass Spectrom, 21(13), 2157-2166.
- Influence of instrumental conditions on the electrospray ionization mass spectrometry of peptides/proteins in mixtures. American Biotechnology Laboratory, 24(2), 32-33.
- Direct infusion electrospray ionization mass spectra of crude cell extracts for microbial characterizations: influence of solvent conditions on the detection of proteins.. Rapid Commun Mass Spectrom, 20(1), 21-30.
- Matrix-suppressed laser desorption/ionisation mass spectrometry and its suitability for metabolome analyses.. Rapid Commun Mass Spectrom, 20(8), 1192-1198.
- A laser desorption ionisation mass spectrometry approach for high throughput metabolomics. METABOLOMICS, 1(3), 243-250.
- Profiling microbial metabolomes: what do we stand to gain?. METABOLOMICS, 1(1), 17-28.
- Introduction: Metabolome analyses for systems biology. Metabolome Analyses: Strategies for Systems Biology, 1-7.
- Metabolome analyses: Strategies for systems biology. Metabolome Analyses: Strategies for Systems Biology, 1-390.
- High-throughput microbial characterizations using electrospray ionization mass spectrometry and its role in functional genomics. Chemical Analysis, 169, 229-256.
- Selective detection of proteins in mixtures using electrospray ionization mass spectrometry: influence of instrumental settings and implications for proteomics.. Anal Chem, 76(17), 5024-5032.
- Metabolomics by numbers: acquiring and understanding global metabolite data.. Trends Biotechnol, 22(5), 245-252.
- From genomes to systems.. Genome Biol, 5(11), 354. View this article in WRRO
- Explanatory optimization of protein mass spectrometry via genetic search.. Anal Chem, 75(23), 6679-6686.
- Influence of morphology on the near-infrared spectra of mycelial biomass and its implications in bioprocess monitoring. BIOTECHNOLOGY AND BIOENGINEERING, 82(6), 715-724.
- Metabolic profiling using direct infusion electrospray ionisation mass spectrometry for the characterisation of olive oils.. Analyst, 127(11), 1457-1462.
- Flow-injection electrospray ionisation mass spectrometry of crude cell extracts for high-throughput bacterial identification.. Journal of the American Society for Mass Spectrometry, 13, 118-128.
- Sample preparation in matrix‐assisted laser desorption/ionization mass spectrometry of whole bacterial cells and the detection of high mass (> 20 kDa) proteins.. Rapid Communications in Mass Spectrometry, 16(13), 1276-1286.
- Assessment of near-infrared spectral information for rapid monitoring of bioprocess quality.. Biotechnol Bioeng, 74(5), 376-388.
- Discrimination of aerobic endospore-forming bacteria via electrospray-ionization mass spectrometry of whole cell suspensions. ANALYTICAL CHEMISTRY, 73(17), 4134-4144.
- Assessment of the structure and predictive ability of models developed for monitoring key analytes in a submerged fungal bioprocess using near-infrared spectroscopy. APPLIED SPECTROSCOPY, 55(4), 444-453.
- Deconvolution of near-infrared spectral information for monitoring mycelial biomass and other key analytes in a submerged fungal bioprocess. ANALYTICA CHIMICA ACTA, 428(1), 41-59.
- At-line monitoring of a submerged filamentous bacterial cultivation using near-infrared spectroscopy.. Enzyme Microb Technol, 27(9), 691-697.
- Critical evaluation of models developed for monitoring an industrial submerged bioprocess for antibiotic production using near-infrared spectroscopy.. Biotechnol Prog, 16(6), 1098-1105.
- Fundamental investigations on the near-infrared spectra of microbial biomass as applicable to bioprocess monitoring. ANALYST, 124(2), 157-162.
- Monitoring of submerged bioprocesses. CRITICAL REVIEWS IN BIOTECHNOLOGY, 19(4), 277-316.
- Correction to: Influence of nutrient status on the biohydrogen and lipid productivity in Parachlorella kessleri: a biorefinery approach. Applied Microbiology and Biotechnology.
- Influence of nutrient status on the biohydrogen and lipid productivity in Parachlorella kessleri: a biorefinery approach. Applied Microbiology and Biotechnology.
- Capture agents, conversion mechanisms, biotransformations and biomimetics: general discussion. Faraday Discuss., 183, 463-487.
- Microwave-Assisted Extraction for Microalgae: From Biofuels to Biorefinery. Biology, 7(1). View this article in WRRO
Chapters
- Microbial Consortia: Concept and Application in Fruit Crop Management In Srivastava AK & Hu C (Ed.), Fruit Crops Diagnosis and Management of Nutrient Constraints (pp. 353-366). Elsevier View this article in WRRO
- Microbial consortia: Concept and application in fruit crop management, Fruit Crops (pp. 353-366). Elsevier
- Understanding the behaviour of pathogenic cells: proteome and metabolome analyses. In Griffiths M (Ed.), Understanding Pathogen Behaviour (pp. 3-52). CRC Press
- Proteome and metabolome analyses for food authentication In Lees M (Ed.), Food authenticity and traceability [electronic resource] (pp. 71-100). Woodhead Publishing
- Metabolome and Proteome Profiling for Microbial Characterization, Metabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis (pp. 9-38). Springer US
- Metabolome and proteome profiling for microbial characterization: Mass spectrometric applications. In Harrigan GG & Goodacre R (Ed.), Metabolic Profiling (pp. 9-38). Springer
- Contributor contact details, Food Authenticity and Traceability (pp. xiii-xvii). Elsevier
- Proteome and metabolome analyses for food authentication, Food Authenticity and Traceability (pp. 71-100).
Conference proceedings papers
- Vapour-mediated ion activation for enhanced SIMS imaging. SURFACE AND INTERFACE ANALYSIS, Vol. 45(1) (pp 290-293)
- Cellular metabolic profiling using ToF-SIMS. SURFACE AND INTERFACE ANALYSIS, Vol. 45(1) (pp 255-259)
- ANYL 380-Matrix effects in biomolecular imaging using ToF-SIMS. ABSTR PAP AM CHEM S, Vol. 238
- BIOT 402-Seeking the message in the medium: Metabolic footprints of microalgal cultivations for bioenergy. ABSTR PAP AM CHEM S, Vol. 238
- Uncovering new challenges in bio-analysis with ToF-SIMS. APPLIED SURFACE SCIENCE, Vol. 255(4) (pp 1264-1270)
- TOF-SIMS investigation of Streptomyces coelicolor, a mycelial bacterium. APPLIED SURFACE SCIENCE, Vol. 255(4) (pp 922-925)
- Exploratory analysis of TOF-SIMS data from biological surfaces. APPL SURF SCI, Vol. 255(4) (pp 1599-1602)
- Proteome and metabolome analyses for rapid authentication of food.. Rapid Methods Europe 2005 (pp 29-48). Noordwijk aan Zee, the Netherlands, 24 May 2005 - 25 May 2005.
- Electrospray-ionization mass spectrometry of protein mixtures: Influence of instrumental settings and proteomic implications.. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, Vol. 229 (pp U185-U185)
- Metabolomic investigations using laser desorption ionisation mass spectrometry on porous silicon. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, Vol. 229 (pp U245-U245)
- Metabolite and protein profiling of whole cells using soft-ionization mass spectrometry for rapid microbial characterization.. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, Vol. 225 (pp U199-U199)
- Rapid, high-throughput microbial characterization by metabolite and protein profiling of whole cells using soft-ionization mass spectrometry.. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, Vol. 224 (pp U199-U199)
- Measurement of mycelial biomass in a submerged bioprocess using near infrared spectroscopy.. NIRS-’99 - Proceedings of the 9th International conference on Near-infrared spectroscopy (pp 429-433). Chichester, UK
Preprints
- Metabolome Analyses:. Springer.
- Research group
-
Our current research focus is in developing and establishing microalgae-based value chains and processes that can be carbon negative and offer environmentally sustainable solutions with wider impact in the chemicals, materials, energy, food and health sectors. We are working with a diverse group of microalgae, including Chalmydomonas sp., Chlorella sp., Dunaliella salina, Scenedesmus sp., Phaeodactylum tricornutum, Nannochloropsis oceanica, Porphyridium purpureum, etc. The investigations include molecular level understanding and identification of relevant metabolic pathways, metabolic modelling, systems level characterisations, chemical and biochemical process engineering, techno-economic assessments, resource utilisation towards a circular bio-economy. We have been funded by UKRI BBSRC and EPSRC o develop an understanding of lipid accumulation in microalgae towards sustainable biofuels production, and by EU H2020, through an MSCFA to study nutrient uptake by microalgae.
We have identified key delineating features suitable for lipid accumulation in marine microalgae that would help in selecting appropriate strains and process conditions suitable for oil production in microalgae [1]. We have studied nutrient uptake in the context of lipid accumulation in P. tricornutum and N. oceanica [2], as well as in N. salina and D. salina [3] and have reported on the differences in the capacity between species to respond to the supply of nitrogen and exposure to high intensity light towards increased lipid accumulation. We have reported on cryopreservation of Chlorella to preserve its lipid accumulating capacity [4]. We are working towards a better understanding of carbon uptake by microalgae [5] to enable appropriate interventions for carbon capture and utilisation. Methods to characterise dissolved inorganic carbon [6], intracellular biochemical compositions [7,8], proteomic and metabolomic data acquisition in microalgae [9,10,11,12] have been established. We are developing strategies for microalgae based microbial co-culture systems for better bioproduct formations [13, 14]. Accumulation of the health-promoting polyunsaturated fatty acids, such as EPA, in the diatom, P. tricornutum have been characterised in pilot-scale outdoor PBRs, as a part of BBSRC funded research (PHYCBIV-28), as well as cell lysis for extraction of products from microalgae (PHYCBIV-13). The development of a biorefinery concept with microalgal cultivations to sustainably sequester CO 2 and produce economically viable processes is being explored with the diatom P. tricornutum [15, 16]. These include downstream processing considerations [17, 18].
We wish to build on these findings and develop relevant microalgae-based value chains and materials to enable sustainable interventions in diverse sectors, including renewable energy generation [19, 20], agriculture [21], aquaculture practice, food production, nutrition, health, bulk and fine chemical manufacture. These interventions are aimed at developing environmentally inclusive, economically impacting routes to future food security, chemical manufacturing, health and energy generation. We have wider expertise in microbial characterisations, omic analyses, mass spectrometric imaging, bioinformatics, bioprocess monitoring and microbial process engineering.
- Teaching activities
-
- CPE403/6030 - Environment: Gaseous Emissions
- CPE401 - Research Project (MEng)
- CPE6009 – Bio-energy
- CPE6016 – Bioanalytical Techniques (MSc BBE)