Biomolecular Discovery and Design Research Centre

Research Output 1980 2019

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2019

A portable nucleic acid detection system using natural convection combined with a smartphone

Rajendran, V. K., Bakthavathsalam, P., Bergquist, P. L. & Sunna, A., 1 Jun 2019, In : Biosensors and Bioelectronics. 134, p. 68-75 8 p.

Research output: Contribution to journalArticleResearchpeer-review

Convection
Smartphones
Nucleic acids
Natural convection
Nucleic Acids

Cell-free enzymatic conversion of spent coffee grounds into the platform chemical lactic acid

Kopp, D., Willows, R. D. & Sunna, A., Dec 2019, In : Frontiers in Bioengineering and Biotechnology. 7, p. 1-13 13 p., 389.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Coffee
Lactic acid
Mannose
Lactic Acid
Enzymes

Characterisation of the first archaeal mannonate dehydratase from Thermoplasma acidophilum and its potential role in the catabolism of D-Mannose

Kopp, D., Willows, R. & Sunna, A., Mar 2019, In : Catalysts. 9, 3, p. 1-14 14 p., 234.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
catabolism
Mannose
genes
xylose
Xylose

Comparative proteomics investigation of central carbon metabolism in Euglena gracilis grown under predominantly phototrophic, mixotrophic and heterotrophic cultivations

Hasan, M. T., Sun, A., Khatiwada, B., McQuade, L., Mirzaei, M., Te'o, J., Hobba, G., Sunna, A. & Nevalainen, H., Nov 2019, In : Algal Research. 43, 11 p., 101638.

Research output: Contribution to journalArticleResearchpeer-review

Euglena gracilis
proteomics
metabolism
carbon
enzymes

Development of screening strategies for the identification of paramylon-degrading enzymes

Gissibl, A., Care, A., Sun, Y., Hobba, G., Nevalainen, H. & Sunna, A., Jun 2019, In : Journal of Industrial Microbiology and Biotechnology. 46, 6, p. 769-781 13 p.

Research output: Contribution to journalArticleResearchpeer-review

Screening
Enzymes
Euglena gracilis
Assays
Escherichia coli

Differential involvement of glycans in the binding of Staphylococcus epidermidis and Corynebacterium spp. to human sweat

Lin, C-H., Peterson, R. A., Gueniche, A., de Beaumais, S. A., Hourblin, V., Breton, L., Dalko, M. & Packer, N. H., Mar 2019, In : Microbiological Research. 220, p. 53-60 8 p.

Research output: Contribution to journalArticleResearchpeer-review

Corynebacterium
Staphylococcus epidermidis
Sweat
Polysaccharides
Fucose

Experimental and theoretical tools to elucidate the binding mechanisms of solid-binding peptides

Bansal, R., Care, A., Lord, M. S., Walsh, T. R. & Sunna, A., 25 Sep 2019, In : New Biotechnology. 52, p. 9-18 10 p.

Research output: Contribution to journalArticleResearchpeer-review

Peptides
Nanobiotechnology
Biomolecules
Substrates

Interactions of an emerging fungal pathogen Scedosporium aurantiacum with human lung epithelial cells

Kaur, J., Kautto, L., Penesyan, A., Meyer, W., Elbourne, L. D. H., Paulsen, I. T. & Nevalainen, H., 22 Mar 2019, In : Scientific Reports. 9, 10 p., 5035.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Scedosporium
Fungal Spores
Epithelial Cells
Lung
Infection

Linker-protein G mediated functionalization of polystyrene-encapsulated upconversion nanoparticles for rapid gene assay using convective PCR

Potluri, P. R., Rajendran, V. K., Tran, C. T., McKenzie, D. R. & Sunna, A., Jun 2019, In : Microchimica Acta. 186, 6, p. 1-9 9 p., 346.

Research output: Contribution to journalArticleResearchpeer-review

Polystyrenes
Assays
Genes
Nanoparticles
Digoxigenin

Mixed-mode liquid chromatography for the rapid analysis of biocatalytic glucaric acid reaction pathways

Petroll, K., Care, A., Waterstraat, M., Bergquist, P. & Sunna, A., 20 Aug 2019, In : Analytica Chimica Acta. 1066, p. 136-145 10 p.

Research output: Contribution to journalArticleResearchpeer-review

Glucaric Acid
Liquid chromatography
Liquid Chromatography
liquid chromatography
acid

Nuclear transformation of the versatile microalga Euglena gracilis

Khatiwada, B., Kautto, L., Sunna, A., Sun, A. & Nevalainen, H., Jan 2019, In : Algal Research. 37, p. 178-185 8 p.

Research output: Contribution to journalArticleResearchpeer-review

Euglena gracilis
biolistics
electroporation
Agrobacterium
DNA

Post-column make-up flow (PCMF) enhances the performance of capillary-flow PGC-LC-MS/MS-based glycomics

Hinneburg, H., Chatterjee, S., Schirmeister, F., Nguyen-Khuong, T., Packer, N. H., Rapp, E. & Thaysen-Andersen, M., 2 Apr 2019, In : Analytical Chemistry. 91, 7, p. 4559-4567 9 p.

Research output: Contribution to journalArticleResearchpeer-review

Capillary flow
Polysaccharides
2-Propanol
Organic solvents
Glycoproteins

Protein paucimannosylation is an enriched N-glycosylation signature of human cancers

Chatterjee, S., Lee, L. Y., Kawahara, R., Abrahams, J. L., Adamczyk, B., Anugraham, M., Ashwood, C., Sumer-Bayraktar, Z., Briggs, M. T., Chik, J. H. L., Everest-Dass, A., Förster, S., Hinneburg, H., Leite, K. R. M., Loke, I., Möginger, U., Moh, E. S. X., Nakano, M., Recuero, S., Sethi, M. K. & 14 othersSrougi, M., Stavenhagen, K., Venkatakrishnan, V., Wongtrakul-Kish, K., Diestel, S., Hoffmann, P., Karlsson, N. G., Kolarich, D., Molloy, M. P., Muders, M. H., Oehler, M. K., Packer, N. H., Palmisano, G. & Thaysen-Andersen, M., Nov 2019, In : Proteomics. 19, 21-22, p. 1-13 13 p., 1900010.

Research output: Contribution to journalArticleResearchpeer-review

Glycosylation
Polysaccharides
Tumors
Tissue
Neoplasms

Smartphone detection of antibiotic resistance using convective PCR and a lateral flow assay

Rajendran, V. K., Bakthavathsalam, P., Bergquist, P. L. & Sunna, A., 1 Nov 2019, In : Sensors and Actuators, B: Chemical. 298, p. 1-10 10 p., 126849.

Research output: Contribution to journalArticleResearchpeer-review

antibiotics
Smartphones
Nucleic acids
nucleic acids
Antibiotics
2018

Comparative assessment of the Euglena gracilis var. saccharophila variant strain as a producer of the β-1,3-glucan paramylon under varying light conditions

Sun, A., Hasan, M. T., Hobba, G., Nevalainen, H. & Te'o, J., Aug 2018, In : Journal of Phycology. 54, 4, p. 529-538 10 p.

Research output: Contribution to journalArticleResearchpeer-review

Euglena gracilis
beta-glucans
plastid
glucose
proteomics

Detection of the cyanotoxins L-BMAA uptake and accumulation in primary neurons and astrocytes

Tan, V. X., Mazzocco, C., Varney, B., Bodet, D., Guillemin, T. A., Bessede, A. & Guillemin, G. J., Jan 2018, In : Neurotoxicity Research. 33, 1, p. 55–61 7 p.

Research output: Contribution to journalArticleResearchpeer-review

Astrocytes
Neurons
Toxicity
Brain
Neurodegenerative diseases

Glycomics@ExPASy: bridging the gap

Mariethoz, J., Alocci, D., Gastaldello, A., Horlacher, O., Gasteiger, E., Rojas-Macias, M., Karlsson, N. G., Packer, N. H. & Lisacek, F., 1 Nov 2018, In : Molecular and Cellular Proteomics. 17, 11, p. 2164-2176 13 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Glycomics
Bioinformatics
Computational Biology
Databases
Reference Values

Growth and protease secretion of Scedosporium aurantiacum under conditions of hypoxia

Han, Z., Kautto, L., Meyer, W., Chen, S. C-A. & Nevalainen, H., Nov 2018, In : Microbiological Research. 216, p. 23-29 7 p.

Research output: Contribution to journalArticleResearchpeer-review

Scedosporium
Peptide Hydrolases
Growth
Cysteine Proteases
Virulence

Microwave pretreatment of paramylon enhances the enzymatic production of soluble β-1,3-glucans with immunostimulatory activity

Gissibl, A., Care, A., Parker, L. M., Iqbal, S., Hobba, G., Nevalainen, H. & Sunna, A., 15 Sep 2018, In : Carbohydrate Polymers. 196, p. 339-347 9 p.

Research output: Contribution to journalArticleResearchpeer-review

Microwaves
Glucan 1,3-beta-Glucosidase
Hydrolysis
Polymerization
Enzymatic hydrolysis

Overview of gene expression using filamentous fungi

Nevalainen, H., Peterson, R. & Curach, N., Apr 2018, In : Current Protocols in Protein Science. 92, 1, p. 1-10 10 p., e55.

Research output: Contribution to journalArticleResearchpeer-review

Fungi
Gene expression
Gene Expression
Proteins
Secretory Pathway

Proteomic phenotyping of metastatic melanoma reveals putative signatures of MEK inhibitor response and prognosis

Krisp, C., Parker, R., Pascovici, D., Hayward, N. K., Wilmott, J. S., Thompson, J. F., Mann, G. J., Long, G. V., Scolyer, R. A. & Molloy, M. P., 17 Aug 2018, In : British Journal of Cancer. 119, 6, p. 713–723 11 p.

Research output: Contribution to journalArticleResearchpeer-review

Mitogen-Activated Protein Kinase Kinases
Proteomics
Melanoma
Proteins
Biomarkers

Raw N-glycan mass spectrometry imaging data on formalin-fixed mouse kidney

Gustafsson, O. J. R., Briggs, M. T., Condina, M. R., Winderbaum, L. J., Pelzing, M., McColl, S. R., Everest-Dass, A. V., Packer, N. H. & Hoffmann, P., 1 Dec 2018, In : Data in Brief. 21, p. 185-188 4 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Formaldehyde
Mass spectrometry
Polysaccharides
Imaging techniques
Metadata

Transition of mesenchymal and epithelial cancer cells depends on α1-4 galactosyltransferase-mediated glycosphingolipids

Jacob, F., Alam, S., Konantz, M., Liang, C. Y., Kohler, R. S., Everest-Dass, A. V., Huang, Y-L., Rimmer, N., Fedier, A., Schötzau, A., Lopez, M. N., Packer, N. H., Lengerke, C. & Heinzelmann-Schwarz, V., 1 Jun 2018, In : Cancer Research. 78, 11, p. 2952-2965 14 p.

Research output: Contribution to journalArticleResearchpeer-review

Galactosyltransferases
Glycosphingolipids
Epithelial Cells
Globosides
Neoplasms
2017

A comprehensive assessment of the biosynthetic pathways of ascorbate, alpha-tocopherol and free amino acids in Euglena gracilis var. saccharophila

Hasan, M. T., Sun, A., Mirzaei, M., Te'o, J., Hobba, G., Sunna, A. & Nevalainen, H., Nov 2017, In : Algal Research. 27, p. 140-151 12 p.

Research output: Contribution to journalArticleResearchpeer-review

Euglena gracilis
free amino acids
alpha-tocopherol
biochemical pathways
proteomics

An innovative approach to bioremediation of mercury contaminated soils from industrial mining operations

McCarthy, D., Edwards, G. C., Gustin, M. S., Care, A., Miller, M. B. & Sunna, A., Oct 2017, In : Chemosphere. 184, p. 694-699 6 p.

Research output: Contribution to journalArticleResearchpeer-review

Environmental Biodegradation
Bioremediation
Mercury
bioremediation
Soil

Applications of fipronil (Adonis 3UL) and Metarhizium acridum for use against locusts have minimal effect on litter decomposition and microbial functional diversity in Australian arid grassland

Maute, K., Story, P., Hose, G. C., Bull, C. M. & French, K., 2017, In : Soil Research. 55, 2, p. 172-181 10 p.

Research output: Contribution to journalArticleResearchpeer-review

Adonis
Metarhizium
fipronil
locust
functional diversity

A Versatile upconversion surface evaluation platform for bio-nano surface selection for the nervous system

Fu, L., Morsch, M., Shi, B., Wang, G., Lee, A., Radford, R., Lu, Y., Jin, D. & Chung, R., 17 Aug 2017, In : Nanoscale. 9, 36, p. 13683-13692 10 p.

Research output: Contribution to journalArticleResearchpeer-review

Neurology
Nanoparticles
Neurodegenerative diseases
Cytotoxicity
Polyethylene glycols

Epigenetics and the evolution of instincts: instincts may evolve from learning and share the same cellular and molecular mechanisms

Robinson, G. E. & Barron, A. B., 7 Apr 2017, In : Science. 356, 6333, p. 26-27 2 p.

Research output: Contribution to journalArticleResearchpeer-review

Genomics and the evolution of antibiotic resistance

Gillings, M. R., Paulsen, I. T. & Tetu, S. G., 1 Jan 2017, In : Annals of the New York Academy of Sciences. 1388, 1, p. 92-107 16 p.

Research output: Contribution to journalArticleResearchpeer-review

Microbial Drug Resistance
Genomics
Genes
Anti-Bacterial Agents
DNA

Secretion of proteases by an opportunistic fungal pathogen Scedosporium aurantiacum

Han, Z., Kautto, L. & Nevalainen, H., 6 Jan 2017, In : PLoS ONE. 12, 1, p. 1-19 19 p., e0169403.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Scedosporium
Pathogens
Peptide Hydrolases
proteinases
secretion

Solid-binding peptides for immobilisation of thermostable enzymes to hydrolyse biomass polysaccharides

Care, A., Petroll, K., Gibson, E. S. Y., Bergquist, P. L. & Sunna, A., 2 Feb 2017, In : Biotechnology for Biofuels. 10, 1, p. 1-16 16 p., 29.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Polysaccharides
polysaccharide
Immobilization
peptide
Biomass

The weighted groundwater health index: Improving the monitoring and management of groundwater resources

Korbel, K. L. & Hose, G. C., 1 Apr 2017, In : Ecological Indicators. 75, p. 164-181 18 p.

Research output: Contribution to journalArticleResearchpeer-review

groundwater resource
groundwater
monitoring
ecosystem health
catchment
2016
Open Access
File
Protease Inhibitors
Edetic Acid
Blood
Plasmas
Electrophoresis
2015

Linking structural features of protein complexes and biological function

Sowmya, G., Breen, E. J. & Ranganathan, S., 1 Sep 2015, In : Protein Science. 24, 9, p. 1486-1494 9 p.

Research output: Contribution to journalArticleResearchpeer-review

Proteins
Solvation
Nonparametric Statistics
Genomics
Binding energy
2014

The necrotrophic effector protein SnTox3 re-programs metabolism and elicits a strong defence response in susceptible wheat leaves

Winterberg, B., Du Fall, L. A., Song, X., Pascovici, D., Care, N., Molloy, M., Ohms, S. & Solomon, P. S., 15 Aug 2014, In : BMC Plant Biology. 14, p. 1-15 15 p., 215.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Leptosphaeria nodorum
Triticum
wheat
metabolism
homocysteine
2013

An improved method for the detection and enrichment of low-abundant membrane and lipid raft-residing proteins

Kan, A., Mohamedali, A., Tan, S. H., Cheruku, H. R., Slapetova, I., Lee, L. Y. & Baker, M. S., 1 Feb 2013, In : Journal of Proteomics. 79, p. 299-304 6 p.

Research output: Contribution to journalArticleResearchpeer-review

Membrane Lipids
Urokinase Plasminogen Activator Receptors
Membrane Proteins
Immunoglobulin G
Immunoprecipitation

BacillOndex: an integrated data resource for systems and synthetic biology.

Misirli, G., Wipat, A., Mullen, J., James, K., Pocock, M., Smith, W., Allenby, N. & Hallinan, J. S., 2013, In : Journal of integrative bioinformatics. 10, 2, p. 1-14 14 p., 224.

Research output: Contribution to journalArticleResearchpeer-review

Synthetic Biology
Systems Biology
Bacillus subtilis
Information Systems
Single Nucleotide Polymorphism

Characterization of the Kynurenine pathway and quinolinic acid production in macaque macrophages

Lim, C. K., Yap, M. M. C., Kent, S. J., Gras, G., Samah, B., Batten, J. C., De Rose, R., Heng, B., Brew, B. J. & Guillemin, G. J., 2013, In : International Journal of Tryptophan Research. 6, p. 7-19 13 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Quinolinic Acid
Kynurenine
Macrophages
Macaca
Metabolism
2012

Microbase2.0: a generic framework for computationally intensive bioinformatics workflows in the cloud.

Flanagan, K., Nakjang, S., Hallinan, J., Harwood, C., Hirt, R. P., Pocock, M. R. & Wipat, A., 2012, In : Journal of integrative bioinformatics. 9, 2, p. 212 1 p.

Research output: Contribution to journalArticleResearchpeer-review

Workflow
Computational Biology
Technology
Archaea
Eukaryota
2011

Is the distribution of Prochlorococcus and Synechococcus ecotypes in the Mediterranean Sea affected by global warming?

Mella-Flores, D., Mazard, S., Humily, F., Partensky, F., Mahé, F., Bariat, L., Courties, C., Marie, D., Ras, J., Mauriac, R., Jeanthon, C., Mahdi Bendif, E., Ostrowski, M., Scanlan, D. J. & Garczarek, L., 2011, In : Biogeosciences. 8, 9, p. 2785-2804 20 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Prochlorococcus
Synechococcus
ecotype
ecotypes
Mediterranean Sea
2010

Differential metabolic response of cultured rice (Oryza sativa) cells exposed to high- And low-temperature stress

Gammulla, C. G., Pascovici, D., Atwell, B. J. & Haynes, P. A., Aug 2010, In : Proteomics. 10, 16, p. 3001-3019 19 p.

Research output: Contribution to journalArticleResearchpeer-review

Temperature
Cell culture
Proteomics
Proteins
Cell Culture Techniques

IV Neurotoxicity Society Meeting: Neurochemical Mechanisms of Neurodegenerative Disorders

Segura-Aguilar, J., Kostrzewa, R., Caviedes, P., Danysz, W., Guillemin, G., Sulzer, D., Díaz-Grez, F., Cadet, J. L. & Calaf, G., Jul 2010, In : Neurotoxicity Research. 18, 1, p. 1 1 p.

Research output: Contribution to journalArticleResearchpeer-review

The humanized NOD/SCID mouse as a preclinical model to study the fate of encapsulated human islets

Vaithilingam, V., Oberholzer, J., Guillemin, G. J. & Tuch, B. E., Mar 2010, In : The review of diabetic studies : RDS. 7, 1, p. 62-73 12 p.

Research output: Contribution to journalArticleResearchpeer-review

Inbred NOD Mouse
SCID Mice
Interleukin-4
Interleukin-10
Animal Models
2009

Impact of 27-hydroxycholesterol on amyloid-β peptide production and ATP-binding cassette transporter expression in primary human neurons

Scott Kim, W., Chan, S. L., Hill, A. F., Guillemin, G. J. & Garner, B., 2009, In : Journal of Alzheimer's Disease. 16, 1, p. 121-131 11 p.

Research output: Contribution to journalArticleResearchpeer-review

ATP-Binding Cassette Transporters
Amyloid beta-Peptides
Neurons
Cholesterol
Cholestanetriol 26-Monooxygenase
2008

Functional analyses reveal an important role for tyrosine residues in the staphylococcal multidrug efflux protein QacA

Wu, J., Hassan, K. A., Skurray, R. A. & Brown, M. H., 2008, In : BMC Microbiology. 8, p. 1-7 7 p., 147.

Research output: Contribution to journalArticleResearchpeer-review

Tyrosine
Pharmaceutical Preparations
Proteins
Aromatic Amino Acids
Phenylalanine
2007

A multiple optimal stopping rule for sums of independent random variables

Nikolaev, M. L. & Sofronov, G. Y., 11 Dec 2007, In : Discrete Mathematics and Applications. 17, 5, p. 463-473 11 p.

Research output: Contribution to journalArticleResearchpeer-review

Optimal Stopping Rule
Sums of Independent Random Variables
Ecology
Random variables
Sales
2006

An aldosterone-related system in the ventrolateral medulla oblongata of spontaneously hypertensive and Wistar-Kyoto rats

Kumar, N. N., Goodchild, A. K., Li, Q. & Pilowsky, P. M., Jan 2006, In : Clinical and Experimental Pharmacology and Physiology. 33, 1-2, p. 71-75 5 p.

Research output: Contribution to journalArticleResearchpeer-review

Medulla Oblongata
Inbred WKY Rats
Aldosterone
Inbred SHR Rats
Arachidonate 12-Lipoxygenase
2004

A yeast intron as a translational terminator in a plasmid shuttle vector

Gibbs, M. D., Reeves, R. A., Sunna, A. & Bergquist, P. L., Mar 2004, In : FEMS Yeast Research. 4, 6, p. 573-577 5 p.

Research output: Contribution to journalArticleResearchpeer-review

Genetic Vectors
Introns
Plasmids
Yeasts
Escherichia coli
2003

A gene encoding a novel extremely thermostable 1,4-β-xylanase isolated directly from an environmental DNA sample

Sunna, A. & Bergquist, P. L., 2003, In : Extremophiles. 7, 1, p. 63-70 8 p.

Research output: Contribution to journalArticleResearchpeer-review

Endo-1,4-beta Xylanases
Ribosomal DNA
Glycoside Hydrolases
Polymerase Chain Reaction
Sequence Analysis
Paecilomyces
Chitinases
Serine Proteases
Gels
Peptide Hydrolases