Biomolecular Discovery and Design Research Centre

Research Output 1980 2019

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

Bioproducts From Euglena gracilis: synthesis and applications

Gissibl, A., Sun, A., Care, A., Nevalainen, H. & Sunna, A., 15 May 2019, In : Frontiers in Bioengineering and Biotechnology. 7, 16 p., 108.

Research output: Contribution to journalReview articleResearchpeer-review

Open Access
File
Euglena gracilis
Dietary Proteins
Vitamins
Metabolism
Lipids

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., 16 Aug 2019, (Accepted/In press) In : Proteomics.

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

Tools and strategies for constructing cell-free enzyme pathways

Petroll, K., Kopp, D., Care, A., Bergquist, P. L. & Sunna, A., Jan 2019, In : Biotechnology Advances. 37, 1, p. 91-108 18 p.

Research output: Contribution to journalReview articleResearchpeer-review

Enzymes
Biocatalysis
Artificial Cells
Biofuels
Coenzymes
2018

Bioengineering strategies for protein-based nanoparticles

Diaz, D., Care, A. & Sunna, A., 23 Jul 2018, In : Genes. 9, 7, p. 1-30 30 p., 370.

Research output: Contribution to journalReview articleResearchpeer-review

Open Access
File
Bioengineering
Nanoparticles
Proteins
Biocatalysis
Synthetic Biology

Biological, biochemical and molecular aspects of Scedosporium aurantiacum, a primary and opportunistic fungal pathogen

Nevalainen, H., Kaur, J., Han, Z., Kautto, L., Ramsperger, M., Meyer, W. & Chen, S. C. A., Jun 2018, In : Fungal Biology Reviews. 32, 3, p. 156-165 10 p.

Research output: Contribution to journalReview articleResearchpeer-review

Scedosporium
Lung
Molecular Diagnostic Techniques
Gene Knockout Techniques
Virulence Factors

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

Human disease glycomics: technology advances enabling protein glycosylation analysis – part 2

Everest-Dass, A. V., Moh, E. S. X., Ashwood, C., Shathili, A. M. M. & Packer, N. H., 2018, In : Expert Review of Proteomics. 15, 4, p. 341-352 12 p.

Research output: Contribution to journalReview articleResearchpeer-review

Glycomics
Glycosylation
Polysaccharides
Technology
Proteins

Human disease glycomics: technology advances enabling protein glycosylation analysis – part 1

Everest-Dass, A. V., Moh, E. S. X., Ashwood, C., Shathili, A. M. M. & Packer, N. H., 1 Feb 2018, In : Expert Review of Proteomics. 15, 2, p. 165-182 18 p.

Research output: Contribution to journalReview articleResearchpeer-review

Glycomics
Glycosylation
Polysaccharides
Technology
Proteins

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

Blueprint for living cities: policy to practice

Davies, P., Corkery, L., Nipperess, D., Barnett, G., Bishop, M., Hochuli, D., Hose, G., Joei, C., Lin, B., Keane, A., Osmond, P., Pelleri, N., Staas, L., Threlfall, C., van den Berg, F. & Wilkinson, S., May 2017, National Green Infrastructure Network. 67 p.

Research output: Book/ReportCommissioned reportResearchpeer-review

Open Access
File

Databases and associated tools for glycomics and glycoproteomics

Lisacek, F., Mariethoz, J., Alocci, D., Rudd, P. M., Abrahams, J. L., Campbell, M. P., Packer, N. H., Ståhle, J., Widmalm, G., Mullen, E., Adamczyk, B., Rojas-Macias, M. A., Jin, C. & Karlsson, N. G., 2017, High-Throughput Glycomics and Glycoproteomics: Methods and Protocols, Methods in Molecular Biology. Lauc, G. & Wuhrer, M. (eds.). New York: Humana Press Inc., Vol. 1503. p. 235-264 30 p. (Methods in Molecular Biology; vol. 1503).

Research output: Chapter in Book/Report/Conference proceedingChapterResearchpeer-review

Glycomics
Polysaccharides
Databases
Proteins
Oligosaccharides

De novo peptide sequencing: Deep mining of high-resolution mass spectrometry data

Islam, M. T., Mohamedali, A., Fernandes, C. S., Baker, M. S. & Ranganathan, S., 2017, Proteome Bioinformatics: Methods in Molecular Biology. Keerthikumar, S. & Mathivanan, S. (eds.). New York: Humana Press Inc., Vol. 1549. p. 119-134 16 p. (Methods in Molecular Biology; vol. 1549).

Research output: Chapter in Book/Report/Conference proceedingChapterResearchpeer-review

High-Throughput Nucleotide Sequencing
Mass Spectrometry
Peptides
Proteome
Proteomics

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

Lateral gene transfer, bacterial genome evolution, and the Anthropocene

Gillings, M. R., 1 Feb 2017, In : Annals of the New York Academy of Sciences. 1389, 1, p. 20-36 17 p.

Research output: Contribution to journalArticleResearchpeer-review

Gene transfer
Bacterial Genomes
Horizontal Gene Transfer
Genes
Virulence

Peptides and peptide-based biomaterials and their biomedical applications

Sunna, A. (ed.), Care, A. (ed.) & Bergquist, P. L. (ed.), 2017, Cham: Springer, Springer Nature. 300 p. (Advances in experimental medicine and biology; vol. 1030)

Research output: Book/ReportEdited Book/AnthologyResearchpeer-review

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

Solid-binding peptides in biomedicine

Care, A., Bergquist, P. L. & Sunna, A., 2017, Peptides and Peptide-based Biomaterials and their Biomedical Applications. Sunna, A., Care, A. & Bergquist, P. L. (eds.). Cham, Switzerland: Springer, Springer Nature, p. 21-36 16 p. (Advances in experimental medicine and biology; vol. 1030). (Advances in Experimental Medicine and Biology).

Research output: Chapter in Book/Report/Conference proceedingChapterResearchpeer-review

Nanostructures
Nanostructured materials
Peptides
Metals
Biocompatibility

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

Yeast's balancing act between ethanol and glycerol production in low-alcohol wines

Goold, H. D., Kroukamp, H., Williams, T. C., Paulsen, I. T., Varela, C. & Pretorius, I. S., 1 Mar 2017, In : Microbial Biotechnology. 10, 2, p. 264-278 15 p.

Research output: Contribution to journalReview articleResearchpeer-review

Open Access
File
Wine
Glycerol
Yeast
Alcohols
Ethanol

Выживаемость и пути онтогенеза слоевищ эпифитного лишайника эвернии сливовой (Evernia prunastri (L.) Ach.)

Suetina, Y. G., Dmitrieva, S. V., Trubyanov, A. B., Sofronov, G. Y., Ivanov, S. M. & Glotov, N. V., 2017, Проблемы популяционной биологии: Материалы XII Всероссийского популяционного семинара памяти Николая Васильевича Глотова (1939–2016). Russia: Mari State University, p. 220-222 3 p.

Research output: Chapter in Book/Report/Conference proceedingConference proceeding contributionResearch

Регрессионная модель для упорядоченных классов и ее применение при анализе онтогенетической структуры популяций

Ivanov, S. M., Sofronov, G. Y., Suetina, Y. G. & Ryzhova, L. V., 2017, Проблемы популяционной биологии: Материалы XII Всероссийского популяционного семинара памяти Николая Васильевича Глотова (1939–2016). Russia: Mari State University, p. 106-108 3 p.

Research output: Chapter in Book/Report/Conference proceedingConference proceeding contributionResearch

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

Interactions between armpit specific bacteria and components of sweat, in particular glycoproteins

Packer, N., 2014, Paris, France: L'Oreal France.

Research output: Book/ReportCommissioned reportResearch

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