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Article ; Online: High-throughput strategy for identification of Mycobacterium tuberculosis membrane protein expression conditions using folding reporter GFP.

Grāve, Kristīne / Bennett, Matthew D / Högbom, Martin

2022 Volume 198, Page(s) 106132

Abstract: Mycobacterium tuberculosis membrane protein biochemistry and structural biology studies are often hampered by challenges in protein expression and selection for well-expressing protein candidates, suitable for further investigation. Here we present a ... ...

Abstract	Mycobacterium tuberculosis membrane protein biochemistry and structural biology studies are often hampered by challenges in protein expression and selection for well-expressing protein candidates, suitable for further investigation. Here we present a folding reporter GFP (frGFP) assay, adapted for M. tuberculosis membrane protein screening in Escherichia coli Rosetta 2 (DE3) and Mycobacterium smegmatis mc
MeSH term(s)	Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Green Fluorescent Proteins/genetics ; Green Fluorescent Proteins/metabolism ; Membrane Proteins/genetics ; Membrane Proteins/metabolism ; Mycobacterium smegmatis/genetics ; Mycobacterium smegmatis/metabolism ; Mycobacterium tuberculosis/genetics ; Mycobacterium tuberculosis/metabolism ; Promoter Regions, Genetic
Chemical Substances	Bacterial Proteins ; Membrane Proteins ; Green Fluorescent Proteins (147336-22-9)
Language	English
Publishing date	2022-06-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1055455-5
ISSN	1096-0279 ; 1046-5928
ISSN (online)	1096-0279
ISSN	1046-5928
DOI	10.1016/j.pep.2022.106132
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Article: VALIDATING FORWARD MODELING AND INVERSIONS OF HELIOSEISMIC HOLOGRAPHY MEASUREMENTS.

DeGrave, K / Braun, D C / Birch, A C / Crouch, A D / Javornik, B

The Astrophysical journal

2020 Volume 863, Issue 1

Abstract: Here we use synthetic data to explore the performance of forward models and inverse methods for helioseismic holography. Specifically, this work presents the first comprehensive test of inverse modeling for flows using lateral-vantage (deep-focus) ... ...

Abstract	Here we use synthetic data to explore the performance of forward models and inverse methods for helioseismic holography. Specifically, this work presents the first comprehensive test of inverse modeling for flows using lateral-vantage (deep-focus) holography. We derive sensitivity functions in the Born approximation. We then use these sensitivity functions in a series of forward models and inversions of flows from a publicly available magnetohydrodynamic quiet-Sun simulation. The forward travel times computed using the kernels generally compare favorably with measurements obtained by applying holography, in a lateral-vantage configuration, on a 15-hour time series of artificial Dopplergrams extracted from the simulation. Inversions for the horizontal flow components are able to reproduce the flows in the upper 3Mm of the domain, but are compromised by noise at greater depths.
Language	English
Publishing date	2020-01-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	2960-9
ISSN	0004-637X
ISSN	0004-637X
DOI	10.3847/1538-4357/aacffd
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Article ; Online: Automated detection of toxicophores and prediction of mutagenicity using PMCSFG algorithm.

Schietgat, Leander / Cuissart, Bertrand / De Grave, Kurt / Efthymiadis, Kyriakos / Bureau, Ronan / Crémilleux, Bruno / Ramon, Jan / Lepailleur, Alban

Molecular informatics

2023 Volume 42, Issue 3, Page(s) e2200232

Abstract: Maximum common substructures (MCS) have received a lot of attention in the chemoinformatics community. They are typically used as a similarity measure between molecules, showing high predictive performance when used in classification tasks, while being ... ...

Abstract	Maximum common substructures (MCS) have received a lot of attention in the chemoinformatics community. They are typically used as a similarity measure between molecules, showing high predictive performance when used in classification tasks, while being easily explainable substructures. In the present work, we applied the Pairwise Maximum Common Subgraph Feature Generation (PMCSFG) algorithm to automatically detect toxicophores (structural alerts) and to compute fingerprints based on MCS. We present a comparison between our MCS-based fingerprints and 12 well-known chemical fingerprints when used as features in machine learning models. We provide an experimental evaluation and discuss the usefulness of the different methods on mutagenicity data. The features generated by the MCS method have a state-of-the-art performance when predicting mutagenicity, while they are more interpretable than the traditional chemical fingerprints.
MeSH term(s)	Mutagens/chemistry ; Algorithms ; Mutagenesis ; Machine Learning
Chemical Substances	Mutagens
Language	English
Publishing date	2023-02-02
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2537668-8
ISSN	1868-1751 ; 1868-1743
ISSN (online)	1868-1751
ISSN	1868-1743
DOI	10.1002/minf.202200232
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Article ; Online: Structure of

Grāve, Kristīne / Bennett, Matthew D / Högbom, Martin

Communications biology

2019 Volume 2, Page(s) 175

Abstract: Tuberculosis causes over one million yearly deaths, and drug resistance is rapidly developing. ...

Abstract	Tuberculosis causes over one million yearly deaths, and drug resistance is rapidly developing.
MeSH term(s)	Amino Acid Substitution ; Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; CDP-Diacylglycerol-Inositol 3-Phosphatidyltransferase/chemistry ; CDP-Diacylglycerol-Inositol 3-Phosphatidyltransferase/genetics ; CDP-Diacylglycerol-Inositol 3-Phosphatidyltransferase/metabolism ; Catalytic Domain/genetics ; Crystallography, X-Ray ; Cytidine Diphosphate Diglycerides/metabolism ; Humans ; Inositol Phosphates/metabolism ; Magnesium/metabolism ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Mutagenesis, Site-Directed ; Mycobacterium tuberculosis/enzymology ; Mycobacterium tuberculosis/genetics ; Static Electricity ; Substrate Specificity
Chemical Substances	Bacterial Proteins ; Cytidine Diphosphate Diglycerides ; Inositol Phosphates ; inositol 3-phosphate (2831-74-5) ; CDP-Diacylglycerol-Inositol 3-Phosphatidyltransferase (EC 2.7.8.11) ; Magnesium (I38ZP9992A)
Language	English
Publishing date	2019-05-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-019-0427-1
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Article ; Online: On the complexity of haplotyping a microbial community.

Nicholls, Samuel M / Aubrey, Wayne / De Grave, Kurt / Schietgat, Leander / Creevey, Christopher J / Clare, Amanda

Bioinformatics (Oxford, England)

2021 Volume 37, Issue 10, Page(s) 1360–1366

Abstract: Motivation: Population-level genetic variation enables competitiveness and niche specialization in microbial communities. Despite the difficulty in culturing many microbes from an environment, we can still study these communities by isolating and ... ...

Abstract	Motivation: Population-level genetic variation enables competitiveness and niche specialization in microbial communities. Despite the difficulty in culturing many microbes from an environment, we can still study these communities by isolating and sequencing DNA directly from an environment (metagenomics). Recovering the genomic sequences of all isoforms of a given gene across all organisms in a metagenomic sample would aid evolutionary and ecological insights into microbial ecosystems with potential benefits for medicine and biotechnology. A significant obstacle to this goal arises from the lack of a computationally tractable solution that can recover these sequences from sequenced read fragments. This poses a problem analogous to reconstructing the two sequences that make up the genome of a diploid organism (i.e. haplotypes) but for an unknown number of individuals and haplotypes. Results: The problem of single individual haplotyping was first formalized by Lancia et al. in 2001. Now, nearly two decades later, we discuss the complexity of 'haplotyping' metagenomic samples, with a new formalization of Lancia et al.'s data structure that allows us to effectively extend the single individual haplotype problem to microbial communities. This work describes and formalizes the problem of recovering genes (and other genomic subsequences) from all individuals within a complex community sample, which we term the metagenomic individual haplotyping problem. We also provide software implementations for a pairwise single nucleotide variant (SNV) co-occurrence matrix and greedy graph traversal algorithm. Availability and implementation: Our reference implementation of the described pairwise SNV matrix (Hansel) and greedy haplotype path traversal algorithm (Gretel) is open source, MIT licensed and freely available online at github.com/samstudio8/hansel and github.com/samstudio8/gretel, respectively.
Language	English
Publishing date	2021-01-14
Publishing country	England
Document type	Journal Article
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btaa977
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Article ; Online: The Bacillus anthracis class Ib ribonucleotide reductase subunit NrdF intrinsically selects manganese over iron

Grave, K. / Griese, J.J. / Berggren, G. / Bennett, M.D. / Hogbom, M.

2020

Abstract: Correct protein metallation in the complex mixture of the cell is a prerequisite for metalloprotein function. While some metals, such as Cu, are commonly chaperoned, specificity towards metals earlier in the Irving Williams series is achieved through ... ...

Abstract	Correct protein metallation in the complex mixture of the cell is a prerequisite for metalloprotein function. While some metals, such as Cu, are commonly chaperoned, specificity towards metals earlier in the Irving Williams series is achieved through other means, the determinants of which are poorly understood. The dimetal carboxylate family of proteins provides an intriguing example, as different proteins, while sharing a common fold and the same 4 carboxylate 2 histidine coordination sphere, are known to require either a Fe Fe, Mn Fe or Mn Mn cofactor for function. We previously showed that the R2lox proteins from this family spontaneously assemble the heterodinuclear Mn Fe cofactor. Here we show that the class Ib ribonucleotide reductase R2 protein from Bacillus anthracis spontaneously assembles a Mn Mn cofactor in vitro, under both aerobic and anoxic conditions, when the metal free protein is subjected to incubation with MnII and FeII in equal concentrations. This observation provides an example of a protein scaffold intrinsically predisposed to defy the Irving Williams series and supports the assumption that the Mn Mn cofactor is the biologically relevant cofactor in vivo. Substitution of a second coordination sphere residue changes the spontaneous metallation of the protein to predominantly form a heterodinuclear Mn Fe cofactor under aerobic conditions and a Mn Mn metal center under anoxic conditions. Together, the results describe the intrinsic metal specificity of class Ib RNR and provide insight into control mechanisms for protein metallation
Keywords	Large scale facilities for research with photons neutrons and ions
Subject code	612
Language	Undetermined
Publishing date	2020-01-01
Publishing country	de
Document type	Article ; Online
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Article: A pharmaco-epidemiological study of antibacterial treatments and bacterial diseases in Norwegian aquaculture from 2011 to 2016.

Lillehaug, Atle / Børnes, Christine / Grave, Kari

Diseases of aquatic organisms

2018 Volume 128, Issue 2, Page(s) 117–125

Abstract: The sales and prescription of antibacterials for use in Norwegian fish-farming according to diagnosis, fish species and production stage from 2011 to 2016 are analysed. The study is based on antibacterial sales data from wholesalers, pharmacies and feed ... ...

Abstract	The sales and prescription of antibacterials for use in Norwegian fish-farming according to diagnosis, fish species and production stage from 2011 to 2016 are analysed. The study is based on antibacterial sales data from wholesalers, pharmacies and feed mills and on prescription data obtained from a register of all prescriptions of antibacterials used in farmed fish. The results show that the fish-farming industry uses very small volumes of antibacterials. In 2016, a total of 212 kg were sold; the only antibacterial substances sold were florfenicol and oxolinic acid. The total amount corresponded to 0.16 mg kg-1 fish slaughtered, or to approximately 0.14% of the fish produced that year. The majority of prescriptions were for non-specific bacterial infections; as most common diseases are under control by vaccination. Most prescriptions for salmonid fish were during early production stages. However, due to higher biomasses of fish, the highest quantities of antibacterials were prescribed during the seawater production phase of Atlantic salmon Salmo salar. An increasing proportion of the prescriptions was for other species, including cleaner fish used for salmon lice control; in 2016 most prescriptions were for this fish category. Due to the negligible use of antibacterials in Norwegian aquaculture, in particular for on-growers, the risk of development of antimicrobial resistance and its transmission to humans through consumption of fish is considered negligible.
MeSH term(s)	Animals ; Anti-Bacterial Agents/administration & dosage ; Aquaculture ; Bacterial Infections/drug therapy ; Bacterial Infections/veterinary ; Drug Utilization ; Fish Diseases/drug therapy ; Fish Diseases/microbiology ; Fishes ; Norway
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2018-05-07
Publishing country	Germany
Document type	Journal Article
ISSN	0177-5103
ISSN	0177-5103
DOI	10.3354/dao03219
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Article ; Online: The management of risk arising from the use of antimicrobial agents in veterinary medicine in EU/EEA countries - a review.

Törneke, K / Torren-Edo, J / Grave, K / Mackay, D K J

Journal of veterinary pharmacology and therapeutics

2015 Volume 38, Issue 6, Page(s) 519–528

Abstract: Antimicrobials are essential medicines for the treatment of many microbial infections in humans and animals. Only a small number of antimicrobial agents with new mechanisms of action have been authorized in recent years for use in either humans or ... ...

Abstract	Antimicrobials are essential medicines for the treatment of many microbial infections in humans and animals. Only a small number of antimicrobial agents with new mechanisms of action have been authorized in recent years for use in either humans or animals. Antimicrobial resistance (AMR) arising from the use of antimicrobial agents in veterinary medicine is a concern for public health due to the detection of increasing levels of resistance in foodborne zoonotic bacteria, particularly gram-negative bacteria, and due to the detection of determinants of resistance such as Extended-spectrum beta-lactamases (ESBL) in bacteria from animals and in foodstuffs of animal origin. The importance and the extent of the emergence and spread of AMR from animals to humans has yet to be quantified. Likewise, the relative contribution that the use of antimicrobial agents in animals makes to the overall risk to human from AMR is currently a subject of debate that can only be resolved through further research. Nevertheless, risk managers have agreed that the impact on public health of the use of antimicrobials in animals should be minimized as far as possible and a variety of measures have been introduced by different authorities in the EU to achieve this objective. This article reviews a range of measures that have been implemented within European countries to reduce the occurrence and the risk of transmission of AMR to humans following the use of antimicrobial agents in animals and briefly describes some of the alternatives to the use of antimicrobial agents that are being developed.
MeSH term(s)	Animals ; Animals, Domestic/microbiology ; Anti-Infective Agents/adverse effects ; Anti-Infective Agents/therapeutic use ; Drug Resistance, Microbial ; European Union ; Humans ; Risk Factors ; Risk Management/methods ; Veterinary Medicine/methods
Chemical Substances	Anti-Infective Agents
Language	English
Publishing date	2015-12
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	435216-6
ISSN	1365-2885 ; 0140-7783
ISSN (online)	1365-2885
ISSN	0140-7783
DOI	10.1111/jvp.12226
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Article ; Online: The Bacillus anthracis class Ib ribonucleotide reductase subunit NrdF intrinsically selects manganese over iron.

Grāve, Kristīne / Griese, Julia J / Berggren, Gustav / Bennett, Matthew D / Högbom, Martin

Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry

2020 Volume 25, Issue 4, Page(s) 571–582

Abstract	Correct protein metallation in the complex mixture of the cell is a prerequisite for metalloprotein function. While some metals, such as Cu, are commonly chaperoned, specificity towards metals earlier in the Irving-Williams series is achieved through other means, the determinants of which are poorly understood. The dimetal carboxylate family of proteins provides an intriguing example, as different proteins, while sharing a common fold and the same 4-carboxylate 2-histidine coordination sphere, are known to require either a Fe/Fe, Mn/Fe or Mn/Mn cofactor for function. We previously showed that the R2lox proteins from this family spontaneously assemble the heterodinuclear Mn/Fe cofactor. Here we show that the class Ib ribonucleotide reductase R2 protein from Bacillus anthracis spontaneously assembles a Mn/Mn cofactor in vitro, under both aerobic and anoxic conditions, when the metal-free protein is subjected to incubation with Mn
MeSH term(s)	Bacillus anthracis/enzymology ; Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Crystallography, X-Ray ; Iron/chemistry ; Iron/metabolism ; Manganese/chemistry ; Manganese/metabolism ; Models, Molecular ; Protein Conformation ; Ribonucleotide Reductases/chemistry ; Ribonucleotide Reductases/genetics ; Ribonucleotide Reductases/metabolism
Chemical Substances	Bacterial Proteins ; Manganese (42Z2K6ZL8P) ; Iron (E1UOL152H7) ; NrdF protein, bacteria (EC 1.17.4.-) ; Ribonucleotide Reductases (EC 1.17.4.-)
Language	English
Publishing date	2020-04-15
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1464026-0
ISSN	1432-1327 ; 0949-8257
ISSN (online)	1432-1327
ISSN	0949-8257
DOI	10.1007/s00775-020-01782-3
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Article: The use of the hand and wrist radiograph in skeletal age assessment; and why skeletal age assessment is important.

Grave, K

Australian orthodontic journal

1994 Volume 13, Issue 3, Page(s) 196

MeSH term(s)	Adolescent ; Age Determination by Skeleton/methods ; Hand/diagnostic imaging ; Humans ; Maxillofacial Development ; Patient Care Planning ; Wrist/diagnostic imaging
Language	English
Publishing date	1994-10
Publishing country	Australia
Document type	Journal Article
ZDB-ID	410066-9
ISSN	0587-3908
ISSN	0587-3908
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