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Article ; Online: Evaluation and prediction of salt effects on pig muscle by deep UV and machine learning.

El Karam, Saïd Abou / Ferrand, Maxime / Astruc, Thierry / Germond, Arno

2023 Volume 199, Page(s) 109136

Abstract: The salting process for meat transformation is a crucial step in conventional industry. Recent developments in label-free spectrometry techniques combined with machine learning hold great promise for high-precision salt processing. In this study, we ... ...

Abstract	The salting process for meat transformation is a crucial step in conventional industry. Recent developments in label-free spectrometry techniques combined with machine learning hold great promise for high-precision salt processing. In this study, we applied UV fluorescence to characterize salting treatments in pig's Teres major muscle and predict NaCl concentrations. t-SNE analyses based on spectral measurements revealed clear differences between NaCl-free and salted treatments. However, salt treatments were not clearly identified. We then highlighted and exploited a variability seen in the emission spectra at the wavelengths 300, 318, and 360 nm, which reflected structural or compositional changes. Using this information, predictive models could accurately identify the five salted treatments with a high specificity and sensitivity or predict salt concentrations. This study paves the way toward the possibility for industrials to precisely adjust NaCl concentrations with precision during processing.
MeSH term(s)	Animals ; Swine ; Food Handling/methods ; Sodium Chloride/analysis ; Meat/analysis ; Muscles/chemistry ; Sodium Chloride, Dietary ; Machine Learning
Chemical Substances	Sodium Chloride (451W47IQ8X) ; Sodium Chloride, Dietary
Language	English
Publishing date	2023-02-08
Publishing country	England
Document type	Journal Article
ZDB-ID	753319-6
ISSN	1873-4138 ; 0309-1740
ISSN (online)	1873-4138
ISSN	0309-1740
DOI	10.1016/j.meatsci.2023.109136
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Article ; Online: Correction to "Toward Gene-Correlated Spatially Resolved Metabolomics with Fingerprint Coherent Raman Imaging".

Poorna, Rajas / Chen, Wei-Wen / Germond, Arno / Qiu, Peng / Cicerone, Marcus T

The journal of physical chemistry. B

2023 Volume 127, Issue 33, Page(s) 7416

Language	English
Publishing date	2023-08-09
Publishing country	United States
Document type	Published Erratum
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.3c05167
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Discriminating cell line specific features of antibiotic-resistant strains of Escherichia coli from Raman spectra via machine learning analysis.

Zahn, Jessica / Germond, Arno / Lundgren, Alice Y / Cicerone, Marcus T

Journal of biophotonics

2022 Volume 15, Issue 7, Page(s) e202100274

Abstract: While Raman spectroscopy can provide label-free discrimination between highly similar biological species, the discrimination is often marginal, and optimal use of spectral information is imperative. Here, we compare two machine learning models, an ... ...

Abstract	While Raman spectroscopy can provide label-free discrimination between highly similar biological species, the discrimination is often marginal, and optimal use of spectral information is imperative. Here, we compare two machine learning models, an artificial neural network and a support vector machine, for discriminating between Raman spectra of 11 bacterial mutants of Escherichia coli MDS42. While we find that both models discriminate the 11 bacterial strains with similarly high accuracy, sensitivity and specificity, it is clear that the models form different class boundaries. By extracting strain-specific (and function-specific) spectral features utilized by the models, we find that both models utilize a small subset of high intensity peaks while separate subsets of lower intensity peaks are utilized by only one method or the other. This analysis highlights the need for methods to use the complete spectral information more effectively, beginning with a better understanding of the distinct information gained from each model.
MeSH term(s)	Anti-Bacterial Agents ; Bacteria ; Cell Line ; Escherichia coli/genetics ; Escherichia coli Infections ; Humans ; Machine Learning ; Spectrum Analysis, Raman/methods ; Support Vector Machine
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2022-04-06
Publishing country	Germany
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2390063-5
ISSN	1864-0648 ; 1864-063X
ISSN (online)	1864-0648
ISSN	1864-063X
DOI	10.1002/jbio.202100274
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Article ; Online: An Integrated Raman Spectroscopy and Mass Spectrometry Platform to Study Single-Cell Drug Uptake, Metabolism, and Effects.

Ali, Ahmed / Abouleila, Yasmine / Germond, Arno

Journal of visualized experiments : JoVE

2020 , Issue 155

Abstract: Cells are known to be inherently heterogeneous in their responses to drugs. Therefore, it is essential that single-cell heterogeneity is accounted for in drug discovery studies. This can be achieved by accurately measuring the plethora of cellular ... ...

Abstract	Cells are known to be inherently heterogeneous in their responses to drugs. Therefore, it is essential that single-cell heterogeneity is accounted for in drug discovery studies. This can be achieved by accurately measuring the plethora of cellular interactions between a cell and drug at the single-cell level (i.e., drug uptake, metabolism, and effect). This paper describes a single-cell Raman spectroscopy and mass spectrometry (MS) platform to monitor metabolic changes of cells in response to drugs. Using this platform, metabolic changes in response to the drug can be measured by Raman spectroscopy, while the drug and its metabolite can be quantified using mass spectrometry in the same cell. The results suggest that it is possible to access information about drug uptake, metabolism, and response at a single-cell level.
MeSH term(s)	Biological Transport/physiology ; Mass Spectrometry/methods ; Spectrum Analysis, Raman/methods
Language	English
Publishing date	2020-01-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Video-Audio Media
ZDB-ID	2259946-0
ISSN	1940-087X ; 1940-087X
ISSN (online)	1940-087X
ISSN	1940-087X
DOI	10.3791/60449
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Article ; Online: Evaluation and prediction of salt effects on pig muscle by deep UV and machine learning

El Karam, Saïd Abou / Ferrand, Maxime / Astruc, Thierry / Germond, Arno

Meat Science. 2023 Feb. 08, p.109136-

2023 , Page(s) 109136–

Abstract	The salting process for meat transformation is a crucial step in conventional industry. Recent developments in label-free spectrometry techniques combined with machine learning hold great promise for high-precision salt processing. In this study, we applied UV fluorescence to characterize salting treatments in pig's Teres major muscle and predict NaCl concentrations. t-SNE analyses based on spectral measurements revealed clear differences between NaCl-free and salted treatments. However, salt treatments were not clearly identified. We then highlighted and exploited a variability seen in the emission spectra at the wavelengths 300, 318, and 360 nm, which reflected structural or compositional changes. Using this information, predictive models could accurately identify the five salted treatments with a high specificity and sensitivity or predict salt concentrations. This study paves the way toward the possibility for industrials to precisely adjust NaCl concentrations with precision during processing.
Keywords	fluorescence ; industry ; meat ; meat science ; muscles ; prediction ; spectroscopy ; swine ; Pig meat ; Salting ; Deep-UV ; Machine learning ; PLS
Language	English
Dates of publication	2023-0208
Publishing place	Elsevier Ltd
Document type	Article ; Online
Note	Pre-press version ; Use and reproduction
ZDB-ID	753319-6
ISSN	1873-4138 ; 0309-1740
ISSN (online)	1873-4138
ISSN	0309-1740
DOI	10.1016/j.meatsci.2023.109136
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Analysis of the stability of 70 housekeeping genes during iPS reprogramming.

Panina, Yulia / Germond, Arno / Watanabe, Tomonobu M

Scientific reports

2020 Volume 10, Issue 1, Page(s) 21711

Abstract: Studies on induced pluripotent stem (iPS) cells highly rely on the investigation of their gene expression which requires normalization by housekeeping genes. Whether the housekeeping genes are stable during the iPS reprogramming, a transition of cell ... ...

Abstract	Studies on induced pluripotent stem (iPS) cells highly rely on the investigation of their gene expression which requires normalization by housekeeping genes. Whether the housekeeping genes are stable during the iPS reprogramming, a transition of cell state known to be associated with profound changes, has been overlooked. In this study we analyzed the expression patterns of the most comprehensive list to date of housekeeping genes during iPS reprogramming of a mouse neural stem cell line N31. Our results show that housekeeping genes' expression fluctuates significantly during the iPS reprogramming. Clustering analysis shows that ribosomal genes' expression is rising, while the expression of cell-specific genes, such as vimentin (Vim) or elastin (Eln), is decreasing. To ensure the robustness of the obtained data, we performed a correlative analysis of the genes. Overall, all 70 genes analyzed changed the expression more than two-fold during the reprogramming. The scale of this analysis, that takes into account 70 previously known and newly suggested genes, allowed us to choose the most stable of all genes. We highlight the fact of fluctuation of housekeeping genes during iPS reprogramming, and propose that, to ensure robustness of qPCR experiments in iPS cells, housekeeping genes should be used together in combination, and with a prior testing in a specific line used in each study. We suggest that the longest splice variants of Rpl13a, Rplp1 and Rps18 can be used as a starting point for such initial testing as the most stable candidates.
MeSH term(s)	Animals ; Cells, Cultured ; Cellular Reprogramming/genetics ; Gene Expression ; Genes, Essential/genetics ; Induced Pluripotent Stem Cells/physiology ; Mice ; Neural Stem Cells/physiology ; Ribosomal Proteins
Chemical Substances	RPLP1 protein, mouse ; Ribosomal Proteins ; Rpl13a protein, mouse
Language	English
Publishing date	2020-12-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-78863-5
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Analysis of the stability of 70 housekeeping genes during iPS reprogramming

Yulia Panina / Arno Germond / Tomonobu M. Watanabe

Scientific Reports, Vol 10, Iss 1, Pp 1-

2020 Volume 10

Abstract: Abstract Studies on induced pluripotent stem (iPS) cells highly rely on the investigation of their gene expression which requires normalization by housekeeping genes. Whether the housekeeping genes are stable during the iPS reprogramming, a transition of ...

Abstract	Abstract Studies on induced pluripotent stem (iPS) cells highly rely on the investigation of their gene expression which requires normalization by housekeeping genes. Whether the housekeeping genes are stable during the iPS reprogramming, a transition of cell state known to be associated with profound changes, has been overlooked. In this study we analyzed the expression patterns of the most comprehensive list to date of housekeeping genes during iPS reprogramming of a mouse neural stem cell line N31. Our results show that housekeeping genes’ expression fluctuates significantly during the iPS reprogramming. Clustering analysis shows that ribosomal genes’ expression is rising, while the expression of cell-specific genes, such as vimentin (Vim) or elastin (Eln), is decreasing. To ensure the robustness of the obtained data, we performed a correlative analysis of the genes. Overall, all 70 genes analyzed changed the expression more than two-fold during the reprogramming. The scale of this analysis, that takes into account 70 previously known and newly suggested genes, allowed us to choose the most stable of all genes. We highlight the fact of fluctuation of housekeeping genes during iPS reprogramming, and propose that, to ensure robustness of qPCR experiments in iPS cells, housekeeping genes should be used together in combination, and with a prior testing in a specific line used in each study. We suggest that the longest splice variants of Rpl13a, Rplp1 and Rps18 can be used as a starting point for such initial testing as the most stable candidates.
Keywords	Medicine ; R ; Science ; Q
Subject code	612
Language	English
Publishing date	2020-12-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: The Effects of Postmortem Time on Muscle Trout Biochemical Composition and Structure.

Germond, Arno / Vénien, Annie / Ravel, Christine / Castulovich, Brayan / Rouel, Jacques / Hutin, Morgane / Mezelli, Sara / Lefin, Sandy / Mirade, Pierre-Sylvain / Astruc, Thierry

Foods (Basel, Switzerland)

2023 Volume 12, Issue 10

Abstract: Fish industry operators have to process fish that arrive at ... ...

Abstract	Fish industry operators have to process fish that arrive at various
Language	English
Publishing date	2023-05-11
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2704223-6
ISSN	2304-8158
ISSN	2304-8158
DOI	10.3390/foods12101957
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: An integrated raman spectroscopy and mass spectrometry platform to study single-cell drug uptake, metabolism, and effects

Ali, Ahmed / Abouleila, Yasmine / Germond, Arno

Journal of visualized experiments. 2020 Jan. 09, , no. 155

2020

Abstract	Cells are known to be inherently heterogeneous in their responses to drugs. Therefore, it is essential that single-cell heterogeneity is accounted for in drug discovery studies. This can be achieved by accurately measuring the plethora of cellular interactions between a cell and drug at the single-cell level (i.e., drug uptake, metabolism, and effect). This paper describes a single-cell Raman spectroscopy and mass spectrometry (MS) platform to monitor metabolic changes of cells in response to drugs. Using this platform, metabolic changes in response to the drug can be measured by Raman spectroscopy, while the drug and its metabolite can be quantified using mass spectrometry in the same cell. The results suggest that it is possible to access information about drug uptake, metabolism, and response at a single-cell level.
Keywords	Raman spectroscopy ; drugs ; mass spectrometry ; metabolism ; metabolites
Language	English
Dates of publication	2020-0109
Size	p. e60449.
Publishing place	Journal of Visualized Experiments
Document type	Article
ZDB-ID	2259946-0
ISSN	1940-087X
ISSN	1940-087X
DOI	10.3791/60449
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Genetic diversity of oxytetracycline-resistant bacteria and tet(M) genes in two major coastal areas of South Korea.

Germond, Arno / Kim, Soo-Jin

Journal of global antimicrobial resistance

2015 Volume 3, Issue 3, Page(s) 166–173

Abstract: This study aimed to analyse the prevalence and genetic diversity of the tet(M) resistance gene as well as the species composition of oxytetracycline-resistant bacteria in coastal areas of South Korea. Both culturable and non-culturable bacterial ... ...

Abstract	This study aimed to analyse the prevalence and genetic diversity of the tet(M) resistance gene as well as the species composition of oxytetracycline-resistant bacteria in coastal areas of South Korea. Both culturable and non-culturable bacterial communities were sampled in 2010 and 2011 within two coastal areas (Wando and Geoje). tet(M) and 16S rRNA gene sequences were obtained by PCR and sequencing and were used for phylogenetic analyses. Quantitative PCR (qPCR) was performed to determine the prevalence of tet(M) in sampled areas. Phylogenetic analyses revealed high heterogeneity of tet(M) sequences between Wando and Geoje areas. Sequences found in Wando were highly similar to each other and were similar to sequences found in Japanese aquaculture sites. A larger diversity of tet(M) sequences was obtained from natural assemblage in Geoje. qPCR showed a high prevalence of tet(M) in Wando's aquaculture sites (up to 10
Language	English
Publishing date	2015-09
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2710046-7
ISSN	2213-7173 ; 2213-7165
ISSN (online)	2213-7173
ISSN	2213-7165
DOI	10.1016/j.jgar.2015.04.005
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