Detection of Penicillin G Produced by <i>Penicillium chrysogenum</i> with Raman Microspectroscopy and Multivariate Curve Resolution-Alternating Least-Squares Methods

Horii, Shumpei; Ando, Masahiro; Samuel, Ashok Zachariah; Take, A; Nakashima, Takuji; Matsumoto, Atsuko; Y, Takahashi; Takeyama, Haruko

doi:10.1021/acs.jnatprod.0c00214

Cited by 27 publications

(51 citation statements)

References 41 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In the Raman images, proteins and lipids can be seen more or less continuously distributed throughout the cell. Polyphosphate and cytochrome c are distributed at certain regions of the cell, in agreement with our previous study (38). A protrusion originating from mycelium is indicated with a circle.…”

Section: Resultssupporting

confidence: 92%

Raman microspectroscopy imaging analysis of extracellular vesicles (EVs) biogenesis by filamentous fungus Penicilium chrysogenum

Samuel

Horii

Nakashima

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

Mechanism of production of extracellular vesicles (EVs) and their molecular contents are of great interest owing to their diverse roles in biological systems and are far from being completely understood. Even though, cellular cargo release mediated by EVs have been demonstrated in several cases, their role in secondary metabolite production and release remains elusive. In this study we investigate this aspect in detail using Raman micro-spectroscopic imaging. We provide considerable evidence to suggest that the release of antibiotic penicillin by filamentous fungus Penicillium chrysogenum involves EVs. Morphological modifications of the fungal body during biogenesis, changes in cell composition at the locus of biogenesis, and major molecular contents of the released EVs are also revealed in this study.ImportanceExtracellular vesicles (EVs) play a key role in cellular communications. EVs role in functioning of fungi are relatively less explored. Here we show selective enrichment of chemical contents at certain locations of mycelium of P. chrysogenum forming protruding regions. Secondary metabolite penicillin is excessively localized in them. We provide evidence to show that EVs are released from these protrusions. Raman imaging has been applied for molecular profiling of the mycelium and for characterizing chemical contents of the EVs. Our study suggests a possible general role of EVs in the release of antibiotics from the producing organisms.

show abstract

Section: Resultssupporting

confidence: 92%

Raman microspectroscopy imaging analysis of extracellular vesicles (EVs) biogenesis by filamentous fungus Penicilium chrysogenum

Samuel

Horii

Nakashima

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…Raman microscopy is one of the few single-cell techniques that provides a direct link between metabolites and source organism in a non-destructive way and at the single-cell level and can be applied to diverse questions in microbiological research using commercially available instrumentation. Raman microscopy was previously applied to single-bacterial natural product imaging 37 and to bacterial sorting based on deuterium incorporation 38 , but to our knowledge MERMAID is the first single-cell pipeline that also provides genomic information. This pipeline can be a one-stop, high-throughput system based on microfluidics.…”

Section: Discussionmentioning

confidence: 99%

“…Some Raman-active moieties that do not overlap with those of basic metabolites are conjugated olefins, alkynes, carbon-halogen bonds, heteroaromatic rings, i.e., features present in many secondary metabolites. In some cases, compounds with more common features can also be targeted using analysis with MCR-ALS 37 . As an example for its utility, the platform enabled the rapid identification of the unusual symbiont 'P.…”

Section: Discussionmentioning

confidence: 99%

Single-cell metabolite detection and genomics reveals uncultivated talented producer

Kogawa

Miyaoka

Hemmerling

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

The production of bioactive metabolites is increasingly recognized as an important function of host-associated bacteria. An example is defensive symbiosis that might account for much of the chemical richness of marine invertebrates including sponges (Porifera), one of the oldest metazoans. However, as most complex microbiomes remain largely uncultivated and lack reference genomes, unequivocally linking metabolic functions to a cellular source is a challenge. Here we report an analysis pipeline of microfluidic encapsulation, Raman microscopy, and integrated digital genomics (MERMAID) for an efficient identification of uncultivated producers. We applied this method to the chemically rich bacteriosponge Theonella swinhoei, previously shown to contain ′Entotheonella′ symbionts providing most of its bioactive substances except for the antifungal aurantosides that lacked biosynthetic gene candidates in the metagenome. Raman-guided single-bacterial analysis and sequencing revealed a cryptic, distinct multiproducer, ′Candidatus Poriflexus aureus′ from a new Chloroflexi lineage. Its exceptionally large genome contains numerous biosynthetic loci and suggested an even higher chemical richness of this sponge than previously appreciated. This study highlights the importance of complementary technologies to uncover microbiome functions, reveals remarkable parallels between distantly related symbionts of the same host, and adds functional support for diverse chemically prolific lineages being present in microbial dark matter.

show abstract

“…MCR-ALS, which evolved from SMMA, is a popular matrix factorization algorithm [ 47 , 48 ]. For MCR-ALS, the initial synergy and activation matrices, containing relative content and component information, respectively, are obtained from SMMA.…”

Section: Methodsmentioning

confidence: 99%

A Novel Muscle Synergy Extraction Method Used for Motor Function Evaluation of Stroke Patients: A Pilot Study

Shi

et al. 2021

Sensors

View full text Add to dashboard Cite

In this paper, we present a novel muscle synergy extraction method based on multivariate curve resolution–alternating least squares (MCR-ALS) to overcome the limitation of the nonnegative matrix factorization (NMF) method for extracting non-sparse muscle synergy, and we study its potential application for evaluating motor function of stroke survivors. Nonnegative matrix factorization (NMF) is the most widely used method for muscle synergy extraction. However, NMF is susceptible to components’ sparseness and usually provides inferior reliability, which significantly limits the promotion of muscle synergy. In this study, MCR-ALS was employed to extract muscle synergy from electromyography (EMG) data. Its performance was compared with two other matrix factorization algorithms, NMF and self-modeling mixture analysis (SMMA). Simulated data sets were utilized to explore the influences of the sparseness and noise on the extracted synergies. As a result, the synergies estimated by MCR-ALS were the most similar to true synergies as compared with SMMA and NMF. MCR-ALS was used to analyze the muscle synergy characteristics of upper limb movements performed by healthy (n = 11) and stroke (n = 5) subjects. The repeatability and intra-subject consistency were used to evaluate the performance of MCR-ALS. As a result, MCR-ALS provided much higher repeatability and intra-subject consistency as compared with NMF, which were important for the reliability of the motor function evaluation. The stroke subjects had lower intra-subject consistency and seemingly had more synergies as compared with the healthy subjects. Thus, MCR-ALS is a promising muscle synergy analysis method for motor function evaluation of stroke patients.

show abstract

Detection of Penicillin G Produced by Penicillium chrysogenum with Raman Microspectroscopy and Multivariate Curve Resolution-Alternating Least-Squares Methods

Cited by 27 publications

References 41 publications

Raman microspectroscopy imaging analysis of extracellular vesicles (EVs) biogenesis by filamentous fungus Penicilium chrysogenum

Raman microspectroscopy imaging analysis of extracellular vesicles (EVs) biogenesis by filamentous fungus Penicilium chrysogenum

Single-cell metabolite detection and genomics reveals uncultivated talented producer

A Novel Muscle Synergy Extraction Method Used for Motor Function Evaluation of Stroke Patients: A Pilot Study

Contact Info

Product

Resources

About