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Article ; Online: Non-invasive diagnosis of colorectal cancer by Raman spectroscopy: Recent developments in liquid biopsy and endoscopy approaches.

Noothalapati, Hemanth / Iwasaki, Keita / Yamamoto, Tatsuyuki

Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy

2021 Volume 258, Page(s) 119818

Abstract: Colorectal cancer (CRC) is the third most common cancer diagnosed globally and is also one of the leading causes of cancer deaths in both men and women. The progression of CRC is slow and is often contained in colon but the risk increases with age. Based ...

Abstract	Colorectal cancer (CRC) is the third most common cancer diagnosed globally and is also one of the leading causes of cancer deaths in both men and women. The progression of CRC is slow and is often contained in colon but the risk increases with age. Based on the high certainty that the net benefit of screening in an age group is substantial, screening for CRC is recommended beginning at the age of 50. Currently, most of the incidence is concentrated in developed countries but the rate is increasing rapidly in developing geographies. Detecting CRC at an early stage is critical to reduce morbidity and mortality. Colonoscopy is the most preferred screening method but not very widely implemented due to practical considerations such as cost involved, lack of personnel and facility. To address these concerns, Raman spectroscopy (RS) has been suggested as a viable alternative due to its potential as a rapid non-invasive diagnostic tool. Recently, several studies have been reported but many variations of RS applications in CRC exists and are not well understood by non-specialists. This review focuses particularly on developments of Raman based liquid biopsy and endoscopic studies in order to throw light on each of their significance and limitations. Necessary developments in the future to translate RS into a clinical tool for screening and diagnosis of CRC are also briefly presented.
MeSH term(s)	Colonic Neoplasms ; Colonoscopy ; Colorectal Neoplasms/diagnosis ; Female ; Humans ; Liquid Biopsy ; Male ; Spectrum Analysis, Raman
Language	English
Publishing date	2021-04-16
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	210413-1
ISSN	1873-3557 ; 0370-8322 ; 0584-8539 ; 1386-1425
ISSN (online)	1873-3557
ISSN	0370-8322 ; 0584-8539 ; 1386-1425
DOI	10.1016/j.saa.2021.119818
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Article ; Online: Identification of Molecular Basis for Objective Discrimination of Breast Cancer Cells (MCF-7) from Normal Human Mammary Epithelial Cells by Raman Microspectroscopy and Multivariate Curve Resolution Analysis.

Iwasaki, Keita / Araki, Asuka / Krishna, C Murali / Maruyama, Riruke / Yamamoto, Tatsuyuki / Noothalapati, Hemanth

International journal of molecular sciences

2021 Volume 22, Issue 2

Abstract: Raman spectroscopy (RS), a non-invasive and label-free method, has been suggested to improve accuracy of cytological and even histopathological diagnosis. To our knowledge, this novel technique tends to be employed without concrete knowledge of molecular ...

Abstract	Raman spectroscopy (RS), a non-invasive and label-free method, has been suggested to improve accuracy of cytological and even histopathological diagnosis. To our knowledge, this novel technique tends to be employed without concrete knowledge of molecular changes in cells. Therefore, identification of Raman spectral markers for objective diagnosis is necessary for universal adoption of RS. As a model study, we investigated human mammary epithelial cells (HMEpC) and breast cancer cells (MCF-7) by RS and employed various multivariate analyses (MA) including principal components analysis (PCA), linear discriminant analysis (LDA), and support vector machine (SVM) to estimate diagnostic accuracy. Furthermore, to elucidate the underlying molecular changes in cancer cells, we utilized multivariate curve resolution analysis-alternating least squares (MCR-ALS) with non-negative constraints to extract physically meaningful spectra from complex cellular data. Unsupervised PCA and supervised MA, such as LDA and SVM, classified HMEpC and MCF-7 fairly well with high accuracy but without revealing molecular basis. Employing MCR-ALS analysis we identified five pure biomolecular spectra comprising DNA, proteins and three independent unsaturated lipid components. Relative abundance of lipid 1 seems to be strictly regulated between the two groups of cells and could be the basis for excellent discrimination by chemometrics-assisted RS. It was unambiguously assigned to linoleate rich glyceride and therefore serves as a Raman spectral marker for reliable diagnosis. This study successfully identified Raman spectral markers and demonstrated the potential of RS to become an excellent cytodiagnostic tool that can both accurately and objectively discriminates breast cancer from normal cells.
MeSH term(s)	Biomarkers, Tumor/analysis ; Breast/cytology ; Breast/metabolism ; Breast Neoplasms/diagnosis ; Breast Neoplasms/metabolism ; Discriminant Analysis ; Epithelial Cells/metabolism ; Glycerides/analysis ; Humans ; Least-Squares Analysis ; Linoleic Acid/analysis ; MCF-7 Cells ; Multivariate Analysis ; Principal Component Analysis ; Reproducibility of Results ; Sensitivity and Specificity ; Spectrum Analysis, Raman/methods ; Support Vector Machine
Chemical Substances	Biomarkers, Tumor ; Glycerides ; Linoleic Acid (9KJL21T0QJ)
Language	English
Publishing date	2021-01-14
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms22020800
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Article ; Online: Cell behavior of the highly sticky bacterium Acinetobacter sp. Tol 5 during adhesion in laminar flows.

Furuichi, Yoshihide / Iwasaki, Keita / Hori, Katsutoshi

Scientific reports

2018 Volume 8, Issue 1, Page(s) 8285

Abstract: It is important to characterize how medically, industrially, or environmentally important bacteria adhere to surfaces in liquid flows in order to control their cell adhesion and subsequent biofilm formation. Acinetobacter sp. Tol 5 is a remarkably sticky ...

Abstract	It is important to characterize how medically, industrially, or environmentally important bacteria adhere to surfaces in liquid flows in order to control their cell adhesion and subsequent biofilm formation. Acinetobacter sp. Tol 5 is a remarkably sticky bacterium that autoagglutinates through the adhesive nanofiber protein AtaA, which is applicable to cell immobilization in bioprocesses. In this study, the adhesion and behavior of Tol 5 cells in laminar flows were investigated using flow cell systems. Tol 5 cells autoagglutinated through AtaA and formed cell clumps during flowing. The cell clumps rather than single cells went downward due to gravity and adhered to the bottom surface. Under appropriate shear stress, a twin vortex was caused by a separated flow generated at the rear of the pre-immobilized cell clumps and carried the small cell clumps to this location, resulting in their stacking there. The rearward immobilized cell clumps developed into a large, stable aggregate with a streamlined shape, independent of cell growth. Cell clumps hardly ever developed under weak shear stress that could not generate a twin vortex and were broken up under excessively strong shear stress. These cell behaviors including the importance of clumping are interesting features in the bacterial adhesion processes.
MeSH term(s)	Acinetobacter/metabolism ; Acinetobacter/physiology ; Adhesins, Bacterial/metabolism ; Bacteria/metabolism ; Bacterial Adhesion/physiology ; Biofilms ; Cell Adhesion/physiology ; Cells, Immobilized/metabolism ; Hydrodynamics ; Tissue Adhesions
Chemical Substances	Adhesins, Bacterial
Language	English
Publishing date	2018-05-29
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/s41598-018-26699-5
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Article ; Online: Differences in microplastic degradation in the atmosphere and coastal water environment from two island nations: Japan and New Zealand

Nagato, Edward G. / Noothalapati, Hemanth / Kogumasaka, Chihiro / Kakii, Sota / Hossain, Sarwar / Iwasaki, Keita / Takai, Yuki / Shimasaki, Yohei / Honda, Masato / Hayakawa, Kazuichi / Yamamoto, Tatsuyuki / Archer, Stephen D.J.

Environmental Pollution. 2023 Sept., v. 333 p.122011-

2023

Abstract: Microplastics are subject to environmental forces that can change polymer organization on a molecular scale. However, it is not clear to what extent these changes occur in the environment and whether microplastics in the atmospheric and water environment ...

Abstract	Microplastics are subject to environmental forces that can change polymer organization on a molecular scale. However, it is not clear to what extent these changes occur in the environment and whether microplastics in the atmospheric and water environment differ. Here we identify structural differences between microplastics in the atmosphere and water environment from Japan and New Zealand, representing two archipelagos differing in their proximity to nearby countries and highly populated areas. We first highlight the propensity for smaller microplastics to arrive via air masses from the Asian continent to the Japan Sea coastal area, while New Zealand received larger, locally derived microplastics. Analyses of polyethylene in the Japanese atmosphere indicate that microplastics transported to the Japanese coastal areas were more crystalline than polyethylene particles in the water, suggesting that the plastics arriving by air were relatively more aged and brittle. By contrast, polypropylene particles in New Zealand waters were more degraded than the microplastic particles in the air. Due to the lack of abundance, both polyethylene and polypropylene could not be analyzed for both countries. Nevertheless, these findings show the structural variation in microplastics between environments in markedly different real-world locations, with implications for the toxic potential of these particles.
Keywords	Japan ; air ; brittleness ; coastal water ; coasts ; microplastics ; pollution ; polyethylene ; polypropylenes ; toxicity ; New Zealand ; Environmental pollution ; Atmospheric microplastics ; Polymer crystallinity ; Raman spectroscopy ; Human health
Language	English
Dates of publication	2023-09
Publishing place	Elsevier Ltd
Document type	Article ; Online
ZDB-ID	280652-6
ISSN	1873-6424 ; 0013-9327 ; 0269-7491
ISSN (online)	1873-6424
ISSN	0013-9327 ; 0269-7491
DOI	10.1016/j.envpol.2023.122011
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Article ; Online: Predictive correction of serum sodium concentration with formulas derived from the Edelman equation in patients with severe hyponatremia.

Nagase, Koya / Watanabe, Tsuyoshi / Nomura, Akihiro / Nagase, Fumika N / Iwasaki, Keita / Nakamura, Yoshihiro / Ikai, Hiroki / Yamamoto, Mari / Murai, Yukari / Yokoyama-Kokuryo, Waka / Takizawa, Naoho / Shimizu, Hideaki / Fujita, Yoshiro

Scientific reports

2023 Volume 13, Issue 1, Page(s) 1783

Abstract: Severe hyponatremia can cause life-threatening cerebral edema. Treatment comprises rapid elevation of serum sodium concentration; however, overcorrection can result in osmotic demyelination. This study investigated potential factors, including predictive ...

Abstract	Severe hyponatremia can cause life-threatening cerebral edema. Treatment comprises rapid elevation of serum sodium concentration; however, overcorrection can result in osmotic demyelination. This study investigated potential factors, including predictive correction based on the Edelman equation, associated with appropriate correction in 221 patients with a serum sodium concentration ≤ 120 mEq/L who were admitted to a hospital in Nagoya, Japan. Appropriate correction was defined as an elevation in serum sodium concentration in the range of 4-10 mEq/L in the first 24 h and within 18 mEq/L in the first 48 h after the start of the correction. Appropriate corrections were made in 132 (59.7%) of the 221 patients. Multivariate analysis revealed that predictive correction with an infusate and fluid loss formula derived from the Edelman equation was associated with appropriate correction of serum sodium concentration (adjusted odds ratio, 7.84; 95% confidence interval, 2.97-20.64). Relative without its use, the predictive equation results in a lower proportion of undercorrection (14.3% vs. 48.0%, respectively) and overcorrection (1.0% vs. 12.2%, respectively). These results suggest that predictive correction of serum sodium concentrations using the formula derived from the Edelman equation can play an essential role in the appropriate management of patients with severe hyponatremia.
MeSH term(s)	Humans ; Behavior Therapy ; Brain Edema ; Hyponatremia/therapy ; Sodium
Chemical Substances	Sodium (9NEZ333N27)
Language	English
Publishing date	2023-01-31
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/s41598-023-28380-y
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Article ; Online: Biological and Medical Applications of Multivariate Curve Resolution Assisted Raman Spectroscopy.

Noothalapati, Hemanth / Iwasaki, Keita / Yamamoto, Tatsuyuki

Analytical sciences : the international journal of the Japan Society for Analytical Chemistry

2017 Volume 33, Issue 1, Page(s) 15–22

Abstract: Biological specimens such as cells, tissues and biofluids (urine, blood) contain mixtures of many different biomolecules, all of which contribute to a Raman spectrum at any given point. The separation and identification of pure biochemical components ... ...

Abstract	Biological specimens such as cells, tissues and biofluids (urine, blood) contain mixtures of many different biomolecules, all of which contribute to a Raman spectrum at any given point. The separation and identification of pure biochemical components remains one of the biggest challenges in Raman spectroscopy. Multivariate curve resolution, a matrix factorization method, is a powerful, yet flexible, method that can be used with constraints, such as non-negativity, to decompose a complex spectroscopic data matrix into a small number of physically meaningful pure spectral components along with their relative abundances. This paper reviews recent applications of multivariate curve resolution by alternating least squares analysis to Raman spectroscopic and imaging data obtained either in vivo or in vitro from biological and medical samples.
Language	English
Publishing date	2017
Publishing country	Japan
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1483376-1
ISSN	1348-2246 ; 0910-6340
ISSN (online)	1348-2246
ISSN	0910-6340
DOI	10.2116/analsci.33.15
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Article ; Online: Differences in microplastic degradation in the atmosphere and coastal water environment from two island nations: Japan and New Zealand.

Nagato, Edward G / Noothalapati, Hemanth / Kogumasaka, Chihiro / Kakii, Sota / Hossain, Sarwar / Iwasaki, Keita / Takai, Yuki / Shimasaki, Yohei / Honda, Masato / Hayakawa, Kazuichi / Yamamoto, Tatsuyuki / Archer, Stephen D J

Environmental pollution (Barking, Essex : 1987)

2023 Volume 333, Page(s) 122011

Abstract	Microplastics are subject to environmental forces that can change polymer organization on a molecular scale. However, it is not clear to what extent these changes occur in the environment and whether microplastics in the atmospheric and water environment differ. Here we identify structural differences between microplastics in the atmosphere and water environment from Japan and New Zealand, representing two archipelagos differing in their proximity to nearby countries and highly populated areas. We first highlight the propensity for smaller microplastics to arrive via air masses from the Asian continent to the Japan Sea coastal area, while New Zealand received larger, locally derived microplastics. Analyses of polyethylene in the Japanese atmosphere indicate that microplastics transported to the Japanese coastal areas were more crystalline than polyethylene particles in the water, suggesting that the plastics arriving by air were relatively more aged and brittle. By contrast, polypropylene particles in New Zealand waters were more degraded than the microplastic particles in the air. Due to the lack of abundance, both polyethylene and polypropylene could not be analyzed for both countries. Nevertheless, these findings show the structural variation in microplastics between environments in markedly different real-world locations, with implications for the toxic potential of these particles.
MeSH term(s)	Microplastics ; Plastics ; Water ; Japan ; New Zealand ; Water Pollutants, Chemical/analysis ; Environmental Monitoring ; Polypropylenes ; Atmosphere ; Polyethylene/analysis
Chemical Substances	Microplastics ; Plastics ; Water (059QF0KO0R) ; Water Pollutants, Chemical ; Polypropylenes ; Polyethylene (9002-88-4)
Language	English
Publishing date	2023-06-09
Publishing country	England
Document type	Journal Article
ZDB-ID	280652-6
ISSN	1873-6424 ; 0013-9327 ; 0269-7491
ISSN (online)	1873-6424
ISSN	0013-9327 ; 0269-7491
DOI	10.1016/j.envpol.2023.122011
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Article: Visualizing wax ester fermentation in single Euglena gracilis cells by Raman microspectroscopy and multivariate curve resolution analysis

Iwasaki, Keita / Kaneko, Asuka / Tanaka, Yuji / Ishikawa, Takahiro / Noothalapati, Hemanth / Yamamoto, Tatsuyuki

Biotechnology for biofuels. 2019 Dec., v. 12, no. 1

2019

Abstract: BACKGROUND: Global demand for energy is on the rise at a time when limited natural resources are fast depleting. To address this issue, microalgal biofuels are being recommended as a renewable and eco-friendly substitute for fossil fuels. Euglena ... ...

Abstract	BACKGROUND: Global demand for energy is on the rise at a time when limited natural resources are fast depleting. To address this issue, microalgal biofuels are being recommended as a renewable and eco-friendly substitute for fossil fuels. Euglena gracilis is one such candidate that has received special interest due to their ability to synthesize wax esters that serve as precursors for production of drop-in jet fuel. However, to realize economic viability and achieve industrial-scale production, development of novel methods to characterize algal cells, evaluate its culture conditions, and construct appropriate genetically modified strains is necessary. Here, we report a Raman microspectroscopy-based method to visualize important metabolites such as paramylon and ester during wax ester fermentation in single Euglena gracilis cells in a label-free manner. RESULTS: We measured Raman spectra to obtain intracellular biomolecular information in Euglena under anaerobic condition. First, by univariate approach, we identified Raman markers corresponding to paramylon/esters and constructed their time-lapse chemical images. However, univariate analysis is severely limited in its ability to obtain detailed information as several molecules can contribute to a Raman band. Therefore, we further employed multivariate curve resolution analysis to obtain chain length-specific information and their abundance images of the produced esters. Accumulated esters in Euglena were particularly identified to be myristyl myristate (C28), a wax ester candidate suitable to prepare drop-in jet fuel. Interestingly, we found accumulation of two different forms of myristyl myristate for the first time in Euglena through our exploratory multivariate analysis. CONCLUSIONS: We succeeded in visualizing molecular-specific information in Euglena during wax ester fermentation by Raman microspectroscopy. It is obvious from our results that simple univariate approach is insufficient and that multivariate curve resolution analysis is crucial to extract hidden information from Raman spectra. Even though we have not measured any mutants in this study, our approach is directly applicable to other systems and is expected to deepen the knowledge on lipid metabolism in microalgae, which eventually leads to new strategies that will help to enhance biofuel production efficiency in the future.
Keywords	Euglena gracilis ; Raman spectroscopy ; biofuels ; economic sustainability ; energy ; fermentation ; fossil fuels ; fuel production ; lipid metabolism ; metabolites ; microalgae ; multivariate analysis ; mutants ; wax esters
Language	English
Dates of publication	2019-12
Size	p. 128.
Publishing place	BioMed Central
Document type	Article
ZDB-ID	2421351-2
ISSN	1754-6834
ISSN	1754-6834
DOI	10.1186/s13068-019-1471-2
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Article ; Online: DNA Fingerprint Analysis of Raman Spectra Captures Global Genomic Alterations in Imatinib-Resistant Chronic Myeloid Leukemia: A Potential Single Assay for Screening Imatinib Resistance.

Mojidra, Rahul / Hole, Arti / Iwasaki, Keita / Noothalapati, Hemanth / Yamamoto, Tatsuyuki / C, Murali Krishna / Govekar, Rukmini

Cells

2021 Volume 10, Issue 10

Abstract: Monitoring the development of resistance to the tyrosine kinase inhibitor (TKI) imatinib in chronic myeloid leukemia (CML) patients in the initial chronic phase (CP) is crucial for limiting the progression of unresponsive patients to terminal phase of ... ...

Abstract	Monitoring the development of resistance to the tyrosine kinase inhibitor (TKI) imatinib in chronic myeloid leukemia (CML) patients in the initial chronic phase (CP) is crucial for limiting the progression of unresponsive patients to terminal phase of blast crisis (BC). This study for the first time demonstrates the potential of Raman spectroscopy to sense the resistant phenotype. Currently recommended resistance screening strategy include detection of BCR-ABL1 transcripts, kinase domain mutations, complex chromosomal abnormalities and BCR-ABL1 gene amplification. The techniques used for these tests are expensive, technologically demanding and have limited availability in resource-poor countries. In India, this could be a reason for more patients reporting to clinics with advanced disease. A single method which can identify resistant cells irrespective of the underlying mechanism would be a practical screening strategy. During our analysis of imatinib-sensitive and -resistant K562 cells, by array comparative genomic hybridization (aCGH), copy number variations specific to resistant cells were detected. aCGH is technologically demanding, expensive and therefore not suitable to serve as a single economic test. We therefore explored whether DNA finger-print analysis of Raman hyperspectral data could capture these alterations in the genome, and demonstrated that it could indeed segregate imatinib-sensitive and -resistant cells. Raman spectroscopy, due to availability of portable instruments, ease of spectrum acquisition and possibility of centralized analysis of transmitted data, qualifies as a preliminary screening tool in resource-poor countries for imatinib resistance in CML. This study provides a proof of principle for a single assay for monitoring resistance to imatinib, available for scrutiny in clinics.
MeSH term(s)	Comparative Genomic Hybridization/methods ; DNA Copy Number Variations/genetics ; DNA Fingerprinting/methods ; Drug Resistance, Neoplasm/drug effects ; Drug Resistance, Neoplasm/genetics ; Humans ; Imatinib Mesylate/pharmacology ; K562 Cells ; Mutation/genetics ; Protein Kinase Inhibitors/pharmacology
Chemical Substances	Protein Kinase Inhibitors ; Imatinib Mesylate (8A1O1M485B)
Language	English
Publishing date	2021-09-22
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells10102506
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Article ; Online: An Acinetobacter trimeric autotransporter adhesin reaped from cells exhibits its nonspecific stickiness via a highly stable 3D structure.

Yoshimoto, Shogo / Nakatani, Hajime / Iwasaki, Keita / Hori, Katsutoshi

Scientific reports

2016 Volume 6, Page(s) 28020

Abstract: Trimeric autotransporter adhesins (TAAs), cell surface proteins of Gram-negative bacteria, mediate bacterial adhesion to host cells and extracellular matrix proteins. However, AtaA, a TAA in the nonpathogenic Acinetobacter sp. strain Tol 5, shows ... ...

Abstract	Trimeric autotransporter adhesins (TAAs), cell surface proteins of Gram-negative bacteria, mediate bacterial adhesion to host cells and extracellular matrix proteins. However, AtaA, a TAA in the nonpathogenic Acinetobacter sp. strain Tol 5, shows nonspecific, high adhesiveness to abiotic material surfaces as well as to biotic surfaces. AtaA is a homotrimer of polypeptides comprising 3,630 amino acids and forms long nanofibers; therefore, it is too large and structurally complex to be produced as a recombinant protein. In this study, we isolated AtaA's passenger domain (AtaA PSD), which is translocated to the cell surface through the C-terminal transmembrane domain and exhibits biological functions, using a new method. We introduced a protease recognition site and reaped AtaA nanofibers 225 nm in length from the cell surface through proteolytic cleavage with a specific protease. Biochemical and biophysical analyses of the purified native AtaA PSD revealed that it has a stable structure under alkaline and acidic conditions. Temperatures above 80 °C, which disrupted AtaA's higher-order structure but maintained the full-length AtaA polypeptide, inactivated AtaA's nonspecific adhesiveness, suggesting that the stickiness of AtaA requires its 3D structure. This finding refutes the widespread but vague speculation that large unfolded polypeptides readily stick to various surfaces.
MeSH term(s)	Acinetobacter/physiology ; Adhesins, Bacterial/chemistry ; Adhesins, Bacterial/genetics ; Adhesins, Bacterial/metabolism ; Amino Acid Sequence ; Bacterial Adhesion/physiology ; Cells, Cultured ; Nanofibers/chemistry ; Protein Conformation
Chemical Substances	Adhesins, Bacterial
Language	English
Publishing date	2016--16
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/srep28020
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