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Article ; Online: Differences in the incidence of nosocomial-onset COVID-19 among hospitalized patients with exposure to SARS-CoV-2.

Nakagawa, Masataka / Fujishiro, Yumiko / Doi, Yohei / Yamakami, Junichi / Honda, Hitoshi

Infection control and hospital epidemiology

2024 , Page(s) 1–3

Abstract: We evaluated the secondary COVID-19 incidence among uninfected hospitalized patients after nosocomial COVID-19 exposure. An exposure source of SARS-CoV-2 was hospitalized patients or healthcare personnel (HCP) newly diagnosed as having COVID-19. Patients ...

Abstract	We evaluated the secondary COVID-19 incidence among uninfected hospitalized patients after nosocomial COVID-19 exposure. An exposure source of SARS-CoV-2 was hospitalized patients or healthcare personnel (HCP) newly diagnosed as having COVID-19. Patients exposed to a COVID-19-infected patient in a shared room more frequently developed COVID-19 than those exposed to an infected HCP.
Language	English
Publishing date	2024-03-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	639378-0
ISSN	1559-6834 ; 0195-9417 ; 0899-823X
ISSN (online)	1559-6834
ISSN	0195-9417 ; 0899-823X
DOI	10.1017/ice.2024.48
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Article ; Online: Efficient expression and purification of tag-free recombinant human procalcitonin (hPCT) with precise sequence in E.coli.

Nakagawa, Masataka / Tomioka, Yui / Akuta, Teruo

Protein expression and purification

2023 Volume 214, Page(s) 106374

Abstract: We present an efficient method for expression and purification of recombinant human procalcitonin (hPCT) in E. coli T7 express LysY/Iq cells, ensuring precise N- and C-terminal amino acid sequences. Our method involves fusing codon-optimized cDNA with ... ...

Abstract	We present an efficient method for expression and purification of recombinant human procalcitonin (hPCT) in E. coli T7 express LysY/Iq cells, ensuring precise N- and C-terminal amino acid sequences. Our method involves fusing codon-optimized cDNA with two distinct tag sequences: eXact tag and chitin binding domain (CBD) tag. To purify the protein, we employ a two-step affinity chromatography process. Firstly, we utilize the N-terminal Profinity eXact tag and purify the protein through Profinity eXact-affinity column chromatography using a resin on which a mutant subtilisin protease was immobilized. The eXact tag was removed by adding NaF to activate the enzyme. Subsequently, the digested sample containing C-terminal CBD tag is directly loaded for the second step of chitin affinity chromatography. Elution is achieved through dithiothreitol (DTT)-catalyzed self-cleavage of the intein sequence from the fusion protein. As a result, the target protein is selectively recovered in the flow-through, completely tag-free, with a purity exceeding 95%. To ensure high purity and eliminate potential contaminants, we effectively remove E. coli host DNA and endotoxins through a combination of streptomycin sulfate, Triton X-114, and ammonium sulfate treatment. The exceptional level of purity obtained eliminates the need for further purification steps in most applications. This highly purified hPCT can be used as a calibrator in procalcitonin or calcitonin immunoassays. Notably, our approach effectively manages small peptides that are prone to degradation by E. coli host proteases, offering a robust solution for various research and application requirements.
MeSH term(s)	Humans ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Recombinant Fusion Proteins/genetics ; Procalcitonin/metabolism ; Recombinant Proteins/chemistry ; Inteins ; Chromatography, Affinity/methods
Chemical Substances	Recombinant Fusion Proteins ; Procalcitonin ; Recombinant Proteins
Language	English
Publishing date	2023-10-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	1055455-5
ISSN	1096-0279 ; 1046-5928
ISSN (online)	1096-0279
ISSN	1046-5928
DOI	10.1016/j.pep.2023.106374
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Article ; Online: Development of a novel two‐dimensional gel electrophoresis protocol with agarose native gel electrophoresis

Nakagawa, Masataka / Tomioka, Yui / Sakuma, Chiaki / Kurosawa, Yasunori / Shibata, Takashi / Arakawa, Tsutomu / Akuta, Teruo

ELECTROPHORESIS. 2023 Sept., v. 44, no. 17-18 p.1446-1460

2023

Abstract: A new protocol for conducting two‐dimensional (2D) electrophoresis was developed by combining the recently developed agarose native gel electrophoresis with either vertical sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis (PAGE) or flat ... ...

Abstract	A new protocol for conducting two‐dimensional (2D) electrophoresis was developed by combining the recently developed agarose native gel electrophoresis with either vertical sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis (PAGE) or flat SDS agarose gel electrophoresis. Our innovative technique utilizes His/MES buffer (pH 6.1) during the first‐dimensional (1D) agarose native gel electrophoresis, which allows for the simultaneous and clear visualization of basic and acidic proteins in their native states or complex structures. Our agarose gel electrophoresis is a true native electrophoresis, unlike blue native–PAGE, which relies on the intrinsic charged states of the proteins and their complexes without the need for dye binding. In the 2D, the gel strip from the 1D agarose gel electrophoresis is soaked in SDS and placed on top of the vertical SDS–PAGE gels or the edge of the flat SDS–MetaPhor high‐resolution agarose gels. This allows for customized operation using a single electrophoresis device at a low cost. This technique has been successfully applied to analyze various proteins, including five model proteins (BSA, factor Xa, ovotransferrin, IgG, and lysozyme), monoclonal antibodies with slightly different isoelectric points, polyclonal antibodies, and antigen–antibody complexes, as well as complex proteins such as IgM pentamer and β‐galactosidase tetramer. Our protocol can be completed within a day, taking approximately 5–6 h, and can be expanded further into Western blot analysis, mass spectrometry analysis, and other analytical methods.
Keywords	Western blotting ; agar gel electrophoresis ; agarose ; dyes ; gels ; lysozyme ; mass spectrometry ; pH ; polyacrylamide gel electrophoresis ; sodium dodecyl sulfate ; two-dimensional gel electrophoresis
Language	English
Dates of publication	2023-09
Size	p. 1446-1460.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	619001-7
ISSN	1522-2683 ; 0173-0835
ISSN (online)	1522-2683
ISSN	0173-0835
DOI	10.1002/elps.202200255
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Article: A case of pancreatic adenosquamous cell carcinoma with a pseudocyst following curative surgery.

Kitasaki, Nao / Abe, Tomoyuki / Inoue, Masashi / Teshima, Marino / Nakagawa, Masataka / Kochi, Masatoshi / Hotta, Ryuichi / Toyota, Kazuhiro

Surgical case reports

2024 Volume 10, Issue 1, Page(s) 74

Abstract: Background: Pancreatic adenosquamous cell carcinoma (PASC) is a relatively rare histological type of pancreatic malignancy, and preoperative diagnosis is difficult because of its rarity. PASC accounts for 1-4% of all pancreatic cancers, and even after ... ...

Abstract	Background: Pancreatic adenosquamous cell carcinoma (PASC) is a relatively rare histological type of pancreatic malignancy, and preoperative diagnosis is difficult because of its rarity. PASC accounts for 1-4% of all pancreatic cancers, and even after curative surgery, its prognosis is poorer than that of ordinary pancreatic adenocarcinoma. Pathologically, it shows glandular and squamous differentiation of cells. Complete resection is the only method to achieve a good long-term prognosis, and an increasing doubling time of PASC is considered to indicate early recurrence after surgery. Here, we report a rare case of PASC with an infected pancreatic cyst that was difficult to treat, along with a review of the literature. Case presentation: A woman in her 80s with a history of breast cancer presented with pericardial pain. Computed tomography revealed a 20-mm hypovascular tumor in the body of the pancreas and a 27-mm pseudocyst. Endoscopic retrograde cholangiopancreatography showed a severe main pancreatic duct stenosis in the body of the pancreas that made cannulation impossible, and contrast media extravasation was due to pancreatic duct disruption in the pancreatic tail. Endoscopic fine-needle aspiration revealed that the tumor was a PASC. Because the patient had an infected pancreatic cyst, central intravenous nutrition and antibiotics were administered, which stabilized her general condition. She was diagnosed with resectable PASC and underwent distal pancreatectomy with lymphadenectomy. The postoperative course was uneventful. Immunohistochemical analysis of the resected specimen confirmed T2N0M0 stage IB. Systemic adjuvant chemotherapy with S-1 is ongoing. Conclusion: Appropriate preoperative management and preoperative accurate staging (T2N0M0 stage IB) of PASC with curative surgery can ensure predictable outcomes.
Language	English
Publishing date	2024-04-01
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2809613-7
ISSN	2198-7793
ISSN	2198-7793
DOI	10.1186/s40792-024-01868-z
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Article ; Online: Ferguson plot analysis of multiple intermediate species of thermally unfolded bovine serum albumin.

Tomioka, Yui / Nagatoishi, Satoru / Nakagawa, Masataka / Tsumoto, Kouhei / Arakawa, Tsutomu / Akuta, Teruo

Biophysical chemistry

2023 Volume 301, Page(s) 107095

Abstract: Ferguson plot was used to characterize the multiple intermediate species of bovine serum albumin (BSA) upon thermal unfolding. Differential scanning calorimetry showed an irreversible melting of BSA in Tris-HCl and phosphate buffers with a mid-transition ...

Abstract	Ferguson plot was used to characterize the multiple intermediate species of bovine serum albumin (BSA) upon thermal unfolding. Differential scanning calorimetry showed an irreversible melting of BSA in Tris-HCl and phosphate buffers with a mid-transition temperature, Tm, of ∼68 °C. Thermally unfolded BSA was analyzed by agarose native gel electrophoresis stained by Coomassie blue and SYPRO Orange staining as a function of pH or protein concentration. SYPRO Orange was used to stain unfolded proteins. BSA heated at 70 and 80 °C, i.e., above the Tm, formed multiple intermediate species, which depended on the pH between 7.0 and 8.0, protein concentration and which buffer was used. These intermediate species were analyzed by Ferguson plot, which showed that BSA heated at 60 °C had a similar size to the native BSA, indicating that they are either native or native-like state consistent with no SYPRO Orange staining. The intermediate species observed at higher temperatures with the mobility less than that of the native BSA showed a steeper Ferguson plot and were stained by SYPRO Orange, indicating that these species had a larger hydrodynamic size than the native BSA and were unfolded.
MeSH term(s)	Calorimetry, Differential Scanning ; Hydrodynamics ; Serum Albumin, Bovine ; Transition Temperature ; Animals ; Cattle
Chemical Substances	Serum Albumin, Bovine (27432CM55Q)
Language	English
Publishing date	2023-08-15
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	185052-0
ISSN	1873-4200 ; 0301-4622
ISSN (online)	1873-4200
ISSN	0301-4622
DOI	10.1016/j.bpc.2023.107095
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Article ; Online: Electrophoresis, a transport technology that transitioned from moving boundary method to zone method.

Arakawa, Tsutomu / Nakagawa, Masataka / Sakuma, Chiaki / Tomioka, Yui / Kurosawa, Yasunori / Ejima, Daisuke / Akuta, Teruo

European biophysics journal : EBJ

2023 Volume 53, Issue 1-2, Page(s) 1–13

Abstract: Gel electrophoresis, a transport technology, is one of the most widely used experimental methods in biochemical and pharmaceutical research and development. Transport technologies are used to determine hydrodynamic or electrophoretic properties of ... ...

Abstract	Gel electrophoresis, a transport technology, is one of the most widely used experimental methods in biochemical and pharmaceutical research and development. Transport technologies are used to determine hydrodynamic or electrophoretic properties of macromolecules. Gel electrophoresis is a zone technology, where a small volume of sample is applied to a large separation gel matrix. In contrast, a seldom-used electrophoresis technology is moving boundary electrophoresis, where the sample is present throughout the separation phase or gel matrix. While the zone method gives peaks of separating macromolecular solutes, the moving boundary method gives a boundary between solute-free and solute-containing phases. We will review electrophoresis as a transport technology of zone and moving boundary methods and describe its principles and applications.
MeSH term(s)	Electrophoresis ; Research Design ; Hydrodynamics
Language	English
Publishing date	2023-12-30
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	283671-3
ISSN	1432-1017 ; 0175-7571
ISSN (online)	1432-1017
ISSN	0175-7571
DOI	10.1007/s00249-023-01694-5
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Article ; Online: Development of a novel two-dimensional gel electrophoresis protocol with agarose native gel electrophoresis.

Nakagawa, Masataka / Tomioka, Yui / Sakuma, Chiaki / Kurosawa, Yasunori / Shibata, Takashi / Arakawa, Tsutomu / Akuta, Teruo

Electrophoresis

2023 Volume 44, Issue 17-18, Page(s) 1446–1460

Abstract: A new protocol for conducting two-dimensional (2D) electrophoresis was developed by combining the recently developed agarose native gel electrophoresis with either vertical sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis (PAGE) or flat ... ...

Abstract	A new protocol for conducting two-dimensional (2D) electrophoresis was developed by combining the recently developed agarose native gel electrophoresis with either vertical sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis (PAGE) or flat SDS agarose gel electrophoresis. Our innovative technique utilizes His/MES buffer (pH 6.1) during the first-dimensional (1D) agarose native gel electrophoresis, which allows for the simultaneous and clear visualization of basic and acidic proteins in their native states or complex structures. Our agarose gel electrophoresis is a true native electrophoresis, unlike blue native-PAGE, which relies on the intrinsic charged states of the proteins and their complexes without the need for dye binding. In the 2D, the gel strip from the 1D agarose gel electrophoresis is soaked in SDS and placed on top of the vertical SDS-PAGE gels or the edge of the flat SDS-MetaPhor high-resolution agarose gels. This allows for customized operation using a single electrophoresis device at a low cost. This technique has been successfully applied to analyze various proteins, including five model proteins (BSA, factor Xa, ovotransferrin, IgG, and lysozyme), monoclonal antibodies with slightly different isoelectric points, polyclonal antibodies, and antigen-antibody complexes, as well as complex proteins such as IgM pentamer and β-galactosidase tetramer. Our protocol can be completed within a day, taking approximately 5-6 h, and can be expanded further into Western blot analysis, mass spectrometry analysis, and other analytical methods.
MeSH term(s)	Sepharose/chemistry ; Proteins/analysis ; Electrophoresis, Gel, Two-Dimensional/methods ; Electrophoresis, Polyacrylamide Gel ; Electrophoresis, Agar Gel/methods ; Gels
Chemical Substances	Sepharose (9012-36-6) ; Proteins ; Gels
Language	English
Publishing date	2023-06-09
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	619001-7
ISSN	1522-2683 ; 0173-0835
ISSN (online)	1522-2683
ISSN	0173-0835
DOI	10.1002/elps.202200255
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Article: Ladder observation of bovine serum albumin by high resolution agarose native gel electrophoresis

Tomioka, Yui / Nakagawa, Masataka / Sakuma, Chiaki / Nagatoishi, Satoru / Tsumoto, Kouhei / Arakawa, Tsutomu / Akuta, Teruo

International journal of biological macromolecules. 2022 June 16,

2022

Abstract: A commercially available bovine serum albumin (BSA) was examined by agarose native gel electrophoresis using two different agarose sources, UltraPure and MetaPhor agarose. While UltraPure agarose up to 5 % showed no clear separation of BSA oligomers, ... ...

Abstract	A commercially available bovine serum albumin (BSA) was examined by agarose native gel electrophoresis using two different agarose sources, UltraPure and MetaPhor agarose. While UltraPure agarose up to 5 % showed no clear separation of BSA oligomers, MetaPhor agarose clearly demonstrated oligomer bands above 4 %, indicating that the latter agarose has greater molecular sieving effects and is hence characterized to have high resolution for size differences, as probed by a greater slope of Ferguson plot. Physical properties are different between two agaroses. In general, UltraPure agarose has physical strength, while MetaPhor agarose is considerably fragile, but MetaPhor agarose solution is less viscous so that even 10 % gel can be made. Cause of oligomers was shown to be not associated with inter-chain disulfide bonds, but is due to association of native or native-like molecules.
Keywords	agarose ; bovine serum albumin ; disulfides ; gel electrophoresis ; gels
Language	English
Dates of publication	2022-0616
Publishing place	Elsevier B.V.
Document type	Article
Note	Pre-press version
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2022.06.118
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Article: Analysis of proteins by agarose native gel electrophoresis in the presence of solvent additives

Tomioka, Yui / Arakawa, Tsutomu / Akuta, Teruo / Nakagawa, Masataka / Ishibashi, Matsujiro

International journal of biological macromolecules. 2022 Feb. 15, v. 198

2022

Abstract: Solvent additives, including NaCl, arginine hydrochloride (ArgHCl), glycine and sucrose, are used to enhance protein stability or reduce protein aggregation. Here, we studied the effects of these additives on proteins using agarose native gel ... ...

Abstract	Solvent additives, including NaCl, arginine hydrochloride (ArgHCl), glycine and sucrose, are used to enhance protein stability or reduce protein aggregation. Here, we studied the effects of these additives on proteins using agarose native gel electrophoresis. Since these additives are used at relatively high concentration, we first confirmed that they do not interfere with the performance of the native gel electrophoresis. Agarose native gel electrophoresis showed that aggregation of bovine serum albumin (BSA) induced by heating was slightly reduced by NaCl and ArgHCl. On the contrary, glycine and sucrose had marginal effects. ArgHCl and NaCl promoted heat aggregation of monoclonal antibody (mAb), while glycine and sucrose stabilized the native mAb. Arginine methyl ester inhibited heat aggregation of lysozyme and, to a much lesser extent, BSA. These results show that agarose native gel electrophoresis can be used to analyze the effects of solvent additives on proteins subjected to heat stresses. SYPRO Orange that stains only unfolded proteins confirmed unfolded structures of soluble aggregates.
Keywords	agarose ; arginine ; bovine serum albumin ; gel electrophoresis ; heat ; lysozyme ; monoclonal antibodies ; solvents ; sucrose
Language	English
Dates of publication	2022-0215
Size	p. 26-36.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2021.12.084
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Article ; Online: Analysis of proteins by agarose native gel electrophoresis in the presence of solvent additives.

Tomioka, Yui / Arakawa, Tsutomu / Akuta, Teruo / Nakagawa, Masataka / Ishibashi, Matsujiro

International journal of biological macromolecules

2021 Volume 198, Page(s) 26–36

Abstract	Solvent additives, including NaCl, arginine hydrochloride (ArgHCl), glycine and sucrose, are used to enhance protein stability or reduce protein aggregation. Here, we studied the effects of these additives on proteins using agarose native gel electrophoresis. Since these additives are used at relatively high concentration, we first confirmed that they do not interfere with the performance of the native gel electrophoresis. Agarose native gel electrophoresis showed that aggregation of bovine serum albumin (BSA) induced by heating was slightly reduced by NaCl and ArgHCl. On the contrary, glycine and sucrose had marginal effects. ArgHCl and NaCl promoted heat aggregation of monoclonal antibody (mAb), while glycine and sucrose stabilized the native mAb. Arginine methyl ester inhibited heat aggregation of lysozyme and, to a much lesser extent, BSA. These results show that agarose native gel electrophoresis can be used to analyze the effects of solvent additives on proteins subjected to heat stresses. SYPRO Orange that stains only unfolded proteins confirmed unfolded structures of soluble aggregates.
MeSH term(s)	Muramidase
Chemical Substances	hen egg lysozyme (EC 3.2.1.-) ; Muramidase (EC 3.2.1.17)
Language	English
Publishing date	2021-12-24
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2021.12.084
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