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  1. Article: Two-Round Treatment With Propidium Monoazide Completely Inhibits the Detection of Dead

    Okada, Ayaka / Tsuchida, Mizuki / Rahman, Md Matiur / Inoshima, Yasuo

    Frontiers in microbiology

    2022  Volume 13, Page(s) 801961

    Abstract: ... ...

    Abstract Campylobacter
    Language English
    Publishing date 2022-04-25
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2022.801961
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Research Note: Detection of Campylobacter spp. in chicken meat using culture methods and quantitative PCR with propidium monoazide.

    Okada, Ayaka / Tsuchida, Mizuki / Aoyagi, Kazuha / Yoshino, Ayaka / Rahman, Md Matiur / Inoshima, Yasuo

    Poultry science

    2023  Volume 102, Issue 9, Page(s) 102883

    Abstract: Globally, Campylobacter spp. are prominent causative agents of food-borne gastroenteritis. These pathogens are commonly detected using conventional culture methods; however, culture methods are unable to detect viable but nonculturable (VBNC) bacteria. ... ...

    Abstract Globally, Campylobacter spp. are prominent causative agents of food-borne gastroenteritis. These pathogens are commonly detected using conventional culture methods; however, culture methods are unable to detect viable but nonculturable (VBNC) bacteria. Currently, the detection rate of Campylobacter spp. on chicken meat does not correlate with the seasonal peak of human campylobacteriosis. We hypothesized that this may be due to the presence of undetectable VBNC Campylobacter spp. Therefore, we previously established a quantitative PCR assay using propidium monoazide (PMA-qPCR), which can detect viable Campylobacter cells. In this study, PMA-qPCR was conducted to detect viable Campylobacter spp. in chicken meat, and the detection rates of PMA-qPCR and the culture method throughout all 4 seasons were compared. A total of 105 chicken meat samples (whole legs, breast fillets, and livers) were screened for the presence of Campylobacter spp. using both PMA-qPCR and the conventional culture method. The detection rates of the 2 methods did not differ significantly; however, the positive and negative samples were not always consistent. Detection rates in March were significantly lower compared to months with the highest detection rates. These results suggest that, to increase the detection rate of Campylobacter spp., the 2 methods should be used in parallel. In this study, PMA-qPCR could not detect VBNC Campylobacter spp. effectively in C. jejuni-spiked chicken meat. Further studies using improved viability-qPCR should be performed to describe the impact of the VBNC state of Campylobacter spp. on the detection of this bacterium in chicken meat.
    MeSH term(s) Humans ; Animals ; Chickens/microbiology ; Real-Time Polymerase Chain Reaction/veterinary ; Real-Time Polymerase Chain Reaction/methods ; Campylobacter/genetics ; Azides ; Propidium ; Meat/microbiology
    Chemical Substances propidium monoazide ; Azides ; Propidium (36015-30-2)
    Language English
    Publishing date 2023-06-18
    Publishing country England
    Document type Journal Article
    ZDB-ID 242586-5
    ISSN 1525-3171 ; 0032-5791
    ISSN (online) 1525-3171
    ISSN 0032-5791
    DOI 10.1016/j.psj.2023.102883
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Analytical characteristics of nano-electrospray operated under super-atmospheric pressure.

    Rahman, Md Matiur / Chen, Lee Chuin

    Analytica chimica acta

    2018  Volume 1021, Page(s) 78–84

    Abstract: High-pressure nanoelectrospray ionization (nanoESI) source is a recently developed technique in which the electrospray ionization is generated inside an enclosed chamber with gas pressure higher than the atmospheric pressure. In this paper, the ... ...

    Abstract High-pressure nanoelectrospray ionization (nanoESI) source is a recently developed technique in which the electrospray ionization is generated inside an enclosed chamber with gas pressure higher than the atmospheric pressure. In this paper, the performance of nanoESI under different gas pressures, emitter position, ion inlet temperature, additive for desalination are presented. Under a pressure of 2 bars, the nanoESI is almost eased from the electrical discharge problem, and that offers a wider tuning window for the emitter potential to produces a higher and more stable ion signal. With optimized ion inlet temperature, the high-pressure operation facilitates the generation of ion species of higher charge-state from the highly aqueous solution, and produced less sodium adducts. A preparation method for the high-throughput analysis of raw biological samples using disposable plastic nanoESI emitter is also described.
    MeSH term(s) Atmospheric Pressure ; Glucose/analysis ; Glucosinolates/analysis ; Malates/analysis ; Nanotechnology ; Plant Roots/chemistry ; Raphanus/chemistry ; Spectrometry, Mass, Electrospray Ionization
    Chemical Substances 4-methylthio-3-butenyl glucosinolate ; Glucosinolates ; Malates ; glucoraphenin ; malic acid (817L1N4CKP) ; Glucose (IY9XDZ35W2)
    Language English
    Publishing date 2018-03-29
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1483436-4
    ISSN 1873-4324 ; 0003-2670
    ISSN (online) 1873-4324
    ISSN 0003-2670
    DOI 10.1016/j.aca.2018.03.026
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Characterization of mRNA Signature in Milk Small Extracellular Vesicles from Cattle Infected with Bovine Leukemia Virus.

    Rahman, Md Matiur / Ishikawa, Hinata / Yamauchi, Marika / Takashima, Shigeo / Kamatari, Yuji O / Shimizu, Kaori / Okada, Ayaka / Inoshima, Yasuo

    Pathogens (Basel, Switzerland)

    2023  Volume 12, Issue 10

    Abstract: This study aimed to characterize the mRNA signature of milk small extracellular vesicles (sEVs) from BLV-infected cattle. A total of 23 mRNAs, which showed greater abundance in milk sEVs from BLV-infected cattle compared to those from BLV-uninfected ( ... ...

    Abstract This study aimed to characterize the mRNA signature of milk small extracellular vesicles (sEVs) from BLV-infected cattle. A total of 23 mRNAs, which showed greater abundance in milk sEVs from BLV-infected cattle compared to those from BLV-uninfected (control) cattle, were identified through microarray analyses conducted in our previous study. To assess the significance of these differences in mRNA abundance, milk was collected from six control cattle and twenty-six cattle infected with BLV. The infected cattle were categorized into two distinct groups based on their proviral loads: a group of eight cattle with low proviral loads (LPVL), characterized by <10,000 copies per 10
    Language English
    Publishing date 2023-10-13
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2695572-6
    ISSN 2076-0817
    ISSN 2076-0817
    DOI 10.3390/pathogens12101239
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Identification of Suitable Internal Control miRNAs in Bovine Milk Small Extracellular Vesicles for Normalization in Quantitative Real-Time Polymerase Chain Reaction.

    Rahman, Md Matiur / Nakanishi, Ryoka / Tsukada, Fumi / Takashima, Shigeo / Wakihara, Yoshiko / Kamatari, Yuji O / Shimizu, Kaori / Okada, Ayaka / Inoshima, Yasuo

    Membranes

    2023  Volume 13, Issue 2

    Abstract: This study aimed to identify a suitable RNA extraction kit and stable internal control microRNA (miRNA) in bovine milk small extracellular vesicles (sEVs) for a quantitative polymerase chain reaction (qPCR) analysis. Two RNA extraction kits, miRNeasy ... ...

    Abstract This study aimed to identify a suitable RNA extraction kit and stable internal control microRNA (miRNA) in bovine milk small extracellular vesicles (sEVs) for a quantitative polymerase chain reaction (qPCR) analysis. Two RNA extraction kits, miRNeasy Micro Kit, and Maxwell RSC miRNA Tissue Kit, were compared and evaluated using bovine milk sEVs via qPCR analysis. Five miRNAs, bta-miR-29a, bta-miR-200a, bta-miR-26b, hsa-miR-27b-3p, and hsa-miR-30b-5p, were selected by microarray analyses, and their cycle threshold (Ct) values were further evaluated mathematically using geNorm, NormFinder, BestKeeper, and ∆Ct algorithms. The results revealed that both the miRNeasy Micro Kit and Maxwell RSC miRNA Tissue Kit are useful for the efficient recovery of RNA from bovine milk sEVs. According to the final stability ranking analyzed by RefFinder, hsa-miR-27b-3p and bta-miR-29a can be used as suitable internal control miRNAs in bovine milk sEVs. The study also indicated that using a suitable internal control miRNA may improve the reliability and accuracy of the qPCR analysis for normalization in bovine milk sEVs. To the best of our knowledge, this is the first study to uncover the suitable internal control miRNAs in bovine milk sEVs.
    Language English
    Publishing date 2023-02-02
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2614641-1
    ISSN 2077-0375
    ISSN 2077-0375
    DOI 10.3390/membranes13020185
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Assessing of the use of proteins A, G, and chimeric protein AG to detect marine mammal immunoglobulins.

    Sakyi, Michael Essien / Kamio, Takashi / Kohyama, Kaoru / Rahman, Md Matiur / Shimizu, Kaori / Okada, Ayaka / Inoshima, Yasuo

    PloS one

    2023  Volume 18, Issue 9, Page(s) e0291743

    Abstract: In recent years, there has been an increase in infectious diseases in marine mammals, including brucellosis, infections of morbillivirus, herpesvirus, and poxvirus. Several serological diagnostic methods, including enzyme-linked immunosorbent assays, ... ...

    Abstract In recent years, there has been an increase in infectious diseases in marine mammals, including brucellosis, infections of morbillivirus, herpesvirus, and poxvirus. Several serological diagnostic methods, including enzyme-linked immunosorbent assays, immunofluorescence assays (ELISA), and western blotting, have been used to detect antibodies against pathogens in marine mammals. However, options for commercial secondary antibodies used to detect antibodies in marine mammals are limited; therefore, the use of proteins A, G, or chimeric protein AG may provide a suitable alternative. This study aimed to assess the use of proteins A, G, and chimeric protein AG to detect marine mammal immunoglobulins. Currently, there are no comparative studies on the use of proteins A, G, and chimeric protein AG for the detection of immunoglobulins in marine mammals. In this study, we used ten pinnipeds' species (Baikal seal, California sea lion, harbor seal, northern fur seal, ringed seal, South American fur seal, South American sea lion, spotted seal, Steller sea lion, and walrus) and five cetacean species (beluga whale, bottlenose dolphin, harbor porpoise, killer whale, and Pacific white-sided dolphin) and compare binding ability to proteins A, G, or chimeric protein AG by ELISA. The results revealed that the immunoglobulins from pinniped and cetacean species reacted more strongly to protein A than protein G. In addition, the immunoglobulins of pinnipeds and cetaceans showed a strong binding ability to chimeric protein AG. These results suggest that proteins A, G, and chimeric protein AG would be used to help further develop serological assays.
    MeSH term(s) Animals ; Sea Lions ; Fur Seals ; Caniformia ; Antibodies ; Seals, Earless ; Beluga Whale ; Phocoena ; Walruses ; Whale, Killer ; Recombinant Fusion Proteins/genetics
    Chemical Substances Antibodies ; Recombinant Fusion Proteins
    Language English
    Publishing date 2023-09-21
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0291743
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Correction to: Direct Analysis of Aqueous Solutions and Untreated Biological Samples Using Nanoelectrospray Ionization Mass Spectrometry with Pipette Tip in Series with High-Ohmic Resistor as Ion Source.

    Rahman, Md Matiur / Wu, Debo / Chingin, Konstantin

    Journal of the American Society for Mass Spectrometry

    2019  Volume 30, Issue 7, Page(s) 1337

    Abstract: Md. Matiur Rahman's name was incorrect in the original publication of this article. ...

    Abstract Md. Matiur Rahman's name was incorrect in the original publication of this article.
    Language English
    Publishing date 2019-03-19
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 1073671-2
    ISSN 1879-1123 ; 1044-0305
    ISSN (online) 1879-1123
    ISSN 1044-0305
    DOI 10.1007/s13361-019-02188-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Online desalting and sequential formation of analyte ions for mass spectrometry characterization of untreated biological samples.

    Rahman, Md Matiur / Chingin, Konstantin / Chen, Huanwen

    Chemical communications (Cambridge, England)

    2019  Volume 55, Issue 62, Page(s) 9188–9191

    Abstract: The metal salts ubiquitously present in biological samples cause serious ion suppression, capillary clogging and signal fluctuation in ESI/nESI. Herein, a current-limited high voltage polarity reversing approach was applied for the online separation of ... ...

    Abstract The metal salts ubiquitously present in biological samples cause serious ion suppression, capillary clogging and signal fluctuation in ESI/nESI. Herein, a current-limited high voltage polarity reversing approach was applied for the online separation of intrinsic metal ions in biological samples, resulting in the generation of protonated analytes at the nESI tip for mass analysis without interference from salt cations. Stable and durable signals (∼30-60 s) were observed for protonated proteins, peptides and metabolites in complex biological samples, including liquids, solids and viscous samples, even with very high salt concentration (100 mM NaCl), allowing comprehensive tandem MS analysis with on average ca. 5-times higher analyte signal intensities compared to the conventional nESI analysis. Therefore this approach offers improved performance of nESI/ESI for the sensitive molecular analysis of untreated biological samples, opening new possibilities in various disciplines, including biology, medicine, chemistry, life sciences, etc.
    MeSH term(s) Ions/analysis ; Peptides/analysis ; Peptides/metabolism ; Proteins/analysis ; Proteins/metabolism ; Protons ; Sodium Chloride/chemistry ; Spectrometry, Mass, Electrospray Ionization/instrumentation
    Chemical Substances Ions ; Peptides ; Proteins ; Protons ; Sodium Chloride (451W47IQ8X)
    Language English
    Publishing date 2019-07-15
    Publishing country England
    Document type Journal Article
    ZDB-ID 1472881-3
    ISSN 1364-548X ; 1359-7345 ; 0009-241X
    ISSN (online) 1364-548X
    ISSN 1359-7345 ; 0009-241X
    DOI 10.1039/c9cc04705k
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Comprehensive Proteomic Analysis Revealed a Large Number of Newly Identified Proteins in the Small Extracellular Vesicles of Milk from Late-Stage Lactating Cows

    Rahman, Md. Matiur / Takashima, Shigeo / Kamatari, Yuji O. / Shimizu, Kaori / Okada, Ayaka / Inoshima, Yasuo

    Animals. 2021 Aug. 26, v. 11, no. 9

    2021  

    Abstract: Bovine milk contains small extracellular vesicles (sEVs) that provide proteins, miRNAs, mRNAs, DNAs, and lipids to target cells and play a role in intracellular communications. Previous studies have characterized proteins in milk sEVs from early- and mid- ...

    Abstract Bovine milk contains small extracellular vesicles (sEVs) that provide proteins, miRNAs, mRNAs, DNAs, and lipids to target cells and play a role in intracellular communications. Previous studies have characterized proteins in milk sEVs from early- and mid-stage lactation. However, the proteins in milk sEVs from late-stage lactation are mostly unexplored. The aim of this study was to determine the proteomic profile of milk sEVs from late-stage lactating cows. A comprehensive nanoliquid chromatography–tandem mass spectrometry (nanoLC-MS/MS) approach was carried out to reveal the proteins in milk sEVs. Additionally, bioinformatics analysis was carried out to interpret the molecular signatures of newly identified proteins in milk sEVs from three late-stage lactating cows. NanoLC-MS/MS analysis revealed a total of 2225 proteins in milk sEVs from cows. Notably, after comparing these identified proteins with previously deposited datasets of proteins in bovine milk sEVs, 429 proteins were detected as newly identified. Bioinformatic analysis indicated that these newly identified proteins in milk sEVs were engaged in a diverse range of molecular phenomena relevant to mammary gland physiology, milk production, immunity, and immune response. These findings suggest that the newly identified proteins could expand the inventory application of molecular cargos, nutritional status, and immune modulation of sEVs in milk during the late-stage lactation.
    Keywords bioinformatics ; data collection ; immune response ; immunomodulation ; inventories ; lactation ; mammary glands ; microRNA ; milk ; milk production ; nutritional status ; proteomics ; tandem mass spectrometry
    Language English
    Dates of publication 2021-0826
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2606558-7
    ISSN 2076-2615
    ISSN 2076-2615
    DOI 10.3390/ani11092506
    Database NAL-Catalogue (AGRICOLA)

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  10. Article: Online desalting and sequential formation of analyte ions for mass spectrometry characterization of untreated biological samples

    Rahman, Md. Matiur / Chingin, Konstantin / Chen, Huanwen

    Chemical communications. 2019 July 30, v. 55, no. 62

    2019  

    Abstract: The metal salts ubiquitously present in biological samples cause serious ion suppression, capillary clogging and signal fluctuation in ESI/nESI. Herein, a current-limited high voltage polarity reversing approach was applied for the online separation of ... ...

    Abstract The metal salts ubiquitously present in biological samples cause serious ion suppression, capillary clogging and signal fluctuation in ESI/nESI. Herein, a current-limited high voltage polarity reversing approach was applied for the online separation of intrinsic metal ions in biological samples, resulting in the generation of protonated analytes at the nESI tip for mass analysis without interference from salt cations. Stable and durable signals (∼30–60 s) were observed for protonated proteins, peptides and metabolites in complex biological samples, including liquids, solids and viscous samples, even with very high salt concentration (100 mM NaCl), allowing comprehensive tandem MS analysis with on average ca. 5-times higher analyte signal intensities compared to the conventional nESI analysis. Therefore this approach offers improved performance of nESI/ESI for the sensitive molecular analysis of untreated biological samples, opening new possibilities in various disciplines, including biology, medicine, chemistry, life sciences, etc.
    Keywords cations ; chemical reactions ; chemical species ; electric potential difference ; mass spectrometry ; medicine ; metabolites ; metal ions ; peptides ; proteins ; salt concentration ; sodium chloride
    Language English
    Dates of publication 2019-0730
    Size p. 9188-9191.
    Publishing place The Royal Society of Chemistry
    Document type Article
    ZDB-ID 1472881-3
    ISSN 1364-548X ; 1359-7345 ; 0009-241X
    ISSN (online) 1364-548X
    ISSN 1359-7345 ; 0009-241X
    DOI 10.1039/c9cc04705k
    Database NAL-Catalogue (AGRICOLA)

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