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  1. Article ; Online: Roles of non-coding RNAs in the metabolism and pathogenesis of bladder cancer.

    Sanya, Daniel Ruben Akiola / Onésime, Djamila

    Human cell

    2023  Volume 36, Issue 4, Page(s) 1343–1372

    Abstract: Bladder cancer (BC) is featured as the second most common malignancy of the urinary tract worldwide with few treatments leading to high incidence and mortality. It stayed a virtually intractable disease, and efforts to identify innovative and effective ... ...

    Abstract Bladder cancer (BC) is featured as the second most common malignancy of the urinary tract worldwide with few treatments leading to high incidence and mortality. It stayed a virtually intractable disease, and efforts to identify innovative and effective therapies are urgently needed. At present, more and more evidence shows the importance of non-coding RNA (ncRNA) for disease-related study, diagnosis, and treatment of diverse types of malignancies. Recent evidence suggests that dysregulated functions of ncRNAs are closely associated with the pathogenesis of numerous cancers including BC. The detailed mechanisms underlying the dysregulated role of ncRNAs in cancer progression are still not fully understood. This review mainly summarizes recent findings on regulatory mechanisms of the ncRNAs, long non-coding RNAs, microRNAs, and circular RNAs, in cancer progression or suppression and focuses on the predictive values of ncRNAs-related signatures in BC clinical outcomes. A deeper understanding of the ncRNA interactive network could be compelling framework for developing biomarker-guided clinical trials.
    MeSH term(s) Humans ; RNA, Untranslated/genetics ; RNA, Untranslated/metabolism ; MicroRNAs/genetics ; MicroRNAs/metabolism ; RNA, Long Noncoding/genetics ; RNA, Long Noncoding/metabolism ; RNA, Circular/genetics ; Urinary Bladder Neoplasms/genetics ; Urinary Bladder Neoplasms/therapy
    Chemical Substances RNA, Untranslated ; MicroRNAs ; RNA, Long Noncoding ; RNA, Circular
    Language English
    Publishing date 2023-05-20
    Publishing country Japan
    Document type Journal Article ; Review
    ZDB-ID 1149134-6
    ISSN 1749-0774 ; 0914-7470
    ISSN (online) 1749-0774
    ISSN 0914-7470
    DOI 10.1007/s13577-023-00915-5
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  2. Article ; Online: New roles for Yarrowia lipolytica in molecules synthesis and biocontrol.

    Sanya, Daniel Ruben Akiola / Onésime, Djamila

    Applied microbiology and biotechnology

    2022  Volume 106, Issue 22, Page(s) 7397–7416

    Abstract: Reprogramming of host metabolism is a common strategy for improving desired compounds in host cells and is essential to generate overproducing strains in biotechnology. As a promising feedstock converter, Yarrowia lipolytica has been engineered to extend ...

    Abstract Reprogramming of host metabolism is a common strategy for improving desired compounds in host cells and is essential to generate overproducing strains in biotechnology. As a promising feedstock converter, Yarrowia lipolytica has been engineered to extend its bioproduction ability related to the synthesis of new value-added molecules relevant to human food and disease treatment. New synthetic tools have been reported and new enzymes with biotechnological importance are recovered. Additionally, metabolic events occurring during substrate utilization and recombinant protein production have been elucidated. Its contributions as feed and in controlling disease in the food industry have also been provided. Likewise, the recent abilities of Yarrowia lipolytica in the bioconversion of food waste into single-cell protein have been reported. These aforementioned events made the novelty of this review compared to the existing ones on this oleaginous yeast. KEY POINTS: • The production of biolipids by the heterotrophic yeast Yarrowia lipolytica is examined. • A Summary of information concerning new value-added molecules has been highlighted. • Special focus on the importance of Yarrowia lipolytica in regulating the immune system has been provided.
    MeSH term(s) Humans ; Yarrowia/genetics ; Yarrowia/metabolism ; Metabolic Engineering ; Food ; Refuse Disposal ; Biotechnology
    Language English
    Publishing date 2022-10-15
    Publishing country Germany
    Document type Journal Article ; Review
    ZDB-ID 392453-1
    ISSN 1432-0614 ; 0171-1741 ; 0175-7598
    ISSN (online) 1432-0614
    ISSN 0171-1741 ; 0175-7598
    DOI 10.1007/s00253-022-12227-z
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  3. Article ; Online: New roles for Yarrowia lipolytica in molecules synthesis and biocontrol

    Sanya, Daniel Ruben Akiola / Onésime, Djamila

    Appl Microbiol Biotechnol. 2022 Nov., v. 106, no. 22 p.7397-7416

    2022  

    Abstract: Reprogramming of host metabolism is a common strategy for improving desired compounds in host cells and is essential to generate overproducing strains in biotechnology. As a promising feedstock converter, Yarrowia lipolytica has been engineered to extend ...

    Abstract Reprogramming of host metabolism is a common strategy for improving desired compounds in host cells and is essential to generate overproducing strains in biotechnology. As a promising feedstock converter, Yarrowia lipolytica has been engineered to extend its bioproduction ability related to the synthesis of new value-added molecules relevant to human food and disease treatment. New synthetic tools have been reported and new enzymes with biotechnological importance are recovered. Additionally, metabolic events occurring during substrate utilization and recombinant protein production have been elucidated. Its contributions as feed and in controlling disease in the food industry have also been provided. Likewise, the recent abilities of Yarrowia lipolytica in the bioconversion of food waste into single-cell protein have been reported. These aforementioned events made the novelty of this review compared to the existing ones on this oleaginous yeast. KEY POINTS: • The production of biolipids by the heterotrophic yeast Yarrowia lipolytica is examined. • A Summary of information concerning new value-added molecules has been highlighted. • Special focus on the importance of Yarrowia lipolytica in regulating the immune system has been provided.
    Keywords Yarrowia lipolytica ; biological control ; biotechnology ; biotransformation ; feedstocks ; food industry ; food waste ; foods ; immune system ; protein synthesis ; recombinant proteins ; single cell protein ; therapeutics ; value added ; yeasts
    Language English
    Dates of publication 2022-11
    Size p. 7397-7416.
    Publishing place Springer Berlin Heidelberg
    Document type Article ; Online
    Note Review
    ZDB-ID 392453-1
    ISSN 1432-0614 ; 0171-1741 ; 0175-7598
    ISSN (online) 1432-0614
    ISSN 0171-1741 ; 0175-7598
    DOI 10.1007/s00253-022-12227-z
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  4. Article ; Online: Recent advances in therapeutic targets identification and development of treatment strategies towards Pseudomonas aeruginosa infections.

    Sanya, Daniel Ruben Akiola / Onésime, Djamila / Vizzarro, Grazia / Jacquier, Nicolas

    BMC microbiology

    2023  Volume 23, Issue 1, Page(s) 86

    Abstract: The opportunistic human pathogen Pseudomonas aeruginosa is the causal agent of a wide variety of infections. This non-fermentative Gram-negative bacillus can colonize zones where the skin barrier is weakened, such as wounds or burns. It also causes ... ...

    Abstract The opportunistic human pathogen Pseudomonas aeruginosa is the causal agent of a wide variety of infections. This non-fermentative Gram-negative bacillus can colonize zones where the skin barrier is weakened, such as wounds or burns. It also causes infections of the urinary tract, respiratory system or bloodstream. P. aeruginosa infections are common in hospitalized patients for which multidrug-resistant, respectively extensively drug-resistant isolates can be a strong contributor to a high rate of in-hospital mortality. Moreover, chronic respiratory system infections of cystic fibrosis patients are especially concerning, since very tedious to treat. P. aeruginosa exploits diverse cell-associated and secreted virulence factors, which play essential roles in its pathogenesis. Those factors encompass carbohydrate-binding proteins, quorum sensing that monitor the production of extracellular products, genes conferring extensive drug resistance, and a secretion system to deliver effectors to kill competitors or subvert host essential functions. In this article, we highlight recent advances in the understanding of P. aeruginosa pathogenicity and virulence as well as efforts for the identification of new drug targets and the development of new therapeutic strategies against P. aeruginosa infections. These recent advances provide innovative and promising strategies to circumvent infection caused by this important human pathogen.
    MeSH term(s) Humans ; Pseudomonas Infections/drug therapy ; Virulence Factors/genetics ; Virulence Factors/metabolism ; Virulence/genetics ; Quorum Sensing ; Pseudomonas aeruginosa/metabolism ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Anti-Bacterial Agents/metabolism
    Chemical Substances Virulence Factors ; Anti-Bacterial Agents
    Language English
    Publishing date 2023-03-30
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2041505-9
    ISSN 1471-2180 ; 1471-2180
    ISSN (online) 1471-2180
    ISSN 1471-2180
    DOI 10.1186/s12866-023-02832-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Roles of RNA-binding proteins in neurological disorders, COVID-19, and cancer.

    Sanya, Daniel Ruben Akiola / Cava, Claudia / Onésime, Djamila

    Human cell

    2022  Volume 36, Issue 2, Page(s) 493–514

    Abstract: RNA-binding proteins (RBPs) have emerged as important players in multiple biological processes including transcription regulation, splicing, R-loop homeostasis, DNA rearrangement, miRNA function, biogenesis, and ribosome biogenesis. A large number of ... ...

    Abstract RNA-binding proteins (RBPs) have emerged as important players in multiple biological processes including transcription regulation, splicing, R-loop homeostasis, DNA rearrangement, miRNA function, biogenesis, and ribosome biogenesis. A large number of RBPs had already been identified by different approaches in various organisms and exhibited regulatory functions on RNAs' fate. RBPs can either directly or indirectly interact with their target RNAs or mRNAs to assume a key biological function whose outcome may trigger disease or normal biological events. They also exert distinct functions related to their canonical and non-canonical forms. This review summarizes the current understanding of a wide range of RBPs' functions and highlights their emerging roles in the regulation of diverse pathways, different physiological processes, and their molecular links with diseases. Various types of diseases, encompassing colorectal carcinoma, non-small cell lung carcinoma, amyotrophic lateral sclerosis, and Severe acute respiratory syndrome coronavirus 2, aberrantly express RBPs. We also highlight some recent advances in the field that could prompt the development of RBPs-based therapeutic interventions.
    MeSH term(s) Humans ; COVID-19 ; MicroRNAs/genetics ; RNA-Binding Proteins/genetics ; Nervous System Diseases ; Neoplasms
    Chemical Substances MicroRNAs ; RNA-Binding Proteins
    Language English
    Publishing date 2022-12-18
    Publishing country Japan
    Document type Journal Article ; Review
    ZDB-ID 1149134-6
    ISSN 1749-0774 ; 0914-7470
    ISSN (online) 1749-0774
    ISSN 0914-7470
    DOI 10.1007/s13577-022-00843-w
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  6. Article ; Online: The native acyltransferase-coding genes DGA1 and DGA2 affect lipid accumulation in Blastobotrys raffinosifermentans differently when overexpressed.

    Sanya, Daniel Ruben Akiola / Onesime, Djamila / Kunze, Gotthard / Neuveglise, Cécile / Crutz-Le Coq, Anne-Marie

    FEMS yeast research

    2021  Volume 20, Issue 8

    Abstract: Blastobotrys raffinosifermentans is an ascomycetous yeast with biotechnological applications, recently shown to be an oleaginous yeast accumulating lipids under nitrogen limitation. Diacylglycerol acyltransferases (DGATs) act in the lipid storage pathway, ...

    Abstract Blastobotrys raffinosifermentans is an ascomycetous yeast with biotechnological applications, recently shown to be an oleaginous yeast accumulating lipids under nitrogen limitation. Diacylglycerol acyltransferases (DGATs) act in the lipid storage pathway, in the last step of triacylglycerol biosynthesis. Two DGAT families are widespread in eukaryotes. We first checked that B. raffinosifermentans strain LS3 possessed both types of DGAT, and we then overexpressed the native DGAT-encoding genes, DGA1 and DGA2, separately or together. DGA2 (from the DGAT1 family) overexpression was sufficient to increase lipid content significantly in LS3, to up to 26.5% of dry cell weight (DCW), 1.6 times the lipid content of the parental strain (16.90% of DCW) in glucose medium under nitrogen limitation. By contrast, DGA1 (of the DGAT2 type) overexpression led to a large increase (up to 140-fold) in the amount of the corresponding transcript, but had no effect on overall lipid content relative to the parental strain. Analysis of the expression of the native genes over time in the parental strain revealed that DGA2 transcript levels quadrupled between 8 and 24 h in the N-limited lipogenic medium, whereas DGA1 transcript levels remained stable. This survey highlights the predominant role of the DGAT1 family in lipid accumulation and demonstrates the suitability of B. raffinosifermentans for engineering for lipid production.
    MeSH term(s) Amino Acid Sequence ; Diacylglycerol O-Acyltransferase/genetics ; Diacylglycerol O-Acyltransferase/metabolism ; Fatty Acids/analysis ; Lipid Metabolism ; Microorganisms, Genetically-Modified ; Saccharomycetales/enzymology ; Saccharomycetales/genetics
    Chemical Substances Fatty Acids ; Diacylglycerol O-Acyltransferase (EC 2.3.1.20)
    Language English
    Publishing date 2021-02-05
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2036775-2
    ISSN 1567-1364 ; 1567-1356
    ISSN (online) 1567-1364
    ISSN 1567-1356
    DOI 10.1093/femsyr/foaa060
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  7. Article ; Online: Yeasts of the Blastobotrys genus are promising platform for lipid-based fuels and oleochemicals production.

    Sanya, Daniel Ruben Akiola / Onésime, Djamila / Passoth, Volkmar / Maiti, Mrinal K / Chattopadhyay, Atrayee / Khot, Mahesh B

    Applied microbiology and biotechnology

    2021  Volume 105, Issue 12, Page(s) 4879–4897

    Abstract: Strains of the yeast genus Blastobotrys (subphylum Saccharomycotina) represent a valuable biotechnological resource for basic biochemistry research, single-cell protein, and heterologous protein production processes. Species of this genus are dimorphic, ... ...

    Abstract Strains of the yeast genus Blastobotrys (subphylum Saccharomycotina) represent a valuable biotechnological resource for basic biochemistry research, single-cell protein, and heterologous protein production processes. Species of this genus are dimorphic, non-pathogenic, thermotolerant, and can assimilate a variety of hydrophilic and hydrophobic substrates. These can constitute a single-cell oil platform in an emerging bio-based economy as oleaginous traits have been discovered recently. However, the regulatory network of lipogenesis in these yeasts is poorly understood. To keep pace with the growing market demands for lipid-derived products, it is critical to understand the lipid biosynthesis in these unconventional yeasts to pinpoint what governs the preferential channelling of carbon flux into lipids instead of the competing pathways. This review summarizes information relevant to the regulation of lipid metabolic pathways and prospects of metabolic engineering in Blastobotrys yeasts for their application in food, feed, and beyond, particularly for fatty acid-based fuels and oleochemicals. KEY POINTS: • The production of biolipids by heterotrophic yeasts is reviewed. • Summary of information concerning lipid metabolism regulation is highlighted. • Special focus on the importance of diacylglycerol acyltransferases encoding genes in improving lipid production is made.
    MeSH term(s) Biofuels ; Biotechnology ; Lipids ; Metabolic Engineering ; Metabolic Networks and Pathways ; Yeasts/genetics
    Chemical Substances Biofuels ; Lipids
    Language English
    Publishing date 2021-06-10
    Publishing country Germany
    Document type Journal Article ; Review
    ZDB-ID 392453-1
    ISSN 1432-0614 ; 0171-1741 ; 0175-7598
    ISSN (online) 1432-0614
    ISSN 0171-1741 ; 0175-7598
    DOI 10.1007/s00253-021-11354-3
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  8. Article: Yeasts of the Blastobotrys genus are promising platform for lipid-based fuels and oleochemicals production

    Sanya, Daniel Ruben Akiola / Onésime, Djamila / Passoth, Volkmar / Maiti, Mrinal K. / Chattopadhyay, Atrayee / Khot, Mahesh B.

    Applied microbiology and biotechnology. 2021 June, v. 105, no. 12

    2021  

    Abstract: Strains of the yeast genus Blastobotrys (subphylum Saccharomycotina) represent a valuable biotechnological resource for basic biochemistry research, single-cell protein, and heterologous protein production processes. Species of this genus are dimorphic, ... ...

    Abstract Strains of the yeast genus Blastobotrys (subphylum Saccharomycotina) represent a valuable biotechnological resource for basic biochemistry research, single-cell protein, and heterologous protein production processes. Species of this genus are dimorphic, non-pathogenic, thermotolerant, and can assimilate a variety of hydrophilic and hydrophobic substrates. These can constitute a single-cell oil platform in an emerging bio-based economy as oleaginous traits have been discovered recently. However, the regulatory network of lipogenesis in these yeasts is poorly understood. To keep pace with the growing market demands for lipid-derived products, it is critical to understand the lipid biosynthesis in these unconventional yeasts to pinpoint what governs the preferential channelling of carbon flux into lipids instead of the competing pathways. This review summarizes information relevant to the regulation of lipid metabolic pathways and prospects of metabolic engineering in Blastobotrys yeasts for their application in food, feed, and beyond, particularly for fatty acid-based fuels and oleochemicals. KEY POINTS: • The production of biolipids by heterotrophic yeasts is reviewed. • Summary of information concerning lipid metabolism regulation is highlighted. • Special focus on the importance of diacylglycerol acyltransferases encoding genes in improving lipid production is made.
    Keywords Blastobotrys ; biosynthesis ; biotechnology ; carbon ; diacylglycerol acyltransferase ; heat tolerance ; heterologous gene expression ; hydrophilicity ; hydrophobicity ; lipids ; lipogenesis ; markets ; microbial oils ; single cell protein ; yeasts
    Language English
    Dates of publication 2021-06
    Size p. 4879-4897.
    Publishing place Springer Berlin Heidelberg
    Document type Article
    Note Review
    ZDB-ID 392453-1
    ISSN 1432-0614 ; 0171-1741 ; 0175-7598
    ISSN (online) 1432-0614
    ISSN 0171-1741 ; 0175-7598
    DOI 10.1007/s00253-021-11354-3
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  9. Article ; Online: A review of approaches to control bacterial leaf blight in rice.

    Sanya, Daniel Ruben Akiola / Syed-Ab-Rahman, Sharifah Farhana / Jia, Aiqun / Onésime, Djamila / Kim, Kyung-Min / Ahohuendo, Bonaventure Cohovi / Rohr, Jason R

    World journal of microbiology & biotechnology

    2022  Volume 38, Issue 7, Page(s) 113

    Abstract: The Gram-negative bacteria Xanthomonas oryzae pv. oryzae, the causative agent of bacterial leaf blight (BLB), received attention for being an economically damaging pathogen of rice worldwide. This damage prompted efforts to better understand the ... ...

    Abstract The Gram-negative bacteria Xanthomonas oryzae pv. oryzae, the causative agent of bacterial leaf blight (BLB), received attention for being an economically damaging pathogen of rice worldwide. This damage prompted efforts to better understand the molecular mechanisms governing BLB disease progression. This research revealed numerous virulence factors that are employed by this vascular pathogen to invade the host, outcompete host defence mechanisms, and cause disease. In this review, we emphasize the virulence factors and molecular mechanisms that X. oryzae pv. oryzae uses to impair host defences, recent insights into the cellular and molecular mechanisms underlying host-pathogen interactions and components of pathogenicity, methods for developing X. oryzae pv. oryzae-resistant rice cultivars, strategies to mitigate disease outbreaks, and newly discovered genes and tools for disease management. We conclude that the implementation and application of cutting-edge technologies and tools are crucial to avoid yield losses from BLB and ensure food security.
    MeSH term(s) Bacterial Proteins/genetics ; Host-Pathogen Interactions ; Oryza/microbiology ; Plant Diseases/microbiology ; Plant Diseases/prevention & control ; Virulence/genetics ; Virulence Factors ; Xanthomonas/genetics
    Chemical Substances Bacterial Proteins ; Virulence Factors
    Language English
    Publishing date 2022-05-17
    Publishing country Germany
    Document type Journal Article ; Review
    ZDB-ID 1499109-3
    ISSN 1573-0972 ; 0959-3993
    ISSN (online) 1573-0972
    ISSN 0959-3993
    DOI 10.1007/s11274-022-03298-1
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  10. Article: A review of approaches to control bacterial leaf blight in rice

    SANYA, Daniel Ruben Akiola / Syed-Ab-Rahman, Sharifah Farhana / Jia, Aiqun / Onésime, Djamila / Kim, Kyung-Min / Ahohuendo, Bonaventure Cohovi / Rohr, Jason R.

    World journal of microbiology & biotechnology. 2022 July, v. 38, no. 7

    2022  

    Abstract: The Gram-negative bacteria Xanthomonas oryzae pv. oryzae, the causative agent of bacterial leaf blight (BLB), received attention for being an economically damaging pathogen of rice worldwide. This damage prompted efforts to better understand the ... ...

    Abstract The Gram-negative bacteria Xanthomonas oryzae pv. oryzae, the causative agent of bacterial leaf blight (BLB), received attention for being an economically damaging pathogen of rice worldwide. This damage prompted efforts to better understand the molecular mechanisms governing BLB disease progression. This research revealed numerous virulence factors that are employed by this vascular pathogen to invade the host, outcompete host defence mechanisms, and cause disease. In this review, we emphasize the virulence factors and molecular mechanisms that X. oryzae pv. oryzae uses to impair host defences, recent insights into the cellular and molecular mechanisms underlying host-pathogen interactions and components of pathogenicity, methods for developing X. oryzae pv. oryzae-resistant rice cultivars, strategies to mitigate disease outbreaks, and newly discovered genes and tools for disease management. We conclude that the implementation and application of cutting-edge technologies and tools are crucial to avoid yield losses from BLB and ensure food security.
    Keywords Xanthomonas oryzae pv. oryzae ; biotechnology ; cultivars ; disease control ; disease progression ; food security ; leaf blight ; pathogens ; rice ; virulence
    Language English
    Dates of publication 2022-07
    Size p. 113.
    Publishing place Springer Netherlands
    Document type Article
    Note Review
    ZDB-ID 1499109-3
    ISSN 1573-0972 ; 0959-3993
    ISSN (online) 1573-0972
    ISSN 0959-3993
    DOI 10.1007/s11274-022-03298-1
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