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Book ; Online: Genetic and Genome-Wide Insights into Microbes Studied for Bioenergy

Minton, Nigel / Louis, Ed / Pappas, Katherine M. / Mukhopadhyay, Biswarup / Yang, Shane

2017

Abstract: ... significantly contribute to the emerging insights regarding microbial-derived energy production. Katherine M ... Pappas, 2016 ...

Abstract	The global mandate for safer, cleaner and renewable energy has accelerated research on microbes that convert carbon sources to end-products serving as biofuels of the so-called first, second or third generation - e.g., bioethanol or biodiesel derived from starchy, sugar-rich or oily crops; bioethanol derived from composite lignocellulosic biomass; and biodiesels extracted from oil-producing algae and cyanobacteria, respectively. Recent advances in 'omics' applications are beginning to cast light on the biological mechanisms underlying biofuel production. They also unravel mechanisms important for organic solvent or high-added-value chemical production, which, along with those for fuel chemicals, are significant to the broader field of Bioenergy. The Frontiers in Microbial Physiology Research Topic that led to the current e-book publication, operated from 2013 to 2014 and welcomed articles aiming to better understand the genetic basis behind Bioenergy production. It invited genetic studies of microbes already used or carrying the potential to be used for bioethanol, biobutanol, biodiesel, and fuel gas production, as also of microbes posing as promising new catalysts for alternative bioproducts. Any research focusing on the systems biology of such microbes, gene function and regulation, genetic and/or genomic tool development, metabolic engineering, and synthetic biology leading to strain optimization, was considered highly relevant to the topic. Likewise, bioinformatic analyses and modeling pertaining to gene network prediction and function were also desirable and therefore invited in the thematic forum. Upon e-book development today, we, at the editorial, strongly believe that all articles presented herein - original research papers, reviews, perspectives and a technology report - significantly contribute to the emerging insights regarding microbial-derived energy production. Katherine M. Pappas, 2016
Keywords	Microbiology ; Science (General)
Size	1 electronic resource (186 p.)
Publisher	Frontiers Media SA
Document type	Book ; Online
Note	English ; Open Access
HBZ-ID	HT020095007
ISBN	9782889450855 ; 2889450856
Database	ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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Article: Cryptococcal Meningoencephalitis in Phenotypically Normal Patients.

Cumagun, Pia M / Moore, Mary Katherine / McCarty, Todd P / McGwin, Gerald / Pappas, Peter G

Pathogens (Basel, Switzerland)

2023 Volume 12, Issue 11

Abstract: Cryptococcosis is an invasive fungal infection found worldwide that causes significant morbidity and mortality among a broad range of hosts. There are approximately 223,000 new cases of cryptococcosis annually throughout the world, and at least 180,000 ... ...

Abstract	Cryptococcosis is an invasive fungal infection found worldwide that causes significant morbidity and mortality among a broad range of hosts. There are approximately 223,000 new cases of cryptococcosis annually throughout the world, and at least 180,000 deaths are attributed to this infection each year. Most of these are due to complications of cryptococcal meningoencephalitis among HIV-infected patients in resource-limited environments. The majority of individuals diagnosed with cryptococcosis have underlying conditions associated with immune dysfunction such as HIV, solid organ transplant, hematologic malignancy, organ failure syndromes, and/or the use of immunosuppressive agents such as glucocorticosteroids and biologic agents. In most clinical series, there is a small proportion of patients with cryptococcosis who are phenotypically normal; that is, they have no clinically obvious predisposition to disease. Cryptococcal meningoencephalitis (CME) presentation and management differ substantially between these normal individuals and their immunocompromised counterparts. In this review, we will focus on CME in the phenotypically normal host and underscore differences in the clinical presentation, management, outcome, and potential risk factors for these patients compared to immunocompromised persons who develop this potential devastating invasive fungal infection.
Language	English
Publishing date	2023-10-31
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens12111303
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Evaluation of the lignocellulose degradation potential of Mediterranean forests soil microbial communities through diversity and targeted functional metagenomics.

Kalntremtziou, Maria / Papaioannou, Ioannis A / Vangalis, Vasileios / Polemis, Elias / Pappas, Katherine M / Zervakis, Georgios I / Typas, Milton A

Frontiers in microbiology

2023 Volume 14, Page(s) 1121993

Abstract: The enzymatic arsenal of several soil microorganisms renders them particularly suitable for the degradation of lignocellulose, a process of distinct ecological significance with promising biotechnological implications. In this study, we investigated the ... ...

Abstract	The enzymatic arsenal of several soil microorganisms renders them particularly suitable for the degradation of lignocellulose, a process of distinct ecological significance with promising biotechnological implications. In this study, we investigated the spatiotemporal diversity and distribution of bacteria and fungi with 16S and Internally Trascribed Spacer (ITS) ribosomal RNA next-generation-sequencing (NGS), focusing on forest mainland
Language	English
Publishing date	2023-02-27
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2023.1121993
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Article ; Online: Zymomonas mobilis metabolism: Novel tools and targets for its rational engineering.

Kalnenieks, Uldis / Pappas, Katherine M / Bettenbrock, Katja

Advances in microbial physiology

2020 Volume 77, Page(s) 37–88

Abstract: Zymomonas mobilis is an α-proteobacterium that interests the biofuel industry due to its perfect ethanol fermentation yields. From its first description as a bacterial isolate in fermented alcoholic beverages to date, Z. mobilis has been rigorously ... ...

Abstract	Zymomonas mobilis is an α-proteobacterium that interests the biofuel industry due to its perfect ethanol fermentation yields. From its first description as a bacterial isolate in fermented alcoholic beverages to date, Z. mobilis has been rigorously studied in directions basic and applied. The Z. mobilis powerful Entner-Doudoroff glycolytic pathway has been the center of rigorous biochemical studies and, aside from ethanol, it has attracted interest in terms of high-added-value chemical manufacturing. Energetic balances and the effects of respiration have been explored in fundamental directions as also in applications pursuing strain enhancement and the utilization of alternative carbon sources. Metabolic modeling has addressed the optimization of the biochemical circuitry at various conditions of growth and/or substrate utilization; it has been also critical in predicting desirable end-product yields via flux redirection. Lastly, stress tolerance has received particular attention, since it directly determines biocatalytical performance at challenging bioreactor conditions. At a genetic level, advances in the genetic engineering of the organism have brought forth beneficial manipulations in the Z. mobilis gene pool, e.g., knock-outs, knock-ins and gene stacking, aiming to broaden the metabolic repertoire and increase robustness. Recent omic and expressional studies shed light on the genomic content of the most applied strains and reveal landscapes of activity manifested at ambient or reactor-based conditions. Studies such as those reviewed in this work, contribute to the understanding of the biology of Z. mobilis, enable insightful strain development, and pave the way for the transformation of Z. mobilis into a consummate organism for biomass conversion.
Language	English
Publishing date	2020-10-22
Publishing country	England
Document type	Journal Article
ZDB-ID	174-0
ISSN	2162-5468 ; 0065-2911
ISSN (online)	2162-5468
ISSN	0065-2911
DOI	10.1016/bs.ampbs.2020.08.001
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Article: One-step separation system of bio-functional lipid compounds from natural sources.

Tsoupras, Alexandros / Pappas, Katherine M / Sotiroudis, Theodore G / Demopoulos, Constantinos A

MethodsX

2021 Volume 8, Page(s) 101380

Abstract: Lipids are a very heterogeneous class of biomolecules with distinct structures and functions. Total lipids (TLs) obtained from natural sources are regularly further separated into lipid subclasses, with the two major ones being the polar lipids (PLs) and ...

Abstract	Lipids are a very heterogeneous class of biomolecules with distinct structures and functions. Total lipids (TLs) obtained from natural sources are regularly further separated into lipid subclasses, with the two major ones being the polar lipids (PLs) and neutral lipids (NLs). Traditional analytical methods for fractionating TLs into NLs, PLs, and their subclasses, usually comprise difficult, costly and time-consuming steps. Instead, several benefits and applications are derived by implementing a novel one-step semi-preparative and reversed-phase HPLC-analysis for separating TLs into all kinds of lipid subclasses. This method allows a one-step separation/fractionation of several subclasses of bio-functional PLs (i.e. phospholipids, glycolipids, phenolic compounds, N-acyl-homoserine-lactones, etc.) and NLs (i.e. triacylglycerols, fatty acids, esters, etc.) from TL-extracts of a natural source, prior to further testing them for their bio-functionality (i.e. in bioassays/cell models) and structure-activity relationships (i.e. LC-MS/GC-MS).•This method can be applied in several natural sources, such as animal and marine sources, plants, microorganisms of biotechnological and agricultural interest, foods, beverages and related products, and by-products.•This method can also be applied for separating specific bio-functional lipids from complex medical and pharmaceutical samples (i.e. cells, tissues, blood, plasma, liposomes, etc.), either for evaluating their role in diseases (i.e. PAF/PAF-like molecules) or by elucidating their protective roles (i.e. PLs rich in ω3 PUFA) for supplements and nutraceuticals' applications.
Language	English
Publishing date	2021-05-08
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2830212-6
ISSN	2215-0161
ISSN	2215-0161
DOI	10.1016/j.mex.2021.101380
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Article: Transcriptomic Adjustments of

Efthimiou, Georgios / Tsiamis, George / Typas, Milton A / Pappas, Katherine M

Frontiers in microbiology

2019 Volume 10, Page(s) 2393

Abstract: Methicillin- ... ...

Abstract	Methicillin-resistant
Language	English
Publishing date	2019-10-18
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2019.02393
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Article ; Online: Farm animal exposure, respiratory illnesses, and nasal cell gene expression.

Brownell, Joshua / Lee, Kristine E / Chasman, Deborah / Gangnon, Ronald / Bendixsen, Casper G / Barnes, Katherine / Grindle, Kristine / Pappas, Tressa / Bochkov, Yury A / Dresen, Amy / Hou, Christine / Haslam, David B / Seroogy, Christine M / Ong, Irene M / Gern, James E

The Journal of allergy and clinical immunology

2024

Abstract: Background: Farm exposures in early life reduce the risks for childhood allergic diseases and asthma. There is less information about how farm exposures relate to respiratory illnesses and mucosal immune development.: Objective: We hypothesized that ... ...

Abstract	Background: Farm exposures in early life reduce the risks for childhood allergic diseases and asthma. There is less information about how farm exposures relate to respiratory illnesses and mucosal immune development. Objective: We hypothesized that children raised in farm environments have a lower incidence of respiratory illnesses over the first 2 years of life than nonfarm children. We also analyzed whether farm exposures or respiratory illnesses were related to patterns of nasal cell gene expression. Methods: The Wisconsin Infant Study Cohort included farm (n = 156) and nonfarm (n = 155) families with children followed to age 2 years. Parents reported prenatal farm and other environmental exposures. Illness frequency and severity were assessed using illness diaries and periodic surveys. Nasopharyngeal cell gene expression in a subset of 64 children at age 2 years was compared to farm exposure and respiratory illness history. Results: Farm versus nonfarm children had nominally lower rates of respiratory illnesses (rate ratio 0.82 [95% CI, 0.69, 0.97]) with a stepwise reduction in illness rates in children exposed to 0, 1, or ≥2 animal species, but these trends were nonsignificant in a multivariable model. Farm exposures and preceding respiratory illnesses were positively related to nasal cell gene signatures for mononuclear cells and innate and antimicrobial responses. Conclusions: Maternal and infant exposure to farms and farm animals was associated with nonsignificant trends for reduced respiratory illnesses. Nasal cell gene expression in a subset of children suggests that farm exposures and respiratory illnesses in early life are associated with distinct patterns of mucosal immune expression.
Language	English
Publishing date	2024-02-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	121011-7
ISSN	1097-6825 ; 1085-8725 ; 0091-6749
ISSN (online)	1097-6825 ; 1085-8725
ISSN	0091-6749
DOI	10.1016/j.jaci.2024.01.019
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Article: Anti-inflammatory and anti-thrombotic properties of lipid bioactives from the entomopathogenic fungus Beauveria bassiana.

Tsoupras, Alexandros / Kouvelis, Vassili N / Pappas, Katherine M / Demopoulos, Constantinos A / Typas, Milton A

Prostaglandins & other lipid mediators

2021 Volume 158, Page(s) 106606

Abstract: In the present work the entomopathogenic fungus B. bassiana lipids were studied against the potent pro-inflammatory and thrombotic mediators implicated in several disorders, platelet-activating factor (PAF) and thrombin. Bioactivities of lipid extracts ... ...

Abstract	In the present work the entomopathogenic fungus B. bassiana lipids were studied against the potent pro-inflammatory and thrombotic mediators implicated in several disorders, platelet-activating factor (PAF) and thrombin. Bioactivities of lipid extracts from B. bassiana cells and culture supernatants and of their lipid fractions separated by a one-step HPLC-analysis ere assessed against the PAF/Thrombin-induced aggregation of washed rabbit platelets. Lipid extracts from both cell-biomass and supernatant inhibited strongly PAF/Thrombin-activities and platelet-aggregation, exhibiting higher specificity against PAF. Similarly, HPLC-derived lipid-fractions of phenolics/glycolipids, Sphingomyelins and Phosphatidylcholines (PC) showed strong anti-PAF potency. PC PAF-like molecules exhibited the strongest antagonistic anti-PAF effects, while in higher amounts they agonistically inhibited PAF-activities. Some bioactive lipids with strong anti-PAF effects are exo-cellularly secreted in the culture media during fungal growth, while others are not. The presence of such lipid bioactives in B. bassiana with strong anti-inflammatory and anti-thrombotic properties, provide new perspectives and putative future applications for this entomopathogenic fungus.
MeSH term(s)	Animals ; Anti-Inflammatory Agents/pharmacology ; Beauveria ; Chromatography, High Pressure Liquid ; Platelet Activating Factor/pharmacology ; Platelet Aggregation ; Rabbits
Chemical Substances	Anti-Inflammatory Agents ; Platelet Activating Factor
Language	English
Publishing date	2021-12-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	1426962-4
ISSN	2212-196X ; 1098-8823 ; 0090-6980
ISSN (online)	2212-196X
ISSN	1098-8823 ; 0090-6980
DOI	10.1016/j.prostaglandins.2021.106606
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Article ; Online: Mini-Mu transposon mutagenesis of ethanologenic Zymomonas mobilis.

Pappas, Katherine M

Methods in molecular biology (Clifton, N.J.)

2011 Volume 765, Page(s) 419–434

Abstract: Zymomonas mobilis is a facultatively anaerobic α-proteobacterium with a considerable potential for industrial ethanol production. An important tool in the generation of stable mutants for this organism is described in this chapter; it entails insertional ...

Abstract	Zymomonas mobilis is a facultatively anaerobic α-proteobacterium with a considerable potential for industrial ethanol production. An important tool in the generation of stable mutants for this organism is described in this chapter; it entails insertional mutagenesis with the help of the transposable element mini-Mu. The latter is delivered into Z. mobilis with the use of plasmid pULB113 (RP4::mini-Mu) that self-transfers in the organism at notable frequencies and remains highly stable even under nonselective conditions. Transposition of mini-Mu and subsequent mutagenesis occur readily in Z. mobilis pULB113 transconjugants and result in the generation of large numbers of random mutants. This can be demonstrated by the isolation of various auxotrophs with single or multiple nutritional requirements, the vast majority of which bears insertions at different chromosomal locations, even when exhibiting the same requirement. Therefore, transposon mutagenesis with the use of mini-Mu serves as a simple and effective tool for indiscriminate mutant production in Z. mobilis.
MeSH term(s)	Bacteriophage mu/genetics ; DNA Transposable Elements/genetics ; Mutagenesis, Insertional/genetics ; Zymomonas/genetics ; Zymomonas/virology
Chemical Substances	DNA Transposable Elements
Language	English
Publishing date	2011
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-61779-197-0_25
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: One-step separation system of bio-functional lipid compounds from natural sources

Alexandros Tsoupras / Katherine M. Pappas / Theodore G. Sotiroudis / Constantinos A. Demopoulos

MethodsX, Vol 8, Iss , Pp 101380- (2021)

2021

Abstract	Lipids are a very heterogeneous class of biomolecules with distinct structures and functions. Total lipids (TLs) obtained from natural sources are regularly further separated into lipid subclasses, with the two major ones being the polar lipids (PLs) and neutral lipids (NLs). Traditional analytical methods for fractionating TLs into NLs, PLs, and their subclasses, usually comprise difficult, costly and time-consuming steps.Instead, several benefits and applications are derived by implementing a novel one-step semi-preparative and reversed-phase HPLC-analysis for separating TLs into all kinds of lipid subclasses. This method allows a one-step separation/fractionation of several subclasses of bio-functional PLs (i.e. phospholipids, glycolipids, phenolic compounds, N-acyl-homoserine-lactones, etc.) and NLs (i.e. triacylglycerols, fatty acids, esters, etc.) from TL-extracts of a natural source, prior to further testing them for their bio-functionality (i.e. in bioassays/cell models) and structure-activity relationships (i.e. LC-MS/GC-MS). • This method can be applied in several natural sources, such as animal and marine sources, plants, microorganisms of biotechnological and agricultural interest, foods, beverages and related products, and by-products. • This method can also be applied for separating specific bio-functional lipids from complex medical and pharmaceutical samples (i.e. cells, tissues, blood, plasma, liposomes, etc.), either for evaluating their role in diseases (i.e. PAF/PAF-like molecules) or by elucidating their protective roles (i.e. PLs rich in ω3 PUFA) for supplements and nutraceuticals’ applications.
Keywords	HPLC ; Reversed phase ; Total lipids ; Polar lipids ; Glycolipids ; Phospholipids ; Science ; Q
Subject code	572
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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