DOCSLIB.ORG

Dynamic Alterations of the Distal Intestinal Microbiota, Transcriptome, and Metabolome of Hybrid Grouper by Β-Conglycinin With

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Dynamic Alterations of the Distal Intestinal Microbiota, Transcriptome, and Metabolome of Hybrid Grouper by Β-Conglycinin With fmars-08-705332 July 13, 2021 Time: 16:51 # 1 ORIGINAL RESEARCH published: 19 July 2021 doi: 10.3389/fmars.2021.705332 Dynamic Alterations of the Distal Intestinal Microbiota, Transcriptome, and Metabolome of Hybrid Grouper by b -Conglycinin With Reconciliations by Sodium Butyrate in Feed Bin Yin1,2,3, Hongyu Liu1,2,3*, Beiping Tan1,2,3*, Xiaohui Dong1,2,3, Shuyan Chi1,2,3, Qihui Yang1,2,3 and Shuang Zhang1,2,3 1 Laboratory of Aquatic Animal Nutrition and Feed, Fisheries College, Guangdong Ocean University, Zhanjiang, China, Edited by: 2 Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Centre of Guangdong Province, Ikram Belghit, Zhanjiang, China, 3 Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry Norwegian Institute of Marine of Agriculture, Zhanjiang, China Research (IMR), Norway Reviewed by: Different doses of b-conglycinin produce different regulations on the intestinal health Fotini Kokou, Wageningen University and Research, of aquatic animals, affecting the absorption of nutrients, indirectly changing water Netherlands quality. Sodium butyrate (NaB) can effectively alleviate the negative effects caused Seyyed Morteza Hoseini, Iranian Fisheries Science Research by high-dose b-conglycinin. We investigated the positive response to low-dose Institute (IFSRI), Iran (1.5%, bL) and negative response to high-dose (6.0%, bH) b-conglycinin and *Correspondence: supplementation with NaB (6.0% b-conglycinin + 0.13% NaB, bHNaB) in terms of water Hongyu Liu pollutants, microbiota, transcriptome, and metabolome in hybrid grouper (Epinephelus [email protected] Beiping Tan fuscoguttatus × E. lanceolatus ). The ammonia nitrogen, nitrite, total nitrogen, and [email protected] total phosphorus♀ contents were♂ significantly higher in the water from bH than from FMb, bL, and bHNaB. Supplementing with NaB significantly reduced the ammonia Specialty section: This article was submitted to nitrogen, nitrite, total nitrogen, and total phosphorus contents. Low-dose b-conglycinin Aquatic Physiology, increased the relative abundance of Pelagibacterium, Pediococcus, Staphylococcus, a section of the journal Frontiers in Marine Science and Lactobacillus and promoted the “ribosome,” “peroxisome proliferator-activated Received: 05 May 2021 receptor (PPAR) signaling” and “histidine metabolism.” High-dose b-conglycinin Accepted: 23 June 2021 increased the relative abundance of pathogenic bacteria Ralstonia and Photobacterium Published: 19 July 2021 and inhibited the “cell cycle” “PPAR signaling” and “starch and proline metabolism.” NaB Citation: supplementation at high-dose b-conglycinin reduced the Ralstonia and Photobacterium Yin B, Liu H, Tan B, Dong X, Chi S, Yang Q and Zhang S (2021) abundance and promoted the “cell cycle,” “linoleic acid metabolism,” and “ABC Dynamic Alterations of the Distal transporters.” Overall, these results reveal differences in the effects of high- and low- Intestinal Microbiota, Transcriptome, and Metabolome of Hybrid Grouper dose b-conglycinin, as well as NaB supplementation, on the utilization of proteins, by β -Conglycinin With carbohydrates, and lipids and on substance transport and signaling among distal Reconciliations by Sodium Butyrate intestinal cells of hybrid grouper. A total of 15 differential metabolite biomarkers were in Feed. Front. Mar. Sci. 8:705332. doi: 10.3389/fmars.2021.705332 identified: FMb vs. bL contained 10-methylimidazole acetic acid, N-acetyl histamine, Frontiers in Marine Science| www.frontiersin.org 1 July 2021| Volume 8| Article 705332 fmars-08-705332 July 13, 2021 Time: 16:51 # 2 Yin et al. b-Conglycinin and Sodium-Butyrate on Grouper urocanic acid, creatinine, glutathione, taurine, nervonic acid, stearic acid, docosanoic acid, and D-serine; FMb vs. bH contained 4-L-fucose, sucrose, a,a-trehalose, and quercetin; and bH vs. bHNaB contained 4-N-acetyl histamine, urocanic acid, creatinine, and S-adenosylhomocysteine, respectively. Our study provides new insights into the regulation of intestinal health by b-conglycinin in aquatic animals and the protective mechanism of NaB. Keywords: hybrid grouper (Epinephelus fuscoguttatus × E. lanceolatus ), b-conglycinin, sodium butyrate, intestinal microbiota, transcriptome, metabolome ♀ ♂ INTRODUCTION It is accepted that b-conglycinin (7S) of soybean meal is a major factor in the induction of intestinal injury. b-Conglycinin, The hybrid grouper (Epinephelus fuscoguttatus one of the major antigen proteins in soybean, often causes allergic × E. lanceolatus ) is an economically important fish along♀ reactions in young animals, causing inflammatory damage to the southern coast♂ of China, with a fast growth rate and strong intestinal epithelial cells accompanied by lipid peroxidation environmental tolerance. In 2017, groupers were officially of cell membranes, negatively affecting the function of tight included in the construction of China’s National Marine Fish junction protein structures and increasing intestinal epithelial Industry Technology System. As a typical carnivorous fish, it permeability (Zhao et al., 2014). The unbalanced amino acid usually requires up to about 50% of protein in its feed (Jiang in soybean meal may lead to increased excretion of nitrogen et al., 2016). Fishmeal is a high quality protein source and it and phosphorus by fish (Tantikitti et al., 2005), which is not has been traditionally used as the main protein source in the conducive to the healthy and sustainable development of the aquafeed industry. However, due to the high demand for fishmeal aquaculture industry. As a widely used additive in livestock and leading to a high price and lack of sources, the farming industry poultry animals, sodium butyrate (NaB) can not only act as a had to find dietary alternative ingredients. The high nitrogen food attractant, but also improve the tight junctions of intestinal and phosphorus content in the fishmeal feeds is not completely epithelium (Huang et al., 2015) and alleviate inflammation by absorbed by hybrid grouper and is most likely to be excreted inhibiting nuclear factor kappa B (NF-kB) (Albino et al., 2012), along with the feces, leading to serious contamination of the and it also has a positive regulatory effect on the host’s intestinal farmed water. Currently, the use of soybean meal to replace fish microbiota (Zou et al., 2019). The active ingredient in NaB is meal can relieve the pressure of fish meal shortage and greatly butyric acid, which is a short-chain, volatile fatty acid (O’Hara promote the sustainable development of aquaculture industry et al., 2018). In aquatic animals, NaB can stimulate the growth and (Yang et al., 2011; Smith et al., 2017; Miao et al., 2018). However, proliferation of intestinal mucosa and inhibit the proliferation owing to low tolerance to soybean meal, excessive intake of of intestinal pathogenic microorganisms, thus, promoting the soybean meal can lead to varying degrees of intestinal injury growth of fish and enhancing intestinal digestion and antioxidant (Zhang et al., 2019). capacity (Tian et al., 2017; Jesus et al., 2018; Fu et al., 2019). The intestines of aquatic animals are responsible for the Nevertheless, the physiological mechanisms of intestinal injury dual functions of digestion and absorption. The mucosa of the and inflammation in hybrid grouper caused by b-conglycinin intestinal tract is the main interface between the internal and and the protective effects of NaB on the intestinal tract are not external environments of the organism. The intestinal tract is well understood. the main site of nutrient exchange and infection or initiation In a previous study, we demonstrated that ingestion of high of infection by many pathogens (Jiang et al., 2019) and is levels of soybean meal by hybrid grouper resulted in intestinal highly susceptible to the effects of feed ingredients and living injury (Zhang et al., 2019). The inhibitory effects of b-conglycinin environmental conditions (Duan et al., 2017). Thus, it is essential on the growth of fish is usually thought to be due to intestinal to maintain the health and stability of the intestinal tracts of inflammation (Zhang et al., 2013); nevertheless, the reports of aquatic animals. The presence of a large number of microbiota whether b-conglycinin can negatively affect other physiological in the intestinal tract is the result of long-term evolution, and functions in fish are rare. In this study, we investigated the they are closely related to the immune function and nutritional effects of b-conglycinin and the protective mechanism of NaB on requirements of the organism (Yang et al., 2018). Intestinal transcription, intestinal microbiota, and metabolites in the distal microbiota can participate in the mediation of multiple metabolic intestine of hybrid grouper. Then, transcriptomic, intestinal pathways in the host, interacting with host metabolism and microbiota, and metabolomic means were combined to model signal transduction to form a physiologically connected gut- the associations among host metabolism, intestinal microbiota, immune-inflammation axis (Matsumoto et al., 2012). Similarly, and aquaculture water pollutants at the system biology level. This intestinal health status could also influence the composition of will help us understand the metabolic processes of the microflora microorganisms. Therefore, the relationship between intestinal in the host and their effects on host transcription, as well as their flora and metabolite associations and host intestinal health interactions with each
Load more

Recommended publications
  • Cell Death Via Lipid Peroxidation and Protein Aggregation Diseases
    biology Review Cell Death via Lipid Peroxidation and Protein Aggregation Diseases Katsuya Iuchi * , Tomoka Takai and Hisashi Hisatomi Department of Materials and Life Science, Faculty of Science and Technology, Seikei University, 3-3-1 Kichijojikitamachi, Musashino-shi, Tokyo 180-8633, Japan; [email protected] (T.T.); [email protected] (H.H.) * Correspondence: [email protected] or [email protected]; Tel.: +81-422-37-3523 Simple Summary: It is essential for cellular homeostasis that biomolecules, such as DNA, proteins, and lipids, function properly. Disturbance of redox homeostasis produces aberrant biomolecules, including oxidized lipids and misfolded proteins, which increase in cells. Aberrant biomolecules are removed by excellent cellular clearance systems. However, when excess aberrant biomolecules remain in the cell, they disrupt organelle and cellular functions, leading to cell death. These aberrant molecules aggregate and cause apoptotic and non-apoptotic cell death, leading to various protein aggregation diseases. Thus, we investigated the cell-death cross-linking between lipid peroxidation and protein aggregation. Abstract: Lipid peroxidation of cellular membranes is a complicated cellular event, and it is both the cause and result of various diseases, such as ischemia-reperfusion injury, neurodegenerative diseases, and atherosclerosis. Lipid peroxidation causes non-apoptotic cell death, which is associated with cell fate determination: survival or cell death. During the radical chain reaction of lipid peroxidation, Citation: Iuchi, K.; Takai, T.; various oxidized lipid products accumulate in cells, followed by organelle dysfunction and the Hisatomi, H. Cell Death via Lipid induction of non-apoptotic cell death. Highly reactive oxidized products from unsaturated fatty acids Peroxidation and Protein are detected under pathological conditions.
    [Show full text]
  • Amino Acid Metabolism: Amino Acid Degradation & Synthesis
    Amino Acid Metabolism: Amino Acid Degradation & Synthesis Dr. Diala Abu-Hassan, DDS, PhD All images are taken from Lippincott’s Biochemistry textbook except where noted CATABOLISM OF THE CARBON SKELETONS OF AMINO ACIDS The pathways by which AAs are catabolized are organized according to which one (or more) of the seven intermediates is produced from a particular amino acid. GLUCOGENIC AND KETOGENIC AMINO ACIDS The classification is based on which of the seven intermediates are produced during their catabolism (oxaloacetate, pyruvate, α-ketoglutarate, fumarate, succinyl coenzyme A (CoA), acetyl CoA, and acetoacetate). Glucogenic amino acids catabolism yields pyruvate or one of the TCA cycle intermediates that can be used as substrates for gluconeogenesis in the liver and kidney. Ketogenic amino acids catabolism yields either acetoacetate (a type of ketone bodies) or one of its precursors (acetyl CoA or acetoacetyl CoA). Other ketone bodies are 3-hydroxybutyrate and acetone Amino acids that form oxaloacetate Hydrolysis Transamination Amino acids that form α-ketoglutarate via glutamate 1. Glutamine is converted to glutamate and ammonia by the enzyme glutaminase. Glutamate is converted to α-ketoglutarate by transamination, or through oxidative deamination by glutamate dehydrogenase. 2. Proline is oxidized to glutamate. 3. Arginine is cleaved by arginase to produce Ornithine (in the liver as part of the urea cycle). Ornithine is subsequently converted to α-ketoglutarate. Amino acids that form α-ketoglutarate via glutamate 4. Histidine is oxidatively deaminated by histidase to urocanic acid, which then forms N-formimino glutamate (FIGlu). Individuals deficient in folic acid excrete high amounts of FIGlu in the urine FIGlu excretion test has been used in diagnosing a deficiency of folic acid.
    [Show full text]
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
    [Show full text]
  • Pyrrolidone Carboxylic Acid Synthesis in Guinea Pig Epidermis
    0022-202X/ 83/ 8102-0122$02.00/0 THE JOURNAL OF INVESTIGATIVE DERMATOLOGY, 81:122-124, 1983 Vol. 81, No.2 Copyright © 1983 by The Williams & Wilkins Co. Printed in U.S.A. Pyrrolidone Carboxylic Acid Synthesis in Guinea Pig Epidermis JoHN G. BARRETT, B.Sc. AND IAN R ScoTT, M.A., PH.D. Environmental Safety Laboratory, Unilever Research, Sharnbrook, Bedford, U. K. To establish the in vivo mechanism of synthesis and MATERIALS AND METHODS accumulation of epidermal pyrrolidone carboxylic acid (PCA), enzymes potentially capable of PCA synthesis Enzyme Assays and Separation of Viable Cells and Stratum have been quantified and located within the guinea pig Corneum epidermis. Intermediates in the synthesis of eHJPCA from a pulse of [3H]glutamine have been identified and All enzyme assays were essentially as described previously [8] except quantified to determine which of the several possible for two modifications. Firstly, the sensitivity of the assays for enzymic PCA formation from glutamine and glutamic acid was increased by metabolic routes occurs in vivo. PCA appears to be syn­ 3 1 thesized from substrate derived from the breakdown using [G- H] substrate (40-90 JLCi mmol- , Radiochemical Centre, Amersham). PCA was separated from glutamic acid and glutamine on within the stratum corneum of protein synthesized sev­ a small column (2.0 ml bed volume) of Ag50W-X8 ion-exchange resin eral days earlier. The predominant route is probably via (200-400 mesh; Bio-Rad). Secondly, epidermal homogenates were pre­ the nonenzymic cyclization of free glutamine liberated pared in 0.5 M Tris-HCl buffer, pH 7.0, then microcentrifuge desalted from this protein.
    [Show full text]
  • Regulation of Mitochondrial and Nonmitochondrial Protein Turnover by the PINK1-Parkin Pathway
    Regulation of mitochondrial and nonmitochondrial protein turnover by the PINK1-Parkin pathway Evelyn S. Vincow A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2013 Reading Committee: Leo J. Pallanck, Chair Sandra M. Bajjalieh Michael J. MacCoss Program Authorized to Offer Degree: Neurobiology and Behavior © Copyright 2013 Evelyn S. Vincow University of Washington Abstract Regulation of mitochondrial and nonmitochondrial protein turnover by the PINK1-Parkin pathway Evelyn Sandra Vincow Chair of the Supervisory Committee: Associate Professor Leo J. Pallanck Genome Sciences The accumulation of damaged mitochondria has been proposed as a key factor in aging and in the pathogenesis of many common age-related diseases, including Parkinson disease (PD). Recently, in vitro studies of the PD-related proteins Parkin and PINK1 have found that these factors act in a common pathway to promote the selective autophagic degradation of damaged mitochondria (mitophagy). However, whether PINK1 and Parkin promote mitophagy in vivo is unknown. To address this question, I used a proteomic approach in Drosophila to study the effects of null mutations in parkin or PINK1 on mitochondrial protein turnover. The parkin null mutants showed a significant overall slowing of mitochondrial protein turnover, similar to but less severe than the slowing seen in autophagy-deficient Atg7 mutants, consistent with the model that Parkin acts upstream of Atg7 to promote mitophagy. By contrast, the turnover of many mitochondrial respiratory chain (RC) subunits showed greater impairment in parkin than in Atg7 mutants, and RC turnover was also selectively impaired in PINK1 mutants. These findings demonstrate that the PINK1-Parkin pathway promotes mitophagy in vivo and, unexpectedly, also promotes selective turnover of mitochondrial RC components.
    [Show full text]
  • An ACSL4 Hemizygous Intragenic Deletion in a Patient with Childhood Stroke
    Pediatric Neurology 100 (2019) 100e101 Contents lists available at ScienceDirect Pediatric Neurology journal homepage: www.elsevier.com/locate/pnu Clinical Letter An ACSL4 Hemizygous Intragenic Deletion in a Patient With Childhood Stroke Caitlin A. Chang, MD a, Julie Lauzon, MD, MHSc a, b, Adam Kirton, MD, MSc b, c, * Bob Argiropoulos, PhD a, b, d, a Department of Medical Genetics, Alberta Children's Hospital, Calgary, Alberta, Canada b Alberta Children's Hospital Research Institute for Child and Maternal Health, Alberta Children's Hospital, Calgary, Alberta, Canada c Department of Pediatrics and Clinical Neurosciences, Pediatric Neurology, Alberta Children's Hospital, Calgary, Alberta, Canada d Genetic Laboratory Services, Cytogenetics Laboratory, Alberta Children's Hospital, Calgary, Alberta, Canada article info Article history: Received 4 March 2019 Accepted 22 June 2019 Available online 28 June 2019 Keywords: Childhood stroke ACSL4 X-linked intellectual disability Ischemia Developmental delay We describe a male with a maternally inherited 9.75-kb intra- was present. Additional evaluation for stroke risk factors, including genic deletion of ACSL4. Fewer than 25 individuals have been re- lumbar puncture, echocardiogram, and examination of blood for fl ported with ACSL4-related X-linked intellectual disability (XLID). thrombophilia and in ammatory markers were negative. This individual highlights a unique presentation of ACSL4-related At three years, severe communication delays were evident. fi XLID and reveals additional pathways for investigation. Behavioral dif culties included frequent outbursts, irritability, and tantrums. There were no limitations in gross or fine motor func- Patient description tioning. At 4.5 years, he developed seizures characterized by eye deviation and automatisms.
    [Show full text]
  • Supplementary Material
    BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) J Neurol Neurosurg Psychiatry Page 1 / 45 SUPPLEMENTARY MATERIAL Appendix A1: Neuropsychological protocol. Appendix A2: Description of the four cases at the transitional stage. Table A1: Clinical status and center proportion in each batch. Table A2: Complete output from EdgeR. Table A3: List of the putative target genes. Table A4: Complete output from DIANA-miRPath v.3. Table A5: Comparison of studies investigating miRNAs from brain samples. Figure A1: Stratified nested cross-validation. Figure A2: Expression heatmap of miRNA signature. Figure A3: Bootstrapped ROC AUC scores. Figure A4: ROC AUC scores with 100 different fold splits. Figure A5: Presymptomatic subjects probability scores. Figure A6: Heatmap of the level of enrichment in KEGG pathways. Kmetzsch V, et al. J Neurol Neurosurg Psychiatry 2021; 92:485–493. doi: 10.1136/jnnp-2020-324647 BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) J Neurol Neurosurg Psychiatry Appendix A1. Neuropsychological protocol The PREV-DEMALS cognitive evaluation included standardized neuropsychological tests to investigate all cognitive domains, and in particular frontal lobe functions. The scores were provided previously (Bertrand et al., 2018). Briefly, global cognitive efficiency was evaluated by means of Mini-Mental State Examination (MMSE) and Mattis Dementia Rating Scale (MDRS). Frontal executive functions were assessed with Frontal Assessment Battery (FAB), forward and backward digit spans, Trail Making Test part A and B (TMT-A and TMT-B), Wisconsin Card Sorting Test (WCST), and Symbol-Digit Modalities test.
    [Show full text]
  • Identification of ACSL4 As a Biomarker and Contributor of Ferroptosis In
    Identication of ACSL4 as a biomarker and contributor of ferroptosis in clear cell renal cell carcinoma na guo ( [email protected] ) Primary research Keywords: Acyl-CoA synthetase long-chain family member 4 (ACSL4), biomarker, ferroptosis, clear cell renal cell carcinoma (ccRCC) Posted Date: May 15th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-24079/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/17 Abstract Background ACSL4 has been reported to be related to tumor genesis and involved in the processes of ferroptosis. However, the expression levels and prognostic value of ACSL4 in clear cell renal cell carcinoma (ccRCC) remain unclear. Methods The Oncomine and TCGA databases were used to predict the expression of ACSL4 mRNA in ccRCC and its association with ccRCC prognosis. The expression levels of ACSL4 were determined in human RCC tissues by real-time PCR. Kaplan-Meier curves were used to analyze the diagnostic and prognostic signicance of ACSL4 in ccRCC. A ferroptosis inducer (erastin) was used to investigate the effects of ACSL4 on ferroptosis in ccRCC cell lines. Results The expression level of ACSL4 was signicantly down-regulated in ccRCC tissues (P < 0.001), which was consistent with the analysis of the Oncomine and TCGA database. Then, immunohistochemical results demonstrated that the ACSL4 was weak or not detected in ccRCC tissues than that in normal tissues. ACSL4 differential expression level was signicantly related to gender, ccRCC subtypes, nodal invasion, tumor grade and cancer stages (all P < 0.001). Survival analysis revealed that overall survival was favorable in ccRCC patients with ACSL4 high expression (P = 0.014).
    [Show full text]
  • Bacterial Biofilms on Microplastics in the Baltic Sea – Composition, Influences, and Interactions with Their Environment
    Bacterial biofilms on microplastics in the Baltic Sea – Composition, influences, and interactions with their environment kumulative Dissertation zur Erlangung des akademischen Grades Doctor rerum naturalium (Dr. rer. nat.) der Mathematisch-Naturwissenschaftlichen Fakultät der Universität Rostock vorgelegt von Katharina Kesy, geb. am 06.11.1985 in Berlin aus Rostock Rostock, 17.09.2019 https://doi.org/10.18453/rosdok_id00002636 Gutachter: Prof. Dr. Matthias Labrenz, Sektion Biologische Meereskunde, Leibniz-Institut für Ostseeforschug Warnemünde Assist. Prof. Dr. Melissa Duhaime, Department of Computational Medicine and Bioinformatics, University of Michigan, USA Jahr der Einreichung: 2019 Jahr der Verteidigung: 2020 Table of contents i Table of contents Summary/Zusammenfassung ............................................................................................. 1 General introduction ........................................................................................................... 6 Biofilms, their formation, and influential factors ............................................................. 6 The ecological importance of biofilms in aquatic systems ............................................... 8 Microplastics in aquatic environments: a newly available habitat for surface associated microorganisms and possible vector for potential pathogens ........................................... 9 Description of research aims ............................................................................................ 15 Summary
    [Show full text]
  • Architecture, Component, and Microbiome of Biofilm Involved In
    www.nature.com/npjbiofilms ARTICLE OPEN Architecture, component, and microbiome of biofilm involved in the fouling of membrane bioreactors Tomohiro Inaba1, Tomoyuki Hori1, Hidenobu Aizawa1, Atsushi Ogata1 and Hiroshi Habe1 Biofilm formation on the filtration membrane and the subsequent clogging of membrane pores (called biofouling) is one of the most persistent problems in membrane bioreactors for wastewater treatment and reclamation. Here, we investigated the structure and microbiome of fouling-related biofilms in the membrane bioreactor using non-destructive confocal reflection microscopy and high-throughput Illumina sequencing of 16S rRNA genes. Direct confocal reflection microscopy indicated that the thin biofilms were formed and maintained regardless of the increasing transmembrane pressure, which is a common indicator of membrane fouling, at low organic-loading rates. Their solid components were primarily extracellular polysaccharides and microbial cells. In contrast, high organic-loading rates resulted in a rapid increase in the transmembrane pressure and the development of the thick biofilms mainly composed of extracellular lipids. High-throughput sequencing revealed that the biofilm microbiomes, including major and minor microorganisms, substantially changed in response to the organic-loading rates and biofilm development. These results demonstrated for the first time that the architectures, chemical components, and microbiomes of the biofilms on fouled membranes were tightly associated with one another and differed considerably depending on the organic-loading conditions in the membrane bioreactor, emphasizing the significance of alternative indicators other than the transmembrane pressure for membrane biofouling. npj Biofilms and Microbiomes (2017) 3:5 ; doi:10.1038/s41522-016-0010-1 INTRODUCTION improvement of confocal reflection microscopy (CRM).9, 10 This Membrane bioreactors (MBRs) have been broadly exploited for the unique analytical technique uses a special installed beam splitter treatment of municipal and industrial wastewaters.
    [Show full text]
  • Global Ubiquitylation Analysis of Mitochondria in Primary Neurons
    bioRxiv preprint doi: https://doi.org/10.1101/2021.04.01.438131; this version posted April 1, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Global ubiquitylation analysis of mitochondria in primary neurons identifies physiological Parkin targets following activation of PINK1 Odetta Antico1#, Alban Ordureau2#, Michael Stevens1, Francois Singh1, Marek φ Gierlinski3, Erica Barini1 , Mollie L. Rickwood1, Alan Prescott4, Rachel Toth1, Ian G. Ganley1, J. Wade Harper2*, and Miratul M. K. Muqit1* 1MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom, DD1 5EH, U.K. 2Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA 3Data Analysis Group, Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom, DD1 5EH, U.K. 4Dundee Imaging Facility, School of Life Sciences, University of Dundee, Dundee, United Kingdom, DD1 5EH, U.K #Denotes Equal Contribution φCurrent address: AbbVie Deutschland GmbH & Co, Knollstr, 67061, Ludwigshafen, Germany *Correspondence: [email protected] or [email protected] Keywords Neurons, PINK1, Parkin, ubiquitin, Parkinson’s disease, Mitochondria, Running Title: Ubiquitin analysis of mitochondria in neurons 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.04.01.438131; this version posted April 1, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
    [Show full text]
  • Microbial Cell Factories Biomed Central
    Microbial Cell Factories BioMed Central Research Open Access Differential gene expression in recombinant Pichia pastoris analysed by heterologous DNA microarray hybridisation Michael Sauer1, Paola Branduardi2, Brigitte Gasser1, Minoska Valli1, Michael Maurer1, Danilo Porro2 and Diethard Mattanovich*1 Address: 1Institute of Applied Microbiology, Department of Biotechnology, University of Natural Resources and Applied Life Sciences, Muthgasse 18, A-1190 Vienna, Austria and 2Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, I-20126 Milan, Italy Email: Michael Sauer - [email protected]; Paola Branduardi - [email protected]; Brigitte Gasser - [email protected]; Minoska Valli - [email protected]; Michael Maurer - [email protected]; Danilo Porro - [email protected]; Diethard Mattanovich* - [email protected] * Corresponding author Published: 20 December 2004 Received: 26 November 2004 Accepted: 20 December 2004 Microbial Cell Factories 2004, 3:17 doi:10.1186/1475-2859-3-17 This article is available from: http://www.microbialcellfactories.com/content/3/1/17 © 2004 Sauer et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Pichia pastoris is a well established yeast host for heterologous protein expression, however, the physiological and genetic information about this yeast remains scanty. The lack of a published genome sequence renders DNA arrays unavailable, thereby hampering more global investigations of P. pastoris from the beginning.
    [Show full text]