Insights on bio-degumming of kenaf bast based on metagenomi and proteomics

Abstract Background: Microbes play important roles in kanef-degumming. This study aims at identifying the key candidate microbes and proteins responsible for the degumming of kenaf bast (Hibiscus cannabinus). Kenaf bast was cut into pieces and immersed into microbia fermentation liquid collected from different sites. Fermentation liquid samples were collected at 0, 40, 110 and 150 h and then subjected to the 16S/18S rRNA sequencing analysis and isobaric tag for relative and absolute quantitation (iTRAQ) analysis. The microbial (bacterial and fungal) diversity and the differentially expressed proteins/peptides (DEPs) were identified.Results: With the prolonged degumming time, the weight loss rate increased, the bacterial diversity was decreased. [Weeksellaceae], Enterobacteriaceae and Moraxellaceae were rapidly increased at 0~40 h, and then decreased and were gradually replaced by Bacteroidaceae from 40 h to 150 h. Similarly, Chryseobacterium and Dysgonomonas were gradually increased at 0~110 h and then decreased; Acinetobacter and Lactococcus were increased at 0~40 h, followed by decrease. Bacteroides was the dominant genus at 150 h. Sequencing 18S rRNA-seq showed the gradually decreased Wallemia hederae and increased Codosiga hollandica during degumming. iTRAQ data analysis showed Rds1, and pyruvate kinase I was decreased and increased in the kanef-degumming, respectively. Other DEPs of ferredoxin I, superoxide dismutase and aconitatehydratase were identified to be related to the Glyoxylate and dicarboxylate metabolism (ko00630).Conclusions: Bacteria including Chryseobacterium, Dysgonomonas, Acinetobacter, Lactococcus and Bacteroidesand fungi like Wallemia hederae and Codosiga hollandica are key candidate microbes for kanef degumming.

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Insights on bio-degumming of kenaf bast based on metagenomi and proteomics

10.21203/rs.2.14508/v3 ◽

2020 ◽

Author(s):

Shengwen Duan ◽

Lifeng Cheng ◽

Xiangyuan Feng ◽

Qi Yang ◽

Zhiyuan Liu ◽

...

Keyword(s):

18S Rrna ◽

Hibiscus Cannabinus ◽

Sequencing Analysis ◽

Absolute Quantitation ◽

Itraq Analysis ◽

Fermentation Liquid ◽

Rrna Sequencing ◽

Isobaric Tag ◽

Ferredoxin I ◽

Kenaf Bast

Abstract Background: Microbial play important roles in kanef-degumming. This study aims at identifying the key candidate microbial and proteins responsible for the degumming of kenaf bast ( Hibiscus cannabinus ). Kenaf bast was cut into pieces and immersed into microbial fermentation liquid collected from different sites. Fermentation liquid samples were collected at 0, 40, 110 and 150 h and then subjected to the 16S/18S rRNA sequencing analysis and isobaric tag for relative and absolute quantitation (iTRAQ) analysis. The microbial (bacterial and fungal) diversity and the differentially expressed proteins/peptides (DEPs) were identified. Results: With the prolonged degumming time, the weight loss rate increased, the bacterial diversity was decreased. [Weeksellaceae], Enterobacteriaceae and Moraxellaceae were rapidly increased at 0~40 h, and then decreased and were gradually replaced by Bacteroidaceae from 40 h to 150 h. Similarly, Chryseobacterium and Dysgonomonas were gradually increased at 0~110 h and then decreased; Acinetobacter and Lactococcus were increased at 0~40 h, followed by decrease. Bacteroides was the dominant genus at 150 h. 18S rRNA-seq showed the gradually decreased Wallemia_hederae and increased Codosiga_hollandica during degumming. iTRAQ data analysis showed Rds1, and pyruvate kinase I was decreased and increased in the kanef-degumming, respectively. Other DEPs of ferredoxin I, superoxide dismutase and aconitatehydratase were identified to be related to the Glyoxylate and dicarboxylate metabolism (ko00630). Conclusions : Bacteria including Chryseobacterium , Dysgonomonas , Acinetobacter , Lactococcus and Bacteroides and fungi like Wallemia_hederae and Codosiga_hollandica are key candidate microbial for kanef degumming.

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Insights on bio-degumming of kenaf bast based on metagenomic and proteomics

10.21203/rs.2.14508/v2 ◽

2019 ◽

Author(s):

Shengwen Duan ◽

Lifeng Cheng ◽

Xiangyuan Feng ◽

Qi Yang ◽

Zhiyuan Liu ◽

...

Keyword(s):

18S Rrna ◽

Hibiscus Cannabinus ◽

Sequencing Analysis ◽

Absolute Quantitation ◽

Itraq Analysis ◽

Fermentation Liquid ◽

Rrna Sequencing ◽

Isobaric Tag ◽

Ferredoxin I ◽

Kenaf Bast

Abstract Background: Microbial play important roles in kanef-degumming. This study aims at identifying the key candidate microbial and proteins responsible for the degumming of kenaf bast ( Hibiscus cannabinus ). Kenaf bast was cut into pieces and immersed into microbial fermentation liquid collected from different sites. Fermentation liquid samples were collected at 0, 40, 110 and 150 h and then subjected to the 16S/18S rRNA sequencing analysis and isobaric tag for relative and absolute quantitation (iTRAQ) analysis. The microbial (bacterial and fungal) diversity and the differentially expressed proteins/peptides (DEPs) were identified. Results: With the prolonged degumming time, the weight loss rate increased, the bacterial diversity was decreased. [Weeksellaceae], Enterobacteriaceae and Moraxellaceae were rapidly increased at 0~40 h, and then decreased and were gradually replaced by Bacteroidaceae from 40 h to 150 h. Similarly, Chryseobacterium and Dysgonomonas were gradually increased at 0~110 h and then decreased; Acinetobacter and Lactococcus were increased at 0~40 h, followed by decrease. Bacteroides was the dominant genus at 150 h. 18S rRNA-seq showed the gradually decreased Wallemia_hederae and increased Codosiga_hollandica during degumming. iTRAQ data analysis showed Rds1, and pyruvate kinase I was decreased and increased in the kanef-degumming, respectively. Other DEPs of ferredoxin I, superoxide dismutase and aconitatehydratase were identified to be related to the Glyoxylate and dicarboxylate metabolism (ko00630). Conclusions : Bacteria including Chryseobacterium , Dysgonomonas , Acinetobacter , Lactococcus and Bacteroides and fungi like Wallemia_hederae and Codosiga_hollandica are key candidate microbial for kanef degumming.

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Insights on bio-degumming of kenaf bast based on metagenomi and proteomics

10.21203/rs.2.14508/v4 ◽

2020 ◽

Author(s):

Shengwen Duan ◽

Lifeng Cheng ◽

Xiangyuan Feng ◽

Qi Yang ◽

Zhiyuan Liu ◽

...

Keyword(s):

18S Rrna ◽

Hibiscus Cannabinus ◽

Sequencing Analysis ◽

Absolute Quantitation ◽

Itraq Analysis ◽

Fermentation Liquid ◽

Rrna Sequencing ◽

Isobaric Tag ◽

Ferredoxin I ◽

Kenaf Bast

Abstract Background: Microbial play important roles in kanef-degumming. This study aims at identifying the key candidate microbial and proteins responsible for the degumming of kenaf bast ( Hibiscus cannabinus ). Kenaf bast was cut into pieces and immersed into microbial fermentation liquid collected from different sites. Fermentation liquid samples were collected at 0, 40, 110 and 150 h and then subjected to the 16S/18S rRNA sequencing analysis and isobaric tag for relative and absolute quantitation (iTRAQ) analysis. The microbial (bacterial and fungal) diversity and the differentially expressed proteins/peptides (DEPs) were identified. Results: With the prolonged degumming time, the weight loss rate increased, the bacterial diversity was decreased. [Weeksellaceae], Enterobacteriaceae and Moraxellaceae were rapidly increased at 0~40 h, and then decreased and were gradually replaced by Bacteroidaceae from 40 h to 150 h. Similarly, Chryseobacterium and Dysgonomonas were gradually increased at 0~110 h and then decreased; Acinetobacter and Lactococcus were increased at 0~40 h, followed by decrease. Bacteroides was the dominant genus at 150 h. 18S rRNA-seq showed the gradually decreased Wallemia_hederae and increased Codosiga_hollandica during degumming. iTRAQ data analysis showed Rds1, and pyruvate kinase I was decreased and increased in the kanef-degumming, respectively. Other DEPs of ferredoxin I, superoxide dismutase and aconitatehydratase were identified to be related to the Glyoxylate and dicarboxylate metabolism (ko00630). Conclusions : Bacteria including Chryseobacterium , Dysgonomonas , Acinetobacter , Lactococcus and Bacteroides and fungi like Wallemia_hederae and Codosiga_hollandica are key candidate microbial for kanef degumming.

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Cardiac proteomics reveals the potential mechanism of microtubule associated protein 4 phosphorylation-induced mitochondrial dysfunction

Burns & Trauma ◽

10.1186/s41038-019-0146-3 ◽

2019 ◽

Vol 7 ◽

Cited By ~ 2

Author(s):

Lingfei Li ◽

Junhui Zhang ◽

Qiong Zhang ◽

Yuesheng Huang ◽

Jiongyu Hu

Keyword(s):

Mitochondrial Dysfunction ◽

Seed Proteins ◽

Enrichment Analysis ◽

Heart Tissue ◽

Reduced Form ◽

Potential Mechanism ◽

Absolute Quantitation ◽

Interacting Protein ◽

Itraq Analysis ◽

Isobaric Tag

Abstract Background Our previous work suggested that microtubule associated protein 4 (MAP4) phosphorylation led to mitochondrial dysfunction in MAP4 phosphorylation mutant mice with cardiomyopathy, but the detailed mechanism was still unknown. Thus, the aim of this study was to investigate the potential mechanism involved in mitochondrial dysfunction responsible for cardiomyopathy. Methods The present study was conducted to explore the potential mechanism underlying the mitochondrial dysfunction driven by MAP4 phosphorylation. Strain of mouse that mimicked constant MAP4 phosphorylation (S737 and S760) was generated. The isobaric tag for relative and absolute quantitation (iTRAQ) analysis was applied to the heart tissue. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and protein-protein interaction (PPI) were all analyzed on the basis of differential expressed proteins (DEPs). Results Among the 72 cardiac DEPs detected between the two genotypes of mice, 12 were upregulated and 60 were downregulated. GO analysis showed the biological process, molecular function, and cellular component of DEPs, and KEGG enrichment analysis linked DEPs to 96 different biochemical pathways. In addition, the PPI network was also extended on the basis of DEPs as the seed proteins. Three proteins, including mitochondrial ubiquitin ligase activator of NF-κB 1, reduced form of nicotinamide adenine dinucleotide (NADH)-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial and growth arrest, and DNA-damage-inducible proteins-interacting protein 1, which play an important role in the regulation of mitochondrial function, may correlate with MAP4 phosphorylation-induced mitochondrial dysfunction. Western blot was used to validate the expression of the three proteins, which was consistent with iTRAQ experiments. Conclusions These findings revealed that the DEPs caused by MAP4 phosphorylation in heart tissue using iTRAQ technique and may provide clues to uncover the potential mechanism of MAP4 phosphorylation-induced mitochondrial dysfunction.

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Protein composition and function of red and white skeletal muscle mitochondria

AJP Cell Physiology ◽

10.1152/ajpcell.00496.2010 ◽

2011 ◽

Vol 300 (6) ◽

pp. C1280-C1290 ◽

Cited By ~ 40

Author(s):

Brian Glancy ◽

Robert S. Balaban

Keyword(s):

Skeletal Muscle ◽

Mitochondrial Protein ◽

Protein Composition ◽

Metabolic Demand ◽

Absolute Quantitation ◽

Itraq Analysis ◽

Palmitoyl Carnitine ◽

Protein Contamination ◽

Isobaric Tag ◽

And Function

Red and white muscles are faced with very different energetic demands. However, it is unclear whether relative mitochondrial protein expression is different between muscle types. Mitochondria from red and white porcine skeletal muscle were isolated with a Percoll gradient. Differences in protein composition were determined using blue native (BN)-PAGE, two-dimensional differential in gel electrophoresis (2D DIGE), optical spectroscopy, and isobaric tag for relative and absolute quantitation (iTRAQ). Complex IV and V activities were compared using BN-PAGE in-gel activity assays, and maximal mitochondrial respiration rates were assessed using pyruvate (P) + malate (M), glutamate (G) + M, and palmitoyl-carnitine (PC) + M. Without the Percoll step, major cytosolic protein contamination was noted for white mitochondria. Upon removal of contamination, very few protein differences were observed between red and white mitochondria. BN-PAGE showed no differences in the subunit composition of Complexes I–V or the activities of Complexes IV and V. iTRAQ analysis detected 358 mitochondrial proteins, 69 statistically different. Physiological significance may be lower: at a 25% difference, 48 proteins were detected; at 50%, 14 proteins were detected; and 3 proteins were detected at a 100%. Thus any changes could be argued to be physiologically modest. One area of difference was fat metabolism where four β-oxidation enzymes were ∼25% higher in red mitochondria. This was correlated with a 40% higher rate of PC+M oxidation in red mitochondria compared with white mitochondria with no differences in P+M and G+M oxidation. These data suggest that metabolic demand differences between red and white muscle fibers are primarily matched by the number of mitochondria and not by significant alterations in the mitochondria themselves.

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Molecular Characterization of Ciliate Diversity in Stream Biofilms

Applied and Environmental Microbiology ◽

10.1128/aem.01438-07 ◽

2008 ◽

Vol 74 (6) ◽

pp. 1740-1747 ◽

Cited By ~ 52

Author(s):

Andrew Dopheide ◽

Gavin Lear ◽

Rebecca Stott ◽

Gillian Lewis

Keyword(s):

18S Rrna ◽

Pcr Primers ◽

18S Rrna Gene ◽

Sequence Diversity ◽

Rrna Genes ◽

Rrna Gene ◽

Sequencing Analysis ◽

Specific Pcr ◽

Stream Biofilms

ABSTRACT Free-living protozoa are thought to be of fundamental importance in aquatic ecosystems, but there is limited understanding of their diversity and ecological role, particularly in surface-associated communities such as biofilms. Existing eukaryote-specific PCR primers were used to survey 18S rRNA gene sequence diversity in stream biofilms but poorly revealed protozoan diversity, demonstrating a need for protozoan-targeted primers. Group-specific PCR primers targeting 18S rRNA genes of the protozoan phylum Ciliophora were therefore designed and tested using DNA extracted from cultured protozoan isolates. The two most reliable primer combinations were applied to stream biofilm DNA, followed by cloning and sequencing analysis. Of 44 clones derived from primer set 384F/1147R, 86% were of probable ciliate origin, as were 25% of 44 clones detected by primer set 121F/1147R. A further 29% of 121F/1147R-detected clones matched sequences from the closely related phylum Apicomplexa. The highly ciliate-specific primer set 384F/1147R was subsequently used in PCRs on biofilm DNA from four streams exhibiting different levels of human impact, revealing differences in ciliate sequence diversity in samples from each site. Of a total of 240 clones, 73% were of probable ciliate origin; 54 different putative ciliate sequences were detected from throughout seven taxonomic ciliate classes. Sequences from Oligohymenophorea were most commonly detected in all samples, followed by either Spirotrichea or Phyllopharyngea. Restriction fragment length polymorphism profile-based analysis of clones suggested a potentially higher level of diversity than did sequencing. Nevertheless, newly designed PCR primers 384F/1147R were considered to provide an effective molecular basis for characterization of ciliate diversity in stream biofilms.

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Fast and slow-growing breeds: characterisation of broiler caecal microbiota development throughout the growing period

10.21203/rs.3.rs-22748/v1 ◽

2020 ◽

Author(s):

Laura Montoro Dasí ◽

Arantxa Villagra ◽

Maria de Toro ◽

María Teresa Pérez-Gracia ◽

Santiago Vega ◽

...

Keyword(s):

16S Rrna ◽

Animal Health ◽

Resistant Bacteria ◽

Production Cycle ◽

Sequencing Analysis ◽

Poultry Production ◽

Growing Period ◽

Rrna Sequencing ◽

Slow Growing ◽

Caecal Microbiota

Abstract Background: The caecal microbiota and its modulation play an important role in animal health, productivity and disease control in poultry production. In this sense, it could be considered as a biomarker of poultry health. Furthermore, due to the emergence of resistant bacteria and the increasing social pressure to establish animal-friendly management on farms, producers are motivated to select more extensive and antibiotic-free breeds. It is therefore necessary to gain better knowledge on the development of major bacteria in healthy broilers, both in commercial fast-growing and in new slow-growing breeds. Hence, the aim of this study was to characterise caecal microbiota in two genetic poultry breeds throughout the growing period using 16S rRNA sequencing analysis. Results: A total of 50 caecal pools (25 per breed) were sequenced by the 16S rRNA method. The complexity of caecal microbiota composition increased significantly as animals grew. Furthermore, there were statistical differences between breeds at the end of the growing period. The dominant phyla throughout the production cycle were Firmicutes, Bacteroidetes and Proteobacteria. The predominantly identified genera were Ruminococcus spp., Lactobacillus spp. and Bacteroides spp.Conclusion: The results showed that the main caecal bacteria for both breeds were similar. Thus, these phyla or genera should be considered as biomarkers of poultry health in the evaluation of different treatments applied to animals.

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Treponema Whipplei Endocarditis Masquerading as a Calcified Amorphous Aortic Valve Tumor

10.22541/au.163308888.85093982/v1 ◽

2021 ◽

Author(s):

Elian Massoud ◽

Justin Watson ◽

Amy Fiedler

Keyword(s):

Aortic Valve ◽

16S Rrna ◽

Transient Ischemic Attack ◽

18S Rrna ◽

Tropheryma Whipplei ◽

Gram Positive ◽

Rrna Sequencing ◽

Aortic Tumor ◽

Ischemic Attack ◽

Culture Negative

Whipple’s endocarditis is a rare culture-negative endocarditis caused by Tropheryma whipplei, an intracellular gram-positive organism. Here, we present a case of a 60-year-old male who presented with transient ischemic attack and was found to have an aortic valve mass. Following successful excision, histopathologic assessment of the lesion was consistent with calcified amorphous aortic tumor, a rare non-neoplastic hamartomatous mass of the heart. However, 16s rRNA and 18s rRNA sequencing detected Tropheryma whipplei, and the diagnosis of Whipple’s endocarditis was made.

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Partial Proteome Map of Campylobacter Jejuni Strain Nctc11168 by Gel-Free Proteomics Analysis

International Journal of Applied Sciences and Biotechnology ◽

10.3126/ijasbt.v2i4.11253 ◽

2014 ◽

Vol 2 (4) ◽

pp. 464-477

Author(s):

Zilun Shi ◽

Chris Dawson ◽

Stephen L.W. On ◽

Malik Altaf Hussain

Keyword(s):

Campylobacter Jejuni ◽

Foodborne Pathogen ◽

Brain Heart Infusion ◽

Cell Protein ◽

Absolute Quantitation ◽

Whole Cell ◽

Itraq Analysis ◽

Proteomic Approach ◽

Whole Cell Protein ◽

Isobaric Tags

A proteome map of the foodborne pathogen Campylobacter jejuni NCTC11168 was analyzed using a state-of-the-art gel-free proteomic approach for the first time. A whole cell protein extract was prepared from the C. jejuni strain NCTC11168 grown in brain heart infusion (BHI) broth at 42°C under microaerobic conditions. A gel-free technique using isobaric tags for relative and absolute quantitation (iTRAQ) was employed to create a protein expression profile of the strain. Liquid chromatography-mass spectrometry (LC-MS/MS) was used to identify the proteins. Protein functionalities were searched to classify them. A total of 235 proteins were identified in the whole cell protein fraction of C. jejuni NCTC11168 cells using iTRAQ analysis. Functional grouping of the identified proteins showed that forty percent of these proteins were associated with energy metabolism, protein synthesis and genetic information processing. iTRAQ was faster, easier and proved more sensitive than two-dimensional gel-based proteomics approaches previously applied to C. jejuni, making it an attractive tool for further studies of cellular physiological response. DOI: http://dx.doi.org/10.3126/ijasbt.v2i4.11253 Int J Appl Sci Biotechnol, Vol. 2(4): 464-477

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