scholarly journals Proteomic Analysis of the Periodontal Pathogen Prevotella Intermedia Secretomes in Biofilm and Planktonic Lifestyles

2021 ◽  
Author(s):  
Maribasappa Karched ◽  
Radhika Bhardwaj ◽  
Muawia Qudeimat ◽  
Areej Al-Khabbaz ◽  
Arjuna Ellepola
Keyword(s):  
Molecular Mechanisms ◽  
Profile Analysis ◽  
Nitrogen Compound ◽  
Metabolic Process ◽  
Periodontal Pathogen ◽  
Superoxide Reductase ◽  
Prevotella Intermedia ◽  
Important Species ◽  
Threonine Synthase ◽  
Virulence Potential

Abstract Prevotella intermedia is an important species associated with periodontitis. Despite the remarkable clinical significance, little is known about the molecular basis for its virulence. The aim of this study was to characterize the secretome of P. intermedia in biofilm and planktonic life mode. The biofilm secretome showed 109 proteins while the planktonic secretome showed 136 proteins. The biofilm and the planktonic secretomes contained 17 and 33 signal-peptide bearing proteins, 13 and 18 lipoproteins, respectively. Superoxide reductase, sensor histidine kinase, C40 family peptidase, elongation factor Tu, threonine synthase etc. were unique to biofilm. Of the ~30 proteins with predicted virulence potential from biofilm and planktonic secretomes, only 6 were common between the two groups, implying large differences between biofilm and planktonic modes of P. intermedia. From gene ontology biofilm secretome displayed a markedly higher percent proteins compared to planktonic secretome in terms of cellular amino acid metabolic process, nitrogen compound metabolic process etc. Inflammatory cytokine profile analysis revealed that only the biofilm secretome, not the planktonic one, induced important cytokines such as MIP-1a/MIP-1b, IL-1b, and IL-8. In conclusion, the revealed differences in the protein profiles of P. intermedia biofilm and planktonic secretomes may trigger further questions about molecular mechanisms how this species exerts its virulence potential in the oral cavity.

scholarly journals Transcriptomic profile analysis of the halophyte Suaeda rigida response and tolerance under NaCl stress

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Zhan-Jiang Han ◽  
Yang Sun ◽  
Min Zhang ◽  
Jun-Tuan Zhai
Keyword(s):  
Cell Wall ◽  
Salt Tolerance ◽  
Protein Transport ◽  
Profile Analysis ◽  
Nitrogen Compound ◽  
Enrichment Analysis ◽  
Plant Type ◽  
Ecological Value ◽  
Annotation Database ◽  
Cell Wall Biogenesis

Abstract Suaeda rigida is a lignified, true haplotype that predominantly grows in the Tarim basin, China. It has significant economic and ecological value. Herein, with aim to determine the genes associated with salt tolerance, transcriptome sequencing was performed on its stem, leaves and root over three set NaCl gradients regimens at treatment intervals of 3 h and 5 days. From our findings, we identified 829,095 unigenes, with 331,394 being successfully matched to at least one annotation database. In roots, under 3 h treatment, no up-regulated DEGs were identified in 100 and 500 mM NaCl treated samples. Under 5 days treatment, 97, 60 and 242 up-regulated DEGs were identified in 100, 300, 500 mM NaCl treated samples, respectively. We identified 50, 22 and 255 down-regulated DEGs in 100, 300, 500 mM NaCl treated samples, respectively. GO biological process enrichment analysis established that down-regulated DEGs were associated with nitrogen compound transport, organic substance transport and intracellular protein transport while the up-regulated genes were enriched in cell wall biogenesis, such as plant-type cell wall biogenesis, cell wall assembly, extracellular matrix organization and plant-type cell wall organization. These findings provide valuable knowledge on genes associated with salt tolerance of Suaeda rigida, and can be applied in other downstream haplotype studies.

scholarly journals Chlorella Vulgaris Biomass Supplementation Increased the Abundance of Hepatic Antioxidant Proteins in Relation to Oxidative Stress Reduction in Rabbits

2020 ◽  
Author(s):  
Akeem Babatunde Sikiru ◽  
Arangasamy Arunachalam ◽  
Stephen Sunday Acheneje Egena ◽  
Sejian Veerasamy ◽  
Ippala Janardhan Reddy ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Chlorella Vulgaris ◽  
Molecular Mechanisms ◽  
Profile Analysis ◽  
Control Group ◽  
Antioxidant Enzyme Activities ◽  
Control Groups ◽  
Antioxidant Genes ◽  
Significant Difference ◽  
Antioxidant Proteins

Abstract Background Chlorella vulgaris is a unicellular microalga that is rich in antioxidant, its supplementation has been reported to reduce oxidative stress via upregulations of antioxidant genes. However, there are scarce reports on its effect on antioxidant protein expressions in rabbits – a situation which necessitate an untargeted proteomic profile analysis due to its supplementation. This is because untargeted proteomics profiling is an approach suitable for assessing the effectiveness of genes code translation into polypeptide chains folded into functional proteins used for specific sub-cellular or extracellular physiological activities. It remains one of the comparative avenues for evaluating the efficacies of drugs and nutraceutical agents including antioxidants. In this study, the antioxidant efficacy of a microalga Chlorella vulgaris was evaluated at molecular levels using its hepatic protein expression in rabbit models. Results After 120 days of the microalga supplementation, protein was extracted from liver of the rabbits for untargeted proteomics profiling using LC-MS/Orbitrap Fusion Tribrid™ peptides quantifier and sequencer. There were five-hundred and eleven (511) proteins identified; and among the proteins, 191 were specific to the control group while 186 were specific to the Treatment group; and 134 were common to both groups. Independent samples t-test of the protein abundance indicated that there was a significant difference (p = 0.01) between the treatment and the control groups. There was also a significant reduction in the malondialdehyde concentrations (p = 0.01), higher total antioxidant capacities (p = 0.002), and increased antioxidant enzyme activities (p = 0.05) between the treatment and control groups.Conclusion The study concluded that one of the molecular mechanisms associated with Chlorella vulgaris intake reduction of the hepatic oxidative stress is increased abundances of antioxidant proteins and reduction of the lipid peroxidation and these led to a suggestion that the microalga is a potent antioxidant agent suitable for protecting against oxidative stress in rabbits and other domestic food producing animals.

scholarly journals MicroRNA Expression Profile Analysis of Chlamydomonas reinhardtii during Lipid Accumulation Process under Nitrogen Deprivation Stresses

2021 ◽  
Vol 9 (1) ◽  
pp. 6
Author(s):  
Jingxian Zhang ◽  
Jiping Shi ◽  
Chenyang Yuan ◽  
Xiangcen Liu ◽  
Guilin Du ◽  
...  
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Lipid Accumulation ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Profile Analysis ◽  
Critical Role ◽  
Lipid Transport ◽  
Nitrogen Deprivation ◽  
Sequencing Platform ◽  
Novel Mirna

Lipid accumulation in various microalgae has been found induced by nitrogen deprivation, and it controls many different genes expression. Yet, the underlying molecular mechanisms still remain largely unknown. MicroRNA (miRNAs) play a critical role in post-transcriptional gene regulation. In this study, miRNAs were hypothesized involved in lipid accumulation by nitrogen deprivation. A deep-sequencing platform was used to explore miRNAs-mediated responses induced by nitrogen deprivation in Chlamydomonas reinhardtii. The eukaryotic orthologous groups of proteins (KOG) function in the predicted target genes of miRNA with response to nitrogen deprivation were mainly involved in signal transduction mechanisms, including transcription, lipid transport, and metabolism. A total of 109 miRNA were predicted, including 79 known miRNA and 30 novel miRNA. A total of 29 miRNAs showed significantly differential expressions after nitrogen deprivation, and most of them were upregulated. A total of 10 miRNAs and their targeting genes might involve in lipid transport and metabolism biological process. This study first investigates nitrogen deprivation-regulated miRNAs in microalgae and broadens perspectives on miRNAs importance in microalgae lipid accumulation via nitrogen deprivation. This study provides theoretical guidance for the application of microalgae in bio-oil engineering production.

scholarly journals RNA-Seq Reveals Differentially Expressed Genes and Pathways Affecting Intramuscular Fat Metabolism in Huangshan Black Chicken Population

2020 ◽  
Vol 12 (3) ◽  
pp. 117
Author(s):  
S. H. Yang ◽  
C. S. He ◽  
C. H. Li ◽  
G. Q. Liu
Keyword(s):  
Fatty Acid ◽  
Candidate Genes ◽  
Meat Quality ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Interaction Network ◽  
Intramuscular Fat ◽  
Metabolic Process ◽  
Differentially Expressed ◽  
Thigh Muscle

Intramuscular fat (IMF) plays an important role in meat quality due to its positive correlation with juiciness, tenderness, and flavor. However, for chickens, the molecular mechanisms underlying IMF deposition in thigh muscle have not yet been determined. Here, to identify candidate genes and signaling pathways related to IMF deposition, we deeply explored the chicken transcriptome from thigh muscles of Huangshan Black Chickens with extremely high and low phenotypic values for intramuscular fat content. A total of 128 genes differentially expressed genes (DEGs) were detected, of which 94 were up-regulated and 34 were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways revealed these DEGs (including FABP4, G0S2, PLIN1, SCD1, LFABP, SLC1A6, SLC45A3, ACSBG1, LY86, ST8SIA5, SNAI2, HPGD, EDN2, and THRSP) were significantly enriched in lipid biosynthetic process, steroid biosynthetic and metabolic process, fatty acid metabolic process, and regulation of unsaturated fatty acid metabolic pathways. Additionally, we concluded an interaction network related to lipid metabolism, which might be contributed to the IMF deposition in chicken. Overall, we proposed some new candidate genes and interaction networks that can be associated with IMF deposition and used as biomarkers in meat quality improvement.

scholarly journals Physiological and transcriptome analysis reveal molecular mechanism in Salvia miltiorrhiza leaves of near-isogenic male fertile lines and male sterile lines

2019 ◽  
Author(s):  
Ruihong Wang ◽  
Hongbo Guo ◽  
Juane Dong
Keyword(s):  
Plant Growth ◽  
Crop Production ◽  
Molecular Mechanisms ◽  
Leaf Gas Exchange ◽  
Salvia Miltiorrhiza ◽  
Underlying Mechanism ◽  
Metabolic Process ◽  
Primary Metabolism ◽  
Male Sterile ◽  
Physiological Analysis

Abstract Background: Our previous study found that male sterility in Salvia miltiorrhiza could result in stunted growth, decrease biomass, inhibit primary metabolism, and promote secondary metabolism, but their molecular mechanisms have not yet been elucidated. In this article, we investigated the underlying mechanism of plant growth and metabolism by using physiological analysis and mRNA sequencing (RNA-Seq). Results: In this study, transcriptomic and physiological analyses were performed to identify the effect on plant growth and metabolic production in male sterile mutants. Through GO and KEGG analysis it was found that the pathways were mainly enriched in processes including organ development, primary metabolic process and secondary metabolic process. Physiological analyses showed that the chloroplast structure of male sterile mutants of Salvia miltiorrhiza was abnormally developed, which could result in decrease in leaf gas exchange (A, E and gs), chlorophyll fluorescence (Fv, Fm and Fv/Fm), and the chlorophyll content. Transcriptomic analyses indicated that disproportionating enzyme 1 (DPE1) catalyzed the degradation of starch, while sucrose synthase 3 (SUS3) and cytosolic invertase 2 (CINV2) catalyzed the degradation of sucrose in S. miltiorrhiza. The results suggested that phenylalanine ammonialyase (PAL) played an important role in the biosynthesis of rosmarinic acid and salvianolic acid B, and flavone synthase (FLS) was an important enzyme catalyzing steps of flavonoid biosynthesis. High expression level of these enzyme genes in male sterile mutants resulted in high content of secondary metabolites. Conclusions: Our results from the physiological and transcriptome analyses reveal underlying mechanism of plant growth and metabolism in male sterile mutants, and provide insight into the crop production of S. miltiorrhiza.

scholarly journals Comparative transcriptome combined with metabolome analyses revealed key factors involved in nitric oxide (NO)-regulated cadmium stress adaptation in tall fescue

2020 ◽  
Author(s):  
Huihui Zhu ◽  
Honglian Ai ◽  
Zhengrong Hu ◽  
Dongyun Du ◽  
Jie Sun ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Secondary Metabolites ◽  
Tall Fescue ◽  
Molecular Mechanisms ◽  
Antioxidant Activities ◽  
Profile Analysis ◽  
Cadmium Stress ◽  
Metabolite Profile ◽  
Glutathione Metabolism ◽  
No Donor

Abstract Background: It has been reported that nitric oxide (NO) could ameliorate cadmium (Cd) toxicity in tall fescue; however, the underlying mechanisms of NO mediated Cd detoxification are largely unknown. In this study, we investigated the possible molecular mechanisms of Cd detoxification process by comparative transcriptomic and metabolomic approaches. Results: The application of Sodium nitroprusside (SNP) as NO donor decreased the Cd content of tall fescue by 11% under Cd stress (T1 treatment), but the Cd content was increased by 24% when treated with Carboxy-PTIO (c-PTIO) together with Nitro-L-arginine methyl ester (L-NAME) (T2 treatment). RNA-seq analysis revealed that 904 (414 up- and 490 down-regulated) and 118 (74 up- and 44 down-regulated) DEGs were identified in the T1 vs Cd (only Cd treatment) and T2 vs Cd comparisons, respectively. Moreover, metabolite profile analysis showed that 99 (65 up- and 34-down- regulated) and 131 (45 up- and 86 down-regulated) metabolites were altered in the T1 vs Cd and T2 vs Cd comparisons, respectively. The integrated analyses of transcriptomic and metabolic data showed that 81 DEGs and 15 differentially expressed metabolites were involved in 20 NO-induced pathways. The dominant pathways were antioxidant activities such as glutathione metabolism, arginine and proline metabolism, secondary metabolites such as flavone and flavonol biosynthesis and phenylpropanoid biosynthesis, ABC transporters, and nitrogen metabolism.Conclusions: In general, the results revealed that there are three major mechanisms involved in NO-mediated Cd detoxification in tall fescue, including (a) antioxidant capacity enhancement; (b) accumulation of secondary metabolites related to cadmium chelation and sequestration; and (c) regulation of cadmium ion transportation, such as ABC transporter activation. In conclusion, this study provides new insights into the NO-mediated cadmium stress response.

scholarly journals Characterization of the microRNA Expression Profiles in the Goat Kid Liver

2022 ◽  
Vol 12 ◽  
Author(s):  
Xiaodong Zhao ◽  
Zhibin Ji ◽  
Rong Xuan ◽  
Aili Wang ◽  
Qing Li ◽  
...  
Keyword(s):  
Differential Expression ◽  
Fatty Acid Synthase ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Metabolic Process ◽  
Liver Development ◽  
Hormone Synthesis ◽  
Liver Tissues

The liver is the largest digestive gland in goats with an important role in early metabolic function development. MicroRNAs (miRNA) are crucial for regulating the development and metabolism in the goat liver. In the study, we sequenced the miRNAs in the liver tissues of the goat kid to further research their regulation roles in early liver development. The liver tissues were procured at 5-time points from the Laiwu black goats of 1 day (D1), 2 weeks (W2), 4 weeks (W4), 8 weeks (W8), and 12 weeks (W12) after birth, respectively with five goats per time point, for a total of 25 goats. Our study identified 214 differential expression miRNAs, and the expression patterns of 15 randomly selected miRNAs were examined among all five age groups. The Gene ontology annotation results showed that differential expression miRNA (DE miRNA) target genes were significantly enriched in the fatty acid synthase activity, toxin metabolic process, cell surface, and antibiotic metabolic process. The KEGG analysis result was significantly enriched in steroid hormone synthesis and retinol metabolism pathways. Further miRNA-mRNA regulation network analysis reveals 9 differently expressed miRNA with important regulation roles. Overall, the DE miRNAs were mainly involved in liver development, lipid metabolism, toxin related metabolism-related biological process, and pathways. Our results provide new information about the molecular mechanisms and pathways in the goat kid liver development.

scholarly journals iTRAQ-Based Quantitative Proteome Revealed Metabolic Changes in Winter Turnip Rape (Brassica rapa L.) under Cold Stress

2018 ◽  
Vol 19 (11) ◽  
pp. 3346 ◽  
Author(s):  
Yaozhao Xu ◽  
Xiucun Zeng ◽  
Jian Wu ◽  
Fenqin Zhang ◽  
Caixia Li ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Cold Stress ◽  
Brassica Rapa ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Pentose Phosphate ◽  
Metabolic Process ◽  
Cellular Process ◽  
Turnip Rape

Winter turnip rape (Brassica rapa L.) is a large-scale winter-only oil crop cultivated in Northwest China. However, its cold-resistant molecular mechanism remains inadequate. Studying the cold adaptation mechanisms of winter turnip rape based on the proteomic technique of isobaric tags for relative and absolute quantification (iTRAQ) offers a solution to this problem. Under cold stress (−4 °C for eight hours), 51 and 94 differently accumulated proteins (DAPs) in Longyou 7 (cold-tolerant) and Tianyou 4 (cold-sensitive) were identified, respectively. These DAPs were classified into 38 gene ontology (GO) term categories, such as metabolic process, cellular process, catalytic activity, and binding. The 142 DAPs identified between the two cold-stressed cultivars were classified into 40 GO terms, including cellular process, metabolic process, cell, catalytic activity, and binding. Kyoto Encyclopedia of Genes and Genomes enrichment analysis indicated that the DAPs participated in 10 pathways. The abundance of most protein functions in ribosomes, carbon metabolism, photosynthesis, and energy metabolism including the citrate cycle, pentose phosphate pathway, and glyoxylate and dicarboxylate metabolism decreased, and the proteins that participate in photosynthesis–antenna and isoflavonoid biosynthesis increased in cold-stressed Longyou 7 compared with those in cold-stressed Tianyou 4. The expression pattern of genes encoding the 10 significant DAPs was consistent with the iTRAQ data. This study provides new information on the proteomic differences between the leaves of Longyou 7 and Tianyou 4 plants and explains the possible molecular mechanisms of cold-stress adaptation in B. rapa.

The surface (S-) layer is a virulence factor of Bacteroides forsythus

Microbiology ◽  
2003 ◽  
Vol 149 (12) ◽  
pp. 3617-3627 ◽  
Author(s):  
M. Sabet ◽  
S.-W. Lee ◽  
R. K. Nauman ◽  
T. Sims ◽  
H.-S. Um
Keyword(s):  
Virulence Factor ◽  
Systemic Disease ◽  
Periodontal Pathogen ◽  
Whole Cells ◽  
Virulence Potential ◽  
Transmission Electron ◽  
Immunization Study ◽  
Antibody Inhibition

Bacteroides forsythus has emerged as a crucial periodontal pathogen with possible implications for systemic disease. The aim of this study was to isolate the S-layer from B. forsythus and examine its virulence potential as a part of efforts to characterize virulence factors of B. forsythus. The role of the S-layer in the haemagglutinating and adherent/invasive activities was evaluated. It was observed that the S-layer alone was able to mediate haemagglutination. In adherent and invasive studies, transmission electron microscopy clearly revealed that B. forsythus cells were able to attach to and invade KB cells, showing the formation of a microvillus-like extension around adherent and intracellular bacteria. The quantitative analysis showed that five different B. forsythus strains exhibited attachment (1·9–2·3 %) and invasion (0·4–0·7 %) capabilities. It was also observed through antibody inhibition assays that adherent/invasive activities of B. forsythus are mediated by the S-layer. Furthermore, an in vivo immunization study adopting a murine abscess model was used to prove that the S-layer is involved in the infectious process of abscess formation. While mice immunized with purified S-layer and B. forsythus whole cells did not develop any abscesses when challenged with viable B. forsythus cells, unimmunized mice developed abscesses. Collectively, the data obtained from these studies indicate that the S-layer of B. forsythus is a virulence factor.

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