scholarly journals Insights from shotgun metagenomics into bacterial species and metabolic pathways associated with NAFLD in obese youth

2021 ◽  
Author(s):  
Todd Testerman ◽  
Zhongyao Li ◽  
Brittany Galuppo ◽  
Joerg Graf ◽  
Nicola Santoro
Keyword(s):  
Amino Acid ◽  
Bacterial Species ◽  
Energy Utilization ◽  
Negative Group ◽  
Healthy Individuals ◽  
Shotgun Metagenomics ◽  
Positive Group ◽  
Obese Youth ◽  
Branched Chain ◽  
Metagenome Sequencing

Abstract Background and Aims NAFLD is the most common form of liver disease and is often the precursor for more serious liver conditions such as NASH and cirrhosis. The gut microbiome has been implicated in the development of NAFLD, but studies have often compared healthy individuals to those with the disease. In this study, we aimed to examine the taxonomic and functional differences between the microbiomes of obese youth with and without NAFLD. Approach and Results Shotgun metagenome sequencing was used to profile the microbial communities of 36 subjects, half of which were diagnosed with NAFLD. Beta diversity analysis showed community-wide differences between the cohorts (p = 0.002). Specific taxonomic differences included the species Fusicatenibacter saccharivorans (p = 0.042), Romboutsia ilealis (p = 0.046), and Actinomyces sp. ICM47 (p = 0.0009) elevated in the NAFLD-positive group and Bacteroides thetaiotamicron (p = 0.0002) elevated in the NAFLD-negative group. At the phylum level, Bacteroidetes (p < 0.0001) was elevated in the NAFLD-negative group. Functionally, branched chain amino acid (p = 0.01343) and aromatic amino acid (p = 0.01343) synthesis pathways were elevated in the NAFLD-positive group along with numerous energy utilization pathways including pyruvate fermentation to acetate (p = 0.01318). Conclusions The link between obesity and NAFLD development in younger individuals has rarely been probed, with most studies focusing on adults and comparing healthy individuals with obese, NAFLD-positive individuals. This study supports the idea that the NAFLD phenotype displays a differentiated microbial and functional signature from the obesity phenotype.

scholarly journals Genotypic identification of presumptive Streptococcus pneumoniae by PCR using four genes highly specific for S. pneumoniae

2006 ◽  
Vol 55 (6) ◽  
pp. 709-714 ◽  
Author(s):  
Nao Suzuki ◽  
Mayumi Yuyama ◽  
Sinsaku Maeda ◽  
Haruhiko Ogawa ◽  
Kazuyuki Mashiko ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Screening Method ◽  
Pcr Amplification ◽  
Oligonucleotide Primer ◽  
Healthy Children ◽  
Negative Group ◽  
Healthy Individuals ◽  
Positive Group ◽  
Genotypic Identification ◽  
Primer Sets

It was previously reported that two oligonucleotide primer sets (spn9802 and spn9828) for discriminating Streptococcus pneumoniae from pneumococcus-like oral streptococcal isolates using PCR had been developed. In this study, PCR amplification of the lytA, ply, spn9802 and spn9828 genes was used to identify presumptive S. pneumoniae. Two genetic groups were identified by analysing sputum samples from 28 patients with community-acquired pneumonia: the lytA-positive, ply-positive, spn9802-positive and spn9828-negative group, and the lytA-positive, ply-positive, spn9802-positive and spn9828-positive group. Isolates of the former group were resistant to optochin, while those of the latter group showed susceptibility to optochin. The lytA-positive, ply-positive, spn9802-negative and spn9828-negative isolates, and lytA-positive, ply-positive, spn9802-negative and spn9828-positive isolates, were not detected in sputum from patients with pneumonia. Subsequently, a total of 92 saliva samples from healthy individuals was screened by PCR using these primer sets. The lytA-positive, ply-positive, spn9802-positive and spn9828-negative group was identified more frequently in saliva from healthy children than in saliva from older healthy individuals and patients with pneumonia. The lytA-positive, ply-positive, spn9802-positive and spn9828-positive group was found frequently in saliva from healthy children, and in saliva and sputum from patients with pneumonia. This study demonstrates a rapid, optimal screening method for the genotypic identification of presumptive S. pneumoniae by PCR using four genes highly specific for S. pneumoniae.

Linkage between H. pylori Infection and TNF-α polymorphism in The Pregnant Women

2018 ◽  
Vol 9 (SPL1) ◽  
Author(s):  
Ghaidaa Raheem Lateef ◽  
Azhar Omaran Al-Thahab
Keyword(s):  
Pregnant Women ◽  
Serum Antibody ◽  
Rapid Test ◽  
Negative Group ◽  
Positive Group ◽  
Gynecology And Obstetrics ◽  
Tnf Α ◽  
Significant Difference ◽  
Pcr Products ◽  
H Pylori

A study was performed on 100 pregnant women in the outpatient department of gynecology and obstetrics of Maternity and Children Hospital in Al-Diwaniya City during the period between (March to September 2016). One hundred blood samples (50 for patients and 50 for control) were collected under the supervision of the treating gynecologist. The detection of Helicobacter. pylori was done by the use of the serum antibody Rapid test. The results showed that 50 (100%) were positive and 50 (100%) were negative for H. pylori in above method.All blood of patients and control samples were used for the extraction of genomic DNA,where the 107 bp PCR product size. Genotyping of the TNF-α-308 SNP (G/A)was performed by restriction fragment length polymorphism PCR (RFLP-PCR). PCR products were digested with restr NcoI iction enzyme. Individuals with the TNF-α-308(GG) homozygote produced digested DNA bands at 80,and 20 bp bp. A heterozygous genotype ofTNF-α-308 (GA)produced 107 bp,80 bp,and 20 bp bands. Individuals with the TNF-α-308 (AA) homozygote genotype had no amplicon digested and generated only one band of 107 bp. There was a significant difference in the frequency of the TNF-α-308(GG)genotype between H. pylori positive group and H. pylori negative group(72%,78% respectively). Also for GA genotype,there was a significant difference between H. pylori positive group and H. pylori negative group(24%,18% respectively). Concerning the frequency of the TNF-α-308 (AA)genotype between H. pylori positive group and H. pylori negative group,there was no significant difference between the two groups.

Amino Acids Sequence-based Analysis of Arginine Deiminase from Different Prokaryotic Organisms: An In Silico Approach

2020 ◽  
Vol 14 (3) ◽  
pp. 235-246
Author(s):  
Sara Abdollahi ◽  
Mohammad H. Morowvat ◽  
Amir Savardashtaki ◽  
Cambyz Irajie ◽  
Sohrab Najafipour ◽  
...  
Keyword(s):  
Amino Acid ◽  
Physicochemical Properties ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
In Silico ◽  
Bacterial Species ◽  
Arginine Deiminase ◽  
Antitumor Effects ◽  
Multiple Sequence ◽  
In Silico Studies

Background: Arginine deiminase is a bacterial enzyme, which degrades L-arginine. Some human cancers such as hepatocellular carcinoma (HCC) and melanoma are auxotrophic for arginine. Therefore, PEGylated arginine deiminase (ADI-PEG20) is a good anticancer candidate with antitumor effects. It causes local depletion of L-arginine and growth inhibition in arginineauxotrophic tumor cells. The FDA and EMA have granted orphan status to this drug. Some recently published patents have dealt with this enzyme or its PEGylated form. Objective: Due to increasing attention to it, we aimed to evaluate and compare 30 arginine deiminase proteins from different bacterial species through in silico analysis. Methods: The exploited analyses included the investigation of physicochemical properties, multiple sequence alignment (MSA), motif, superfamily, phylogenetic and 3D comparative analyses of arginine deiminase proteins thorough various bioinformatics tools. Results: The most abundant amino acid in the arginine deiminase proteins is leucine (10.13%) while the least amino acid ratio is cysteine (0.98%). Multiple sequence alignment showed 47 conserved patterns between 30 arginine deiminase amino acid sequences. The results of sequence homology among 30 different groups of arginine deiminase enzymes revealed that all the studied sequences located in amidinotransferase superfamily. Based on the phylogenetic analysis, two major clusters were identified. Considering the results of various in silico studies; we selected the five best candidates for further investigations. The 3D structures of the best five arginine deiminase proteins were generated by the I-TASSER server and PyMOL. The RAMPAGE analysis revealed that 81.4%-91.4%, of the selected sequences, were located in the favored region of arginine deiminase proteins. Conclusion: The results of this study shed light on the basic physicochemical properties of thirty major arginine deiminase sequences. The obtained data could be employed for further in vivo and clinical studies and also for developing the related therapeutic enzymes.

Potential application of dynamic contrast enhanced ultrasound in predicting microvascular invasion of hepatocellular carcinoma

2021 ◽  
pp. 1-9
Author(s):  
Yi Dong ◽  
Yijie Qiu ◽  
Daohui Yang ◽  
Lingyun Yu ◽  
Dan Zuo ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Area Under The Curve ◽  
Microvascular Invasion ◽  
Contrast Enhanced Ultrasound ◽  
Negative Group ◽  
Clinical Value ◽  
Positive Group ◽  
Quantitative Perfusion ◽  
Dynamic Contrast Enhanced ◽  
Contrast Enhanced

OBJECTIVE: To investigate the clinical value of dynamic contrast enhanced ultrasound (D-CEUS) in predicting the microvascular invasion (MVI) of hepatocellular carcinoma (HCC). PATIENTS AND METHODS: In this retrospective study, 16 patients with surgery and histopathologically proved HCC lesions were included. Patients were classified according to the presence of MVI: MVI positive group (n = 6) and MVI negative group (n = 10). Contrast enhanced ultrasound (CEUS) examinations were performed within a week before surgery. Dynamic analysis was performed by VueBox ® software (Bracco, Italy). Three regions of interests (ROIs) were set in the center of HCC lesions, at the margin of HCC lesions and in the surrounding liver parenchyma accordingly. Time intensity curves (TICs) were generated and quantitative perfusion parameters including WiR (wash-in rate), WoR (wash-out rate), WiAUC (wash-in area under the curve), WoAUC (wash-out area under the curve) and WiPi (wash-in perfusion index) were obtained and analyzed. RESULTS: All of HCC lesions showed arterial hyperenhancement (100 %) and at the late phase as hypoenhancement (75 %) in CEUS. Among all CEUS quantitative parameters, the WiAUC and WoAUC were higher in MVI positive group than in MVI negative group in the center HCC lesions (P <  0.05), WiAUC, WoAUC and WiPI were higher in MVI positive group than in MVI negative group at the margin of HCC lesions. WiR and WoR were significant higher in MVI positive group. CONCLUSIONS: D-CEUS with quantitative perfusion analysis has potential clinical value in predicting the existence of MVI in HCC lesions.

Need for Confirmatory Neutralization Tests for Hepatitis B Surface Antigen Tests in Populations with Intermediate Prevalence

2021 ◽  
Author(s):  
Min Young Lee ◽  
So Young Kang ◽  
Woo In Lee ◽  
Myeong Hee Kim
Keyword(s):  
Hepatitis B ◽  
Surface Antigen ◽  
Neutralization Test ◽  
Hepatitis B Surface Antigen ◽  
False Negative ◽  
Confirmatory Test ◽  
Negative Group ◽  
Positive Group ◽  
Test Kit ◽  
Antigen Tests

Abstract Objective Hepatitis B surface antigen (HBsAg) is known as the hallmark of hepatitis B virus (HBV) infection. This study aimed to determine whether an HBsAg neutralization test is necessary to accurately interpret HBsAg test results. Methods Initially reactive HBsAg specimens from a 5-year period, with cutoff index values between 1.0 and 2.0, were subjected to neutralization confirmatory testing using an Elecsys HBsAg Confirmatory test kit (Roche Diagnostics GmbH. Mannheim, Germany). Results The neutralization test showed 46.1% positive (confirmed positive group) and 53.9% negative (confirmed negative group) results from the total specimens. Among the confirmed negative group, 79.5% of patients were confirmed to be negative for the current infection, whereas 4 patients in the chronic hepatitis B subgroup showed a neutralization percentage close to 40%. More than half of patients in the confirmed positive group were considered to be in the hepatitis B e antigen-negative inactive HBsAg carrier phase. Conclusion In populations with intermediate HBV prevalence, a neutralization test is necessary to confirm an HBsAg result and reduce the false positive and false negative rates of initial HBsAg tests.

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