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Angewandte Chemie (International Ed. in... Nov 2019An accurate, rapid, and cost-effective biosensor for the quantification of disease biomarkers is vital for the development of early-diagnostic point-of-care systems. The...
An accurate, rapid, and cost-effective biosensor for the quantification of disease biomarkers is vital for the development of early-diagnostic point-of-care systems. The recent discovery of the trans-cleavage property of CRISPR type V effectors makes CRISPR a potential high-accuracy bio-recognition tool. Herein, a CRISPR-Cas12a (cpf1) based electrochemical biosensor (E-CRISPR) is reported, which is more cost-effective and portable than optical-transduction-based biosensors. Through optimizing the in vitro trans-cleavage activity of Cas12a, E-CRIPSR was used to detect viral nucleic acids, including human papillomavirus 16 (HPV-16) and parvovirus B19 (PB-19), with a picomolar sensitivity. An aptamer-based E-CRISPR cascade was further designed for the detection of transforming growth factor β1 (TGF-β1) protein in clinical samples. As demonstrated, E-CRISPR could enable the development of portable, accurate, and cost-effective point-of-care diagnostic systems.
Topics: Acidaminococcus; Aptamers, Nucleotide; Biosensing Techniques; CRISPR-Cas Systems; DNA Cleavage; DNA, Viral; Electrochemical Techniques; Electrodes; Human papillomavirus 16; Humans; Immobilized Nucleic Acids; Limit of Detection; Mesenchymal Stem Cells; Parvovirus; Sensitivity and Specificity; Surface Properties; Transforming Growth Factor beta1
PubMed: 31568601
DOI: 10.1002/anie.201910772 -
Nature Communications May 2022Combinatorial CRISPR technologies have emerged as a transformative approach to systematically probe genetic interactions and dependencies of redundant gene pairs....
Combinatorial CRISPR technologies have emerged as a transformative approach to systematically probe genetic interactions and dependencies of redundant gene pairs. However, the performance of different functional genomic tools for multiplexing sgRNAs vary widely. Here, we generate and benchmark ten distinct pooled combinatorial CRISPR libraries targeting paralog pairs to optimize digenic knockout screens. Libraries composed of dual Streptococcus pyogenes Cas9 (spCas9), orthogonal spCas9 and Staphylococcus aureus (saCas9), and enhanced Cas12a from Acidaminococcus were evaluated. We demonstrate a combination of alternative tracrRNA sequences from spCas9 consistently show superior effect size and positional balance between the sgRNAs as a robust combinatorial approach to profile genetic interactions of multiple genes.
Topics: Acidaminococcus; CRISPR-Cas Systems; RNA, Guide, CRISPR-Cas Systems; Staphylococcus aureus; Streptococcus pyogenes
PubMed: 35513429
DOI: 10.1038/s41467-022-30196-9 -
International Journal of Systematic and... Oct 2007Eleven strains of a hitherto unknown, Gram-negative, anaerobic coccus were recovered from various human clinical samples of patients hospitalized in two geographically...
Eleven strains of a hitherto unknown, Gram-negative, anaerobic coccus were recovered from various human clinical samples of patients hospitalized in two geographically distant French hospitals. These strains displayed the morphology and growth characteristics of those related to the genus Acidaminococcus. The clinical isolates shared at least 99.9 and 99.7 % of their nucleotide positions in the 16S and 23S rRNA gene sequences, respectively. They displayed 95.6 and 88.9 % 16S and 23S rRNA gene sequence similarities, respectively, with Acidaminococcus fermentans. The 16S rRNA-based phylogeny revealed that all the clinical isolates grouped in a statistically well supported cluster separate from A. fermentans. Enzymic activity profiles as well as metabolic end product patterns, including propionic acid production, differentiated the novel bacteria from A. fermentans. Finally, phenotypic, genotypic and phylogenetic data, including large-scale chromosome structure and DNA G+C content, supported the proposal of a novel species of the genus Acidaminococcus, for which the name Acidaminococcus intestini sp. nov. is proposed. The type strain is ADV 255.99(T) (=AIP 283.01(T)=CIP 108586(T)=CCUG 50930(T)).
Topics: Acidaminococcus; Adolescent; Adult; Aged; Aged, 80 and over; Anaerobiosis; Bacterial Proteins; Bacterial Typing Techniques; Base Composition; Chromosomes, Bacterial; DNA, Bacterial; DNA, Ribosomal; Enzymes; Female; France; Genes, rRNA; Gram-Negative Bacterial Infections; Humans; Male; Middle Aged; Molecular Sequence Data; Phylogeny; RNA, Bacterial; RNA, Ribosomal, 16S; RNA, Ribosomal, 23S; Sequence Analysis, DNA; Sequence Homology, Nucleic Acid
PubMed: 17911303
DOI: 10.1099/ijs.0.64883-0 -
New Microbes and New Infections Jan 2017We report here the main characteristics of strain Marseille-P2764, isolated from human right colon, and strain Marseille-P2828, isolated from human duodenum.
We report here the main characteristics of strain Marseille-P2764, isolated from human right colon, and strain Marseille-P2828, isolated from human duodenum.
PubMed: 28018604
DOI: 10.1016/j.nmni.2016.11.010 -
The Journal of Biological Chemistry 2021Electron bifurcation uses free energy from exergonic redox reactions to power endergonic reactions. β-FAD of the electron transfer flavoprotein (EtfAB) from the...
Electron bifurcation uses free energy from exergonic redox reactions to power endergonic reactions. β-FAD of the electron transfer flavoprotein (EtfAB) from the anaerobic bacterium Acidaminococcus fermentans bifurcates the electrons of NADH, sending one to the low-potential ferredoxin and the other to the high-potential α-FAD semiquinone (α-FAD). The resultant α-FAD hydroquinone (α-FADH) transfers one electron further to butyryl-CoA dehydrogenase (Bcd); two such transfers enable Bcd to reduce crotonyl-CoA to butyryl-CoA. To get insight into the mechanism of these intricate reactions, we constructed an artificial reaction only with EtfAB containing α-FAD or α-FAD to monitor formation of α-FAD or α-FADH, respectively, using stopped flow kinetic measurements. In the presence of α-FAD, we observed that NADH transferred a hydride to β-FAD at a rate of 920 s, yielding the charge-transfer complex NAD:β-FADH with an absorbance maximum at 650 nm. β-FADH bifurcated one electron to α-FAD and the other electron to α-FAD of a second EtfAB molecule, forming two stable α-FAD. With α-FAD, the reduction of β-FAD with NADH was 1500 times slower. Reduction of β-FAD in the presence of α-FAD displayed a normal kinetic isotope effect (KIE) of 2.1, whereas the KIE was inverted in the presence of α-FAD. These data indicate that a nearby radical (14 Å apart) slows the rate of a hydride transfer and inverts the KIE. This unanticipated flavin chemistry is not restricted to Etf-Bcd but certainly occurs in other bifurcating Etfs found in anaerobic bacteria and archaea.
Topics: Acidaminococcus; Bacterial Proteins; Electron Transport; Electron-Transferring Flavoproteins; Flavins; Kinetics; Oxidation-Reduction; Phylogeny
PubMed: 33239361
DOI: 10.1074/jbc.RA120.016017 -
European Journal of Biochemistry Aug 19811. Glutaconate CoA-transferase catalyses the transfer of CoAS- from acetyl-CoA preferentially to (E)-glutaconate, but glutarate, (R)-2-hydroxyglutarate, acrylate and...
1. Glutaconate CoA-transferase catalyses the transfer of CoAS- from acetyl-CoA preferentially to (E)-glutaconate, but glutarate, (R)-2-hydroxyglutarate, acrylate and propionate are also good acceptors. No reaction was observed with (Z)-glutaconate and C4-dicarboxylic acids. 2. The product of the reaction of acetyl-CoA with (E)-glutaconate is the 1-isomer of glutaconyl-CoA, i.e. the thiol ester is conjugated with the double bond. Other results indicate, however, that with (R)-2-hydroxyglutarate as substrate both possible isomers are generated. 3. Glutaconate CoA-transferase was purified from cell-free extracts of Acidaminococcus fermentans to apparent homogeneity and crystallized. The relative molecular mass of the enzyme is approximately 275000. It consists of two different polypeptide chains (M, 32000 and 34000). On the catalytic pathway a thiolester is formed between CoASH and a carboxylate of the smaller polypeptide chain. 4. The structural and functional relationships between glutaconate CoA-transferase and other CoA-transferases are discussed. 5. Glutaconate CoA-transferase is also present in other bacteria fermenting glutamate via hydroxyglutarate. Experiments with an antiserum against the enzyme indicate that the transferase is necessary for the decarboxylation of glutaconate but not for the dehydration of (R)-2-hydroxyglutarate.
Topics: Acyl Coenzyme A; Coenzyme A; Coenzyme A-Transferases; Crystallization; Glutarates; Gram-Negative Anaerobic Bacteria; Kinetics; Molecular Weight; Substrate Specificity; Sulfhydryl Reagents; Sulfurtransferases
PubMed: 6945182
DOI: 10.1111/j.1432-1033.1981.tb06404.x -
European Journal of Clinical Nutrition Dec 2022Intrauterine environment can influence the offspring's body adiposity whose distribution affect the cardiometabolic risk. Underlying mechanisms may involve the gut...
UNLABELLED
Intrauterine environment can influence the offspring's body adiposity whose distribution affect the cardiometabolic risk. Underlying mechanisms may involve the gut microbiome. We investigated associations of gestational weight gain with the adult offspring's gut microbiota, body adiposity and related parameters in participants of the Nutritionists' Health Study.
METHODS
This cross-sectional analysis included 114 women who had early life and clinical data, body composition, and biological samples collected. The structure of fecal microbiota was analyzed targeting the V4 region of the 16 S rRNA gene. Beta diversity was calculated by PCoA and PERMANOVA used to test the impact of categorical variables into the diversity. Bacterial clusters were identified based on the Jensen-Shannon divergence matrix and Calinski-Harabasz index. Correlations were tested by Spearman coefficient.
RESULTS
Median age was 28 (IQR 24-31) years and BMI 24.5 (IQR 21.4-28.0) kg/m. Fifty-eight participants were assigned to a profile driven by Prevotella and 56 to another driven by Blautia. Visceral adipose tissue was correlated to abundance of Acidaminococcus genus considering the entire sample (r = 0.37; p < 0.001) and the profiles (Blautia: r = 0.35, p = 0.009, and Prevotella: r = 0.38, p = 0.006). In Blautia-driven profile, the same genus was also correlated to maternal gestational weight gain (r = 0.38, p = 0.006).
CONCLUSIONS
Association of Acidaminococcus with gestational weight gain could reinforce the relevance with mothers' nutritional status for gut colonization at the beginning of life. Whether Acidaminococcus abundance could be a marker for central distribution of adiposity in young women requires further investigation.
Topics: Adult; Humans; Female; Gestational Weight Gain; Adiposity; Acidaminococcus; Body Mass Index; Cross-Sectional Studies; Adult Children; Obesity, Abdominal; Obesity
PubMed: 35906333
DOI: 10.1038/s41430-022-01182-7 -
FEMS Microbiology Letters Oct 1992The phylogenetic position of Acidaminococcus fermentans was determined by comparative sequence analysis of the 16S rRNA. This Gram-negative bacterium is a member of the...
The phylogenetic position of Acidaminococcus fermentans was determined by comparative sequence analysis of the 16S rRNA. This Gram-negative bacterium is a member of the Sporomusa cluster that is defined by other Gram-negative bacteria, i.e. Sporomusa, Megasphaera, Selenomonas, Butyrivibrio, Pectinatus, and Zymophilus. The branching point of this group within the radiation of Gram-positive bacteria of the Clostridium/Bacillus subphylum and adjacent to Peptococcus niger could be confirmed. Chemotaxonomic data were provided for a more detailed characterization of A. fermentans.
Topics: Amino Acids, Diamino; Carbohydrates; Cell Wall; Phylogeny; RNA, Bacterial; RNA, Ribosomal, 16S; Veillonellaceae
PubMed: 1385264
DOI: 10.1016/0378-1097(92)90355-r -
Applied Microbiology Jan 1974Fecal bacterial cultures from 40 normal humans yielded Megasphaera elsdenii from four individuals and Acidaminococcus fermentans from 10 individuals, with two...
Fecal bacterial cultures from 40 normal humans yielded Megasphaera elsdenii from four individuals and Acidaminococcus fermentans from 10 individuals, with two individuals having both organisms.
Topics: Anaerobiosis; Bacteria; Bacteriological Techniques; Cell Count; Feces; Humans
PubMed: 4589136
DOI: 10.1128/am.27.1.274-275.1974 -
International Journal of Systematic... Jul 1994Ruminal fluid which was enriched with trans-aconitate yielded a gram-negative diplococcus (strain AO) which was identified by 16S ribosomal DNA sequence analysis as... (Comparative Study)
Comparative Study
Ruminal fluid which was enriched with trans-aconitate yielded a gram-negative diplococcus (strain AO) which was identified by 16S ribosomal DNA sequence analysis as Acidaminococcus fermentans. In contrast to the original description, the A. fermentans type strain and strain AO were found to utilize citrate as an energy source and to produce hydrogen and hydrogen sulfide. The descriptions of the genus and species are emended accordingly.
Topics: Aconitic Acid; Animals; Cattle; Citrates; Citric Acid; DNA, Bacterial; DNA, Ribosomal; Gram-Negative Anaerobic Bacteria; Molecular Sequence Data; Oxidation-Reduction; Rumen; Species Specificity
PubMed: 8068544
DOI: 10.1099/00207713-44-3-576