human sfb  (Biotechnology Information)

Journal: Nature Communications

Article Title: Segmented filamentous bacteria are worldwide human gut commensals

doi: 10.1038/s41467-026-70010-4

Figure Lengend Snippet: Analysis of fecal samples from bioproject PRJNA234437. a Maximum likelihood phylogenetic tree of 16S rRNA gene sequences from SFB from various hosts; includes Clostridium outgroup species (italic). Tree includes bootstrap values, and the scale is nucleotide substitutions per nucleotide position. Sequences are trimmed to the 16S rRNA gene 1470 bp position but includes shorter sequences, including only the V1-V4 region for mackerel, pinfish, macaque, and shorebird (Supplementary Fig. ). b Percent nucleotide identities across SFB 16S rRNA gene sequences of 1366 bp in length from various hosts (Supplementary Fig. ). c Gram stain of Mouse-SFB-NL from the intestinal content of monocolonized mice. Highlights SFB filament sections that are c (i/ii) thin and smooth with c (i) long primary and c (ii) short secondary segments, as well as c (iii) thick and bulbous sections characteristic of differentiation, and c (iv) a filament section containing spores. d Gram stain of The Gambia (GM) sample 102358 from a non-diarrheal control group child showing a complete filament and zooms (z) to the (z1) smooth filament end; (z2) smooth to bulbous transition; (z3) heavily de-stained bulbous segments towards filament end with crystal violet staining reminiscent of intracellular offsprings; and (z4) white unstained spores at filament end. (z1-z4) Arrows highlight the various features. e Schematic representation of inferred SFB filament stages. f Gram stain of a disintegrating filament in The Gambia sample 102358 with large oval spores at filament end, including a zoom to highlight spores. g Gram stain of the Kenya (KE) sample 401080 from a non-dysentery diarrheal group child showing a filament with a zoom (z1) to the thin, apparently tip-like, end and (z2) to the bulbous filament end. h Gram stains of the Mali (ML) sample 200340 (S340, Human-SFB-ML-1) from a non-diarrheal control group child, including h (i) a filament with a zoom to the characteristically (z1) thin and (z2) bulbous phenotype of SFB, and h (ii) a filament with spores at one end, highlighted with a black arrow. i Gram stain of the Mali sample 200195 (S195, Human-SFB-ML-2) from a non-dysentery diarrheal group child showing filamentous bacteria and a zoom (z) of one filament. a , b , d – i Labeling includes the two-letter country codes of the sample of origin, except YIT, which also originated from Japan. Images in ( d ) and ( g ) include increased bilinear interpolation for clarity.

Article Snippet: The raw sequencing files and the metagenome-assembled genomes (MAGs) for Human-SFB-ML-1 and ML-2 generated in this study have been deposited in the National Center for Biotechnology Information (NCBI) database under bioproject PRJNA1106451 and includes the genome assemblies with accession numbers JBRACM000000000 (Human-SFB-ML-1) and JBRACM000000001 (Human-SFB-ML-2).

Techniques: Staining, Control, Bacteria, Labeling

Journal: Nature Communications

Article Title: Segmented filamentous bacteria are worldwide human gut commensals

doi: 10.1038/s41467-026-70010-4

Figure Lengend Snippet: a , b Fluorescent in situ hybridization of the ML-1 fecal sample showing staining with a , b (i) the SFB-specific (green) and eubacterial (EUB338) (red) 16S rDNA probes or a , b (ii) only the SFB-specific eubacterial probe in black and white. a Image with two SFB filaments, including a zoom (z) in brightfield highlighting the smooth (white arrow) and bulbous (black arrow) morphology of the filament. b Image with an SFB filament of uneven thickness, a potential SFB filament fragment, and two small SFB highlighted (z1/z2) in both color and, for the SFB probe only, in black and white. The small SFB has an apparent teardrop-shaped morphology (white arrows). Images in (z1/z2) include increased bilinear interpolation for clarity. c SEM images c (i/ii) of the Human-SFB-ML-1 (non-diarrheal) fecal sample showing the smooth end and of a filament with zooms to the characteristically SFB tip structure, and for l (ii) also a zoom of filament thickening. d SEM images (i/ii) of the Human-SFB-ML-2 (diarrheal) fecal sample showing disintegrating filaments with zooms of the tip structure. e SEM images of the Human-SFB-ML-1 fecal sample showing e (i/ii) filaments with a contrasting smooth and bulbous morphology along the filament with zooms of opposite filament ends included for ( e (i)); e (iii) a filament with a characteristic segmented phenotype of SFB, and e (iv) a filament, including a zoom, with an irregular and large bulbous segmented phenotype similar to the spore-containing filament segment in the Gram stains of Fig. and Fig. .

Article Snippet: The raw sequencing files and the metagenome-assembled genomes (MAGs) for Human-SFB-ML-1 and ML-2 generated in this study have been deposited in the National Center for Biotechnology Information (NCBI) database under bioproject PRJNA1106451 and includes the genome assemblies with accession numbers JBRACM000000000 (Human-SFB-ML-1) and JBRACM000000001 (Human-SFB-ML-2).

Techniques: In Situ Hybridization, Staining

Journal: Nature Communications

Article Title: Segmented filamentous bacteria are worldwide human gut commensals

doi: 10.1038/s41467-026-70010-4

Figure Lengend Snippet: a Schematic of the components of the glycogen and starch utilization module identified in the Human-SFB-ML genomes. Includes the gene locus tags for Human-SFB-ML-1 (S340) and 2 (S195) for reference. b Sugar-binding affinities of Human-SFB-ML MdxE showing the results for each substrate from two independent experiments for a single purified protein sample. Carbohydrates with a α-(1,4) linkage of glucose subunits are colored in black when linear and gray when circular; Trehalose and isomaltose are dimers of glucose with a α-(1,1) and α-(1,6) linkage, respectively. c Schematic of the biosynthetic pathways for polyamines. Predicted enzymes present in all eight genomes are in green, a Orn/Lys/Arg decarboxylase predicted to be present in all genomes but whose substrate specificity is unclear is in black, and the enzyme predicted to be present only in the Human-SFB-ML genomes is in red. Polyamines are shaded in gray.

Article Snippet: The raw sequencing files and the metagenome-assembled genomes (MAGs) for Human-SFB-ML-1 and ML-2 generated in this study have been deposited in the National Center for Biotechnology Information (NCBI) database under bioproject PRJNA1106451 and includes the genome assemblies with accession numbers JBRACM000000000 (Human-SFB-ML-1) and JBRACM000000001 (Human-SFB-ML-2).

Techniques: Starch, Binding Assay, Purification

Journal: Cell reports

Article Title: Protein-folding chaperones predict structure-function relationships and cancer risk in BRCA1 mutation carriers

doi: 10.1016/j.celrep.2024.113803

Figure Lengend Snippet: (A and B) BRCA1 mutations cataloged in ClinVar (accessed April 27, 2023). (A) Clinical significance of BRCA1 mutations grouped by mutation type. (B) Location of pathogenic missense mutations cataloged in ClinVar with at least a “two-gold-star” review status (n = 285). (C) C-terminal BRCA1 3×FLAG-tagged truncation construct used for LUMIER. The two BRCT subdomains are colored (orange and wheat). pSXXF denotes the BRCT binding phosphopeptide (BACH1). Protein Data Bank (PDB): 1T29. (D) LUMIER with BACON (bait control) approach to quantify chaperone interactions in HEK293T cells. Diagram was created with BioRender. (E) Chaperone binding to benign and pathogenic BRCA1-BRCT variants in ClinVar (including “likely” classifications). Z scores were calculated by averaging non-transfected wells to illustrate the significance of the data. Dashed line indicates the threshold for a statistically significant signal ( Z score > 2.5). Wild-type BRCA1-BRCT values are shown as green-filled triangles. Chaps, chaperones; Patho., pathogenic. (F) BRCA1-BRCT variant levels after pull-down detected by ELISA. (G) Variant ΔΔG values (kcal/mol) predicted by FoldX relative to the wild-type value (ΔΔG = 0). Dashed line indicates the threshold for structure disruption (ΔΔG > 2). (H) HSP70/HSP90 interaction preferences. Diagonal shows the identity line. The unknown group includes variants annotated as having uncertain significance, no significance provided, conflicting interpretations, or “one-gold-star” review status. FANCA variants and a frameshifted (fs) variant encoding an additional out-of-frame HSP70 site shown for comparison. Statistical significance was determined using two-tailed Mann-Whitney t test (E–G). ****p ≤ 0.0001. Data are presented as mean values from at least two independent experiments.

Article Snippet: Plasmids containing human BRCA1 cDNA were a gift from Junjie Chen (Addgene, Plasmid #99394).

Techniques: Mutagenesis, Construct, Binding Assay, Phospho-proteomics, Control, Transfection, Variant Assay, Enzyme-linked Immunosorbent Assay, Disruption, Comparison, Two Tailed Test, MANN-WHITNEY

Journal: Cell reports

Article Title: Protein-folding chaperones predict structure-function relationships and cancer risk in BRCA1 mutation carriers

doi: 10.1016/j.celrep.2024.113803

Figure Lengend Snippet: (A) Variants targeting secondary structure elements in the BRCA1-BRCT domain. (B) Y1845 variants that disrupt or support hydrophobic interactions. FoldX ΔΔG predictions for each variant are shown. (C) T1685 variants that disrupt or support side-chain hydrogen bonding. Two different T1685S codons were tested because these codons previously exhibited different functional effects. (D and E) Chaperone binding predictions to the BRCA1-BRCT variant library. The “disruptor” bin includes variants that introduce prolines in α-helices; truncations within the BRCT domain; buried variants that introduce a charge, decrease hydrophobicity, or create a steric clash; and charged variants that mutate residues in hydrophobic networks or disrupt side-chain hydrogen bonding. The “no effect” bin includes variants that fully delete the BRCT domain; variants outside the BRCT domain; buried variants that retain hydrophobicity; isosteric or quasi-isosteric variants; variants that maintain side-chain hydrogen bonds; and other surface variants not included prior. Dashed line indicates the cutoff for binding (HSP70 score > 0.5). (E) excluded variants previously characterized using protease sensitivity. Statistical significance was determined using a two-tailed Mann-Whitney t test. ****p ≤ 0.0001. Data are presented as mean ± standard deviation values from at least two independent experiments.

Article Snippet: Plasmids containing human BRCA1 cDNA were a gift from Junjie Chen (Addgene, Plasmid #99394).

Techniques: Variant Assay, Functional Assay, Binding Assay, Introduce, Two Tailed Test, MANN-WHITNEY, Standard Deviation

Journal: Cell reports

Article Title: Protein-folding chaperones predict structure-function relationships and cancer risk in BRCA1 mutation carriers

doi: 10.1016/j.celrep.2024.113803

Figure Lengend Snippet: (A and B) Correlation of HSP70 binding with BRCA1-BRCT variant stability. Horizontal dashed line is the average of four double variants that combine strongly chaperone-bound single variants. Vertical dashed line reflects the upper limit of stability measurements owing to variant insolubility. The correlations were fit to a linear regression within the linear regime (FoldX: < 10 kcal/mol, empirical: < 5 kcal/mol). G1788V was not fit because the stability measurement for this variant was previously reported as contradictory. (C and D) HSP70 binding binned according to the functional effect class measured using aggregation/degradation or transcriptional activation assays. (E) Linear correlation of HSP70 binding and variant levels (ELISA) at different concentrations of cell lysates pulled down. Dashed lines indicate the average LUMIER and ELISA signals observed under our standard assay conditions for variants that bound strongly to HSP70. (F and G) BRCA1 variant function in HAP1 (cell fitness) or HeLa (HDR) cells binned according to the degree of HSP70 binding. (H) Integrated functional data from neXtProt binned by the magnitude of HSP70 binding. Percentages calculated using the percentage of variants associated with each HSP70 binding magnitude and phenotype intensity. Func., functional. Statistical significance was determined using Kruskal-Wallis ANOVA test (C, D, F, and G) or chi-squared test (H). ****p ≤ 0.0001, **p ≤ 0.01, and *p ≤ 0.05. Data are presented as mean ± standard deviation values from at least two independent experiments.

Article Snippet: Plasmids containing human BRCA1 cDNA were a gift from Junjie Chen (Addgene, Plasmid #99394).

Techniques: Binding Assay, Variant Assay, Functional Assay, Activation Assay, Enzyme-linked Immunosorbent Assay, Standard Deviation

Journal: Cell reports

Article Title: Protein-folding chaperones predict structure-function relationships and cancer risk in BRCA1 mutation carriers

doi: 10.1016/j.celrep.2024.113803

Figure Lengend Snippet: (A) HSP70 interaction scores for natural human variants observed in patients with cancer (ClinVar and cBioPortal/TCGA , ) or the general population (gno-mAD ). Unknown (unk.) includes variants annotated as having uncertain significance, no significance provided, conflicting interpretations, or one-gold-star review status. (B) The functional severity , of natural BRCA1-BRCT variants grouped by the degree of HSP70 binding. LoF, loss of function. (C) HSP70 binding to natural BRCA1-BRCT human variants binned by the predicted effect on domain structure. Variants were ranked using an informed hierarchical approach (see ). Moderate HSP70-bound variants are colored magenta and overlaid onto the BRCT crystal structure. An example long-range interaction that coordinates the two BRCT subdomains is indicated with an arrow. Struct., structure. (D and E) ROC curves using pathogenicity annotated in ClinVar (D) or mode phenotypic intensity annotated in neXtProt (E) as the target datasets. The neXtProt curves designate mild, moderate, and ambiguous (multimodal) variants as pathogenic. (F) The observed AUCs when mild, moderate, and ambiguous variants in the neXtProt target dataset were designated benign or pathogenic. Statistical significance was determined using Kruskal-Wallis ANOVA test (A and C) or chi-squared test (B). ****p ≤ 0.0001 and **p ≤ 0.01. ns, not significant. Data are presented as mean values from at least two independent experiments.

Article Snippet: Plasmids containing human BRCA1 cDNA were a gift from Junjie Chen (Addgene, Plasmid #99394).

Techniques: Functional Assay, Binding Assay

Journal: Cell reports

Article Title: Protein-folding chaperones predict structure-function relationships and cancer risk in BRCA1 mutation carriers

doi: 10.1016/j.celrep.2024.113803

Figure Lengend Snippet: (A) BRCA1 mutation penetrance likelihood binned by the magnitude of HSP70 binding. Data shown were obtained from the Leiden Open Variation Database (LOVD) (accessed April 24, 2023). (B–D) Age of first cancer diagnosis for patients carrying BRCA1 mutations binned by mutation type (B), missense mutations in domains (C), and the degree of HSP70 binding (D). Statistical significance was determined using two-tailed (A) or one-tailed (B–D) Mann-Whitney t test. ****p ≤ 0.0001, **p ≤ 0.01, and *p ≤ 0.05. The number of variants in each bin is shown in parentheses. Data are presented as mean values from at least two independent experiments.

Article Snippet: Plasmids containing human BRCA1 cDNA were a gift from Junjie Chen (Addgene, Plasmid #99394).

Techniques: Mutagenesis, Binding Assay, Biomarker Discovery, Two Tailed Test, One-tailed Test, MANN-WHITNEY

Journal: Cell reports

Article Title: Protein-folding chaperones predict structure-function relationships and cancer risk in BRCA1 mutation carriers

doi: 10.1016/j.celrep.2024.113803

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Plasmids containing human BRCA1 cDNA were a gift from Junjie Chen (Addgene, Plasmid #99394).

Techniques: Recombinant, Luciferase, Enzyme-linked Immunosorbent Assay, Plasmid Preparation, Western Blot, Mutagenesis, Variant Assay