Datasets:
nopperl
/
pmc-image-text

Dataset card Data Studio Files Community
1
dedup-isc-ft-v107-score
float64
0.3
1
uid
stringlengths
32
32
text
stringlengths
1
17.9k
paper_id
stringlengths
8
11
original_image_filename
stringlengths
7
69
0.420884
8b094c69fb95445c8ec2e9f8742b0812
Replication and PykA catalytic activity analysis in wild-type, pykAT>A, and pykAT>D cells grown in different media. A Ori/ter ratio and C period. B Runout DNA histograms. Numbers in brackets stand for generation times (min). C PykA catalytic activity. Numbers refer to ratios as follows: top row: pykAT>A/wild-type; bottom row: wild-type/pykAT>D. Data in A and C are from 3–6 biological repeats (mean and SD). Representative runout DNA histograms are shown in (B)
PMC9009071
12915_2022_1278_Fig6_HTML.jpg
0.400305
8d2f328b039f475ba29b1baa8b482e54
PykA stimulates the DNA polymerase activity of DnaE. A Representative alkaline agarose gels showing DnaE primer extension time courses (30, 60, 90, 120, and 150 s) with DnaE (10 nM) alone and in the presence or absence of PykA (40 nM tetramer) or BSA (40 nM), as described in “Methods”. Lanes M and C represent DNA size markers and the control radioactive substrate in the absence of any proteins, respectively. B Representative alkaline agarose gels (from three independent experiments) showing DnaE primer extension time courses (30, 60, 90, 120, and 150 s) with DnaE (10 nM) and in the presence or absence of PykA (40 nM tetramer), with molar ratios of DnaE monomer: DnaN dimer: HolB monomer:YqeN monomer:DnaX trimer:PykA tetramer set to 1:1:1:1:1:1, considering the oligomeric states of these proteins. C As in B with 2 nM DnaE and molar ratios of 1:1:1:1:1:1
PMC9009071
12915_2022_1278_Fig7_HTML.jpg
0.446936
643a542fcb96473883495ca60d39f639
PykA directly inhibits the helicase activity of the helicase DnaC and via the primase DnaG. A Time courses (5, 10, 15, 25, and 30 min) showing the helicase activity of DnaC/DnaI in the presence or absence of PykA, as indicated. B Time courses (5, 10, 15, 25, and 30 min) showing the helicase activity of DnaC/DnaI in the presence or absence of PykA and/or DnaG, as indicated. The reactions were carried out as described in “Methods”. Representative native PAGE gels (from two independent experiments) are shown with lanes a and b representing control annealed and fully displaced (boiled) control DNA substrates. Data were plotted as a percentage of displaced primer versus time using GrapPad Prism 4 software. Error bars show the standard deviation from two independent repeat experiments
PMC9009071
12915_2022_1278_Fig8_HTML.jpg
0.458134
576f3d0b3d7f48ef95a79154b8de6861
Intertwining model of PykA catalytic activity regulation and PykA-driven metabolic control of DNA replication. A Regulation of PykA catalytic activity. Several metabolites (PEP, ATP, ADP, AMP, R5P…) are used as signaling molecules for PykA regulation. They gear Cat-metabolite interactions, Cat-PEPut interaction, and TSH motif phosphorylation in PEPut. In response to these signals, PykA adopts different conformations with different types and levels of TSH motif phosphorylation. These multiple forms of PykA typify the cellular metabolic state and drive allosteric regulation of PykA catalytic activity. This regulation impacts the metabolome and the concentration of signaling metabolites. This mechanism can be implemented by posttranslational modifications (PTMs) of PykA. B Metabolic control of DNA replication by PykA. The ability of PykA to sense signaling metabolites (effectors and phosphoryl donors) and adopt multiple forms typifying the nutritional environment is used by cells to convey a metabolic signal to the replication machinery and regulate DNA synthesis in a large range of nutritional conditions. Top panel: metabolic control of initiation. (i) In response to the concentration of a phosphoryl donor and the activity of a kinase/phosphatase system, the phosphorylation level of the T residue in the TSH motif of PEPut varies. Initiation is inhibited at low- and activated at high phosphorylation levels. High phosphorylation level may be powered by a metabolic cycle causing periodic accumulation of the phosphoryl donor at the age of initiation. Bottom panel: metabolic control of elongation. The balance between the multiple forms of PykA is sensed by replication enzymes for modulating elongation. Previous data suggest that receptors of metabolic signals conveyed by PykA are the helicase DnaC, the primase DnaG, and the lagging strand polymerase DnaE which are essential for both replication initiation and elongation (see the “Background” section). The metabolic control of initiation and elongation help cells to properly time replication in the cell cycle in a large range of nutritional conditions
PMC9009071
12915_2022_1278_Fig9_HTML.jpg
0.473367
ad8ae7061805498d81721ecd88a29b05
Overview of method and design of Experiment 1. a Participants first completed an exposure session, in which they viewed 420 objects: five object exemplars in each of two colors in each of 42 different categories. The objects were presented against scene backgrounds for 2 s each. The participants completed a Plausibility-Rating task, in which they rated how likely it would be to encounter an object of that type in a scene of that type on a scale of 1 (extremely likely) to 6 (extremely unlikely). b In the exposure session, two categories were paired that had exemplars with the same two possible colors (e.g., red or blue staplers or pencil sharpeners). These two categories were paired with two different scene background photographs in which each object type might plausibly appear (e.g., classroom and office). The assignment of object colors to scene backgrounds was complementary. For example, in the exposure session red staplers appeared against the classroom background and blue staplers against the office background. This assignment was reversed for sharpeners: blue against the classroom and red against the office. c Participants then completed a visual search session. On each trial, they first saw a scene background for 500 ms, then a text cue describing the target category for 800 ms, followed by a 1 s delay and a search array of eight objects. They searched for the object that matched the category label and reported the orientation of a superimposed letter “F”. The target object in the search array either matched or mismatched the category-specific color of exemplars associated with that background during the exposure session. Note that the category label was always presented in red font color and did not cue the color of the target object.
PMC9010067
13414_2022_2475_Fig1_HTML.jpg
0.4687
4dd77ed224d84df194db6b7aeaafe2a3
Visual search results for Experiment 1 (a) and Experiment 2 (b). Mean search response time (RT) as a function of context match condition. Errors bars are condition-specific, within-subject 95% confidence intervals (Morey, 2008)
PMC9010067
13414_2022_2475_Fig2_HTML.jpg
0.519339
c9d694fd2d1c490e9ef339ebfc44e3e0
A case of vanishing testis showing fibrosis (arrow 1), dystrophic calcifications (arrow 2), and hemosiderin deposits (arrow 3) in H&E stain. Images under ×200 visual field.
PMC9010507
fped-10-834083-g0001.jpg
0.524966
94e1604b66154f26b22b53b70aacc235
(A) A 52 month-old vanishing testis patient. The GCs (arrow) are easily identified in H&E stain, (B) while the GCs (arrow) are negative to Oct3/4. (C) A 17 month-old vanishing testis patient showing the GCs (arrow) with nuclear positive for Oct3/4. (D) Another 28 month-old vanishing testis patient showing the GCs (arrow) with nuclear positive for Sall4. Images under ×200 visual field.
PMC9010507
fped-10-834083-g0002.jpg
0.468859
a63e49288ba846b5bc9c24f67ca31dea
(A) A case of vanishing testis showing Sertoli cell population with immunohistochemical cytoplasmic positivity for anti-AMH (arrow) in SNTs. (B) Another one showing Sertoli cell population with immunohistochemical nuclear positivity for anti-AR (arrow 1) in SNTs, but no Leydig cell with immunohistochemical positivity for anti-AR in interstitial space (arrow 2). Images under ×100 visual field.
PMC9010507
fped-10-834083-g0003.jpg
0.416707
76ae20314f014b2f86cca0e4a9f7b518
Chemical composition of BEO.
PMC9010862
fmicb-13-855905-g001.jpg
0.413907
1ae1545384124cf4844dd3b8eae40e97
Time kill curve of BEO against Listeria monocytogenes (A); TEM images of L. monocytogenes before and after BEO [minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC)] treatment (B).
PMC9010862
fmicb-13-855905-g002.jpg
0.453922
98c1677027de4899b73bc21d341321bf
The effect of BEO on the cell membrane permeability of L. monocytogenes: (A) Propidium iodide (PI) fluorescence picture; (B) Intracellular protein content; and (C) Changes of electrical conductivity and β-galactosidase. Different letters in the figure indicate significant difference ( p <0.05).
PMC9010862
fmicb-13-855905-g003.jpg
0.415915
cc84050098e34c288f4dc1ef6f43817e
Changes in Raman spectra of cell membrane phospholipids (A); One-dimensional 1H NMR spectra of cell membrane phospholipids before (B) and after (C) reaction with linalool.
PMC9010862
fmicb-13-855905-g004.jpg
0.373219
ad49421215e14328a8ec9313d7d7113d
Reactive oxygen species (ROS) fluorescence picture of L. monocytogenes (A); ROS fluorescence intensity (B). Different letters in the figure indicate significant difference ( p <0.05).
PMC9010862
fmicb-13-855905-g005.jpg
0.496508
d5ab80389eaf4817b16c7a7d94be58b8
(A) The molecular docking of α-bergamotene and the key enzymes [phosphofructokinase (PFK), pyruvate kinase (PK)] of the EMP pathway. (B) The effect of BEO on key enzyme activities of EMP pathway. Different letters in the figure indicate significant difference ( p <0.05).
PMC9010862
fmicb-13-855905-g006.jpg
0.454964
ef73e5f77f4c427eaa178e9f448a245f
1H NMR spectra (A) of product isolated from the reaction mixture and precursor. Labels (B) correspond to peaks in spectra.
PMC9011398
lg1c00029_0001.jpg
0.513105
892bafbe448e488bb7ddc78f5886178f
ATR-FTIR spectra of product (top) and precursor (bottom) with essential stretching modes highlighted.
PMC9011398
lg1c00029_0002.jpg
0.428971
a6a4bf4f532b4a91af74e8abe63deeef
DSC traces of PIM-OAc (orange) and precursor (black). The heating rate was set to 20 °C min–1, and the cooling curves were set to 10 °C min–1. Tg was calculated as the local maximum of the first-order derivative of heat flow.
PMC9011398
lg1c00029_0003.jpg
0.434255
b048dec9d18149da812d8c580111e5fa
Flow demonstration of PIM-TFSI at room temperature and the DSC heating traces of PIM-TFSI (blue), PIM-OAc (orange), and the precursor (dotted) the precursor.
PMC9011398
lg1c00029_0004.jpg
0.470897
ea5f183f477840aba4520a47dda3c7db
DSC heating traces for decreasing the monomer concentration in the polymerization from top to bottom.
PMC9011398
lg1c00029_0005.jpg
0.373194
7f081829dccd4f9cac9e9497c922a99b
DSC heating traces for PILs prepared at decreasing carbonyl content from 0.11 to 1.7.
PMC9011398
lg1c00029_0006.jpg
0.504482
cd2d6e9795624b30942d3e7ba47ac83c
(A) Cross-sectional SEM images of the hybrid porous membrane with a relative wt.% ratio of PCMVIm-TFSI/PIM-TFSI-40% = 66:34 and (B) tensile stress–strain plot of hybrid porous membranes with different relative wt.% ratios of PCMVImTFSI:PIM-TFSI-40%.
PMC9011398
lg1c00029_0007.jpg
0.469742
46ed272ece8c49ffb35d1d3b5c44b483
Debus–Radziszewski Reaction toward an Imidazolium-Based Main-Chain Polysiloxane
PMC9011398
lg1c00029_0008.jpg
0.428351
86f41b5e28cf447792ee0eba3ad075ce
(a) The fast electric field changes of the F1907021515 at 130 m and 1.55 km. The electric field measurement antenna at 1.55 km is more sensitive and some parts of data are saturated. (b) The arranged high-speed frames showing the five types of lightning leader, with background removed and contrast enhanced. The arrange interval of IUPL is smaller than those of the other four leaders.
PMC9012797
41598_2022_10366_Fig1_HTML.jpg
0.439577
5bc7ec44c1cb4dddb9cebf36edef1920
(a) Arranged high-speed frames showing the development of SUPL and SCCP. (b–e) The electric figure changes of SUPL and SCCP at 1.55 km expanded in different time scale. The colored triangles indicate the position of SUPL, SCCP, RS1 and RS2. The high-speed frames are represented by these yellow-and-cyan and purple-and-green rectangles respectively to match with the corresponding electric field changes with an uncertainty of 3.8 μs.
PMC9012797
41598_2022_10366_Fig2_HTML.jpg
0.426026
2432aed348b343c49c50763b01c7e977
The electric field changes of DL4 at 1.55 km expanded in different time scale. The electric field waveform is colored to match corresponding high-speed frames with an uncertainty of 3.8 μs. The high-speed frames are background removed, intensity inverted and contrast enhanced to show the propagation process better.
PMC9012797
41598_2022_10366_Fig3_HTML.jpg
0.370256
737faea25e0a4a268dc520f4d980cf87
Differential luminosity from frame-to-frame of the frames in Fig. 3. The color range of each image is from the minimum value to the maximum value of the differential luminosity. The background color usually represents a differential light intensity of 0 which means that the luminosity of the corresponding position of the two frames remains unchanged. According to the color bar, redder means brighter and bluer means darker relative to the background color.
PMC9012797
41598_2022_10366_Fig4_HTML.jpg
0.456778
e416211ae3bd4c18adbb99545c3ad487
The electric field changes of DL13 (top) and DL14 (bottom) with corresponding high-speed frames. The waveform is separated by several grey vertical lines representing these 1 μs dead times to match high-speed frames.
PMC9012797
41598_2022_10366_Fig5_HTML.jpg
0.422224
166e1da433834715b54d4676b52717ed
Features of 48 distinct bipolar pulses superimposed on the electric field at 1.55 km of DL14. The positive and negative peak values of these pulses are reflected by columns with colors representing their durations.
PMC9012797
41598_2022_10366_Fig6_HTML.jpg
0.430816
eeb1f367d758480fac50db9b5b464a09
Propagation speeds variations of sixteen leaders in F1907021515. (a) The speed-position figure of sixteen leaders. The arrow preceding ID of each leader indicates the propagation direction. The upward propagation of bidirectional leader DL4 is also shown. (b) The propagation speeds variations of sixteen leaders. Only the downward propagation of bidirectional leader DL4 is shown. The top border is colored to show the duration of each leader.
PMC9012797
41598_2022_10366_Fig7_HTML.jpg
0.41588
e12d0f8c6e3648d0a5c92a9b1008ada2
Two examples of acceleration leaders whose propagation result in saturation of both high-speed frames and electric field recorded at 1.55 km. The left one is DL2 and the right one is DL7. The electric field at 1.55 km and brightness of high-speed frames get saturated simultaneously. The exposure time of each high-speed frame is 49 μs.
PMC9012797
41598_2022_10366_Fig8_HTML.jpg
0.471649
fd2a1bf4dc85483bbed68afae70f64c8
ND-induced thrombocytopenia in mice. (A) Platelet (PLT) counts, (B) white blood cell (WBC) counts, (C) red blood cell (RBC) counts, of wild type C57Bl/6J mice challenged by TiO2 (5 and 60 nm; 1.25 mg/kg) and various sizes of ND (5-200 nm; 1.25 mg/kg) nanoparticles. (D) Platelet counts of wild type C57Bl/6J mice challenged by various doses (0.625-1.25 mg/kg) of 50 nm ND nanoparticles. n = 6 (three experiments with two mice per group). **P < 0.01, vs. 0 h groups.
PMC9013758
fimmu-13-806686-g001.jpg
0.448081
980e051eca3c48ae9c0074aedd7403bc
ND-induced platelet cell death and aggregation in vitro. (A, B) Treatments of 50 nm NDs induced dose-dependent (0, 30, 1250 μg/mL) platelet aggregation (A) and cell death (B), as measured by flow cytometry (A, gating in Figure S1 ), and Zombie NIR live/dead analysis kit (B), respectively. (C) We observed the ND treatments induced multiple regulated cell death pathways (RCDs) in the dead cell population of mouse platelets. n = 6 (3 experiments with 2 samples per group). *P < 0.05, **P < 0.01, vs. vehicle control (0 μg/mL) groups.
PMC9013758
fimmu-13-806686-g002.jpg
0.482954
98900d473198431cb7d072c303f0a2a2
P-selectin, Nlrp3, caspase-1 and caspase-3 inhibitors protect platelets from ND-induced pyroptosis and apoptosis. Treatments with competitive P-selectin inhibitor rP-sel (100 ng/mL), ROS inhibitor NAC (150 μg/mL), mitochondria-targeted antioxidant MitoTEMPO (10 μMu;), Nlrp3 inhibitor OLT1177 (OLT, 10 μM), caspase 1 inhibitor Z-WEHD-FMK (WEHD, 10 μM) and caspase 3 inhibitor Z-DEVD-FMK (DEVD, 10 μM) rescued ND-induced platelet cell death (A, B). By dividing total cell death (B) into respective RCDs (C–G), we found that pyroptosis and apoptosis are the top 2 RCDs induced by ND challenges. Additional treatments with rP-sel, NAC, MitoTEMPO, OLT1177, Z-WEHD-FMK and Z-DEVD-FMK, all markedly rescued ND-induced platelet pyroptosis (C), apoptosis (G), necroptosis (D) and autophagy (F) levels. Despite overall platelet survival rate increased after the inhibitor treatments, the ferroptosis levels exacerbated (E). n = 6 (3 experiments with 2 samples per group), *P < 0.05, **P < 0.01, vs. vehicle groups.
PMC9013758
fimmu-13-806686-g003.jpg
0.408693
1e3c002ec8fb4142be1e873a46bce08b
Confocal microscopy analyses on the morphology of ND-induced platelet aggregates. (A–I) Example images of platelet (PLT) aggregates that were induced by treatments of ND, with or without additional treatments of inhibitors (rP-sel, NAC, OLT1177, Z-WEHD-FMK and Z-DEVD-FMK) were shown. CellTracker Blue Dye labeled mouse platelets, and red fluorescent 50 nm NDs (NV center > 100 per particle, FND Biotech) were employed in this experiment. (J, K) Quantitative analyses revealed that ND treatments markedly enhanced the platelet aggregate counts (those > 400 pixels) (J), and area (K). All tested inhibitors (rP-sel, NAC, MitoTEMPO, OLT1177, Z-WEHD-FMK and Z-DEVD-FMK) suppressed ND-induced aggregation (K, area; and J, counts; except MitoTEMPO). n = 6 (2 experiments with 3 mice per group). # P < 0.05 vs. vehicle groups. * P < 0.05, ** P < 0.01, vs. ND + vehicle groups. Example images of 3D morphology of ND-induced platelet aggregate are highlighted (H, I; similar result referred to Supplementary Video S1 ). Scale bars: (A–G), 10 μm (G-4); (H, I), 10 μm (I).
PMC9013758
fimmu-13-806686-g004.jpg
0.423789
0bce9bb602f0497fa98a3aa637432e97
P-selectin, Nlrp3 and caspase-1 deficiencies protect platelets from ND-induced pyroptosis and apoptosis. (A, B) Compared with wild type (WT) controls, P-selectin (Selp-/- ), Nlrp3 (Nlrp3-/- ) and caspase 1 (Casp1-/- ) deficient platelets displayed less cell death levels in response to ND treatments. (C–G) Consistent with the cell death analysis, platelets from P-selectin (Selp-/- ), Nlrp3 (Nlrp3-/- ) and caspase 1 (Casp1-/- ) deficient mice displayed less pyroptosis and apoptosis, the 2 major RCDs, levels in response to ND challenges. n = 6 (2 experiments with 3 mice per group), *P < 0.05, **P < 0.01, vs. WT groups.
PMC9013758
fimmu-13-806686-g005.jpg
0.417941
bd26037b84e44cc68fc05f0bd317d554
P-selectin, Nlrp3, caspase-1 and ROS inhibitors protect platelets from ND-induced activation. ND-induced platelet activation, including (A) platelet aggregation, and (B) mitochondrial superoxide levels, could be suppressed with the treatments with P-selectin, ROS inhibitors, Nlrp3, caspase-1 and caspse-3 inhibitors [rP-sel (100 ng/mL), OLT1177 (OLT, 10 μM), Z-WEHD-FMK (WEHD, 10 μM), Z-DEVD-FMK (DEVD, 10 μM), NAC (150 μg/mL), and MitoTEMPO (1 μM)], respectively (A, B). (A) ND + vehicle groups were normalized to 100%; (B) vehicle groups were normalized to 100%. n = 6 (2 experiments with 3 mice per group), ## P < 0.05, vs. respective vehicle groups; **P < 0.01, vs. respective ND + vehicle groups.
PMC9013758
fimmu-13-806686-g006.jpg
0.476544
7622c99f5e304a72aa7671b344e778f9
Treatments of P-selectin, ROS, Nlrp3, caspase-1, and caspase-3 inhibitors ameliorate ND-induced thrombocytopenia in mice. Treatments with P-selectin, ROS, Nlrp3, caspase-1, and caspase-3 inhibitors [rP-sel (0.24 mg/mL), OLT1177 (OLT, 50 mg/kg), NAC (300 mg/kg), and MitoTEMPO (0.1 mg/kg), Z-WEHD-FMK (ZWEHD, 750 μg/kg), Z-DEVD-FMK (DEVD, 6.5 μg/kg)], ameliorated ND (50 nm; 1.25 mg/kg)-induced thrombocytopenia (A), and platelet pyroptosis (B) and apoptosis (C) levels in C57BL/6J mice. (B, C) Vehicle groups were normalized to 100%. n = 6, (2 experiments with 3 mice per group). # P < 0.05, ## P < 0.01, vs. respective vehicle groups; *P < 0.05, **P < 0.01 significantly lower, vs. respective ND + vehicle groups; ++ P < 0.01 significantly higher, vs. ND + vehicle groups.
PMC9013758
fimmu-13-806686-g007.jpg
0.493556
4eacecb32d65437ebbeb1d56d86d76a9
Reversal of ND-induced thrombocytopenia through suppression of NETosis in mice. Flow cytometry gating of NETosis (citrullinated histone H3, CitH3 staining) levels of mouse neutrophils treated with vehicle (A, B), 12-O-tetradecanoylphorbol-13-acetate (C, TPA, a positive control NETosis inducer; 2 nM), and supernatants from 50 nm NDs (30 μg/mL) activated (30 min) wild mice platelets (2 × 106) (PLT ND sup) (E) with or without additional inhibitor (F, OLT) pretreatments (30 min), as compared to the NETosis induced by none-activated platelet supernatants (D, PLT sup). (G) The quantified results indicated that ND can induce NET formation directly (green columns). ND treatments can also enhance NETosis indirectly through soluble factors released from ND-activated platelets (G, PLT+ND sup), and such this “PLT+ND sup”-induced NETosis could be suppressed by treatments of additional inhibitors such as GSK484, rP-sel, NAC, MitoTEMPO, OLT1177, Z-WEHD-FMK and Z-DEVE-FMK (G, blue columns). (H) Treatments NETosis inhibitor GSK484 ameliorated ND-induced thrombocytopenia. (G, H) ## P < 0.01 vs. vehicle groups. (G) + P < 0.05, vs. ND groups; *P < 0.05, **P < 0.01, vs. “PLT + ND sup” groups. (H) *P < 0.05, vs. ND groups. n = 6 (2 experiments with 3 mice per group).
PMC9013758
fimmu-13-806686-g008.jpg
0.428479
5a105343ea824b3093e3d05d9bba5cdd
The distribution of ATP7B gene mutations in 47 neurological WD patients.
PMC9013891
fgene-13-875694-g001.jpg
0.468338
e8d0222f7e6341839e1702d04007fea7
Overall survival for all patients.
PMC9014302
fonc-12-869572-g001.jpg
0.458504
cce8f1c5aed246648b3073f7d60b32d2
(A) Local failure for all lesions. (B) Local failure for lesions stratified by diameter: ≤1 vs. >1 cm.
PMC9014302
fonc-12-869572-g002.jpg
0.48678
65d40341e5ac495eb35f2d02663b0b63
(A) Radionecrosis for all lesions. (B) Radionecrosis for lesions stratified by diameter: ≤1 vs. >1 cm.
PMC9014302
fonc-12-869572-g003.jpg
0.478185
091b1d8afa37430c8622ec9193a30c15
Medication management at home (n=19)
PMC9014897
pharmpract-20-2600-g001.jpg
0.398019
ba25c6f9239546828e0a5b9cb19744f8
NLR receiver operating characteristic (ROC) curve analysis.
PMC9015869
BMRI2022-1149789.001.jpg
0.451737
3cfdb95f8ef84010b6b35f799f221e82
Study design.
PMC9015869
BMRI2022-1149789.002.jpg
0.42847
beb02c93c63646229554ceba979c19e3
The effects of eimultaneous TLR3/4 activation on the intensity of microglia activation. BV2 cells were stimulated with 1 µg/mL LPS and/or 10 µg/mL poly(I:C) in serum-free medium for the times indicated. A Nitrite concentrations in the culture supernatants of the control and stimulated BV2 cells, determined using the Griess assay. Data are presented as means ± standard deviation of five independent experiments, each performed in duplicate. B, C Release of the cytokines IL-6 (B) and TNF-α (C) into the culture supernatants of the control and stimulated BV2 cells, determined using flow cytometry. Data are presented as means ± standard deviation of two independent experiments, each performed in duplicate. *p ˂ 0.05
PMC9016010
12035_2021_2694_Fig1_HTML.jpg
0.500303
57ba2b4f43164b46b3a2792c1728b58e
The effects of simultaneous TLR3/4 activation on cathepsin X expression and activity in microglia. A–D BV2 cells or primary microglia cultures were stimulated with 1 µg/mL LPS and/or 10 µg/mL poly(I:C) in serum-free medium for the times indicated (A, C) or for 24 h (B, D). A, B Cathepsin X protein levels in cell lysates of the control and stimulated cells were measured by ELISA, using a goat anti-cathepsin X capture antibody (AF934) and a mouse anti-cathepsin X detection antibody (3B10). Data are presented as means ± standard deviation of at least two independent experiments, each performed in duplicate. C, D Cathepsin X activity in cell lysates was determined using the cathepsin X-specific substrate Abz-Phe-Glu-Lys(Dnp)-OH. Data are presented as means ± standard deviation of at least two independent experiments, each performed in duplicate. *p ˂ 0.05. E Representative images of double immunofluorescence staining of cadherin (green) and cathepsin X (red) in unstimulated BV2 cells (control) and in BV2 cells stimulated with LPS and/or poly(I:C) for 24 h. Nuclei were counterstained with DAPI (blue). Right: quantification of the relative co-localization areas of cadherin and cathepsin X, presented as means ± standard deviation of pixels (cell numbers ≥ 10). Scale bars: 10 µm. *p ˂ 0.05
PMC9016010
12035_2021_2694_Fig2_HTML.jpg
0.445459
4a9c21caeebf4beb88033d7a813e09fb
Simultaneous TLR3/4 activation affects cathepsin X release and localization in microglia. BV2 cells were stimulated with 1 µg/mL LPS and/or 10 µg/mL poly(I:C) for 24 h. A Cathepsin X protein levels in culture supernatants of control and stimulated BV2 cells were measured by ELISA, using a goat anti-cathepsin X capture antibody (AF934) and a mouse anti-cathepsin X detection antibody (3B10). Data are presented as means ± standard deviation of three independent experiments. B Cathepsin X activity in the culture supernatants was determined using the cathepsin X-specific substrate Abz-Phe-Glu-Lys(Dnp)-OH. Data are presented as means ± standard deviation of three independent experiments
PMC9016010
12035_2021_2694_Fig3_HTML.jpg
0.486085
aefd1cf5b25343549ccfb58f926d5b65
The effects of cathepsin X inhibition on the TLR3/4-mediated inflammatory response in microglia. BV2 cells or primary microglia cultures were pre-treated with cathepsin X inhibitor AMS36 (10 µM) for 1 h and then stimulated with 1 µg/mL LPS and/or 10 µg/mL poly(I:C) for the indicated times. A Nitrite concentrations in the culture supernatants of the control and stimulated BV2 cells, determined using the Griess assay. Data are presented as means ± standard deviation of five independent experiments, each performed in duplicate. B Nitrite concentrations in the culture supernatants of the control and stimulated primary microglia cultures for 24 h, determined using the Griess assay. Data are presented as means ± standard deviation of two independent experiments, each performed in duplicate. C Western blotting for iNOS expression in the BV2 cell lysates (above). The iNOS levels in the control and stimulated BV2 cells were quantified and normalized to the respective total β-actin, used as the loading control. Semi-quantitative densitometry analysis for the iNOS protein levels (below). Data are means of two independent experiments and are expressed relative to the control cells. D, E Release of the cytokines IL-6 (D) and TNF-α (E) into the culture supernatants of the control and stimulated BV2 cells, determined using flow cytometry. Data are means of two independent experiments, each performed in duplicate. *p ˂ 0.05
PMC9016010
12035_2021_2694_Fig4_HTML.jpg
0.484731
193e6f02a0ad483abd6074e231645835
Neuroprotective effects of the cathepsin X inhibitor AMS36 on LPS/poly(I:C)-induced microglia-mediated neurotoxicity in SH-SY5Y cells. Microglia BV2 cells were pre-treated with 10 µM AMS36 for 1 h, followed by stimulation with 1 µg/mL LPS plus 10 µg/mL poly(I:C) for 24 h. Microglia culture supernatants were collected and incubated with neuronal SH-SY5Y cells for the times indicated. Neuronal cell viability was determined using the MTS assay. Data are presented as means ± standard deviation of two independent experiments, each performed in quadruplicate. *p ˂ 0.05; **p ˂ 0.01
PMC9016010
12035_2021_2694_Fig5_HTML.jpg
0.437182
e5d31aceaca848aa975dee54456f1c31
The effects of cathepsin X inhibition on TLR3/4-mediated apoptosis in microglia. BV2 cells were pre-treated with the cathepsin X inhibitor AMS36 (10 µM) for 1 h and then stimulated with 1 µg/mL LPS and/or 10 µg/mL poly(I:C) for the indicated times. A Cell death (apoptosis) of the control and stimulated BV2 cells was determined using propidium iodide (PI) and flow cytometry. Data are relative percentages of PI-positive (PIpos) cells normalized to the appropriate control, presented as means ± standard deviation of four independent experiments. B The proportions (%) of apoptotic cells determined using Annexin V and PI staining and flow cytometry. The quadrant threshold was set according to the control BV2 cells, and the quantitative analysis indicates the proportion (%) of the cells showing apoptosis (i.e., annexin-Vpos and PIpos). Data are presented as means ± standard deviation of two independent assays. C Caspase-3/7 activities in cell lysates of the control and stimulated BV2 cells, determined fluorometrically using the specific substrate for caspase 3/7, Ac-DEVD-AFC. Data are presented as rates of fluorescence changes (ΔF/Δt) with means ± standard deviation of four independent experiments, each performed in duplicate. *p ˂ 0.05
PMC9016010
12035_2021_2694_Fig6_HTML.jpg
0.496253
f1a8b3e9dfd34db2b2c1535a79157a37
LY29004 modulates the LPS/poly(I:C)-induced proinflammatory response and cathepsin X activity. A–D BV2 cells were pre-treated with 10 µM LY29004 or 1 µM wortmannin for 1 h and then stimulated with 1 µg/mL LPS and/or 10 µg/mL poly(I:C) for 24 h. A Nitrite concentrations in the culture supernatants of the control and stimulated BV2 cells, determined using the Griess assay. Data are presented as means ± standard deviation of two independent experiments, each performed in duplicate. B, C Levels of the cytokines IL-6 (B) and TNF-α (C) in the culture supernatants of the control and LPS/poly(I:C)-stimulated BV2 cells, determined using flow cytometry. Data are means of two independent experiments, each performed in duplicate. D Cathepsin X activity in cell lysates was determined using the cathepsin X-specific substrate, Abz-Phe-Glu-Lys(Dnp)-OH. Data are presented as means ± standard deviation of two independent experiments, each performed in duplicate. E Analysis of Akt activation. BV2 cells were pre-treated with the cathepsin X inhibitor AMS36 (10 µM) for 1 h, followed by 1 µg/mL LPS and 10 µg/mL poly(I:C) stimulation for 30 min. Flow cytometry analysis of Akt activation was performed using a specific antibody against phosphorylated Ser473 of Akt. Data are means of two independent experiments, each performed in duplicate. *p ˂ 0.05
PMC9016010
12035_2021_2694_Fig7_HTML.jpg
0.478001
89d18f3d90b249419dabe488862771c9
A library of 115 recombinant cell-surface and secreted proteins from Schistosoma mansoni expressed as secreted enzymatically monobiotinylated recombinant proteins in HEK293 cells. Supernatants were resolved by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) under reducing conditions, blotted, and detected with streptavidin-conjugated horseradish peroxidase. Approximately one third of the protein library consists of membrane-tethered surface proteins, whereas the remainder of the library corresponds to secreted proteins as indicated. Their predicted molecular mass is indicated by a red line. Three proteins (52, 57, 86) migrated faster than expected; 6 proteins (42, 68, 80, 89, 91, 102) exhibited evidence of partial processing; 13 proteins were not detected by Western blotting.
PMC9016452
jiaa329f0001.jpg
0.433272
45bbd8ada46e45f58adf1c886c0e9d57
The majority of recombinant proteins are immunoreactive to sera from individuals living in schistosomiasis-endemic areas and contain heat-labile conformational epitopes. Recombinant proteins were probed with pooled sera from individuals living in schistosomiasis-endemic areas (“infected,” red checked bars) or individuals from the United Kingdom who have never been infected (“control,” green dotted bars). To test for the presence of heat-labile epitopes, recombinant proteins were also heat-treated (80°C, 10 minutes) before being exposed to immune sera (“infected heat treated,” orange hatched bars). All except 2 proteins (18 and 57, shown in blue) were seropositive, as determined by Aprotein > Acontrol + 3SDcontrol ( = 0.201) (red dashed line), where control is the rat Cd4d3 + 4 protein tag. High immunoreactivity was determined as Aprotein > 0.3 (green dotted line). Proteins that exhibited little or no loss of reactivity after heat treatment are shown in italics, including 16 highly reactive proteins (6, 7, 14, 16, 19, 30, 32, 34, 36, 42, 49, 54, 56, 89, 101, 105). All measurements were performed in triplicate; error bars = standard deviation.
PMC9016452
jiaa329f0002.jpg
0.505207
badd10ff16e04f629579a7227ab114dc
Identification of early markers of infection in human volunteers experimentally infected with Schistosoma mansoni male cercariae. Three individuals were each infected with 30 male cercariae, and their antibody response to 103 Schistosoma antigens were monitored every 4 weeks over a period of 20 weeks. The number of positive antigens increased over time with the most highly immunoreactive antigens containing saposin domains (proteins 44, 61, 62, 63, and 65) or belonging to the cathepsin family of proteases (proteins 67, 68, and 83). Colored symbols represent time point readings for each individual. Data points represent mean ± standard deviation; n = 3.
PMC9016452
jiaa329f0003.jpg
0.440712
f537082adcbb4bfaa7026f0adfc61905
Kinetics of human antibody response to early markers of infection using sera from experimental infections by Schistosoma mansoni. Immunoreactivity to S mansoni antigens were quantified on a weekly basis in 3 individuals infected with 30 male cercariae. Reactivity to proteins 44 and 65 could be detected in all volunteers as early as 5 weeks postinfection. The control antigen corresponds to the rat Cd4d3 + 4 protein tag. Data points represent mean ± standard deviation; n = 3.
PMC9016452
jiaa329f0004.jpg
0.405001
200cacb7a7a44b9d935e0e6a8c14b333
Early reactivity to Schistosoma mansoni antigens is detectable in individuals challenged with just 10 cercariae. The immune response from 3 human volunteers infected with 10 male S mansoni cercariae was monitored at 4, 8, and 12 weeks postinfection. Reactivity to antigens 44 and 65 was detected in all participants at 8 weeks and as early as 4 weeks in the case of participant E and antigen 44. With the exception of protein 83, all volunteers were immunoreactive for the antigens tested at 12 weeks postinfection. Data points represent mean ± standard deviation; n = 3.
PMC9016452
jiaa329f0005.jpg
0.445256
6d7bdb62690a42f285969a7bbf8ca927
Analysis of the acquired antibody response to Schistosoma mansoni antigens in experimentally infected mice. Individual sera from 3 mice infected percutaneously (PC) or pooled sera from 3 mice infected intraperitoneally (IP) were analyzed at 8, 21, and 42 days postinfection. The aim was to try and capture the antibody reactivity at different stages of parasite maturation: schistosomule at 8 days, immature adult at 21 days, and mature adult at 42 days. Proteins 44 and 3 were immunopositive at day 21, and 8 additional proteins (10, 41, 62, 63, 64, 67, 68, 106) were immunopositive at day 42. Each data point represents the average of triplicate experiments; error bars = standard deviation.
PMC9016452
jiaa329f0006.jpg
0.365777
aa6b04b49087434c8fac4c8293dcb384
AAQRC generation and its recognition.
PMC9016685
41598_2022_9858_Fig1_HTML.jpg
0.414351
b79acccdd9784b8c9da5798f136dc6d1
An example on AAQRC generation: step 1.
PMC9016685
41598_2022_9858_Fig2_HTML.jpg
0.406175
2ee4a0039ed64a90974b267156ce7536
An example on AAQRC generation: step 2: music score of f2.
PMC9016685
41598_2022_9858_Fig3_HTML.jpg
0.543768
54ef51151680436287c54f0482b893c8
An example on AAQRC recognition: step 3: music score of f3.
PMC9016685
41598_2022_9858_Fig4_HTML.jpg
0.474086
3c99fbd46c034e7d8efccc04976f963d
An example on AAQRC recognition: step 4.
PMC9016685
41598_2022_9858_Fig5_HTML.jpg
0.427346
b0670e3c866249b3beee5936a0ab5ebf
An example on AAQRC recognition: step 3: music score of f3’.
PMC9016685
41598_2022_9858_Fig6_HTML.jpg
0.426315
b5cb019f21884413b77f6aaefa4d74dc
Music scores of the thirty URLs. (a) a1.mid; (b) a2.mid; (c) a3.mid; (d) a4.mid; (e) a5.mid; (f) a6.mid; (g) a7.mid; (h) a8.mid; (i) a9.mid; (j) a10.mid; (k) b1.mid; (l) b2.mid; (m) b3.mid; (n) b4.mid; (o) b5.mid; (p) b6.mid; (q) b7.mid; (r) b8.mid; (s) b9.mid; (t) b10.mid; (u) c1.mid; (v) c2.mid; (w) c3.mid; (x) c4.mid; (y) c5.mid; (z) c6.mid; (aa) c7.mid; (ab) c8.mid; (ac) c9.mid; (ad) c10.mid.
PMC9016685
41598_2022_9858_Fig7_HTML.jpg
0.436192
feec9bf0c7f7473ca20ebdc5ba33dcd2
The proportion of the strings of pitches which are correctly identified in the all strings of pitches (a string of pitches is correctly identified, if the corresponding value of t1 is 1). (a) in Table 6; (b) in Table 7.
PMC9016685
41598_2022_9858_Fig8_HTML.jpg
0.520396
1a5c22b0dbfa417cbe37b12cfc3d3096
A poll on artistry and favorability among 100 persons selected randomly.
PMC9016685
41598_2022_9858_Fig9_HTML.jpg
0.398107
c159345c05354f61bde7b11e2fcb5c8f
Progress of DKP-[Cys(CH2)3COOtBu-Pro] formation under various Fmoc-removal conditions.
PMC9016848
ao2c00214_0002.jpg
0.436414
25ba8b4f8df148899033a3dc7dd3ff88
Comparison of DKP development by 20% piperidine/DMF and 2% DBU, 5% piperazine/NMP treatment of Fmoc–Xaa–Pro–2-Cl-trityl resin (top, total DKP formation), Fmoc–Xaa–Sar–2-Cl-trityl resin (middle, total DKP formation), and Fmoc–Xaa–N-4-F-Bn-Gly–2-Cl-trityl resin (bottom).
PMC9016848
ao2c00214_0003.jpg
0.394256
37aba9162ce94e17800158981e11a7cc
Comparison of DKP development by 20% piperidine/DMF and 2% DBU, 5% piperazine/NMP treatment of Fmoc–Xaa1–Sar/Pro–Xaa3–2-Cl-trityl resin.
PMC9016848
ao2c00214_0004.jpg
0.52049
e2a2d822771b4325a9752948007ed9b6
Mechanism of DKP Formation
PMC9016848
ao2c00214_0005.jpg
0.499739
d6a889a8d1de48a883437e0efcfb750e
Mechanism of 1,4-Bis(9H-fluoren-9-ylmethyl)piperazine Formation through Piperazine-Mediated Fmoc Removal
PMC9016848
ao2c00214_0006.jpg
0.445117
7ae4a954b309403db522d3f6b55f9c54
Surface SEM images and EDX spectra of the oxide coatings grown on the pretreated NiTi wire by hydrothermal reaction in HCl solution (a and b), HNO3 solution (c and d) and glacial acetic acid (e and f) at 150 °C for 12 h.
PMC9017461
d2ra01031c-f1.jpg
0.425234
76559955daad4d709a55aadf60ee213a
Typical chromatograms of SPME-HPLC with the NiTi@TiO2NPs fiber obtained in HNO3 solution (a), the NiTi@TiO2NPs fibers obtained in HCl solution within 6 h (b) and 12 h (c) for CPs, PAEs, UVFs and PAHs.
PMC9017461
d2ra01031c-f2.jpg
0.478927
1afc203f416346578f7325914ae99c50
The extraction capability of the PA fiber and the NiTi@TiO2NPs fiber for UVFs.
PMC9017461
d2ra01031c-f3.jpg
0.427789
2936261a750546a89edf16cb518f9c6c
Dependence of extraction efficiency on ionic strength (a), stirring rate (b), extraction temperature (c), pH (d) as well as extraction time (e) and desorption time (f).
PMC9017461
d2ra01031c-f4.jpg
0.503272
18b4ae8d03ff4ca8a014c473099ed40d
Annual publications trend.
PMC9017514
ECAM2022-7705256.001.jpg
0.479118
c2aba20acb4c4085a49a8d06a8bc8a0d
Co-authorship network of country.
PMC9017514
ECAM2022-7705256.002.jpg
0.537052
4e452ac0e1844caa9f8ff669334fca1f
Institution cooperation network.
PMC9017514
ECAM2022-7705256.003.jpg
0.456716
2a21f4704e3a4f56b0a1e5cc0b0861ac
Author cooperation network map.
PMC9017514
ECAM2022-7705256.004.jpg
0.441986
bfaadc5a20fe42288ab7e016cdb0f980
Density map of journals.
PMC9017514
ECAM2022-7705256.005.jpg
0.43444
9fa3e1a8564f45d0817dd396851257d6
Density map of the co-cited references.
PMC9017514
ECAM2022-7705256.006.jpg
0.394425
6d6399034f5543ac9cf2639526e1bea2
Network of the cited references.
PMC9017514
ECAM2022-7705256.007.jpg
0.435247
c37cb57280fb4f8899001587d0fbf345
Network of keywords.
PMC9017514
ECAM2022-7705256.008.jpg
0.424618
f02fde95d76245379519d7e2bb2f6966
Density map of keywords.
PMC9017514
ECAM2022-7705256.009.jpg
0.38444
91a612aaaf5042cba4747bdd3cd7c918
Overlay visualization of keywords.
PMC9017514
ECAM2022-7705256.010.jpg
0.421891
6af1f966aecd4d4984a0412cf798fbb8
Domain composition of PABPC1(14) and Paip2A(17). PABPC1 is a 636-residue protein with four RNA recognition motifs (RRMs) in the N terminus. Residues 11 to 89, 99 to 175, 191 to 268, and 294 to 370 are RRM1, RRM2, RRM3, and RRM4, respectively. The C terminus contains an unstructured region named as the linker and a PABC (PABP C-terminal domain). Paip2A is a 127-residue protein with PABP-interacting motif 1 (PAM1) in the N terminus and PABP-interacting motif 2 (PAM2) in the C terminus. PABPC1, poly(A)-binding protein C1; Paip2A, PABP-interacting protein 2A.
PMC9019252
gr1.jpg
0.477386
34d64b286c5d42e1b28633d3ae01426d
Schematic representation of the dissociation of PABPC1 from poly(A) by Paip2A. A, in the poly(A)-bound PABPC1, the RRM2–RRM3 region mainly contributes to the poly(A) association. B, as the affinity of the RRM2 region for poly(A) (Kd = 200 μM, Table 1) is 50-fold weaker than that for Paip2A (Kd = 4.0 μM, Table 2), the RRM2 region transfers from poly(A) to RRM2-binding region of Paip2A (blue) when Paip2A approaches sites where the RRM3-binding region of Paip2A (yellow) are partly available for RRM3 binding. Next, Paip2A removes RRM3 from poly(A) because of the threefold higher affinity of RRM3 for Paip2A (Kd = 1.3 μM, Table 2) compared with that for poly(A) (Kd = 4.7 μM, Table 1). PABPC1, poly(A)-binding protein C1; Paip2A, PABP-interacting protein 2A; RRM, RNA recognition motif.
PMC9019252
gr10.jpg
0.474977
bc8f37b469734091a69bedd07046e2e6
Surface plasmon resonance results for the activity of prepared Paip2A(FL) that dissociates PABPC1 and RRM1/2/3/4 from poly(A). 5′-Biotinylated A24 was immobilized on a streptavidin-coated sensor chip. Application periods for 128 nM PABPC1 (A) and RRM1/2/3/4 (B) (81–260 s) and Paip2A(FL) (721–900 s) are indicated as bars above the sensorgrams. PABPC1, poly(A)-binding protein C1; Paip2A(FL), PABP-interacting protein 2A (full length); RRM, RNA recognition motif.
PMC9019252
gr2.jpg
0.432079
b8bc47c0e3574415b966bfbb8204621b
NMR spectral changes in Paip2A(FL) after adding RRM1/2/3/4. A, backbone NMR assignments of Paip2A(FL) identified on the 1H–15N HSQC spectrum. B, overlay of 1H–15N TROSY spectra for 2H, 15N-labeled Paip2A(FL) in the presence (red) and absence (black) of nonlabeled RRM1/2/3/4. The top left panel shows a cross-section of the A32 signals after adding RRM1/2/3/4. The bottom left panel shows unassigned signals that appeared after adding RRM1/2/3/4. The equivalent numbers for RRM1/2/3/4 are shown in each figure, colored as blue (0 equivalent), red (0.25 equivalent), green (0.5 equivalent), purple (0.75 equivalent), yellow (1.0 equivalent), or orange (1.25 equivalent). C, chemical shift changes in each residue of Paip2A(FL). “Perturbed (P)” indicates the residues whose signals disappeared after adding RRM1/2/3/4 and appeared at different positions. Chemical shift changes were calculated using the following equation: δ = Δ1H2+(Δ15N/6.5)2, where Δ1H and Δ15N are the chemical shift changes in the 1H and 15N dimensions, respectively. HSQC, heteronuclear single quantum coherence; Paip2A(FL), PABP-interacting protein 2A (full-length); RRM, RNA recognition motif; TROSY, transverse relaxation optimized spectroscopy.
PMC9019252
gr3.jpg
0.435676
79cbed5c523b402ba92a750164131247
ITC analysis of the interactions of RRM of PABPC1 with poly(A). ITC analysis of the interactions of each RRM ((A) RRM1, (B) RRM2, (C) RRM3, and (D) RRM4) with A7, (E) RRM2/3 with A7, (F) RRM2 with A12, (G) RRM3 with A12, (H) RRM2/3 with A12. Upper panel, A–E, traces of the 19 titrations of 2 μl aliquots of A7 into cells containing RRM, (F) trace of the 91 titrations of 0.4 μl aliquots of RRM2 into cells containing A12, (G) traces of the 19 titrations of 2 μl aliquots of RRM3 into cells containing A12, and (H) traces of the 19 titrations of 2 μl aliquots of RRM2/3 into cells containing A12. Lower panel, the integrated binding isotherms obtained from the experiments were fitted using a “One Set of Sites” model. The parameters obtained from the best fit (solid line) with the error values calculated from the fitting are summarized in Table 1. ITC, isothermal titration calorimetry; PABPC1, poly(A)-binding protein C1; RRM, RNA recognition motif.
PMC9019252
gr4.jpg
0.452278
0c3ff763edfb42f6ac795189f4512ecb
ITC analysis of interactions of the RRM of PABPC1 with Paip2A(25–83). ITC results are shown for the interactions of Paip2A(25–83) with (A) RRM1, (B) RRM2, (C) RRM3, (D) RRM4, and (E) RRM2/3. Upper panel, traces of the 19 titrations of 2 μl aliquots of RRM into cells containing Paip2A(25–83). Lower panel, integrated binding isotherms obtained from the experiments were fitted using a “One Set of Sites” model. The parameters obtained from the best fit (solid line), with error values calculated from the fitting, are summarized in Table 1. ITC, isothermal titration calorimetry; PABPC1, poly(A)-binding protein C1; Paip2A, PABP-interacting protein 2A; RRM, RNA recognition motif.
PMC9019252
gr5.jpg
0.419607
abb5e92cce4a4a0995314a984a12c8e1
Chemical shift perturbation (CSP) analysis of Paip2A(25–83) upon RRM2/3, RRM2, and RRM3 titration.A, backbone NMR assignments of [2H, 13C, 15N] Paip2A(25–83) bound to RRM2/3 identified on the 1H–15N TROSY spectrum. The L-3∗, G-2∗, S-1∗, and L80∗ are derived from the cis isomer of proline. B, chemical shift changes in each residue of Paip2A(25–83) bound to RRM2/3. Chemical shift changes were calculated using the following equation: δ = Δ1H2+(Δ15N/6.5)2, where Δ1H and Δ15N are the chemical shift changes in the 1H and 15N dimensions, respectively. Asterisks indicate unassigned residues. However, the amino-acid types are identified for all unassigned peaks. Empty boxes indicate that the signal for the residue disappeared after RRM2/3 addition. Overlays of the 1H–15N HSQC spectra of 15N-labeled Paip2A(25–83) in the absence (black) or the presence (red) of (C) RRM2 and (D) RRM3. The perturbed and not perturbed signals are indicated in green and blue, respectively. E, chemical shift changes are plotted versus the residue numbers for Paip2A(25–83) after adding RRM2 (upper) or RRM3 (lower). Signals from residues 44 to 70 and 74 to 79 were perturbed after adding RRM2 and those from residues 27 to 70 were perturbed after adding RRM3. Residues 44 to 70 were perturbed after adding either RRM2 or RRM3. Chemical shift changes were calculated using the following equation: δ = Δ1H2+(Δ15N/6.5)2, where Δ1H and Δ15N are the chemical shift changes in the 1H and 15N dimensions, respectively. HSQC, heteronuclear single quantum coherence; Paip2A, PABP-interacting protein 2A; RRM, RNA recognition motif; TROSY, transverse relaxation optimized spectroscopy.
PMC9019252
gr6.jpg
0.391515
6cbdc3d0d55e4bf19a23f12ed83e2955
Chemical shift changes in uniformly15N-labeled RRM2/3 after adding A12.A, overlay of the 1H–15N HSQC spectra of 15N-labeled RRM2/3 in the absence (black) or the presence (red) of 1.0 equivalents of A12. B, chemical shift changes of signals derived from RRM2 and RRM3 from 0 to 1.25 equivalents of A12 titrations. The G141 and R240 are residues in RRM2 and RRM3, respectively. C, schematic drawing of the interactions between RRM2/3 and A12. In the presence of excessive RRM2/3 compared with A12, the RRM3 of RRM2/3 binds to A12 leaving RRM2 unbound (center). In the presence of equimolar A12, both RRM2 and RRM3 in one molecule of RRM2/3 simultaneously bind to A12 (right). D, plot showing the chemical shift changes after adding 1.25 equivalents of A12. The upper bar graph shows the chemical shift changes in the signals derived from RRM2, and the lower bar graph shows those from RRM3. The residues of the upper and lower graphs are arranged based on alignments between RRM2 and RRM3, and a secondary structure of these domains is shown in the graph. The corresponding signals in the A12-bound state were assigned by a series of triple resonance experiments, and their chemical shift changes are plotted in D. Some signals were perturbed after adding A12, and their corresponding signals in the A12-bound state could not be assigned, as the triple resonance signals were not observed. These residues are indicated as “Perturbed (P)” in D. Chemical shift changes were calculated using the following equation: δ = Δ1H2+(Δ15N/6.5)2, where Δ1H and Δ15N are the chemical shift changes in the 1H and 15N dimensions, respectively. The symbols α and β in the graph indicate an α-helix and a β-strand, respectively, as observed in the crystal structure of the RRM1/2–poly(A) complex (Protein Data Bank code: 1CVJ (16)). The red lines at the 0.2 ppm represent the thresholds of residues mapped in Figure 7, E and F. E, RRM2 residues showing large chemical shift changes (>0.2 ppm) and labeled as “Perturbed” were mapped in green onto the crystal structure of RRM2 (Protein Data Bank code: 1CVJ (16)). The upper and lower parts are the ribbon model and surface drawing, respectively. F, RRM3 residues showing large chemical shift changes (>0.2 ppm) and labeled as “Perturbed” were mapped in green onto the homology model of RRM3. HSQC, heteronuclear single quantum coherence; RRM, RNA recognition motif.
PMC9019252
gr7.jpg
0.475354
81a6a40446274c389a98b03e3de89029
Chemical shift changes in uniformly15N-labeled RRM2/3 after adding Paip2A(25–83). A, overlay of 1H–15N HSQC spectra of 15N-labeled RRM2/3 in the absence (black) and the presence (red) of 1.25 equivalents of Paip2A(25–83). B, change in A150 signal of RRM2/3 upon titration of Paip2A(25–83). C, the upper bar graph shows the chemical shift changes in signals derived from RRM2, and the lower bar graph shows those from RRM3. Chemical shift changes were calculated using the following equation: δ = Δ1H2+(Δ15N/6.5)2, where Δ1H and Δ15N are the chemical shift changes in the 1H and 15N dimensions, respectively. The residues of the upper and lower graphs are arranged based on alignment between RRM2 and RRM3, and a secondary structure of these domains is shown in the graph. Signals with green labels were perturbed after adding Paip2A(25–83), and their corresponding signals in the Paip2A(25–83)-bound state could not be assigned because of broadening of the triple resonance signals. These residues are indicated as “Perturbed (P)” in C. The symbols α and β in the graph indicate an α-helix and a β-strand, respectively, as observed in the crystal structure of the RRM1/2–poly(A) complex (Protein Data Bank code: 1CVJ (16)). D, RRM2 residues showing large chemical shift changes labeled as “Perturbed” and I101 (>0.5 ppm) are mapped in green on the crystal structure of RRM2 (Protein Data Bank code: 1CVJ (16)). The upper and lower parts are the ribbon model and surface drawing, respectively. The square labels indicate that the residues interact with poly(A) directly in the crystal structure. E, RRM3 residues showing large chemical shift changes labeled as “Perturbed” were mapped in green onto the homology model of RRM3. The squares indicate the residues that are homologous to the residues of RRM2 that interact with poly(A) directly in the crystal structure. HSQC, heteronuclear single quantum coherence; Paip2A, PABP-interacting protein 2A; RRM, RNA recognition motif.
PMC9019252
gr8.jpg
0.463035
8d0c1ab73d8a409896fb48840a0c063c
1H–15N HSQC spectra of the RRM2/3 in the presence of equimolar A12and Paip2A(25–83). A, overlay of the 1H–15N HSQC spectra of 15N-labeled RRM2/3 in the presence of 1.25 equivalents of A12 (black) and 1.25 equivalents of both A12 and Paip2A(25–83) (red). B, overlay of the 1H–15N HSQC spectra of 15N-labeled RRM2/3 in the presence of 1.25 equivalents of Paip2A(25–83) (blue) and presence of 1.25 equivalents of both A12 and Paip2A(25–83) (red). HSQC, heteronuclear single quantum coherence; Paip2A, PABP-interacting protein 2A; RRM, RNA recognition motif.
PMC9019252
gr9.jpg
0.468572
c1151d2c19284ac3870cc1b47400b185
CBR3-AS1 is overexpressed in CRC. (a) RT-qPCR analysis of CBR3-AS1 expression levels in CRC tissues and adjacent normal tissues. (b) RT-qPCR analysis of CBR3-AS1 expression levels in CRC cell lines and FHC cells. (c) Kaplan-Meier analysis of correlation between CBR3-AS1 expression and overall survival of CRC patients. #P < 0.05 vs. FHC cells.
PMC9019443
JO2022-2260211.001.jpg
0.440153
4c6f4ad7a70741e5b3598cbe35441d78
CBR3-AS1 knockdown inhibits the malignant behaviors of CRC cells. (a) MTT assay showed the proliferation of CRC cells after transfection. (b) Flow cytometry analysis showed the apoptosis of CRC cells after transfection. (c) Transwell assay showed the migration and invasion of CRC cells after transfection. (d) Mammosphere formation assay showed the number of CRC cell mammospheres after transfection. (e) Western blot analysis showed the expression levels of CSC markers in CRC cells after transfection. ∗P < 0.05 vs. si-NC-transfected cells.
PMC9019443
JO2022-2260211.002.jpg
0.488223
aae848389c8840b58f1db4d1c9a8c782
CBR3-AS1 directly binds to miR-145-5p and inhibits its expression in CRC. (a) Cell fractionation analysis showed the subcellular distribution of CBR3-AS1 in CRC cells. (b) The predicted binding site of miR-145-5p within CBR3-AS1 fragment. (c) Dual-luciferase reporter assay validated the binding relation between CBR3-AS1 and miR-145-5p in CRC cells. (d) RIP assay showed the enrichment of CBR3-AS1 in CRC cells after transfection. (e) RT-qPCR analysis of miR-145-5p expression levels in CRC tissues and adjacent normal tissues. (f) An inverse expression correlation between CBR3-AS1 and miR-195-5p in CRC tissues. (g) RT-qPCR analysis of miR-145-5p expression levels in CRC cells after transfection. ∗P < 0.05 vs. mimics control-transfected cells; #P < 0.05 vs. IgG antibody; ^P < 0.05 vs. si-NC-transfected cells.
PMC9019443
JO2022-2260211.003.jpg