Journal: Frontiers in Microbiology

Article Title: Benchmark Evaluation of True Single Molecular Sequencing to Determine Cystic Fibrosis Airway Microbiome Diversity

doi: 10.3389/fmicb.2018.01069

Figure Lengend Snippet: Study subject demographics, cultured bacteria, and treatment antibiotics.

Article Snippet: Approximately 5 μg of dehydrated genomic bacterial DNA for P. aeruginosa (ATCC ® 47085D-5, strain PAO1-LAC), B. cepacia (ATCC ® 25416D-5), and Prevotella melaninogenica (ATCC ® 25845D-5) were obtained from ATCC (Manassas, VA, United States).

Techniques: Cell Culture, Bacteria

Journal: Frontiers in Microbiology

Article Title: Benchmark Evaluation of True Single Molecular Sequencing to Determine Cystic Fibrosis Airway Microbiome Diversity

doi: 10.3389/fmicb.2018.01069

Figure Lengend Snippet: Bacterial and viral taxonomic profile of pre- and post-antibiotic sputum samples in three subjects with cystic fibrosis who grew antibiotic resistant bacteria. Only bacterial and viral species with a minimum total observation count of 0.01% of total reads are shown for PathoScope (A) and Kraken (B) . Only bacterial and viral species with a minimum total observation count of 0.1% of total reads are shown for MetaPhlAn (C) . Burkholderia cepacia was the pathogen identified in culture for subject S1, but the majority of reads were attributed to Burkholderia cenocepacia. Pseudomonas aeruginosa was identified as the predominant bacteria for subjects S2 and S3, and was also identified in corresponding respiratory cultures.

Article Snippet: Approximately 5 μg of dehydrated genomic bacterial DNA for P. aeruginosa (ATCC ® 47085D-5, strain PAO1-LAC), B. cepacia (ATCC ® 25416D-5), and Prevotella melaninogenica (ATCC ® 25845D-5) were obtained from ATCC (Manassas, VA, United States).

Techniques: Bacteria

Journal: Epilepsia open

Article Title: Early preclinical plasma protein biomarkers of brain trauma are influenced by early seizures and levetiracetam.

doi: 10.1002/epi4.12738

Figure Lengend Snippet: FIGURE 2 Plasma protein biomarker levels in LFPI-LEV0, LFPI-LEV200, sham, and naïve control rats at 2 d or 7 d post-craniotomy/ LFPI and equivalent timepoints in controls. (A) Plasma levels of the biomarkers expressed as log2-transformed Y-cept values, representing total biomarker signal intensity of undiluted plasma sample. (B) Summary of significant pairwise differences in plasma biomarker levels. The matrices depict significant pairwise differences of LFPI-LEV0, LFPI-LEV200 or sham vs. the rest of the groups from the same day (2 d or 7 d), using the pairwise Student's t-test results (P < 0.05). “Higher” (red boxes) or “lower” (blue boxes) values indicate higher or lower levels respectively in the reference group (left columns, i.e., LFPI-LEV0 or LFPI-LEV200, or Sham in each table) vs. the comparator group indicated in each column, during the same timepoint. Statistical comparisons were done by linear mixed model analyses, considering repeated measures. Pairwise comparisons were done with Tukey HSD (red arrows indicate P < 0.05) and for exploratory purpose with Student t-tests (blue arrows indicate P < 0.05). d, days; GFAP, glial fibrillary acidic protein; HMGB1, high mobility group box protein 1; HSP70, heat shock protein 70 kD; IFNγ, interferon γ; IL-1β, Interleukin 1β; IL-6, Interleukin-6; LFPI-LEV0, vehicle-treated LFPI rats; LFPI- LEV200, levetiracetam 200 mg/kg bolus i.p. followed by 200 mg/kg/day treated LFPI rats; NFL, neurofilament light chain; pTAU-Thr231, phosphorylated TAU at Thr231; S100B, calcium-binding protein S100B; TAU, microtubule-associated protein; TNF, tumor necrosis factor; UCHL1, ubiquitin C-terminal hydrolase.

Article Snippet: Levetiracetam (LEV) (HY- B0106, MedChem Express) was dissolved in 0.9% sterile saline.

Techniques: Clinical Proteomics, Biomarker Discovery, Control, Transformation Assay, Binding Assay, Ubiquitin Proteomics

Journal: Epilepsia open

Article Title: Early preclinical plasma protein biomarkers of brain trauma are influenced by early seizures and levetiracetam.

doi: 10.1002/epi4.12738

Figure Lengend Snippet: FIGURE 3 Effects of early post-LFPI seizures and LEV upon protein biomarkers in LFPI rats. (A) Plasma levels of the biomarkers expressed as log2-transformed Y-cept values, representing total biomarker signal intensity of undiluted plasma sample, in LFPI-LEV0 (LEV0 in the graphs) and LFPI-LEV200 (LEV200 in the graphs) rats with (Sz) or without seizures (No Sz) at 2 d or 7 d post-LFPI. (B) Summary of the significant pairwise differences in plasma biomarker levels observed in the mixed model analyses with repeated measures shown in panel A. “Higher” (red boxes) or “lower” (blue boxes) indicate higher or lower levels respectively in the reference group [left columns of each table, i.e., LFPI-LEV0 with seizures (LFPI-LEV0, Sz), or LFPI-LEV200 with seizures (LFPI-LEV200, Sz), or LFPI-LEV0 without seizures (LFPI-LEV0, No Sz)] vs. the comparator group indicated in each column of the matrix, during the same timepoint. Early seizures and LEV treatment significantly alter plasma levels of several biomarkers, including pTAU-Thr231, pTAU-Thr231/TAU, UCHL1, IFNγ, HMGB1, NFL. The presence of early seizures is associated with lower levels of 2d-pTAU-Thr231 and 2d-pTAU-Thr231/TAU only in LFPI rats that were not treated with LEV, but this effect is transient and not seen at 7d. LFPI-LEV0 rats with early seizures have higher levels of UCHL1 at 2d than LFPI-LEV200 rats with or without seizures. On the other hand, the presence of early seizures in LFPI-LEV200 rats is marked by higher 2d-IFNγ plasma levels than in LFPI-LEV0 or LFPI rats without early seizures. LFPI-LEV200 rats have higher HMGB1 plasma levels at both 2 d and 7 d, regardless of early seizure presence. LFPI-LEV200 rats have higher NFL plasma levels at 2 d but not at 7 d, regardless of early seizure presence. Significant pairwise differences after linear mixed model analyses and post hoc Tukey HSD (red arrows) or Student's t-test (blue arrows). d, days; GFAP, glial fibrillary acidic protein; HMGB1, high mobility group box protein 1; HSP70, heat shock protein 70 kD; IFNγ, interferon γ; IL-1 β, Interleukin 1β; IL-6, Interleukin-6; LFPI-LEV0, vehicle-treated LFPI rats; LFPI-LEV200, levetiracetam 200 mg/kg bolus i.p. followed by 200 mg/kg/day treated LFPI rats; NFL, neurofilament light chain; pTAU-Thr231, phosphorylated TAU at Thr231; S100B, calcium-binding protein S100B; Sz, early seizures; TAU, microtubule-associated protein; TNF, tumor necrosis factor; UCHL1, ubiquitin C- terminal hydrolase.

Article Snippet: Levetiracetam (LEV) (HY- B0106, MedChem Express) was dissolved in 0.9% sterile saline.

Techniques: Clinical Proteomics, Transformation Assay, Biomarker Discovery, Binding Assay, Ubiquitin Proteomics

Journal: Epilepsia open

Article Title: Early preclinical plasma protein biomarkers of brain trauma are influenced by early seizures and levetiracetam.

doi: 10.1002/epi4.12738

Figure Lengend Snippet: FIGURE 4 Selection of the most predictive biomarkers with the penalized logistic regression with the Lasso penalty. (A) LASSO coefficients of 2d and 7d biomarkers predicting LFPI, LEV treatment or early seizures considering all LFPI rats combined, LFPI-LEV0 only, or LFPI-LEV200 only. The 2 d biomarkers offer better prediction for LFPI status or early seizures whereas both 2 d and 7 d biomarkers were predictive of LEV treatment. (B) LASSO coefficients of 2 d, 7 d, or change from 2 d to 7 d plasma biomarkers predicting neuromotor functional recovery based on composite neuroscore improvement from 2 d to 7 d. Better neuromotor functional recovery (i.e., composite neuroscore improvement) from 2 d to 7 d is predicted by higher S100B and lower HMGB1 plasma levels at 2 d post-LFPI and increase in HMGB1 and decrease in TNF plasma levels from 2 d to 7 d. Although 2d-TNFα and (7d-2d)-GFAP plasma levels had non-zero predictive coefficients, further linear regression showed borderline (P = 0.053) statistical significance for 2d-TNF and no significance for (7d-2d)-GFAP (P = 0.185). d, days; GFAP, glial fibrillary acidic protein; HMGB1, high mobility group box protein 1; HSP70, heat shock protein 70 kD; IFNγ, interferon γ; IL-1β, Interleukin 1β; IL-6, Interleukin-6; LFPI-LEV0, vehicle-treated LFPI rats; LFPI-LEV200, levetiracetam 200 mg/kg bolus i.p. followed by 200 mg/kg/day treated LFPI rats; NFL, neurofilament light chain; pTAU-Thr231, phosphorylated TAU at Thr231; S100B, calcium binding protein S100B; TAU, microtubule-associated protein; TNF, tumor necrosis factor; UCHL1, ubiquitin C-terminal hydrolase.

Article Snippet: Levetiracetam (LEV) (HY- B0106, MedChem Express) was dissolved in 0.9% sterile saline.

Techniques: Selection, Clinical Proteomics, Functional Assay, Binding Assay, Ubiquitin Proteomics

Journal: Epilepsia open

Article Title: Early preclinical plasma protein biomarkers of brain trauma are influenced by early seizures and levetiracetam.

doi: 10.1002/epi4.12738

Figure Lengend Snippet: FIGURE 5 ROC curves of biomarkers of LFPI or craniotomy (A), Levetiracetam (B) and early seizures (C). (A) ROC curves for biomarkers predicting LFPI vs. controls (sham or naïve), LFPI vs. controls only, or Sham ve controls (diagnostic biomarkers). (B) ROC curves for biomarkers predicting LEV treatment among LFPI rats (pharmacodynamic biomarkers). (C) ROC curves for biomarkers predicting early seizures among LFPI-LEV0 (prognostic biomarkers) and LFPI-LEV200 rats (prognostic or response biomarkers). The ROC AUC values (in parentheses) of the selected biomarkers are presented under each ROC. Biomarkers are color matched to the corresponding biomarker's ROC line. “Combined” means combination of the selected predictive biomarkers for each characteristic.

Article Snippet: Levetiracetam (LEV) (HY- B0106, MedChem Express) was dissolved in 0.9% sterile saline.

Techniques: Diagnostic Assay, Biomarker Discovery

Journal: Epilepsia open

Article Title: Early preclinical plasma protein biomarkers of brain trauma are influenced by early seizures and levetiracetam.

doi: 10.1002/epi4.12738

Figure Lengend Snippet: FIGURE 7 Plasma NFL levels at 2d post-TBI are higher in LFPI-LEV200 rats with longer apnea times. (A) Plasma 2d-NFL levels correlate positively with apnea duration in LFPI-LEV200 rats (P = 0.001) but not in LFPI-LEV0 (P = 0.959). Linear regression plots for the two groups are shown in this panel. (B). Plasma 2d-NFL levels are higher in LFPI-LEV200 rats with apneas longer than 20 s (P = 0.02, Exact test, Wilcoxon/Kruskal–Wallis test). ANOVA yielded significant effects for LEV treatment (F = 13.818, P = 0.001), apnea >20 s (F = 8.032, P = 0.009), and the interaction of LEV treatment and apnea >20 s (F = 6.211, P = 0.02). LFPI-LEV0, vehicle-treated LFPI rats; LFPI-LEV200, levetiracetam 200 mg/kg bolus i.p. followed by 200 mg/kg/day treated LFPI rats; NFL, neurofilament light chain.

Article Snippet: Levetiracetam (LEV) (HY- B0106, MedChem Express) was dissolved in 0.9% sterile saline.

Techniques: Clinical Proteomics

Journal: International Journal of Molecular Sciences

Article Title: The Chemokine Receptor CCR3 Is Potentially Involved in the Homing of Prostate Cancer Cells to Bone: Implication of Bone-Marrow Adipocytes

doi: 10.3390/ijms22041994

Figure Lengend Snippet: CCR3 is an important driver in the directed migration of PCa cells towards BM-Ad-CM and its effect is majored in obesity and ageing conditions. In vitro migration of C4-2B ( A ) or PC3 ( B ) . CCR3 (UCB35625, 200 nM), CCR2 (sc-202525, 25 nM), CXCR1/2 (SB225002 inhibitor, 50 nM) or CXCR4 (AMD3100, 100 nM) or with mAbs against CCR3, CXCR1, CXCR2 or CXCR4 (all used at 10 μg/ml). Bar plots represent the percentage of migrating cells relative to the migration of untreated cells (set to 100%). Data are shown as mean ± sem ( n = 4–6). The statistical significance between means of migrating cells (in %) in treated vs. control cells was evaluated by One-way ANOVA with Tukey’s multiple comparisons test. Similar experiments were performed with the indicated cell lines towards BM-Ad-CM obtained either from lean/obese ( C ) or control/aged ( D ) subjects in the presence of CCR3 inhibitors and blocking mAb. Data are shown as mean ± sem ( n = 4–9). The statistical significance between mean of migrating cells (with the control groups set at 100%) was evaluated by Two-way ANOVA with Sidak’s multiple comparisons test. * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001, ns: not significant.

Article Snippet: Cells were also pre-incubated for 30 min at 37 °C with pharmacological inhibitors: 200nM CCR1/CCR3 inhibitor, UCB35625 (Tocris, Bristol, UK), 25nM CCR2 inhibitor, sc-202525 (Santa Cruz Biotechnology, Dallas, TE, USA), 50nM CXCR1/2 inhibitor, SB225002 (Tocris, Bristol, UK) or 100nM CXCR4 inhibitor, AMD3100 (Sigma-Aldrich, Saint Louis, MO, USA).

Techniques: Migration, In Vitro, Control, Blocking Assay