Identifying DNA methylation biomarkers for non-endoscopic detection of Barrett’s esophagus

We report a biomarker-based non-endoscopic method for detecting Barrett’s esophagus (BE), based on detecting methylated DNAs retrieved via a swallowable balloon-based esophageal sampling device. BE is the precursor of, and a major recognized risk factor for, developing esophageal adenocarcinoma (EAC). Endoscopy, the current standard for BE detection, is not cost-effective for population screening. We performed genome-wide screening to ascertain regions targeted for recurrent aberrant cytosine methylation in BE, identifying high-frequency methylation within the CCNA1 locus. We tested CCNA1 DNA methylation as a BE biomarker in cytology brushings of the distal esophagus from 173 individuals with or without BE. CCNA1 DNA methylation demonstrated an area under the curve (AUC)=0.95 for discriminating BE-related metaplasia and neoplasia cases versus normal individuals, performing identically to methylation of VIM DNA, an established BE biomarker. When combined, the resulting two biomarker panel was 95% sensitive and 91% specific. These results were replicated in an independent validation cohort of 149 individuals, who were assayed using the same cutoff values for test positivity established in the training population. To progress toward non-endoscopic esophageal screening, we engineered a well-tolerated, swallowable, encapsulated balloon device able to selectively sample the distal esophagus within 5 minutes. In balloon samples from 86 individuals, tests of CCNA1 plus VIM DNA methylation detected BE metaplasia with 90.3% sensitivity and 91.7% specificity. Combining the balloon sampling device with molecular assays of CCNA1 plus VIM DNA methylation enables an efficient, well-tolerated, sensitive, and specific method of screening at-risk populations for BE

Genome Sequence of a Cellulose-Producing Bacterium, Gluconacetobacter hansenii ATCC 23769▿

The Gram-negative bacterium Gluconacetobacter hansenii is considered a model organism for studying cellulose synthesis. We have determined the genome sequence of strain ATCC 23769

Results of nodule detection along AUV track SO239_115-1_AUV9 (Abyss_175) during SONNE cruise SO239

Images were acquired by the DeepSurvey Camera on board GEOMAR's AUV Abyss. Nodules were delineated by the CoMoNoD algorithm [see related to references]. Result files are computed per AUV dive. Nodule detections below 5cm^2 are neglected as are detections above 707cm^2. Abundance statistics are computed per m^2 and gridded per m^2 as well. For overlapping images, max-pooling has been applied to select the values reported in the result files. Pixel values in the rendered maps correspond to the units reported in the ASCI files (median-nodule-size: cm^2, nodule-number: m^-2, percent-coverage: %, sorting, skewness and pixel-contributions are unit-free)

Comparison of growth of newly emerging third leaves of control and apoplast (T27 and T27R) or Golgi (T28 and T29) FAE expressing plants.

<p>Growth as increase in leaf length (A), distribution of growth within the elongation zone of leaf blades, determined as the relative segmental elongation rate (B), maximum daily extension rate (C), and leaf length at maximum extension rate (D). Mean ± SEM (n = 20–30 from each plant). Third leaves from tillers of 2–3 plants per line were measured until leaf length was constant. Letters indicate significant difference (Tukey’s, α = 0.05) among mean values.</p

Chlorophyll content of leaves of control and an FAE expressing plant (T27R) during leaf senescence.

<p>Chlorophyll content of leaves of control and an FAE expressing plant (T27R) during leaf senescence.</p

Levels of FAE enzyme activity in 10 mm segments along 12–14 cm leaf blades starting at the cell elongation zone of control, apoplast (T27 and T27R) and Golgi (T28 and T29) FAE expressing plants.

<p>Mean ± SEM (n = 2–3 replicates of 25–30 leaf sections from two independent transformed plants). L = ligula; EZ = extension zone. One unit of FAEA activity equals 1 μg ferulic acid released from ethyl ferulate in 24 h at 28°C.</p

Ester linked HCAs in mature roots.

<p><i>p</i>-coumaric acid (A), ferulate monomers (B) and ferulate dimers (C). Ferulate monomers = trans- ferulic+ cis-ferulic acid. Ferulate dimers = 8-0-4’-diferulate + 5–5’ diferulate + 8-5cyclic diferulate (benzo form) + 8–5’-diferulate + an unknown ferulate dimer. Mean ± SEM (n = 2). Different letters indicate significant differences from the control (Tukey’s = 0.05).</p

4-Aminoquinolone Piperidine Amides: Noncovalent Inhibitors of DprE1 with Long Residence Time and Potent Antimycobacterial Activity

4-Aminoquinolone piperidine amides (AQs) were identified as a novel scaffold starting from a whole cell screen, with potent cidality on Mycobacterium tuberculosis (Mtb). Evaluation of the minimum inhibitory concentrations, followed by whole genome sequencing of mutants raised against AQs, identified decaprenylphosphoryl-beta-D-ribose 2'-epimerase (DprE1) as the primary target responsible for the antitubercular activity. Mass spectrometry and enzyme kinetic studies indicated that AQs are noncovalent, reversible inhibitors of DprE1 with slow on rates and long residence times of similar to 100 min on the enzyme. In general, AQs have excellent leadlike properties and good in vitro secondary pharmacology profile. Although the scaffold started off as a single active compound with moderate potency from the whole cell screen, structure-activity relationship optimization of the scaffold led to compounds with potent DprE1 inhibition (IC50 < 10 nM) along with potent cellular activity (MIC = 60 nM) against Mtb