On the identification of differentially-active transcription factors from ATAC-seq data

ATAC-seq has emerged as a rich epigenome profiling technique, and is commonly used to identify Transcription Factors (TFs) underlying given phenomena. A number of methods can be used to identify differentially-active TFs through the accessibility of their DNA-binding motif, however little is known on the best approaches for doing so. Here we benchmark several such methods using a combination of curated datasets with various forms of short-term perturbations on known TFs, as well as semi-simulations. We include both methods specifically designed for this type of data as well as some that can be repurposed for it. We also investigate variations to these methods, and identify three particularly promising approaches (chromVAR-limma with critical adjustments, monaLisa and a combination of GC smooth quantile normalization and multivariate modeling). We further investigate the specific use of nucleosome-free fragments, the combination of top methods, and the impact of technical variation. Finally, we illustrate the use of the top methods on a novel dataset to characterize the impact on DNA accessibility of TRAnscription Factor TArgeting Chimeras (TRAFTAC), which can deplete TFs - in our case NFkB - at the protein level.

Validation of hypermethylated DNA regions found in colorectal cancers as potential aging-independent biomarkers of precancerous colorectal lesions

BACKGROUND

We previously identified 16,772 colorectal cancer-associated hypermethylated DNA regions that were also detectable in precancerous colorectal lesions (preCRCs) and unrelated to normal mucosal aging. We have now conducted a study to validate 990 of these differentially methylated DNA regions (DMRs) in a new series of preCRCs.

METHODS

We used targeted bisulfite sequencing to validate these 990 potential biomarkers in 59 preCRC tissue samples (41 conventional adenomas, 18 sessile serrated lesions), each with a patient-matched normal mucosal sample. Based on differential DNA methylation tests, a panel of candidate DMRs was chosen on a subset of our cohort and then validated on the remaining part of our cohort and two publicly available datasets with respect to their stratifying potential between preCRCs and normal mucosa.

RESULTS

Strong statistical significance for the difference in methylation levels was observed across the full set of 990 investigated DMRs. From these, a selected candidate panel of 30 DMRs correctly identified 58/59 tumors (area under the receiver operating curve: 0.998).

CONCLUSIONS

These validated DNA hypermethylation markers can be exploited to develop more accurate noninvasive colorectal tumor screening assays.

Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability

Computational methods represent the lifeblood of modern molecular biology. Benchmarking is important for all methods, but with a focus here on computational methods, benchmarking is critical to dissect important steps of analysis pipelines, formally assess performance across common situations as well as edge cases, and ultimately guide users on what tools to use. Benchmarking can also be important for community building and advancing methods in a principled way. We conducted a meta-analysis of recent single-cell benchmarks to summarize the scope, extensibility, and neutrality, as well as technical features and whether best practices in open data and reproducible research were followed. The results highlight that while benchmarks often make code available and are in principle reproducible, they remain difficult to extend, for example, as new methods and new ways to assess methods emerge. In addition, embracing containerization and workflow systems would enhance reusability of intermediate benchmarking results, thus also driving wider adoption.

Electronic Barriers Produced at Zno Surfaces By Ion Implantation And Annealing

Modern varistors are made of polycrystalline ZnO, doped to create Schottky-like barriers at the grain boundaries. To allow the study of tailored single barrier junctions, we have implanted ZnO crystals with Bi, Sb and transition metals. The electrical properties and the distribution of Bi and Sb were measured in the implanted crystals as a function of annealing temperature. After implantation and before heating, no barriers can be observed. After heating to 600–800°C, a high voltage (insulating) barrier is created. Heating to above 1000°C produces a 2-1/2 Volt barrier with high nonlinearity. The temperatures at which these barriers appear correspond, respectively, to temperatures at which motion of Sb and Bi first can be observed by ion backscattering techniques, and at which these elements diffuse freely.

Inactivation of foot and mouth disease virus in skimmed milk with propionic acid, citric acid and hydrogen peroxide

In order to protect farm animals from infections such as foot and mouth disease (FMD) and tuberculosis, the pasteurisation of milk and milk products designated for the feeding of animals is compulsory in Switzerland. Nowadays, milk products are often treated chemically with acids or with hydrogen peroxide in order to keep bacterial contamination low. The capacity of these chemical treatments to inactivate FMD virus in skimmed milk within 6 h at 5 degrees C was tested in this study. The results indicated that the addition of 0.1%-0.3% of consumable acids, such as citric acid or propionic acid, could not guarantee the complete inactivation of FMD virus in skimmed milk. Similar results were obtained both with FMD virus deliberately added to skimmed milk and with skimmed milk obtained from naturally infected cows. Hydrogen peroxide in concentrations of 0.1%-0.3% was also an ineffective means of controlling the risk of FMD virus transmission from contaminated milk.

High frequency polarization modulation method for measuring birefringence

A high frequency modulation method utilizing a photoelastic polarization modulator for the measurement of optical birefringence is described and discussed. Although the apparatus has the high sensitivity required to measure very small retardations, the accurate measurement of larger retardations is emphasized and a particularly simple null detection technique for such measurements is described. Results obtained for some common uniaxial crystals are presented and compared with previously obtained results.