Mature enteroendocrine cells contribute to basal and pathological stem cell dynamics in the small intestine.

Lgr5-expressing intestinal stem cells (ISCs) maintain continuous and rapid generation of the intestinal epithelium. Here, we present evidence that dedifferentiation of committed enteroendocrine cells (EECs) contributes to maintenance of the epithelium under both basal conditions and in response to injury. Lineage-tracing studies identified a subset of EECs that reside at +4 position for more than 2 wk, most of which were BrdU-label-retaining cells. Under basal conditions, cells derived from these EECs grow from the bottom of the crypt to generate intestinal epithelium according to neutral drift kinetics that is consistent with dedifferentiation of mature EECs to ISCs. The lineage tracing of EECs demonstrated reserve stem cell properties in response to radiation-induced injury with the generation of reparative EEC-derived epithelial patches. Finally, the enterochromaffin (EC) cell was the predominant EEC type participating in these stem cell dynamics. These results provide novel insights into the +4 reserve ISC hypothesis, stem cell dynamics of the intestinal epithelium, and in the development of EC-derived small intestinal tumors. NEW & NOTEWORTHY The current manuscript demonstrating that a subset of mature enteroendocrine cells (EECs), predominantly enterochromaffin cells, dedifferentiates to fully functional intestinal stem cells (ISCs) is novel, timely, and important. These cells dedifferentiate to ISCs not only in response to injury but also under basal homeostatic conditions. These novel findings provide a mechanism in which a specified cell can dedifferentiate and contribute to normal tissue plasticity as well as the development of EEC-derived intestinal tumors under pathologic conditions.

Masking as an effective quality control method for next-generation sequencing data analysis.

BACKGROUND: Next generation sequencing produces base calls with low quality scores that can affect the accuracy of identifying simple nucleotide variation calls, including single nucleotide polymorphisms and small insertions and deletions. Here we compare the effectiveness of two data preprocessing methods, masking and trimming, and the accuracy of simple nucleotide variation calls on whole-genome sequence data from Caenorhabditis elegans. Masking substitutes low quality base calls with 'N's (undetermined bases), whereas trimming removes low quality bases that results in a shorter read lengths. RESULTS: We demonstrate that masking is more effective than trimming in reducing the false-positive rate in single nucleotide polymorphism (SNP) calling. However, both of the preprocessing methods did not affect the false-negative rate in SNP calling with statistical significance compared to the data analysis without preprocessing. False-positive rate and false-negative rate for small insertions and deletions did not show differences between masking and trimming. CONCLUSIONS: We recommend masking over trimming as a more effective preprocessing method for next generation sequencing data analysis since masking reduces the false-positive rate in SNP calling without sacrificing the false-negative rate although trimming is more commonly used currently in the field. The perl script for masking is available at http://code.google.com/p/subn/. The sequencing data used in the study were deposited in the Sequence Read Archive (SRX450968 and SRX451773).

Analysis of the stabilities of hexameric amyloid-ß(1-42) models using discrete molecular dynamics simulations.

Amyloid-ß (Aß) oligomers appear to play a pivotal role in Alzheimer's disease. A 42 residue long alloform, Aß42, is closely related to etiology of the disease. In vitro results show evidences of hexamers; however structures of these hexamers have not been resolved experimentally. Here, we use discrete molecular dynamics (DMD) to analyze long duration stabilities of Aß42 hexamer models developed previously in our lab. The hydrophobic core of these models is a six-stranded ß-barrel with 3-fold radial symmetry formed by residues 30-40. This core is shielded from water by residues 1-28. The nine models we analyzed differ by the relative positions of the core ß-strands, and whether the other segments surrounding the core contain α helices or ß-strands. A model of an annular protofibril composed of 36 Aß peptides was also simulated. Results of these model simulations were compared with results of aggregation simulations that started from six well separated random coils of Aß42 and with simulations of two known ß-barrel structures. These results can be categorized into three groups: stable models with properties similar or superior to those of experimentally determined ß-barrel proteins, aggregation-prone models, and an amorphous aggregate from random coils. Conformations at the end of the simulation for aggregation-prone models have exposed hydrophobic core with dangling ß-strands on the surface. Hydrogen bond patterns within the ß-barrel were a critical factor for stability of the ß-barrel models. Aggregation-prone conformations imply that the association of these hexamers may be possible, which could lead to the formation of larger assemblies.

MRI volumetric analysis techniques, including hippocampus extraction, based on data from the Honolulu Asia Aging Study (HAAS).

PURPOSE: The purpose of this study is to develop and apply methods for volumetric analyses of magnetic resonance imaging (MRI) data for future comparisons with autopsy findings from the same subjects. METHODS: HAAS MRI data analysis was run using the Oxford Centre for Functional Magnetic Resonance imaging of the Brain's (FMRIB) Software Library (FSL). The Brain Extraction Tool (BET) performed brain extraction and nonlinear noise reduction with FMRIB's Smallest Univalue Segment Assimilating Nucleus (SUSAN), and extraction of hippocampus data was performed with FMRIB's Integrated Registration and Segmentation Tool (FIRST). RESULTS: Scull stripping and the extraction of the hippocampus data created a computerized model. DISCUSSION: MRI analysis techniques can be applied when comparing MRI data to autopsy results. Using the combination of this autopsy and MRI data, this study will make it possible to estimate in vivo states.