A Niche for Adult Neurogenesis: Analysis of BMP Signaling and Transcriptional Profiles of Adult Subventricular Zone Cells

Neurogenesis persists in restricted regions of the adult vertebrate brain. The largest region of adult neurogenesis is the subventricular zone (SVZ) of the lateral ventricle wall. Neural stem cells reside in the SVZ. The S V Z cell types and molecular signals necessary for this neurogenic niche were poorly understood. Here, I first demonstrate that astrocyte-like cells in the SVZ (type B cells) can self-renew and differentiate into mature brain cells. This data contributed to the identification of type B cells as the S V Z stem cell. In vivo, all S V Z cell types are in direct contact with type B cells. By reconstituting cell-cell interactions of dissociated SVZ cells in culture, I defined an in vitro cellular environment that recapitulates SVZ neurogenesis; these cultures provided an in vitro assay for the study of external molecular signals that regulate S V Z neurogenesis. Ependymal cells lie adjacent to the SVZ. I show that the bone morphogenetic protein (BMP) antagonist Noggin is expressed by ependymal cells and that S V Z cells express B M P s as well as their receptors. In vitro, B M P signaling potently inhibited neurogenesis. Conversely, Noggin protein in vitro promoted neurogenesis. Overexpression of BMPs in ependymal cells decreased SVZ cell proliferation and abolished type A cell regeneration. Ectopic Noggin expression in the normally nonneurogenic striatum promoted neuronal differentiation of transplanted S V Z cells. I thus propose that ependymal Noggin production creates a neurogenic niche in the adjacent SVZ by antagonizing B M P signaling. To identify other genes with roles in the SVZ, I utilized high-density oligonucleotide arrays to determine the transcriptional profiles of the S V Z region as well as purified type B and ependymal cells. SVZ regional and cell-specific expression profiles were compared to those of other brain regions. Differential gene expression was validated by Northern blot and histological techniques. This transcriptional profile data provides new markers and candidate regulatory genes for future investigations into the SVZ neurogenic niche

Comparison of Circumferential and Traditional Trabeculotomy in Pediatric Glaucoma

Purpose To compare intraocular pressure (IOP) control of pediatric glaucoma patients undergoing traditional trabeculotomy (<360 degrees or partial) with those receiving 360-degree circumferential trabeculotomy. Methods The medical records of pediatric glaucoma patients receiving trabeculotomy at a single institution from 2000 to 2012were retrospectively reviewed. Patients were divided into two groups: a traditional trabeculotomy group and 360-degree trabeculotomy group. IOP at baseline and at 1, 3, 6, and 12 months’ follow-up were compared within and each groups. Results A total of 77 eyes of 56 patients (age at surgery, 1.52 ± 2.68 years) in the traditional group and 14 eyes of 10 patients in the 360-degree group (age at surgery, 0.61 ± 0.42 years) were included. Mean baseline IOP was similar in both groups (traditional, 28.75 ± 8.80 mm Hg; 360-degree, 30.35 ± 6.04 mm Hg; t test; P = 0.43). Mean 1-year IOP was 17.05 ± 5.92 mm Hg in the traditional group and 11.0 ± 2.31 mm Hg in the 360-degree group. At 1-year, the surgical success rate was 58.44% in the traditional group and 85.71% in the 360-degree group; 32 eyes in the former and 2 eyes in the latter required another glaucoma procedure within 1 year for IOP control. For both groups, compared to baseline values, IOP decreased significantly with all postoperative measurements (paired t test, all P < 0.01). The 360-degree group had significantly lower IOP compared to the traditional group at 1-year (t test, P < 0.01). Conclusions Both 360-degree and traditional trabeculotomy significantly reduced IOP in children through 1 year’s follow-up, although the former procedure shows better 1-year postoperative IOP control, with higher rate of surgical success

The Metal-Insulator Transition in \u3cem\u3eVO\u3csub\u3e2\u3c/sub\u3e\u3c/em\u3e Studied using Terahertz Apertureless Near-Field Microscopy

We have studied the metal-insulator transition in a vanadium dioxide (VO2) thin film using terahertz apertureless near-field optical microscopy. We observe a variation of the terahertz amplitude due to the phase transition induced by an applied voltage across the sample. The change of the terahertz signal is related to the abrupt change of the conductivity of the VO2 film at the metal-insulator transition. The subwavelength spatial resolution of this near-field microscopy makes it possible to detect signatures of micron-scale metallic domains in inhomogeneous VO2 thin films

CRISPRi-based radiation modifier screen identifies long non-coding RNA therapeutic targets in glioma.

BackgroundLong non-coding RNAs (lncRNAs) exhibit highly cell type-specific expression and function, making this class of transcript attractive for targeted cancer therapy. However, the vast majority of lncRNAs have not been tested as potential therapeutic targets, particularly in the context of currently used cancer treatments. Malignant glioma is rapidly fatal, and ionizing radiation is part of the current standard-of-care used to slow tumor growth in both adult and pediatric patients.ResultsWe use CRISPR interference (CRISPRi) to screen 5689 lncRNA loci in human glioblastoma (GBM) cells, identifying 467 hits that modify cell growth in the presence of clinically relevant doses of fractionated radiation. Thirty-three of these lncRNA hits sensitize cells to radiation, and based on their expression in adult and pediatric gliomas, nine of these hits are prioritized as lncRNA Glioma Radiation Sensitizers (lncGRS). Knockdown of lncGRS-1, a primate-conserved, nuclear-enriched lncRNA, inhibits the growth and proliferation of primary adult and pediatric glioma cells, but not the viability of normal brain cells. Using human brain organoids comprised of mature neural cell types as a three-dimensional tissue substrate to model the invasive growth of glioma, we find that antisense oligonucleotides targeting lncGRS-1 selectively decrease tumor growth and sensitize glioma cells to radiation therapy.ConclusionsThese studies identify lncGRS-1 as a glioma-specific therapeutic target and establish a generalizable approach to rapidly identify novel therapeutic targets in the vast non-coding genome to enhance radiation therapy

DNA hybridization to mismatched templates: a chip study

High-density oligonucleotide arrays are among the most rapidly expanding technologies in biology today. In the {\sl GeneChip} system, the reconstruction of the target concentration depends upon the differential signal generated from hybridizing the target RNA to two nearly identical templates: a perfect match (PM) and a single mismatch (MM) probe. It has been observed that a large fraction of MM probes repeatably bind targets better than the PMs, against the usual expectation from sequence-specific hybridization; this is difficult to interpret in terms of the underlying physics. We examine this problem via a statistical analysis of a large set of microarray experiments. We classify the probes according to their signal to noise ($S/N$) ratio, defined as the eccentricity of a (PM, MM) pair's `trajectory' across many experiments. Of those probes having large $S/N$ ($>3$) only a fraction behave consistently with the commonly assumed hybridization model. Our results imply that the physics of DNA hybridization in microarrays is more complex than expected, and they suggest new ways of constructing estimators for the target RNA concentration.Comment: 3 figures 1 tabl

Single-cell analysis of long non-coding RNAs in the developing human neocortex

Single cell transcriptomics of lncRNA expression in K562 cell cultures. A Distributions of median lncRNA expression to median mRNA expression ratios (lncRNA:mRNA) in populations, in silico merged single cells, and single cells from K562 cultures. B Proportion of K562 cells that expressed each lncRNA (blue) and mRNA (red), separated by maximum expression in single cells. C Same as in (B) but grouped by maximum expression quantile. D Distributions of non-zero lncRNA (blue) and mRNA (red) expression in 46 single K562 cells. Green squares, housekeeping genes; black triangles, ERCC Spike-In Controls. (PDF 454 kb

Strong social relationships are associated with decreased longevity in a facultatively social mammal

Data accessibility. Data are available from the Dryad Digital Repository at: https://doi.org/10.5061/dryad.h8n7p [40]. D.T.B. was supported by the National Geographic Society, UCLA (Faculty Senate and the Division of Life Sciences), a Rocky Mountain Biological Laboratory research fellowship and by the NSF (IDBR-0754247, and DEB-1119660 and 1557130 to D.T.B., as well as DBI-0242960, 0731346 and 1226713 to the Rocky Mountain Biological Laboratory).Peer reviewedPostprin

Genomic epidemiology and transmission dynamics of recurrent Clostridioides difficile infection in Western Australia

Recurrent cases of Clostridioides difficile infection (rCDI) remain one of the most common and serious challenges faced in the management of CDI. The accurate distinction between a relapse (caused by infection with the same strain) and reinfection (caused by a new strain) has implications for infection control and prevention, and patient therapy. Here, we used whole-genome sequencing to investigate the epidemiology of 94 C. difficile isolates from 38 patients with rCDI in Western Australia. The C. difficile strain population comprised 13 sequence types (STs) led by ST2 (PCR ribotype (RT) 014, 36.2 %), ST8 (RT002, 19.1 %) and ST34 (RT056, 11.7 %). Among 38 patients, core genome SNP (cgSNP) typing found 27 strains (71%) from initial and recurring cases differed by ≤ 2 cgSNPs, suggesting a likely relapse of infection with the initial strain, while eight strains differed by ≥ 3 cgSNPs, suggesting reinfection. Almost half of patients with CDI relapse confirmed by WGS suffered episodes that occurred outside the widely used 8-week cut-off for defining rCDI. Several putative strain transmission events between epidemiologically unrelated patients were identified. Isolates of STs 2 and 34 from rCDI cases and environmental sources shared a recent evolutionary history, suggesting a possible common community reservoir. For some rCDI episodes caused by STs 2 and 231, within-host strain diversity was observed, characterised by loss/gain of moxifloxacin resistance. Genomics improves discrimination of relapse from reinfection and identifies putative strain transmission events among patients with rCDI. Current definitions of relapse and reinfection based on the timing of recurrence need to be reconsidered