Neil R. Smalheiser

Dicer and eIF2c are enriched at postsynaptic densities in adult mouse brain and are modified by neuronal activity in a calpain-dependent manner.

We have hypothesized that small RNAs may participate in learning and memory mechanisms. Because dendritic spines are important in synaptic plasticity and learning, we asked whether dicer, the rate‐limiting enzyme in the formation of small RNAs, is enriched within dendritic spines. In adult mouse brain, dicer and the RNA‐induced silencing complex (RISC) component eIF2c were expressed in the somatodendritic compartment of principal neurons and some interneurons in many regions, and dicer was enriched in dendritic spines and postsynaptic densities (PSDs). A portion of dicer and eIF2c were associated with each other and with fragile X mental retardation protein (FMRP), as assessed by co‐immunoprecipitation. Calpain I treatment of recombinant dicer or immunopurified brain dicer caused a marked increase in RNAse III activity. Purified PSDs did not exhibit RNAse III activity, but calpain caused release of dicer from PSDs in an enzymatically active form, together with eIF2c. NMDA stimulation of hippocampal slices, or calcium treatment of synaptoneurosomes, caused a 75 kDa dicer fragment to appear in a calpain‐dependent manner. The findings support a model whereby acute neuronal stimulation at excitatory synapses increases intracellular calcium, which activates calpain, which liberates dicer and eIF2c bound to PSDs. This supports the hypothesis that dicer could be involved in synaptic plasticity.

Antidepressants alter cell proliferation in the adult brain in vivo and in neural cultures in vitro.

The action of antidepressants on cell proliferation (bromodeoxyuridine (BrdU) or [3H]thymidine incorporation) was studied in the adult rat hippocampus in vivo and in neural precursors (immature rat cerebellar granule cells) in vitro. In vivo, prolonged (21 days) but not acute (single) intraperitoneal treatment with fluoxetine (5 mg/kg) resulted in a 3.4-fold increase of bromodeoxyuridine-positive cells in the subgranular zone of the dentate gyrus. In cell cultures, at 1 and 10 days in vitro, 48-h fluoxetine exposure (1 microM, which is comparable to therapeutic plasma concentrations) reduced thymidine incorporation when initiated at 1 day in vitro, but increased cell proliferation when initiated at 10 days in vitro. Clomipramine and imipramine produced similar action in vitro; desipramine was ineffective.

Expression of microRNAs and their precursors in synaptic fractions of adult mouse forebrain

We have characterized the expression of microRNAs and selected microRNA precursors within several synaptic fractions of adult mouse forebrain, including synaptoneurosomes, synaptosomes and isolated post‐synaptic densities (PSDs), using methods of microRNA microarray, real time qRT‐PCR, Northern blotting and immunopurification using anti‐PSD95 antibody. The majority of brain microRNAs (especially microRNAs known to be expressed in pyramidal neurons) are detectably expressed in synaptic fractions, and a subset of microRNAs is significantly enriched in synaptic fractions relative to total forebrain homogenate. MicroRNA precursors are also detectable in synaptic fractions at levels that are comparable to whole tissue. Whereas mature microRNAs are predominantly associated with soluble components of the synaptic fractions, microRNA precursors are predominantly associated with PSDs. For seven microRNAs examined, there was a significant correlation between the relative synaptic enrichment of the precursor and the relative synaptic enrichment of the corresponding mature microRNA. These findings support the proposal that microRNAs are formed, at least in part, via processing of microRNA precursors locally within dendritic spines. Dicer is expressed in PSDs but is enzymatically inactive until conditions that activate calpain cause its liberation; thus, we propose that synaptic stimulation may lead to local processing of microRNA precursors in proximity to the synapse.

MicroRNA Expression Is Down-Regulated and Reorganized in Prefrontal Cortex of Depressed Suicide Subjects

Background Recent studies suggest that alterations in expression of genes, including those which regulate neural and structural plasticity, may be crucial in the pathogenesis of depression. MicroRNAs (miRNAs) are newly discovered regulators of gene expression that have recently been implicated in a variety of human diseases, including neuropsychiatric diseases. Methodology/Principal Findings The present study was undertaken to examine whether the miRNA network is altered in the brain of depressed suicide subjects. Expression of miRNAs was measured in prefrontal cortex (Brodmann Area 9) of antidepressant-free depressed suicide (n = 18) and well-matched non-psychiatric control subjects (n = 17) using multiplex RT-PCR plates. We found that overall miRNA expression was significantly and globally down-regulated in prefrontal cortex of depressed suicide subjects. Using individual tests of statistical significance, 21 miRNAs were significantly decreased at p = 0.05 or better. Many of the down-regulated miRNAs were encoded at nearby chromosomal loci, shared motifs within the 5′-seeds, and shared putative mRNA targets, several of which have been implicated in depression. In addition, a set of 29 miRNAs, whose expression was not pairwise correlated in the normal controls, showed a high degree of co-regulation across individuals in the depressed suicide group. Conclusions/Significance The findings show widespread changes in miRNA expression that are likely to participate in pathogenesis of major depression and/or suicide. Further studies are needed to identify whether the miRNA changes lead to altered expression of prefrontal cortex mRNAs, either directly (by acting as miRNA targets) or indirectly (e.g., by affecting transcription factors).

Author name disambiguation in MEDLINE

Background: We recently described “Author-ity,” a model for estimating the probability that two articles in MEDLINE, sharing the same author name, were written by the same individual. Features include shared title words, journal name, coauthors, medical subject headings, language, affiliations, and author name features (middle initial, suffix, and prevalence in MEDLINE). Here we test the hypothesis that the Author-ity model will suffice to disambiguate author names for the vast majority of articles in MEDLINE. Methods: Enhancements include: (a) incorporating first names and their variants, email addresses, and correlations between specific last names and affiliation words; (b) new methods of generating large unbiased training sets; (c) new methods for estimating the prior probability; (d) a weighted least squares algorithm for correcting transitivity violations; and (e) a maximum likelihood based agglomerative algorithm for computing clusters of articles that represent inferred author-individuals. Results: Pairwise comparisons were computed for all author names on all 15.3 million articles in MEDLINE (2006 baseline), that share last name and first initial, to create Author-ity 2006, a database that has each name on each article assigned to one of 6.7 million inferred author-individual clusters. Recall is estimated at ∼98.8%. Lumping (putting two different individuals into the same cluster) affects ∼0.5% of clusters, whereas splitting (assigning articles written by the same individual to >1 cluster) affects ∼2% of articles. Impact: The Author-ity model can be applied generally to other bibliographic databases. Author name disambiguation allows information retrieval and data integration to become person-centered, not just document-centered, setting the stage for new data mining and social network tools that will facilitate the analysis of scholarly publishing and collaboration behavior. Availability: The Author-ity 2006 database is available for nonprofit academic research, and can be freely queried via http://arrowsmith.psych.uic.edu.

A probabilistic similarity metric for Medline records: a model for author name disambiguation.

We present a model for automatically generating training sets and estimating the probability that a pair of Medline records sharing a last and first name initial are authored by the same individual, based on shared title words, journal name, co-authors, medical subject headings, language, and affiliation, as well as distinctive features of the name itself (i.e., presence of middle initial, suffix, and prevalence in Medline).

The Relationship between Perlecan and Dystroglycan and its Implication in the Formation of the Neuromuscular Junction

Perlecan is a major heparan-sulfate proteoglycan (HSPG) within the basement membrane surrounding skeletal muscle fibers. The C-terminus of its core protein contains three globular domain modules which are also found in laminin and agrin, two proteins that bind to dystroglycan (DG, cranin) on the muscle surface with these modules. In this study, we examined whether perlecan can also bind to DG and is involved in signaling the formation of the neuromuscular junction (NMJ). By labeling cultured muscle cells with a polyclonal anti-perlecan antibody, this protein is found both within the extracellular matrix in a fibrillar network and at the cell surface in a punctate pattern. In Xenopus muscle cells, the cell-surface perlecan is precisely colocalized with DG. Both perlecan and DG are clustered at ACh receptor clusters induced by spinal neurons or by beads coated with HB-GAM, a heparin-binding growth factor. Blot overlay assays have shown that perlecan binds alpha-DG in a calcium and heparin-sensitive manner. Furthermore, perlecan is present in muscle lysate immunoprecipitated with an anti-DG antibody. Immunolabeling also showed colocalization between HB-GAM and perlecan and between HB-GAM and DG. These data suggest that perlecan is anchored to muscle surface via DG-dystrophin complex. Since DG is also a site of agrin binding, the neural agrin secreted by motoneurons during NMJ formation may compete with the pre-existing perlecan for cell surface binding. This competition may result in the presentation of perlecan-bound growth factors such as HB-GAM to effect synaptic induction.

EST analyses predict the existence of a population of chimeric microRNA precursor-mRNA transcripts expressed in normal human and mouse tissues.

SummaryA significant population of expressed sequence tags (ESTs) encodes chimeric transcripts containing microRNA (miRNA) precursor sequences as well as pieces of adjacent mRNAs in sense orientation. These chimeric transcripts may potentially be involved in miRNA biosynthesis, and/or affect expression of adjacent mammalian mRNAs.

A reelin-integrin receptor interaction regulates Arc mRNA translation in synaptoneurosomes.

Reelin is synthesized and secreted into extracellular matrix by cortical γ-aminobutyric acid (GABA)ergic interneurons and binds with high affinity to the extracellular domain of integrin receptors expressed in dendritic shaft and spine postsynaptic densities (DSPSD) of pyramidal neurons. In heterozygous reeler mice, reelin bound to DSPSD, and the expression of Arc (activity-regulated cytoskeletal protein) is lower than in wild-type mice. We studied the effect of reelin on Arc and total protein synthesis in synaptoneurosomes (SNSs) prepared from mouse neocortex. Recombinant full-length mouse reelin displaces the high affinity (KD = 60 fM) binding of [125I]echistatin (a competitive integrin receptor antagonist) to integrin receptors with a Ki of 22 pM and with a Hill slope close to 1. Echistatin (50–100 nM) competitively antagonizes and abates reelin binding. The addition of reelin (2–40 pM) to SNSs enhances the incorporation of [35S]methionine into Arc and other rapidly translated proteins in a concentration-dependent manner. This incorporation is virtually abolished by 50–100 nM echistatin or by 5–10 nM rapamycin, a blocker of the mammalian target of rapamycin kinase. We conclude that reelin binds with high affinity to integrin receptors expressed in SNSs and thereby activates Arc protein synthesis.

Linking estrogen to Alzheimer's disease An informatics approach

Epidemiologic studies suggest that estrogen protects against AD.We employ ARROWSMITH, a novel computer-assisted approach, to identify possible links between estrogen and AD that are not explicit in the biomedical literature, by searching for substances or processes that are known targets of estrogen action and that have also been separately studied in relation to AD. Several links appear particularly promising (e.g., estrogens antioxidant activity) and merit attention by neuroscientists. NEUROLOGY 1996;47: 809-810