Age at menopause in Latin America

OBJECTIVE: To assess the age at menopause (AM) in Latin America urban areas. DESIGN: A total of 17,150 healthy women, aged 40 to 59 years, accompanying patients to healthcare centers in 47 cities of 15 Latin American countries, were surveyed regarding their age, educational level, healthcare coverage, history of gynecological surgery, smoking habit, presence of menses, and the use of contraception or hormone therapy at menopause. The AM was calculated using logit analysis. RESULTS: The mean age of the entire sample was 49.4 ± 5.5 years. Mean educational level was 9.9 ± 4.5 years, and the use of hormone therapy and oral contraception was 22.1% and 7.9%, respectively. The median AM of women in all centers was 48.6 years, ranging from 43.8 years in Asuncion (Paraguay) to 53 years in Cartagena de Indias (Colombia). Logistic regression analysis determined that women aged 49 living in cities at 2,000 meters or more above sea level (OR = 2.0, 95% CI: 1.4-2.9, P less than 0.001) and those with lower educational level (OR = 1.9, 95% CI: 1.3-2.8, P less than 0.001) or living in countries with low gross national product (OR = 2.1, 95% CI: 1.5-2.9, P less than 0.001) were more prone to an earlier onset of menopause. CONCLUSIONS: The AM varies widely in Latin America. Lower income and related poverty conditions influence the onset of menopause. © 2006 by The North American Menopause Society

Genome-Wide Identification and Mapping of NBS-Encoding Resistance Genes in Solanum tuberosum Group Phureja

The majority of disease resistance (R) genes identified to date in plants encode a nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domain containing protein. Additional domains such as coiled-coil (CC) and TOLL/interleukin-1 receptor (TIR) domains can also be present. In the recently sequenced Solanum tuberosum group phureja genome we used HMM models and manual curation to annotate 435 NBS-encoding R gene homologs and 142 NBS-derived genes that lack the NBS domain. Highly similar homologs for most previously documented Solanaceae R genes were identified. A surprising ∼41% (179) of the 435 NBS-encoding genes are pseudogenes primarily caused by premature stop codons or frameshift mutations. Alignment of 81.80% of the 577 homologs to S. tuberosum group phureja pseudomolecules revealed non-random distribution of the R-genes; 362 of 470 genes were found in high density clusters on 11 chromosomes

SIMS: A deep-learning label transfer tool for single-cell RNA sequencing analysis

Cell atlases serve as vital references for automating cell labeling in new samples, yet existing classification algorithms struggle with accuracy. Here we introduce SIMS (scalable, interpretable machine learning for single cell), a low-code data-efficient pipeline for single-cell RNA classification. We benchmark SIMS against datasets from different tissues and species. We demonstrate SIMS's efficacy in classifying cells in the brain, achieving high accuracy even with small training sets (<3,500 cells) and across different samples. SIMS accurately predicts neuronal subtypes in the developing brain, shedding light on genetic changes during neuronal differentiation and postmitotic fate refinement. Finally, we apply SIMS to single-cell RNA datasets of cortical organoids to predict cell identities and uncover genetic variations between cell lines. SIMS identifies cell-line differences and misannotated cell lineages in human cortical organoids derived from different pluripotent stem cell lines. Altogether, we show that SIMS is a versatile and robust tool for cell-type classification from single-cell datasets

Allele-Specific Gene Silencing in Two Mouse Models of Autosomal Dominant Skeletal Myopathy

<div><p>We explored the potential of mutant allele-specific gene silencing (ASGS) in providing therapeutic benefit in two established mouse models of the autosomal dominantly-inherited muscle disorders, Malignant Hyperthermia (MH) and Central Core Disease (CCD). Candidate ASGS siRNAs were designed and validated for efficacy and specificity on ryanodine receptor (RyR1) cDNA mini-constructs expressed in HEK293 cells using RT-PCR- and confocal microscopy-based assays. <em>In vivo</em> delivery of the most efficacious identified siRNAs into flexor digitorum brevis (FDB) muscles was achieved by injection/electroporation of footpads of 4–6 month old heterozygous Ryr1^Y524S/+ (YS/+) and Ryr1^I4895T/+ (IT/+) knock-in mice, established mouse models of MH with cores and CCD, respectively. Treatment of IT/+ mice resulted in a modest rescue of deficits in the maximum rate (∼38% rescue) and magnitude (∼78%) of ligand-induced Ca²⁺ release that occurred in the absence of a change in the magnitude of electrically-evoked Ca²⁺ release. Compared to the difference between the caffeine sensitivity of Ca²⁺ release in FDB fibers from YS/+ and WT mice treated with SCR siRNA (EC₅₀: 1.1 mM versus 4.4 mM, respectively), caffeine sensitivity was normalized in FDB fibers from YS/+ mice following 2 (EC₅₀: 2.8 mM) and 4 week (EC₅₀: 6.6 mM) treatment with YS allele-specific siRNA. Moreover, the temperature-dependent increase in resting Ca²⁺ observed in FDB fibers from YS/+ mice was normalized to WT levels after 2 weeks of treatment with YS allele-specific siRNA. As determined by quantitative real time PCR, the degree of functional rescue in YS/+ and IT/+ mice correlated well with the relative increase in fractional WT allele expression.</p> </div

siRNA-mediated Rescue of RyR1 function in FDB fibers from IT/+ knock-in mice.

<p>A) Representative indo-1 ratio traces from FDB fibers from a WT mouse treated for two weeks with control scrambled (SCR) siRNA (<i>left</i>), a IT/+ mouse treated with SCR siRNA (<i>middle</i>), and a IT/+ mouse treated with IT-Dc siRNA (<i>right</i>) during electrical stimulation (arrowheads) and application of 500 µM 4-CMC (black bar). B) Average (±SEM) peak magnitude of electrically-evoked Ca²⁺ release in FDB fibers from WT and IT/+ knock-in mice treated with either SCR or IT-Dc siRNA for two (2 W) or four weeks (4 W) as indicated. C) Average (±SEM) peak magnitude and rate (D) of 500 µM 4-CMC-induced Ca²⁺ release in FDB fibers from WT and IT/+ knock-in mice treated with SCR or IT-Dc siRNA for either two (2 W) or four weeks (4 W) as indicated. Statistically significant differences (p<0.05) from WT SCR are indicated with brackets; number of fibers evaluated is given at the bottom of each bar in B-D. Two identically treated animals were used for each experimental condition and a similar number of fibers were used from each of the two animals.</p

Effect of siRNA Treatment on WT and Mutant Allele Frequency Assessed by qRT-PCR.

<p>A) Schematic diagram depicting the allele-specific PCR primer design used to determine fractional WT and mutant allele expression. The IT (<i>top</i>) and YS (<i>bottom</i>) primer sets amplify 147 and 159 bp PCR products, respectively. Each primer set includes an upstream primer common for both the WT and mutant alleles and a downstream primer designed to specifically anneal to only the WT or mutant template. B) The result of normalized ΔΔCt analysis comparing the fractional contribution of mutant to WT allele frequency (mutant/WT) such that an equal expression is reflected in a value of 1.0 and an increase in fractional WT allele frequency reflected in values <1.0. IT/+ mice were treated for two weeks with either SCR or IT-Dc siRNA. YS/+ mice were treated for two weeks with either SCR or YS-Dc siRNA. A total of n = 4 FDB muscles were used for all conditions. ^* p<0.01.</p

siRNA-mediated Rescue of RyR1 Function in FDB fibers from YS/+ knock-in mice.

<p>A) Representative traces of caffeine concentration-responses from FDB fibers obtained from a WT mouse treated for two weeks with SCR siRNA (<i>top</i>), a YS/+ mouse treated with SCR siRNA (<i>middle</i>), and a YS/+ mouse treated with YS-Dc siRNA (<i>bottom</i>). Scale bars represent 30s (<i>horizontal bar</i>) and 0.5ΔΔR (<i>vertical bar</i>). B) Caffeine-concentration response curves for FDB fibers from WT mice treated with SCR siRNA (<i>filled circles</i>, n = 19, EC₅₀: 4.44 mM, h: 1.88), FDB fibers from YS/+ mice treated with SCR siRNA (<i>open circles</i>, n = 13, EC₅₀: 1.11 mM, h: 2.11), and FDB fibers from YS/+ mice treated with YS-Dc siRNA for either 2 weeks (<i>filled triangles</i>, n = 13, EC₅₀: 2.81 mM, h: 2.80) or 4 weeks (<i>filled diamonds</i>, n = 8, EC₅₀: 6.57 mM, h: 2.53). For clarity, data for FDB fibers from WT mice treated with SCR siRNA for 4 weeks are similar to the 2 week data, and therefore are not included. C) Fractional change in resting fura-2 ratio upon temperature challenge to 32°C (R₃₂/R₂₅) in fibers from WT mice treated with SCR siRNA for 2 weeks and YS/+ mice treated for 2 (2 W) or 4 weeks (4 W) with either SCR or YS-Dc siRNA. The number of experiments for each condition is as follows in the format 25^oC/32^oC: WT SCR: 160/152; YS/+ SCR 2 W: 104/117; YS/+ YS-Dc 2 W: 39/30; YS/+ SCR 4 W: 104/98; YS/+ YS-Dc 4W: 107/101. * p<0.01. Two identically treated animals were used for each experimental condition and a similar number of fibers were used from each of the two animals.</p

siRNA Screening Results at the Protein Level.

<p>Quantification of siRNA knockdown from the ratio of venus:cherry fluorescence intensity evaluated via confocal microscopy. A) Representative venus (<i>left</i>), cherry (<i>middle</i>), and merged (<i>right</i>) images from HEK293 cells co-expressing venus-tagged WT-YS (<i>left</i>) and cherry-tagged YS following transfection of scrambled (<i>top</i>) or YS-Dc (<i>bottom</i>) siRNAs. B) Average (±SEM) siRNA-mediated mRNA knockdown following transfection of either 200 or 400 pmol siRNAs. Venus:cherry ratio was normalized to scrambled control (SCR) for WT-IT versus IT-targeted siRNAs (<i>left</i>) and WT-YS vs. YS siRNAs (<i>right</i>). * p<0.01 or † p<0.05 vs SCR control. Number of experiments is given at the bottom of each bar in B.</p