This dataset was collected to show that direct RNA sequencing using nanopore arrays is an alternative to conventional RNA sequencing approaches, which are complicated by high gene density, overlapping reading frames, and complex splicing patterns. In direct RNA sequencing, individual polyadenylated RNAs are sequenced directly. For this study, direct RNA sequencing was used to profile the herpes simplex...

This dataset was collected to present a spectral alignment method for the identification of protein modifications using high-resolution mass spectrometry proteomics. For this study, they used SAMPEI for spectral alignment-based modified peptide identification. SAMPEI is an open-source algorithm that is designed for the discovery of functional protein and peptide signaling modifications. Human OCI-AML2...

Long interspersed element-1 (LINE-1) is an autonomous retroelement that utilizes copy and paste mechanism to propagate themselves throughout the genome through a process called retrotransposition. The LINE-1 bicistronic mRNA codes for two proteins, ORF1p and ORF2. While LINE-1 transcription is usually repressed in most healthy somatic cells, ORF1p expression has been observed in tumors, including prostate...

Tuberous sclerosis complex (TSC) and focal cortical dysplasia (FCD) are associated with dysfunctional mammalian target of rapamycin (mTOR) signaling, which results in increased cell growth and ribosomal S6 protein phosphorylation. TSC studies suggest mTOR inhibitors can reduce TSC tumor growth and seizure frequency, while FCD studies indicate seizure suppression. This study assessed safety of mTOR...

This study used proteomic analysis, respirometry, and electron microscopy to examine the development of condensed mitochondria. The dataset contains proteomic and imaging data. The data indicate that condensed mitochondria formed from orthodox mitochondria during meiosis in order to support the formation of the acrosomal matrix. Condensed mitochondria also respired more actively and contained more...

Lysosomal dysfunction plays a key role in the pathogenesis of Alzheimer’s disease (AD) and Parkinson’s disease (PD). In early onset of AD, there is loss of Presenilin-1 (PSEN1) function. The loss of PSEN1 function impedes ER to lysosome delivery of chloride channel-7 (ClC-7). In murine blastocysts with different PSEN1 genotypes, isoproterenol and related β2-adrenergic agonists was used to reverse lysosomal...

Neurological dysfunction associated with Down syndrome (DS) is the concomitant basal forebrain cholinergic neuron (BFCN) degeneration and onset of Alzheimer’s disease (AD) pathology. Previously, single population RNA sequencing analysis in the Ts65Dn (Ts) mouse model of DS revealed that the mitochondrial oxidative phosphorylation pathway was significantly impacted, where a large subset of genes within...

Down syndrome (DS) is linked with mitochondrial dysfunction, which results in accumulation of damaged mitochondria. This study revealed that mitophagy, a form of selective autophagy activated to clear damaged mitochondria, is deficient in primary human fibroblasts derived from individuals with DS. This leads to accumulation of damaged mitochondria with consequent increases in oxidative stress. They...

Lysosomal failure plays an important role in the pathogenesis of many congenital neurodegenerative disorders, such as Alzheimer’s disease (AD) and Down syndrome (DS). This study showed that lysosomal dysfunction in DS requires the extra gene copy of amyloid precursor protein (APP) and is specifically mediated by the β cleaved carboxy terminal fragment of APP (APP-βCTF). In primary fibroblasts from...

Patients with Alzheimer’s disease (AD) have altered intestinal microbiota. Studies have shown that reduced intestinal microbiota in AD animal models decreases amyloid-beta (Aβ) plaque deposition. This age-related changes in the microbiota contribute to immunologic and physiologic decline. Previous study indicated that calorie restriction (CR) reduced brain Aβ deposition in Tg2576 mouse model of AD....