Revealing missing human protein isoforms based on Ab initio prediction, RNA-seq and proteomics

Biological and biomedical research relies on comprehensive understanding of protein-coding transcripts. However, the total number of human proteins is still unknown due to the prevalence of alternative splicing. In this paper, we detected 31,566 novel transcripts with coding potential by filtering our ab initio predictions with 50 RNA-seq datasets from diverse tissues/cell lines. PCR followed by MiSeq sequencing showed that at least 84.1% of these predicted novel splice sites could be validated. In contrast to known transcripts, the expression of these novel transcripts were highly tissue-specific. Based on these novel transcripts, at least 36 novel proteins were detected from shotgun proteomics data of 41 breast samples. We also showed L1 retrotransposons have a more significant impact on the origin of new transcripts/genes than previously thought. Furthermore, we found that alternative splicing is extraordinarily widespread for genes involved in specific biological functions like protein binding, nucleoside binding, neuron projection, membrane organization and cell adhesion. In the end, the total number of human transcripts with protein-coding potential was estimated to be at least 204,950.publishedVersio

RecQ dysfunction contributes to social and depressive-like behavior and affects aldolase activity in mice

RecQ helicase family proteins play vital roles in maintaining genome stability, including DNA replication, recombination, and DNA repair. In human cells, there are five RecQ helicases: RECQL1, Bloom syndrome (BLM), Werner syndrome (WRN), RECQL4, and RECQL5. Dysfunction or absence of RecQ proteins is associated with genetic disorders, tumorigenesis, premature aging, and neurodegeneration. The biochemical and biological roles of RecQ helicases are rather well established, however, there is no systematic study comparing the behavioral changes among various RecQ-deficient mice including consequences of exposure to DNA damage. Here, we investigated the effects of ionizing irradiation (IR) on three RecQ-deficient mouse models (RecQ1, WRN and RecQ4). We find abnormal cognitive behavior in RecQ-deficient mice in the absence of IR. Interestingly, RecQ dysfunction impairs social ability and induces depressive-like behavior in mice after a single exposure to IR, suggesting that RecQ proteins play roles in mood and cognition behavior. Further, transcriptomic and metabolomic analyses revealed significant alterations in RecQ-deficient mice, especially after IR exposure. In particular, pathways related to neuronal and microglial functions, DNA damage repair, cell cycle, and reactive oxygen responses were downregulated in the RecQ4 and WRN mice. In addition, increased DNA damage responses were found in RecQ-deficient mice. Notably, two genes, Aldolase Fructose-Bisphosphate B (Aldob) and NADPH Oxidase 4 (Nox4), were differentially expressed in RecQ-deficient mice. Our findings suggest that RecQ dysfunction contributes to social and depressive-like behaviors in mice, and that aldolase activity may be associated with these changes, representing a potential therapeutic target

Clinical Characteristics and Surgical Safety in Congenital Cataract Eyes with Three Pathological Types of Posterior Capsule Abnormalities

Purpose. To observe the clinical characteristics of 3 pathological types of posterior capsule abnormalities (PCAs) in congenital cataracts (CCs) and evaluate the surgical safety in these eyes. Methods. This study involved 239 children (367 eyes) with CC who underwent cataract surgery at the Eye Hospital of Wenzhou Medical University. All surgery videos were collected for detailed reviews. Intraoperative and postoperative complications (within 3 months) were all recorded. Results. The 3 pathological types of PCAs, namely, persistent fetal vasculature (PFV), posterior capsule defect (PCD), and posterior lenticonus (PLC), presented in 129 (35.1%) CC eyes, while 238 (64.9%) eyes were recorded as CC without PCA. The percentages of PFV, PCD, and PLC were 10.9%, 26.7%, and 5.4% in CC eyes (n = 367), respectively. The most common concomitant of PFV eyes was PCD (42.5%), and PFV was the most frequent (17.3%) one in PCD eyes. PLC was only associated with PFV (15%) and PCD (50%). The occurrence rates of surgical complications ranged from 0 to 5.4%, and no statistical difference was found between the eyes with and without PCA (all P>0.05). Conclusions. PFV, PCD, and PLC play a very important role in the CCs. The effect of fetal vessels in PFV eyes might be an abnormally strong attachment on the posterior capsule, leading to PLC and PCD. Even in PCA patients, severe surgical complication can also be avoided with well-designed and skilled operation. This trial is registered with NCT03905044 at http://ClinicalTrials.gov

Early-Onset Hearing Loss in Mouse Models of Alzheimers Disease and Increased DNA Damage in the Cochlea.

There is considerable interest in whether sensory deficiency is associated with the development of Alzheimers disease (AD). Notably, the relationship between hearing impairment and AD is of high relevance but still poorly understood. In this study, we found early-onset hearing loss in two AD mouse models, 3xTgAD and 3xTgAD/Polβ+/-. The 3xTgAD/Polβ+/- mouse is DNA repair deficient and has more humanized AD features than the 3xTgAD. Both AD mouse models showed increased auditory brainstem response (ABR) thresholds between 16 and 32 kHz at 4 weeks of age, much earlier than any AD cognitive and behavioral changes. The ABR thresholds were significantly higher in 3xTgAD/Polβ+/- mice than in 3xTgAD mice at 16 kHz, and distortion product otoacoustic emission signals were reduced, indicating that DNA damage may be a factor underlying early hearing impairment in AD. Poly ADP-ribosylation and protein expression levels of DNA damage markers increased significantly in the cochlea of the AD mice but not in the adjacent auditory cortex. Phosphoglycerate mutase 2 levels and the number of synaptic ribbons in the presynaptic zones of inner hair cells were decreased in the cochlea of the AD mice. Furthermore, the activity of sirtuin 3 was downregulated in the cochlea of these mice, indicative of impaired mitochondrial function. Taken together, these findings provide new insights into potential mechanisms for hearing dysfunction in AD and suggest that DNA damage in the cochlea might contribute to the development of early hearing loss in AD

Presentation_1_Nicotinamide adenine dinucleotide supplementation drives gut microbiota variation in Alzheimer’s mouse model.pdf

Alzheimer’s disease (AD) is the most common neurodegenerative disease. Growing evidence suggests an important role for gut dysbiosis and gut microbiota-host interactions in aging and neurodegeneration. Our previous works have demonstrated that supplementation with the nicotinamide adenine dinucleotide (NAD+) precursor, nicotinamide riboside (NR), reduced the brain features of AD, including neuroinflammation, deoxyribonucleic acid (DNA) damage, synaptic dysfunction, and cognitive impairment. However, the impact of NR administration on the intestinal microbiota of AD remains unknown. In this study, we investigated the relationship between gut microbiota and NR treatment in APP/PS1 transgenic (AD) mice. Compared with wild type (WT) mice, the gut microbiota diversity in AD mice was lower and the microbiota composition and enterotype were significantly different. Moreover, there were gender differences in gut microbiome between female and male AD mice. After supplementation with NR for 8 weeks, the decreased diversity and perturbated microbial compositions were normalized in AD mice. This included the species Oscillospira, Butyricicoccus, Desulfovibrio, Bifidobacterium, Olsenella, Adlercreutzia, Bacteroides, Akkermansia, and Lactobacillus. Our results indicate an interplay between NR and host-microbiota in APP/PS1 mice, suggesting that the effect of NR on gut dysbiosis may be an important component in its therapeutic functions in AD.</p

Identification of the Causative Gene for Simmental Arachnomelia Syndrome Using a Network-Based Disease Gene Prioritization Approach

<div><p>Arachnomelia syndrome (AS), mainly found in Brown Swiss and Simmental cattle, is a congenital lethal genetic malformation of the skeletal system. In this study, a network-based disease gene prioritization approach was implemented to rank genes in the previously reported ∼7 Mb region on chromosome 23 associated with AS in Simmental cattle. The top 6 ranked candidate genes were sequenced in four German Simmental bulls, one known AS-carrier ROMEL and a pooled sample of three known non-carriers (BOSSAG, RIFURT and HIRMER). Two suspicious mutations located in coding regions, a mis-sense mutation c.1303G>A in the bystin-like (<i>BYSL</i>) gene and a 2-bp deletion mutation c.1224_1225delCA in the molybdenum cofactor synthesis step 1 (<i>MOCS1</i>) gene were detected. Bioinformatic analysis revealed that the mutation in <i>MOCS1</i> was more likely to be the causative mutation. Screening the c.1224_1225delCA site in 383 individuals from 12 cattle breeds/lines, we found that only the bull ROMEL and his 12 confirmed progeny carried the mutation. Thus, our results confirm the conclusion of Buitkamp et al. that the 2-bp deletion mutation c.1224_1225delCA in exon 11 of the <i>MOCS1</i> gene is causative for AS in Simmental cattle. Furthermore, a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was developed to detect the causative mutation.</p></div

Additional file 3: of Abnormal circadian oscillation of hippocampal MAPK activity and power spectrums in NF1 mutant mice

Supplementary tables were shown as the spike firing rates of pyramidal cells in mice. (ZIP 106 kb

Additional file 2: Figure S2. of Abnormal circadian oscillation of hippocampal MAPK activity and power spectrums in NF1 mutant mice

In vivo recording in CA1 demonstrates alterations in hippocampal rhythmic oscillations and firing rates in Nf1 +/− mice. a The local field potentials (LFPs) recordings in CA1(WT mice). First trace- unfiltered LFPs, second trace- alpha oscillations (filtered 7–12 Hz). b Histograms show the averaged power spectral density of the neuronal rhythmic oscillations (alpha). Data are expressed as mean ± SEM (WT, n = 5; Nf1 +/− , n = 5). Two-way analysis of variance with repeated measures and post hoc Bonferroni tests was used to evaluate differences in local field potential power spectrum density in day and night recordings in Nf1 +/− and WT groups. ***p < 0.001. (PDF 212 kb