RNA sampling time on postmortem avian carcasses in the wild

Genetic sampling, especially high‐quality RNA from wild avian populations, is challenging in wildlife biology due to rapid RNA degradation. Although carcasses could be a potential RNA source, the optimal postmortem sampling time on the avian carcasses under field conditions remains unclear. Here, we carried out a field experiment on the Qinghai‐Tibet Plateau (QTP) and evaluated the relationship between PMI and RNA degradation in three tissue types (muscle, brain, and liver) of the domestic chicken Gallus gallus domesticus carcasses. In the muscle and brain tissues, we found that the RNA Integrity Number (RIN) of samples collected within 60 h postmortem was more than 7.0, suggesting a high RNA extract quality. The following RNA‐seq experiment demonstrated that gene expression profiles of the samples collected within 36 h postmortem were comparable to those of fresh samples (i.e. 0 h), with a low percentage of differentially expressed genes (< 3.0%) observed between samples at 0 and 36 h postmortem. However, in the liver tissue, RNA samples already degraded at 12 h postmortem, showing low RIN values (< 7.0), different gene expression profiles from fresh samples, and a high percentage of differentially expressed genes (15.6%). Therefore, our study suggests that samples from muscle and brain tissues collected within 36 h postmortem are qualified for RNA‐seq analyses. In contrast, only the fresh RNA samples from liver tissue are qualified. Our study provides a practicable and efficient sampling strategy for the transcriptome study on avian populations under extreme environment such as the QTP

Transcription-associated mutation promotes RNA complexity in highly expressed genes - a major new source of selectable variation

Alternatively spliced transcript isoforms are thought to play a critical role for functional diversity. However, the mechanism generating the enormous diversity of spliced transcript isoforms remains unknown, and its biological significance remains unclear. We analyzed transcriptomes in saker falcons, chickens, and mice to show that alternative splicing occurs more frequently, yielding more isoforms, in highly expressed genes. We focused on hemoglobin in the falcon, the most abundantly expressed genes in blood, finding that alternative splicing produces 10-fold more isoforms than expected from the number of splice junctions in the genome. These isoforms were produced mainly by alternative use of de novo splice sites generated by transcription-associated mutation (TAM), not by the RNA editing mechanism normally invoked. We found that high expression of globin genes increases mutation frequencies during transcription, especially on nontranscribed DNA strands. After DNA replication, transcribed strands inherit these somatic mutations, creating de novo splice sites, and generating multiple distinct isoforms in the cell clone. Bisulfate sequencing revealed that DNA methylation may counteract this process by suppressing TAM, suggesting DNA methylation can spatially regulate RNA complexity. RNA profiling showed that falcons living on the high Qinghai–Tibetan Plateau possess greater global gene expression levels and higher diversity of mean to high abundance isoforms (reads per kilobases per million mapped reads ≥18) than their low-altitude counterparts, and we speculate that this may enhance their oxygen transport capacity under low-oxygen environments. Thus, TAM-induced RNA diversity may be physiologically significant, providing an alternative strategy in lifestyle evolution

The Role of Autophagy in Parkinson's Disease: Rotenone-Based Modeling

Background: Autophagy-mediated self-digestion of cytoplasmic inclusions may be protective against neurodegenerative diseases such as Parkinson’s disease (PD). However, excessive autophagic activation evokes autophagic programmed cell death. Methods: In this study, we aimed at exploring the role of autophagy in the pathogenesis of rotenone-induced cellular and animal models for PD. Results: Reactive oxygen species over-generation, mitochondrial membrane potential reduction or apoptosis rate elevation occurred in a dose-dependent fashion in rotenone-treated human neuroblastoma cell line SH-SY5Y. The time- and dose-dependent increases in autophagic marker microtubule-associated protein1 light chain 3 (LC3) expression and decreases in autophagic adaptor protein P62 were observed in this cellular model. LC3-positive autophagic vacuoles were colocalized with alpha-synuclein-overexpressed aggregations. Moreover, the number of autophagic vacuoles was increased in rotenone-based PD models in vitro and in vivo. Conclusions: These data, along with our previous finding showing rotenone-induced toxicity was prevented by the autophagy enhancers and was aggravated by the autophagy inhibitors in SH-SY5Y, suggest that autophagy contributes to the pathogenesis of PD, attenuates the rotenone toxicity and possibly represents a new subcellular target for treating PD

Photochemical origin of SiC2_2 in the circumstellar envelope of carbon-rich AGB stars revealed by ALMA

Whether SiC$_2$ is a parent species, that is formed in the photosphere or as a by-product of high-temperature dust formation, or a daughter species, formed in a chemistry driven by the photodestruction of parent species in the outer envelope, has been debated for a long time. Here, we analyze the ALMA observations of four SiC$_2$ transitions in the CSEs of three C-rich AGB stars (AI Vol, II Lup, and RAFGL 4211), and found that SiC$_2$ exhibits an annular, shell-like distribution in these targets, suggesting that SiC$_2$ can be a daughter species in the CSEs of carbon-rich AGB stars. The results can provide important references for future chemical models.Comment: Accepted in Frontiers in Astronomy and Space Science

Determination of relevance between surface free energy and adsorption capacity of cement particles

ABSTRACT The compatibility between superplasticizer and cement was influenced by the adsorption capacity of cement particles. This study investigated the relevance between the adsorption capability and surface free energy. Adsorption capacity and surface free energy of both sulphoaluminate cement and portland cement were measured. The adsorption capacity of cement particles was measured by ultraviolet spectrophotometry. The test showed that particles of sulphoaluminate cement adsorbed more molecules of superplasticizer than portland cement particles. The weight of superplasticizer adsorbed by 2g of sulphoaluminate cement and portland cement were 0.28mg and 0.159mg respectively. Surface free energy of cement particles was calculated by contact angle and the contact angles were determined by the thin-layer wicking technique and washburn equation which is theoretical basis of thin-layer wiching technique presented by Chibowski E. The sulphoaluminate cement, portland cement's surface free energy were 51.46 mJ·m-2 and 49.36 mJ·m-2 respectively. The results showed that the higher adsorption capacity of particles was usual accompanied by higher surface free energy. The fluidity of cement paste was influenced by the adsorption capacity of cement particles because the more molecules of superplasticizer was adsorbed by cement particles there were lacking superplasticizer in the paste. The macro-behaviour of higher adsorption capacity is that the cement paste need more superplasticizer to reach the needed fluidity

Determination of relevance between surface free energy and adsorption capacity of cement particles

ABSTRACT The compatibility between superplasticizer and cement was influenced by the adsorption capacity of cement particles. This study investigated the relevance between the adsorption capability and surface free energy. Adsorption capacity and surface free energy of both sulphoaluminate cement and portland cement were measured. The adsorption capacity of cement particles was measured by ultraviolet spectrophotometry. The test showed that particles of sulphoaluminate cement adsorbed more molecules of superplasticizer than portland cement particles. The weight of superplasticizer adsorbed by 2g of sulphoaluminate cement and portland cement were 0.28mg and 0.159mg respectively. Surface free energy of cement particles was calculated by contact angle and the contact angles were determined by the thin-layer wicking technique and washburn equation which is theoretical basis of thin-layer wiching technique presented by Chibowski E. The sulphoaluminate cement, portland cement's surface free energy were 51.46 mJ·m-2 and 49.36 mJ·m-2 respectively. The results showed that the higher adsorption capacity of particles was usual accompanied by higher surface free energy. The fluidity of cement paste was influenced by the adsorption capacity of cement particles because the more molecules of superplasticizer was adsorbed by cement particles there were lacking superplasticizer in the paste. The macro-behaviour of higher adsorption capacity is that the cement paste need more superplasticizer to reach the needed fluidity