Entropy subspace separation-based clustering for noise reduction (ENCORE) of scRNA-seq data

Single-cell RNA sequencing enables us to characterize the cellular heterogeneity in single cell resolution with the help of cell type identification algorithms. However, the noise inherent in single-cell RNA-sequencing data severely disturbs the accuracy of cell clustering, marker identification and visualization. We propose that clustering based on feature density profiles can distinguish informative features from noise. We named such strategy as ‘entropy subspace’ separation and designed a cell clustering algorithm called ENtropy subspace separation-based Clustering for nOise REduction (ENCORE) by integrating the ‘entropy subspace’ separation strategy with a consensus clustering method. We demonstrate that ENCORE performs superiorly on cell clustering and generates high-resolution visualization across 12 standard datasets. More importantly, ENCORE enables identification of group markers with biological significance from a hard-to-separate dataset. With the advantages of effective feature selection, improved clustering, accurate marker identification and high-resolution visualization, we present ENCORE to the community as an important tool for scRNA-seq data analysis to study cellular heterogeneity and discover group markers.     

敲减神经肽F基因(npf)对亚洲玉米螟取食、生长发育和繁殖的影响

【目的】神经肽F(neuropeptide F, NPF)是无脊椎动物特有的一类神经肽,因其C末端是苯丙氨酸(F)而命名,参与昆虫的取食、生物节律、学习记忆等多种生理功能的调控。本研究旨在明确NPF对亚洲玉米螟Ostrinia furnacalis生长发育的影响,为害虫防治提供重要依据。【方法】采用一种基于工程菌高效合成靶向昆虫基因的dsRNA的方法经济有效地敲降npf,用低浓度(0.01%)和高浓度(0.02%)dsNPF和dsGFP(对照)分别饲喂亚洲玉米螟1龄初、3龄初和5龄初幼虫直至化蛹,检测5龄幼虫平均取食量、体重、体长、存活率和化蛹率,蛹羽化率和成虫产卵量,以及幼虫各龄期、蛹发育历期和成虫寿命。【结果】从亚洲玉米螟1, 3和5龄初幼虫开始饲喂0.01%和0.02% dsNPF时,与饲喂相应浓度dsGFP的对照相比,除个别点外,5龄幼虫的取食量、体重、体长、存活率和化蛹率,蛹羽化率和成虫单雌产卵量均显著降低,幼虫各龄期、蛹发育历期均显著延长,成虫寿命显著缩短。且dsNPF处理幼虫的龄期越早对发育的影响越大。其中0.01% dsNPF处理的1龄幼虫和0.02% dsNPF处理的3龄幼虫有90%的个体在蛹期死亡,而0.02%dsNPF处理的1龄幼虫有90%的个体在幼虫期死亡。【结论】结果提示NPF对亚洲玉米螟的发育和取食具有调控作用,这为探索新型绿色的害虫防治提供了依据。     

Effects of Exogenous Application of GA4+7 and NAA on Sugar Accumulation and Related Gene Expression in Peach Fruits During Developing and Ripening Stages

Sweetness is one of the key factors determining peach fruit quality. To better understand the molecular basis of gibberellic acid (GA) and 1-naphthaleneacetic acid (NAA) interference with sugar biosynthesis, a middle-late maturing commercial cultivar, ‘Jinxiu’ yellow peach fruit, was treated with three different concentrations of GA₄₊₇ and four of NAA. Fruit weight, firmness, total soluble solids, different sugar contents and the expression level of sugar-related genes were evaluated. The results showed that maximum increase in cv. ‘Jinxiu’ peach fruit size and sucrose content was with 1.25 mM GA₄₊₇, compared to control fruits and the other treatments during the ripening stages. The sucrose-phosphate synthase gene (PpSPS₂) which had a high level of expression and positive correlation with sucrose content was significantly regulated by 1.25 mM GA₄₊₇ in the final ripening stages. 0.5 mM NAA treatments significantly reduced the sucrose content and fruit size. Ninety percent of the fruits were deformed or dropped from the trees with treatments of 1 mM NAA and 2 mM NAA in the early development period. The crosstalk of different phytohormones and the related genes will be further investigated to get an insight into the inherent association between hormone control and sugar accumulation.

     

Effects of 5-HT7 receptors on circadian rhythm of mice anesthetized with isoflurane

ABSTRACT

The role of the serotonin 7 receptor (5-HT₇ receptor) subtype in a number of domains has been widely recognized, but its role in the regulation of changes of the circadian rhythm after anesthesia is still unclear. We used intraperitoneal injection of 5-HT₇ receptor agonist LP-211 or antagonist SB-269970 in mice to influence the level of 5-HT₇ receptor protein in the SCN and to observe the role of this receptor on circadian rhythm changes after isoflurane anesthesia. Our results show the appropriate dose of SB-269970 significantly alleviated the circadian rhythm disorder induced by isoflurane anesthesia, while LP-211 significantly aggravated it after anesthesia, which is different from the phase shift that can be caused by the administration of LP-211 before anesthesia. These findings may indicate the 5-HT₇ receptor plays a complex role in the regulation of circadian rhythm after anesthesia. Our findings may provide some positive significance for alleviating circadian rhythm disorder in patients after anesthesia and ultimately promoting rapid postoperative recovery.     

Inhibiting roles of FOXA2 in liver cancer cell migration and invasion by transcriptionally suppressing microRNA-103a-3p and activating the GREM2/LATS2/YAP axis

Cytotechnology - Forkhead box A2 (FOXA2) has emerged as a tumor inhibitor in several human malignancies. This work focused on the effect of FOXA2 on liver cancer (LC) cell invasion and migration...     

Offspring performance and female preference of Pagiophloeus tsushimanus (coleoptera: curculionidae) on three Lauraceae tree species: A potential risk of host shift caused by larval experience

The weevil Pagiophloeus tsushimanus Morimoto (Coleoptera: Curculionidae), native to Eastern Asia, is a wood-boring pest that causes severe damage to camphor trees (Cinnamomum sp.) in Shanghai, China. Other Lauraceae tree species that grew sympatrically with this pest in close proximity could face a potential threat. To assess the potential risks of host shift, we explored the phenotypic associations between preference and performance in P. tsushimanus reared on three Lauraceae tree species. In a no-choice experiment offering branches of each plant as diet material and oviposition sites, we found that individuals reared on Cinnamomum camphora (L.) Presl (Laurales: Lauraceae) exhibited the strongest performance with shorter development time, higher survival and growth rate in the immature stage, longer longevity and greater fecundity in adults. In contrast, those on novel Lauraceae tree species (Cinnamomum chekiangensis Nakai and Phoebe chekiangensis Shang) had difficulty completing their whole life cycle due to significantly lower survival and reproduction. In a multiple-choice experiment, C. camphora was established as the preferred host. However, we found that the larval experiences on the non-preferred host plants contributed to an increased preference for that plant species. These results indicated that both the preference-performance hypothesis and the Hopkins’ host selection principle are applicable in this weevil under experimental conditions. It is possible that although the weevil performed poorly on two novel Lauraceae tree species, under favourable conditions their surviving offspring could evolve into a new host-specific population. Consequently, this weevil pest needs to be monitored on these novel Lauraceae tree species.     

Histone H3K27 dimethylation landscapes contribute to genome stability and genetic recombination during wheat polyploidization

Bread wheat (Triticum aestivum) is an allohexaploid that was formed via two allopolyploidization events. Growing evidence suggests histone modifications are involved in the response to ‘genomic shock’ and environmental adaptation during polyploid formation and evolution. However, the role of histone modifications, especially histone H3 lysine-27 dimethylation (H3K27me2), in genome evolution remains elusive. Here we analyzed H3K27me2 and H3K27me3 profiles in hexaploid wheat and its tetraploid and diploid relatives. Although H3K27me3 levels were relatively stable among wheat species with different ploidy levels, H3K27me2 intensities increased concurrent with increased ploidy levels, and H3K27me2 peaks were colocalized with massively amplified DTC transposons (CACTA family) in euchromatin, which may silence euchromatic transposons to maintain genome stability during polyploid wheat evolution. Consistently, the distribution of H3K27me2 is mutually exclusive with another repressive histone mark, H3K9me2, that mainly silences transposons in heterochromatic regions. Remarkably, the regions with low H3K27me2 levels (named H3K27me2 valleys) were associated with the formation of DNA double-strand breaks in genomes of wheat, maize (Zea mays) and Arabidopsis. Our results provide a comprehensive view of H3K27me2 and H3K27me3 distributions during wheat evolution, which support roles for H3K27me2 in silencing euchromatic transposons to maintain genome stability and in modifying genetic recombination landscapes. These genomic insights may empower breeding improvement of crops.     

Correction to: lncRNA MEG3, Acting as a ceRNA,Modulates RPE Differentiation Through the miR-7-5p/Pax6 Axis

Biochemical Genetics - A correction to this paper has been published: https://doi.org/10.1007/s10528-021-10086-3