Bayesian estimation and use of high-throughput remote sensing indices for quantitative genetic analyses of leaf growth

Key message

We develop Bayesian function-valued trait models that mathematically isolate genetic mechanisms underlying leaf growth trajectories by factoring out genotype-specific differences in photosynthesis. Remote sensing data can be used instead of leaf-level physiological measurements.

Abstract

Characterizing the genetic basis of traits that vary during ontogeny and affect plant performance is a major goal in evolutionary biology and agronomy. Describing genetic programs that specifically regulate morphological traits can be complicated by genotypic differences in physiological traits. We describe the growth trajectories of leaves using novel Bayesian function-valued trait (FVT) modeling approaches in Brassica rapa recombinant inbred lines raised in heterogeneous field settings. While frequentist approaches estimate parameter values by treating each experimental replicate discretely, Bayesian models can utilize information in the global dataset, potentially leading to more robust trait estimation. We illustrate this principle by estimating growth asymptotes in the face of missing data and comparing heritabilities of growth trajectory parameters estimated by Bayesian and frequentist approaches. Using pseudo-Bayes factors, we compare the performance of an initial Bayesian logistic growth model and a model that incorporates carbon assimilation (A _max) as a cofactor, thus statistically accounting for genotypic differences in carbon resources. We further evaluate two remotely sensed spectroradiometric indices, photochemical reflectance (pri2) and MERIS Terrestrial Chlorophyll Index (mtci) as covariates in lieu of A _max, because these two indices were genetically correlated with A _max across years and treatments yet allow much higher throughput compared to direct leaf-level gas-exchange measurements. For leaf lengths in uncrowded settings, including A _max improves model fit over the initial model. The mtci and pri2 indices also outperform direct A _max measurements. Of particular importance for evolutionary biologists and plant breeders, hierarchical Bayesian models estimating FVT parameters improve heritabilities compared to frequentist approaches.

     

Autophagy mediates cytotoxicity of human colorectal cancer cells treated with garcinielliptone FC

The tautomeric pair of garcinielliptone FC (GFC) is a novel tautomeric pair of polyprenyl benzophenonoid isolated from the pericarps of Garcinia subelliptica Merr. (G. subelliptica, Clusiaceae), a tree with abundant sources of polyphenols. Our previous report demonstrated that GFC induced apoptosis on various types of human cancer cell lines including chemoresistant human colorectal cancer HT‐29 cells. In the present study, we observed that many autophagy‐related genes in GFC‐treated HT‐29 cells were up‐ and down‐regulated using a cDNA microarray containing oncogenes and kinase genes. GFC‐induced autophagy of HT‐29 cells was confirmed by observing the formation of acidic vesicular organelles, LC3 puncta, and double‐membrane autophagic vesicles using flow cytometry, confocal microscopy, and transmission electron microscopy, respectively. Inhibition of AKT/mTOR/P70S6K signaling as well as formation of Atg5‐Atg12 and PI3K/Beclin‐1 complexes were observed using Western blot. Administration of autophagy inhibitor (3‐methyladenine and shRNA Atg5) and apoptosis inhibitor Z‐VAD showed that the GFC‐induced autophagy was cytotoxic form and GFC‐induced apoptosis enhanced GFC‐induced autophagy. Our data suggest the involvement of autophagy and apoptosis in GFC‐induced anticancer mechanisms of human colorectal cancer.     

不同因素对六盘山地区甘肃鼢鼠肠道细菌多样性的影响

【目的】研究甘肃鼢鼠肠道细菌的群落结构和多样性,探讨不同环境因素对六盘山地区甘肃鼢鼠肠道细菌多样性的影响。【方法】通过Illumina高通量测序技术,对甘肃鼢鼠的36个盲肠样品进行16S rRNA V3–V4区的高通量测序,分析了肠道细菌多样性、丰度和群落结构,探讨地域、性别和季节等因素对甘肃鼢鼠肠道细菌多样性的影响。【结果】甘肃鼢鼠肠道细菌群落主要包括3个门,其中Firmicutes门占主导地位,其次是Bacteroidetes和Proteobacteri。在属水平,优势菌属分别为Oscillospira、Ruminococcus、Coprococcus和Desulfovibrio等。不同县(区)样品中,彭阳县、隆德县和泾源县三个县的甘肃鼢鼠肠道细菌菌群结构相似度较高,海原县甘肃鼢鼠肠道细菌群落结构在组内相似度高,与其他县(区)相似度低;雌性甘肃鼢鼠肠道细菌群落结构相似性高,而雄性细菌群落结构在样品间差异较大;甘肃鼢鼠肠道细菌菌群多样性秋季显著高于春季,细菌群落结构相似度秋季高于春季。【结论】不同地域、性别和季节因素对甘肃鼢鼠肠道细菌群落结构产生显著的影响,甘肃鼢鼠肠道细菌群落结构和多样性的变化对基于食源的季节性变化具有积极的响应。     

Effect of Selenium on Ion Profiles and Antioxidant Defense in Mice Livers

Se entering the mammalian body from diverse sources shows different liver accumulation patterns. However, the effects of Se from diverse sources on the body’s I on spectrum and the relationship between the changes in the ion spectrum and antioxidant function are not clear. In this study, 80 3-week-old female mice were randomly divided into four groups: a control group, sodium selenite group, yeast Se group, and seaweed Se group. The estimated Se contents were 0.03, 0.23, 0.23, and 0.23 mg/kg, respectively. The liver was collected from mice on day 60. The results showed that, compared with the control group, sodium selenite significantly reduced Na and Li contents and significantly increased Cr, Ni, Se, and Sb contents (P < 0.05); yeast Se significantly increased Mg, Ca, Si, Cr, Fe, Co, Cu, Se, Sb, and Al contents, and significantly reduced Tl, As, and Hg contents (P < 0.05); seaweed Se significantly increased B, Si, Cr, Fe, Se, As, and Hg contents, and significantly reduced Zn and Tl contents (P < 0.05). The results of antioxidant parameter analysis showed that Se from three sources increased total superoxide dismutase content and significantly reduced malondialdehyde content (P < 0.05), whereas no clear effect was observed on total antioxidant capacity (P > 0.05). Combined with the ion spectrum and antioxidant test results, yeast Se was found to most effectively promote the accumulation of beneficial elements, enhance antioxidant capacity, and reduce the concentration of toxic elements. The variety of ion spectrum antioxidants followed a similar trend, which indicated that the ion spectrum might be related to antioxidant activity.     

Neuroprotection of Cytisine Against Cerebral Ischemia–Reperfusion Injury in Mice by Regulating NR2B-ERK/CREB Signal Pathway

The aim of the study was to elucidate the therapeutic effects of Cytisine (CYT) on cerebral ischemia–reperfusion injury in mice. Male ICR mice were pretreated with reagents (drug), and then subjected to 2 h focal cerebral ischemia and 24 h reperfusion. Morphologically, the histopathological impairment were estimated by the TTC, HE and TUNEL staining. The expression of GluN2B-containing NMDA receptor, phosphorylation of extracellular regulated protein kinases, total ERK, phosphorylation of cAMP-response element binding protein and total CREB were determined by immunofluorescence and Western blot assay, respectively. The mRNA expression of NR2B, ERK and CREB were quantified by the real-time RT-PCR. CYT significantly diminished the infarct size and neuronal apoptosis. Additionally, it ameliorated histopathological lesion dramatically. CYT promoted the phosphorylation of ERK, CREB and their mRNA expression. In contrast, the expression of NR2B was suppressed in concomitant with the down-regulation of genes. The overall results thus far suggest that CYT confers the neuroprotection against cerebral I/R injury by regulating the NR2B-ERK/CREB signal pathway.     

Cellulose type chiral stationary phase based on reduced graphene oxide@silica gel for the enantiomer separation of chiral compounds

The graphene oxide (GO) was covalently coupled to the surfaces of silica gel (SiO₂) microspheres by amide bond to get the graphene oxide@silica gel (GO@SiO₂). Then, the GO@SiO₂ was reduced with hydrazine to the reduced graphene oxide@silica gel (rGO@SiO₂), and the cellulose derivatives were physically coated on the surfaces of rGO@SiO₂ to prepare a chiral stationary phase (CSP) for high performance liquid chromatography. Under the optimum experimental conditions, eight benzene‐enriched enantiomers were separated completely, and the resolution of trans‐stilbene oxide perfectly reached 4.83. Compared with the blank column of non‐bonded rGO, the separation performance is better on the new CSP, which is due to the existence of rGO to produce special retention interaction with analytes, such as π‐π stacking, hydrophobic effect, π‐π electron‐donor–acceptor interaction, and hydrogen bonding. Therefore, the obtained CSP shows special selectivity for benzene‐enriched enantiomers, improves separation selectivity and efficiency, and rGO plays a synergistic effect with cellulose derivatives on enantioseparation.     

PlpA,a PilZ‐like protein,regulates directed motility of the bacterium Myxococcus xanthus

The rod‐shaped bacterium Myxococcus xanthus moves on surfaces along its long cell axis and reverses its moving direction regularly. Current models propose that the asymmetric localization of a Ras‐like GTPase, MglA, to leading cell poles determines the moving direction of cells. However, cells are still motile in the mutants where MglA localizes symmetrically, suggesting the existence of additional regulators that control moving direction. In this study, we identified PlpA, a P ilZ‐l ike p rotein that regulates the direction of motility. PlpA and MglA localize into opposite asymmetric patterns. Deletion of the plpA gene abolishes the asymmetry of MglA localization, increases the frequency of cellular reversals and leads to severe defects in cell motility. By tracking the movements of single motor particles, we demonstrated that PlpA and MglA co‐regulated the direction of gliding motility through direct interactions with the gliding motor. PlpA inhibits the reversal of individual gliding motors while MglA promotes motor reversal. By counteracting MglA near lagging cell poles, PlpA reinforces the polarity axis of MglA and thus stabilizes the direction of motility.     

茉莉酸甲酯对马尾松萜类合成酶活性及其细胞化学定位的影响

马尾松(Pinus massoniana)是我国南方生态建设与造林用材的主要树种,为了揭示马尾松抗虫机理尤其是诱导抗虫性的分子机制,该研究以马尾松幼苗为材料,通过外源喷施茉利酸甲酯(Me JA),分析了处理与对照间植株针叶显微结构、萜类合成酶活性及其细胞化学定位的变化。结果表明:在0.2 mmol·L~(-1)Me JA处理下马尾松植株松针中萜类物质,尤其是单萜、二萜的相对含量增加,马尾松毛虫拒食性明显,诱导抗性增强。显微观测中,针叶叶肉细胞内树脂道分泌物增加,叶绿体数目减少,但叶绿体体积增大,叶绿体片层结构增加。Me JA处理4周后,针叶中萜类合成酶活性增加,通过电镜酶细胞化学观察,膜系统尤其是叶绿体膜上萜类合成酶活性定位明显增强。这说明Me JA诱导的马尾松诱导抗性可能与改变的叶绿体结构及绿色质体萜类合成酶活性密切相关。     

表观调控rDNA转录的研究进展

rDNA是控制细胞核糖体生物合成的串联重复基因,影响着整体蛋白质的翻译水平,与细胞生长代谢息息相关.由于rDNA序列具有多拷贝的重复特征,其转录除了受一般转录机制的调节外,还受多重表观调控机制的调节,精细调控着rDNA的转录状态.一般认为rDNA分为活跃和沉默两种状态,分别与活跃染色质标记和异染色质标记相关.近些年来,发现一种平衡态rDNA的存在,更加丰富了rDNA表观机制的研究.H3.3是一种H3组蛋白变体,是近些年来的研究热点,已有报道H3.3可能在分子伴侣HIRA的介导下整合进入活跃rDNA,然而沉默rDNA的维持是否也与H3.3的作用相关需要更多的探索.CTCF是rDNA重复单元间的绝缘子成分,与H3.3相关但并不清楚是否也调控着rDNA的转录.该综述讨论了几种调控rDNA表观状态的机制,并对可能参与该过程的新机制提出了设想.