Design principles and developmental mechanisms underlying retinal mosaics

Most structures within the central nervous system (CNS) are composed of different types of neuron that vary in both number and morphology, but relatively little is known about the interplay between these two features, i.e. about the population dynamics of a given cell type. How such arrays of neurons are distributed within a structure, and how they differentiate their dendrites relative to each other, are issues that have recently drawn attention in the invertebrate nervous system, where the genetic and molecular underpinnings of these organizing principles are being revealed in exquisite detail. The retina is one of the few locations where these principles have been extensively studied in the vertebrate CNS, indeed, where the design principles of ‘mosaic regularity’ and ‘uniformity of coverage’ were first explicitly defined, quantified, and related to each other. Recent studies have revealed a number of genes that influence the formation of these histotypical features in the retina, including homologues of those invertebrate genes, although close inspection reveals that they do not always mediate comparable developmental processes nor elucidate fundamental design principles. The present review considers just how pervasive these features of ‘mosaic regularity’ and ‘uniform dendritic coverage’ are within the mammalian retina, discussing the means by which such features can be assessed in the mature and developing nervous system and examining the limitations associated with those assessments. We then address the extent to which these two design principles co‐exist within different populations of neurons, and how they are achieved during development. Finally, we consider the neural phenotypes obtained in mutant nervous systems, to address whether a prospective gene of interest underlies those very design principles.     

The single-cell stereo-seq reveals region-specific cell subtypes and transcriptome profiling in Arabidopsis leaves

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代谢组与转录组联合解析赤皮青冈叶片黄化变异机制

为揭示赤皮青冈叶色黄化变异机制,该研究以赤皮青冈叶色变异植株和正常植株的叶片为试验材料,采用超高效液相色谱串联质谱法和高通量RNA测序技术分别进行代谢组和转录组分析。结果表明:(1)代谢组在正离子(POS)、负离子(NEG)模式下分别检测出正常植株和突变体之间存在257个和357个显著差异代谢物(SCMs),其中槲皮素、白矢车菊素、杨梅素等多种黄酮类化合物及其糖苷衍生物(吡喃酮啡肽A、异鼠李素3-葡糖苷酸等)在突变体中显著上调,而叶绿素a、叶绿素b、类胡萝卜素等色素含量则显著下降。(2)转录组测序检测出4 146个差异表达基因(DEGs),其中1 711个基因上调表达,2 435个基因下调表达。(3)KEGG富集分析表明,SCMs和DEGs显著富集到光合作用、卟啉与叶绿素代谢、类黄酮生物合成等途径。综上表明,突变体叶色黄化可能是受到叶绿素合成受阻、叶绿体发育异常及黄酮物质合成增加等因素的综合影响。此外,MYB和bHLH家族基因在突变体中显著上调,证实该两类转录因子参与调控类黄酮生物合成。该研究结果为植物黄化突变的分子机制研究提供了新的见解,也为叶色功能基因挖掘与园林植物育种工作提供了参考。     

Metabolome and transcriptome profiling reveals quality variation and underlying regulation of three ecotypes for Cistanche deserticola

Plant Molecular Biology - Cistanche deserticola is a plant used both as food and medicine. We are interested in understanding how C. deserticola responds to environmental conditions. Samples were...     

Biochemical and developmental characterization of multiple forms of catalase in tobacco leaves

Leaf extracts of both Nicotiana tabacum and Nicotiana sylvestris contain multiple forms of catalase (H₂O₂:H₂O₂ oxidoreductase, EC 1.11.1.6) which are separable at different pH values by chromatofocusing columns. Marked changes in distribution of these catalases occur during seedling development and leaf maturation. The form of catalase eluting first (peak 1) was predominant during early seedling growth and present at all stages of development. Two more acidic forms (peaks 2 and 3) appeared later and comprised 29% of the total activity by 11 days postgermination. Mature leaves of N. tabacum contained peak 1 catalase, but peaks 2 and 3 represented 62% of the total activity. No interconversion of peaks 1, 2, and 3 was detected. The three forms of catalase differed in thermal stability with peak 1 > peak 2 peak 3. For N. sylvestris, t_½ at 55°C was 31.5 and 3.0 min for peaks 1 and 3, respectively, and for N. tabacum, t_½ was 41.5 and 3.2 min, respectively. All forms of catalase in tobacco show peroxidatic (measured as ethanol to acetaldehyde conversion) as well as catalatic activities. However, for both Nicotiana species the ratio peroxidatic/catalatic activity is at least 30-fold higher in peak 3 than in peaks 1 and 2. Chromatofocusing of extracts from spinach leaves separated at least four peaks of catalase activity, one of which had a 10-fold higher ratio of peroxidatic/catalatic activity than the others. Short-term growth (5 days) of tobacco seedlings under atmospheric conditions suppressing photorespiration (1% CO₂/21% O₂) reduced total catalase activity and caused a decline in peak 1 catalase and a substantial increase in the activity of peaks 2 and 3 relative to air-grown seedlings at the same stage.     

Comparative transcriptome profiling of amyloid precursor protein family members in the adult cortex

Background

SOX2 is a key gene implicated in maintaining the stemness of embryonic and adult stem cells. SOX2 appears to re-activate in several human cancers including glioblastoma multiforme (GBM), however, the detailed response program of SOX2 in GBM has not yet been defined.

Results

We show that knockdown of the SOX2 gene in LN229 GBM cells reduces cell proliferation and colony formation. We then comprehensively characterize the SOX2 response program by an integrated analysis using several advanced genomic technologies including ChIP-seq, microarray profiling, and microRNA sequencing. Using ChIP-seq technology, we identified 4883 SOX2 binding regions in the GBM cancer genome. SOX2 binding regions contain the consensus sequence wwTGnwTw that occurred 3931 instances in 2312 SOX2 binding regions. Microarray analysis identified 489 genes whose expression altered in response to SOX2 knockdown. Interesting findings include that SOX2 regulates the expression of SOX family proteins SOX1 and SOX18, and that SOX2 down regulates BEX1 (brain expressed X-linked 1) and BEX2 (brain expressed X-linked 2), two genes with tumor suppressor activity in GBM. Using next generation sequencing, we identified 105 precursor microRNAs (corresponding to 95 mature miRNAs) regulated by SOX2, including down regulation of miR-143, -145, -253-5p and miR-452. We also show that miR-145 and SOX2 form a double negative feedback loop in GBM cells, potentially creating a bistable system in GBM cells.

Conclusions

We present an integrated dataset of ChIP-seq, expression microarrays and microRNA sequencing representing the SOX2 response program in LN229 GBM cells. The insights gained from our integrated analysis further our understanding of the potential actions of SOX2 in carcinogenesis and serves as a useful resource for the research community.     

Plant Proteus: brown algal morphological plasticity and underlying developmental mechanisms

Brown algae are multicellular photosynthetic marine organisms, ubiquitous on rocky intertidal shores at cold and temperate latitudes. Nevertheless, little is known about many aspects of their biology, particularly their development. Given their phylogenetic distance (1.6 billion years) from other plant organisms (land plants, and green and red algae), brown algae harbor a high, as-yet undiscovered diversity of biological mechanisms governing their development. They also show great morphological plasticity, responding to specific environmental constraints, such as sea currents, reduced light availability, grazer attacks, desiccation and UV exposure. Here, we show that brown algal morphogenesis is rather simple and flexible, and review recent genomic data on the cellular and molecular mechanisms known to date that can possibly account for this developmental strategy.     

Stem cell-based modeling and single-cell multiomics reveal gene-regulatory mechanisms underlying human skeletal development

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