森林碳循环模型概述

森林碳循环是陆地碳循环研究的重要内容,碳循环模型是进行森林生态系统碳循环机理研究和碳通量估算的重要手段.本文在总结主要碳循环模型的基础上,将森林碳循环模型归纳为斑块尺度的森林碳循环模型和区域尺度的陆地碳循环模型两大类,并评述了各类型的代表性模型及其特点,最后指出了我国森林碳循环模型研究的未来发展方向.     

CCPE: cell cycle pseudotime estimation for single cell RNA-seq data

Pseudotime analysis from scRNA-seq data enables to characterize the continuous progression of various biological processes, such as the cell cycle. Cell cycle plays an important role in cell fate decisions and differentiation and is often regarded as a confounder in scRNA-seq data analysis when analyzing the role of other factors. Therefore, accurate prediction of cell cycle pseudotime and identification of cell cycle stages are important steps for characterizing the development-related biological processes. Here, we develop CCPE, a novel cell cycle pseudotime estimation method to characterize cell cycle timing and identify cell cycle phases from scRNA-seq data. CCPE uses a discriminative helix to characterize the circular process of the cell cycle and estimates each cell''s pseudotime along the cell cycle. We evaluated the performance of CCPE based on a variety of simulated and real scRNA-seq datasets. Our results indicate that CCPE is an effective method for cell cycle estimation and competitive in various applications compared with other existing methods. CCPE successfully identified cell cycle marker genes and is robust to dropout events in scRNA-seq data. Accurate prediction of the cell cycle using CCPE can also effectively facilitate the removal of cell cycle effects across cell types or conditions.     

喜树与南方红豆杉混交群落生活史型谱特征

研究了不同生境条件下喜树和南方红豆杉混交群落中喜树和南方红豆杉的生活史型谱特征。结果表明,喜树和南方红豆杉在S生活史型得分和比例均为0。喜树和南方红豆杉生活史型V主成分得分均以山地2最高,而纯林的生活史型V主成分得分最低,C也表现为山地2最高,而纯林最低。喜树种群的生活史型比例按照从山地、坡地、平地、纯林排序,V型比例逐渐上升而C型比例逐渐下降的趋势,这就构成了混交群落中喜树种群的生活史型谱。南方红豆杉种群的生活史型谱特征,主要表现为山地2和坡地V型比例最小,而C型比例最大,纯林种植中V型比例较高,而以纯林1的V型比例最高,C型比例最小。     

冻融胚胎移植中三种不同内膜准备方法的妊娠结局比较

目的：比较三种不同内膜准备方法中复苏胚胎移植的妊娠结局。方法：对因女方输卵管因素不孕的248个冻融囊胚移植周期的临床资料进行回顾性分析。将内膜准备方法分为自然周期组、全激素替代周期组和半激素替代周期组三种,分别对各组的着床率、临床妊娠率、生化妊娠率和早期流产率进行分析比较。结果：自然周期组的子宫内膜厚度显著高于全激素周期组和半激素替代周期组（P〈0．05）,差异有统计学意义。而这三组病人在年龄、不孕年限和移植胚胎数目上则均无明显差异（P〉0．05）。另外,三种内膜准备方法的着床率、临床妊娠率、早期流产率及生化妊娠流产率亦无显著性差异（P〉O．05）。结论：冻融胚胎移植中,对于排卵正常患者我们建议采用自然周期法更为经济、方便。而对于月经周期不正常,排卵障碍的病人应依实际情况采用全激素周期或半激素周期方案。     

Lighting The Circle of Life: Fluorescent Sensors for Covert Surveillance of the Cell Cycle

The cell cycle is the collective mechanism through which all of us develop, exist and in many cases, when it goes wrong, die. Despite enormous progress in unravelling the complexity of the cell cycle through intensive study over the past 100 years, development of new tools to analyse the process and associated cellular events has not kept pace. All standard cell cycle analysis methods preclude real time dynamic analysis of the cell cycle in live cells at single cell resolution. To address the needs of cell cycle investigations across a range of analysis platforms we are currently developing a range of cell cycle phase markers based on GFP expression controlled by well characterised cell cycle components to allow covert surveillance of the cell cycle in living cells.     

Lighting the circle of life: fluorescent sensors for covert surveillance of the cell cycle

The cell cycle is the collective mechanism through which all of us develop, exist and in many cases, when it goes wrong, die. Despite enormous progress in unravelling the complexity of the cell cycle through intensive study over the past 100 years, development of new tools to analyse the process and associated cellular events has not kept pace. All standard cell cycle analysis methods preclude real time dynamic analysis of the cell cycle in live cells at single cell resolution. To address the needs of cell cycle investigations across a range of analysis platforms we are currently developing a range of cell cycle phase markers based on GFP expression controlled by well characterised cell cycle components to allow covert surveillance of the cell cycle in living cells.     

Life cycle replacement by gene introduction under an allee effect in periodical cicadas

Periodical cicadas (Magicicada spp.) in the USA are divided into three species groups (-decim, -cassini, -decula) of similar but distinct morphology and behavior. Each group contains at least one species with a 17-year life cycle and one with a 13-year cycle; each species is most closely related to one with the other cycle. One explanation for the apparent polyphyly of 13- and 17-year life cycles is that populations switch between the two cycles. Using a numerical model, we test the general feasibility of life cycle switching by the introduction of alleles for one cycle into populations of the other cycle. Our results suggest that fitness reductions at low population densities of mating individuals (the Allee effect) could play a role in life cycle switching. In our model, if the 13-year cycle is genetically dominant, a 17-year cycle population will switch to a 13-year cycle given the introduction of a few 13-year cycle alleles under a moderate Allee effect. We also show that under a weak Allee effect, different year-classes ("broods") with 17-year life cycles can be generated. Remarkably, the outcomes of our models depend only on the dominance relationships of the cycle alleles, irrespective of any fitness advantages.     

Chemical inhibitors: a tool for plant cell cycle studies

Synchrony provides a large number of cells at defined points of the cell cycle. Highly synchronised cells are powerful and effective tools for molecular analyses and for studying the biochemical events of the cell cycle in plants. Usually, plant cell suspensions can be synchronised by chemical agents, which arrest the cell cycle by acting on the driving forces of the cell cycle engine such as cyclin-dependent kinase activity, enzymes involved in DNA synthesis or proteolysis of cell cycle regulators or by acting on the cell cycle apparatus (mitotic spindle). The specificity, reversibility and efficiency of each type of cell cycle inhibitor are described and related to their mode of action.     

Morphogenesis and cell cycle progression in Candida albicans

Candida albicans, an opportunistic human pathogen, displays three modes of growth: yeast, pseudohyphae and true hyphae, all of which differ both in morphology and in aspects of cell cycle progression. In particular, in hyphal cells, polarized growth becomes uncoupled from other cell cycle events. Yeast or pseudohyphae that undergo a cell cycle delay also exhibit polarized growth, independent of cell cycle progression. The Spitzenk?rper, an organelle composed of vesicles associated with hyphal tips, directs continuous hyphal elongation in filamentous fungal species and also in C. albicans hyphae. A polarisome mediates cell cycle dependent growth in yeast and pseudohyphae. Regulation of morphogenesis and cell cycle progression is dependent upon specific cyclins, all of which affect morphogenesis and some of which function specifically in yeast or hyphal cells. Future work will probably focus on the cell cycle checkpoints involved in connecting morphogenesis to cell cycle progression.     

Simultaneous flow cytometric DNA and volume measurements of bone marrow cells as sensitive indicator of abnormal proliferation patterns in rat leukemias.

Simultaneous flow cytometric DNA and volume analysis of normal rat bone marrow cells shows three populations of nucleated cells with different mean volume. Each of these populations proliferates in a distinct cell cycle (alpha, beta, gamma). Normally the alpha-cell cycle has the highest amplitude, the beta-cell cycle is intermediate, and the gamma-cell cycle is low. The alpha-cell cycle was very significantly depressed and the beta + gamma-cell cycle was increased in three different rat leukemias (L5222, Shay, BNML), growing on three different rat strains (BDIX, Holtzmann, Brown Norway). The two parameter analysis further revealed that cells of the beta + gamma-cell cycle were slightly hyperdiploid and hypertetraploid in leukemic animals. The decrease of the alpha-cell cycle and the hyperploidies were more sensitive indicators for the abnormal proliferation pattern than the analysis of one parameter DNA distributions which remained within normal limits in all three leukemias.     

外周血淋巴细胞凋亡依赖于细胞周期运行

目的以培养的人类正常外周血淋巴细胞（peripheral blood lymphocytes,PBLs）为模型,模拟细胞周期运行的不同状态,研究细胞凋亡与细胞周期运行的关系。方法将PHA及咖啡因处理前后的PBLs,分别用喜树碱（CPT）、X-射线、抗Fas抗体和肿瘤坏死因子TNF-α诱导,流式细胞术方法对细胞凋亡进行定量检测。结果PBLs经PHA刺激后进入细胞周期并发生凋亡,在凋亡因子打击作用下凋亡明显增加,用咖啡因废除细胞周期检测点后对凋亡打击敏感性降低。未经PHA刺激的PBLs对凋亡打击无应答。结论细胞进入细胞周期总是伴随细胞凋亡的发生,细胞不进入周期,则不会发生凋亡,细胞周期不停止,也不会凋亡。细胞周期检测点是联结细胞周期和细胞凋亡的重要位点。     

Metabolic cycle, cell cycle, and the finishing kick to Start

Slowly growing budding yeast store carbohydrate, then liquidate it in late G1 phase of the cell cycle, superimposing a metabolic cycle on the cell cycle. This metabolic cycle may separate biochemically incompatible processes. Alternatively it may provide a burst of energy and material for commitment to the cell cycle. Stored carbohydrate could explain the size requirement for cells passing the Start point.     

Graded requirement for the spliceosome in cell cycle progression

Genome stability is ensured by multiple surveillance mechanisms that monitor the duplication, segregation, and integrity of the genome throughout the cell cycle. Depletion of components of the spliceosome, a macromolecular machine essential for mRNA maturation and gene expression, has been associated with increased DNA damage and cell cycle defects. However, the specific role for the spliceosome in these processes has remained elusive, as different cell cycle defects have been reported depending on the specific spliceosome subunit depleted. Through a detailed cell cycle analysis after spliceosome depletion, we demonstrate that the spliceosome is required for progression through multiple phases of the cell cycle. Strikingly, the specific cell cycle phenotype observed after spliceosome depletion correlates with the extent of depletion. Partial depletion of a core spliceosome component results in defects at later stages of the cell cycle (G2 and mitosis), whereas a more complete depletion of the same component elicits an early cell cycle arrest in G1. We propose a quantitative model in which different functional dosages of the spliceosome are required for different cell cycle transitions.     

Change in Photosynthetic Capacity over the Cell Cycle in Light/Dark-Synchronized Amphidinium carteri Is Due Solely to the Photocycle

Cell cycle dependent photosynthesis in the marine dinoflagellate Amphidinium carteri was studied under constant illumination and light/dark (L/D) photocycles to distinguish intrinsic cell cycle control from environmental influences. Cells were grown in constant light and on a 14:10 L:D cycle at light intensities that would yield a population growth rate of 1 doubling per day. In the former case division was asynchronous, and cells were separated according to cell cycle stage using centrifugal elutriation. Cells grown on the L:D cycle were synchronized, with division restricted to the dark period. Cell cycle stage distributions were quantified by flow cytometry. Various cell age groups from the two populations were compared as to their photosynthetic response (photosynthetic rate versus irradiance) to determine whether or not the response was modulated primarily by cell cycle constraints or the periodic L/D cycle. Cell cycle variation in photosynthetic capacity was found to be determined solely by the L/D cycle; it was not present in cells grown in constant light.     

Effect of regulated expression of the fragile histidine traid gene on cell cycle and proliferation

The mechanism of tumor suppressor action of the fragile histidine triad (FHIT) gene is unknown. Disruption of cell cycle regulation leads to the tumor formation and many tumor suppressor genes suppress tumorigenesis through their effect on cell cycle regulation. We examined the expression of FHIT during the cell cycle, and determined whether overexpression of FHIT affects cell cycle kinetics and apoptosis. The FHIT cDNA was cloned into the ecdysone-inducible expression vector in both the sense and antisense orientations. Overexpression of the sense or antisense construct did not affect cell proliferation, cell cycle distribution or apoptosis in human 293T cells. Analysis of the FHIT expression in 293T cells collected at various cell cycle phases showed that the expression of FHIT is not under cell cycle regulation. These results indicate that the tumor suppressor activity of the FHIT gene may be independent of an effect on the cell cycle and apoptosis mechanisms.     

Transcription profiling during the cell cycle shows that a subset of Polycomb-targeted genes is upregulated during DNA replication

Genome-wide gene expression analyses of the human somatic cell cycle have indicated that the set of cycling genes differ between primary and cancer cells. By identifying genes that have cell cycle dependent expression in HaCaT human keratinocytes and comparing these with previously identified cell cycle genes, we have identified three distinct groups of cell cycle genes. First, housekeeping genes enriched for known cell cycle functions; second, cell type-specific genes enriched for HaCaT-specific functions; and third, Polycomb-regulated genes. These Polycomb-regulated genes are specifically upregulated during DNA replication, and consistent with being epigenetically silenced in other cell cycle phases, these genes have lower expression than other cell cycle genes. We also find similar patterns in foreskin fibroblasts, indicating that replication-dependent expression of Polycomb-silenced genes is a prevalent but unrecognized regulatory mechanism.     

Systematic Characterization of Cell Cycle Phase-dependent Protein Dynamics and Pathway Activities by High-content Microscopy-assisted Cell Cycle Phenotyping

Cell cycle progression is coordinated with metabolism, signaling and other complex cellular functions. The investigation of cellular processes in a cell cycle stage-dependent manner is often the subject of modern molecular and cell biological research. Cell cycle synchronization and immunostaining of cell cycle markers facilitate such analysis, but are limited in use due to unphysiological experimental stress, cell type dependence and often low flexibility. Here, we describe high-content microscopy-assisted cell cycle phenotyping（hi MAC）, which integrates high-resolution cell cycle profiling of asynchronous cell populations with immunofluorescence microscopy. hi MAC is compatible with cell types from any species and allows for statistically powerful, unbiased, simultaneous analysis of protein interactions, modifications and subcellular localization at all cell cycle stages within a single sample. For illustration, we provide a hi MAC analysis pipeline tailored to study DNA damage response and genomic instability using a 3–4-day protocol,which can be adjusted to any other cell cycle stage-dependent analysis.     

Cell cycle in the fucus zygote parallels a somatic cell cycle but displays a unique translational regulation of cyclin-dependent kinases

In eukaryotic cells, the basic machinery of cell cycle control is highly conserved. In particular, many cellular events during cell cycle progression are controlled by cyclin-dependent kinases (CDKs). The cell cycle in animal early embryos, however, differs substantially from that of somatic cells or yeasts. For example, cell cycle checkpoints that ensure that the sequence of cell cycle events is correct have been described in somatic cells and yeasts but are largely absent in embryonic cells. Furthermore, the regulation of CDKs is substantially different in the embryonic and somatic cells. In this study, we address the nature of the first cell cycle in the brown alga Fucus, which is evolutionarily distant from the model systems classically used for cell cycle studies in embryos. This cycle consists of well-defined G1, S, G2, and M phases. The purine derivative olomoucine inhibited CDKs activity in vivo and in vitro and induced different cell cycle arrests, including at the G1/S transition, suggesting that, as in somatic cells, CDKs tightly control cell cycle progression. The cell cycle of Fucus zygotes presented the other main features of a somatic cell cycle, such as a functional spindle assembly checkpoint that targets CDKs and the regulation of the early synthesis of two PSTAIRE CDKs, p32 and p34, and the associated histone H1 kinase activity as well as the regulation of CDKs by tyrosine phosphorylation. Surprisingly, the synthesis after fertilization of p32 and p34 was translationally regulated, a regulation not described previously for CDKs. Finally, our results suggest that the activation of mitotic CDKs relies on an autocatalytic amplification mechanism.