Genome-wide identification and expression analysis of rice cell cycle genes

Cyclins, cyclin-dependent kinases, and a number of other proteins control the progression of plant cell cycle. Although extensive studies have revealed the roles of some cell cycle regulators and the underlying mechanisms in Arabidopsis, relatively a small number of cell cycle regulators were functionally analyzed in rice. In this study, we describe 41 regulators in the rice genome. Our results indicate that the rice genome contains a less number of the core cell cycle regulators than the Arabidopsis one does, although the rice genome is much larger than the Arabidopsis one. Eight groups of CDKs similar to those in Arabidopsis were identified in the rice genome through phylogenetic analysis, and the corresponding members in the different groups include E2F, CKI, Rb, CKS and Wee. The structures of the core cell regulators were relatively conserved between the rice and Arabidopsis genomes. Furthermore, the expression of the majority of the core cell cycle genes was spatially regulated, and the most closely related ones showed very similar patterns of expression, suggesting functional redundancy and conservation between the highly similar core cell cycle genes in rice and Arabidopsis. Following auxin or cytokinin treatment, the expression of the core cell cycle genes was either upregulated or downregulated, suggesting that auxin and/or cytokinin may directly regulate the expression of the core cell cycle genes. Our results provide basic information to understand the mechanism of cell cycle regulation and the functions of the rice cell cycle genes. Electronic supplementary material The online version of this article (doi: ) contains supplementary material, which is available to authorized users. Jing Guo and Jian Song have contributed equally.     

Life cycle cost analysis of three renewed street lighting installations in Finland

Purpose  

Outdoor lighting is facing major changes due to the EU legislation on ecodesign of energy-related products, such as the ban of high-pressure mercury (HPM) lamps widely used in outdoor lighting. This article presents life cycle costs (LCC) of three examples of replacing HPM lamps in street lighting in Finland. The purpose of the article is to assess how the development of light-emitting diode (LED) technology affects LCCs and how the division of LCCs differentiates in the cases.     

Unique aspects of the grass cell wall

Grasses are amongst the most important crops worldwide, and the composition of their cell walls is critical for uses as food, feed, and energy crops. Grass cell walls differ dramatically from dicot cell walls in terms of the major structural polysaccharides present, how those polysaccharides are linked together, and the abundance and importance of pectins, proteins and phenolic compounds. Recent advances, spurred by the availability of genomic resources for several plant species, include the characterization of cellulose synthase like (Csl) gene families that are unique to the grasses and the demonstration that members of one of those gene families, CslF, are responsible for making the mixed linkage glucans that are unique to the order Poales.     

Efficiency of expression of transfected genes depends on the cell cycle

Lipofection, a lipid-mediated DNA transfection procedure, was used to transfect synchronized L929 mouse fibroblast cells with a reporter plasmid containing the bacterial chloramphenicol acetyltransferase gene. The efficiency of gene expression was investigated on transfection of cells at different stages of the cell cycle. Our data show that expression of the reporter gene was minimal when transfection was performed in G0-phase and parallel experimental data disproved the possibility that the reduced expression observed was due to differential uptake at different times in the cell cycle. Investigation into the condensation state of the plasmid has shown that the low chloramphenicol acetyltransferase gene expression could be a direct consequence of the packaging of the plasmid into condensed chromatin when transfection occurs in G0-phase. The inactivation of the reporter gene is not reversed by growth of the cells in high serum or by treatment with Trichostatin A, a specific inhibitor of histone deacetylase, suggesting that the inactive chromatin formed in G0-phase cells lacks associated histone acetylase activity. In contrast, the high activity seen when cells in S-phase are transfected is enhanced even further by treatment with Trichostatin A.     

Factors regulating the expression of cell cycle genes in individual buds ofPopulus

The early and differential responses of the individual buds along a shoot have remained largely unknown due to the difficulties of analyzing early indicators that allow the monitoring of the effects of subtle changes in the environment on the growth activity of the individual bud. To overcome this problem, we transformed poplar [Populus tremula (L.) xP. alba (L.)] with two chimeric genes,Pcdc2a-gus andPcycl At-gus, the expression of which is closely linked to cell division inArabidopsis thaliana (L.) Heynh. We analyzed the expression levels of both chimeric genes in individual buds of the same tree, and under different conditions known to promote or retard growth in the buds. The expression levels of both chimeric genes were found to reflect closely the growth activity of the buds. After decapitation of the shoot, the expression ofPcdc2a-gus andPcycl At-gus revealed rapid and selective changes in the cell cycle, even when no morphological changes were observed. Furthermore, on the basis of the expression of the chimeric cell cycle genes, different degrees of growth activity and dormancy could be discriminated in the axillary buds. In addition, the expression ofPcycl At-gus was found to be closely associated with the day length, which is critical for dormancy induction in poplar.Abbreviations GUS -glucuronidase - MU methylumbelliferone     

Naringenin regulates expression of genes involved in cell wall synthesis in Herbaspirillum seropedicae

Five thousand mutants of Herbaspirillum seropedicae SmR1 carrying random insertions of transposon pTnMod-OGmKmlacZ were screened for differential expression of LacZ in the presence of naringenin. Among the 16 mutants whose expression was regulated by naringenin were genes predicted to be involved in the synthesis of exopolysaccharides, lipopolysaccharides, and auxin. These loci are probably involved in establishing interactions with host plants.     

In vivo robustness analysis of cell division cycle genes in Saccharomyces cerevisiae

Intracellular biochemical parameters, such as the expression level of gene products, are considered to be optimized so that a biological system, including the parameters, works effectively. Those parameters should have some permissible range so that the systems have robustness against perturbations, such as noise in gene expression. However, little is known about the permissible range in real cells because there has been no experimental technique to test it. In this study, we developed a genetic screening method, named “genetic tug-of-war” (gTOW) that evaluates upper limit copy numbers of genes in a model eukaryote Saccharomyces cerevisiae, and we applied it for 30 cell-cycle related genes (CDC genes). The experiment provided unique quantitative data that could be used to argue the system-level properties of the cell cycle such as robustness and fragility. The data were used to evaluate the current computational model, and refinements to the model were suggested.     

Genome-wide annotation and expression profiling of cell cycle regulatory genes in Chlamydomonas reinhardtii

Eukaryotic cell cycles are driven by a set of regulators that have undergone lineage-specific gene loss, duplication, or divergence in different taxa. It is not known to what extent these genomic processes contribute to differences in cell cycle regulatory programs and cell division mechanisms among different taxonomic groups. We have undertaken a genome-wide characterization of the cell cycle genes encoded by Chlamydomonas reinhardtii, a unicellular eukaryote that is part of the green algal/land plant clade. Although Chlamydomonas cells divide by a noncanonical mechanism termed multiple fission, the cell cycle regulatory proteins from Chlamydomonas are remarkably similar to those found in higher plants and metazoans, including the proteins of the RB-E2F pathway that are absent in the fungal kingdom. Unlike in higher plants and vertebrates where cell cycle regulatory genes have undergone extensive duplication, most of the cell cycle regulators in Chlamydomonas have not. The relatively small number of cell cycle genes and growing molecular genetic toolkit position Chlamydomonas to become an important model for higher plant and metazoan cell cycles.     

绵羊MHC区段3个预测基因的验证与表达分析

对新疆美利奴细毛羊基因组MHC(Major histocompatibility complex)区段细菌人工染色体(BAC)文库的DNA序列进行测定,经过序列比对分析,首次预测了约130个新基因,其中有8个CDS(Coding sequences)未在其他物种中发现其同源序列,推测可能系绵羊所特有。在此基础上,文章对绵羊MHC区段预测的3个新基因(分别命名为OaN2、OaN5、OaN6)进行了实验验证和表达分析。从绵羊肺组织中克隆到了OaN2的cDNA序列,其长度为270 bp;从肠系淋巴结中扩增得到OaN5和OaN6的cDNA序列,长度分别为309 bp和205 bp。上述3个基因的GenBank登录号分别为JF330782、JF330783和JF330784。利用Northern blotting技术进行转录本水平分析,发现这3个新基因均在免疫器官肠系淋巴结中高表达。通过Western blotting和原位免疫组化技术对OaN2蛋白水平进行了表达谱分析,结果表明OaN2蛋白在绵羊脾脏和肠系淋巴结等免疫器官中高表达,在心、肝及胰脏中不表达。这是首次通过实验验证绵羊MHC区段的3个预测的新基因,为其在绵羊免疫器官中的功能研究奠定了基础。     

Oncogenes and cell cycle genes

The relationships between oncogenes, cell-cycle control genes, and growth-related genes are described. An important generalization from the data is that all the oncogenes and cell-cycle control genes so far characterized appear to be genes for growth factors or for receptors to growth factors, or to be involved in the general metabolism and structure of the cell. It is suggested that the transition in cell growth from quiescence to the proliferative state, in early G₁, may be less specific than previously thought and involve a general priming of the cells for more specific later stimuli.     

Analysis of expressed genes in ethylene-treated potato leaves using expressed sequence tags

To isolate useful and interesting plant genes in large quantities, random sequencing of cDNA clones from potato leaf library treated with ethylene was performed. Partial sequences of randomly selected 210 clones with the insert of longer than 500 base pair (bp) as well as poly (A) tail have been compared with sequences in GeneBank, EMBL and DDBJ nucleic acid databases and fostered 193 expressed sequence tags (ESTs). The 210 cDNA clones identified are related to various aspect of metabolic pathways such as glycolysis, amino acid synthesis, translation mechanism, ribosome synthesis, hormone response, stress response, regulation of gene expression, and signal transduction. Among the 193 ESTs, 12 ESTs (29 cDNA clones) appeared more than once and 181 ESTs appeared once regarded as a solitary group. Out of 210 clones, 29 clones (13.8%) have no similarity to the known nucleotide sequences and could serve as a potentially useful resource for plant molecular biology referring to particular genes. Nucleotide sequencing to generate more ESTs from ethylene-induced as well as non-induced potato leaf is in progress as well.     

Life cycle analysis of algae biodiesel

Background, aim, and scope  

Algae biomass has great promise as a sustainable alternative to conventional transportation fuels. In this study, a well-to-pump life cycle assessment (LCA) was performed to investigate the overall sustainability and net energy balance of an algal biodiesel process. The goal of this LCA was to provide baseline information for the algae biodiesel process.     

Deregulated expression of circadian clock and clock-controlled cell cycle genes in chronic lymphocytic leukemia

Circadian rhythms are endogenous and self-sustained oscillations of multiple biological processes with approximately 24-h rhythmicity. Circadian genes and their protein products constitute the molecular components of the circadian oscillator that form positive/negative feedback loops and generate circadian rhythms. The circadian regulation extends from core clock genes to various clock-controlled genes that include various cell cycle genes. Aberrant expression of circadian clock genes, therefore, may lead to genomic instability and accelerated cellular proliferation potentially promoting carcinogenesis. The current study encompasses the investigation of simultaneous expression of four circadian clock genes (Bmal1, Clock, Per1 and Per2) and three clock-controlled cell cycle genes (Myc, Cyclin D1 and Wee1) at mRNA level and determination of serum melatonin levels in peripheral blood samples of 37 CLL (chronic lymphocytic leukemia) patients and equal number of age- and sex-matched healthy controls in order to indicate association between deregulated circadian clock and manifestation of CLL. Results showed significantly down-regulated expression of Bmal1, Per1, Per2 and Wee1 and significantly up-regulated expression of Myc and Cyclin D1 (P < 0.0001) in CLL patients as compared to healthy controls. When expression of these genes was compared between shift-workers and non-shift-workers within the CLL group, the expression was found more aberrant in shift-workers as compared to non-shift-workers. However, this difference was found statistically significant for Myc and Cyclin D1 only (P < 0.05). Serum melatonin levels were found significantly low (P < 0.0001) in CLL subjects as compared to healthy controls whereas melatonin levels were found still lower in shift-workers as compared to non-shift-workers within CLL group (P < 0.01). Our results suggest that aberrant expression of circadian clock genes can lead to aberrant expression of their downstream targets that are involved in cell proliferation and apoptosis and hence may result in manifestation of CLL. Moreover, shift-work and low melatonin levels may also contribute in etiology of CLL by further perturbing of circadian clock.     

Life cycle assessment of retaining wall backfilled with shredded tires

Purpose

This life cycle assessment (LCA) study compares energy consumption, greenhouse gas emissions, and environmental damages for two methods of constructing retaining structures, a traditional method involving a retaining wall backfilled with sand, and an alternative method involving a retaining wall backfilled with shredded tires.

Methods

Taking into account the extraction and production of the used construction materials, loading, transport and installation, the cumulative energy demand (CED), global warming potential (GWP), acidification potential, Human Health Criteria Air-mobile, aquatic eutrophication potential, ozone depletion potential, and smog potential is determined for each construction method. The seven environmental impact categories are calculated using the software tool, ATHENA® Environmental Impact Estimator (ATHENA® EIE) for Buildings v5.2.0118.

Results and discussion

The seven impact categories were reduced significantly by using shredded tires as retaining wall backfill; this is due to the decrease in the amounts of concrete, reinforcing steel, and fuel quantity consumed by building machines and vehicles transporting construction materials.

Conclusions

The study concludes that in all examined impact categories alternative method provides a larger environmental benefit than the traditional method. Also, the results clearly demonstrate that the use of shredded tires is very effective as a sustainable alternative to retaining structures.