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OALib Journal期刊

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Certain amplified genomic-DNA fragments (AGFs) may be involved in cell-cycle progression and chloroquine was found to induce the production of cell-cycle-associated AGFs (CAGFs) in Plasmodium falciparum
Gao-De Li
Quantitative Biology , 2015,
Abstract: It is well known that cyclins are a family of proteins that control cell-cycle progression by activating cyclin-dependent kinase. In this paper we propose a novel hypothesis that certain amplified genomic-DNA fragments (AGFs) may also be required for cell-cycle progression and thus could be named as cell-cycle-associated AGFs (CAGFs). Like fluctuation in cyclin levels during cell-cycle progression, these CAGFs are amplified and degraded at different points of the cell cycle. The functions of CAGFs are unknown, but we speculate that the CAGFs might be involved in regulation of gene expression, genome protection, and formation of certain macromolecular complexes required for the dynamic genome architecture during cell-cycle progression. Our preliminarily experimental results showed that chloroquine induced the production of CAGFs in Plasmodium falciparum, suggesting that targeting cell-cycle progression could be the primary mechanism of chloroquine's antimalarial, anticancer, and immunomodulatory actions.
Pfcrmp May Play a Key Role in Chloroquine Antimalarial Action and Resistance Development
Gao-De Li
Quantitative Biology , 2015,
Abstract: It was proposed earlier that Pfcrmp (Plasmodium falciparum chloroquine resistance marker protein) may be the chloroquine's target protein in nucleus. In this communication, further evidence is presented to support the view that Pfcrmp may play a key role in chloroquine antimalarial actions as well as resistance development.
“Natural Site-Directed Mutagenesis” Might Exist in Eukaryotic Cells  [PDF]
Gao-De Li
Open Access Library Journal (OALib Journal) , 2016, DOI: 10.4236/oalib.1102595
Abstract: Site-directed mutagenesis refers to a man-made molecular biology method that is used to make genetic alterations in the DNA sequence of a gene of interest. But based on our recently published experimental findings, we propose that “natural site-directed mutagenesis” might exist in eukaryotic cells, which is triggered by harmful agents and co-directed by special transcription hotspots and mutation-contained intranuclear primers.
A Possible Mechanism of DNA to DNA Transcription in Eukaryotic Cells: Endonuclease Dependent Transcript Cutout  [PDF]
Gao-De Li
Open Access Library Journal (OALib Journal) , 2016, DOI: 10.4236/oalib.1102758
Abstract:
We previously proposed the existence of DNA to DNA transcription in eukaryotic cells, but the mechanism by which single-stranded DNA (ssDNA) transcript is produced and released from the genome remains unknown. We once speculated that the mechanism of DNA to DNA transcription might be similar to that of DNA to RNA transcription, but now we propose that endonuclease dependent transcript cutout may be a possible mechanism of DNA to DNA transcription, in which a copy of ssDNA fragment (transcript) between two nicks produced by nicking endonuclease is released from double-stranded DNA (dsDNA) region in the genome by an unknown ssDNA fragment releasing enzyme. The gap in the dsDNA will be filled through DNA repair mechanism. Occasionally, multiple copies of ssDNA transcripts could be produced through multiple rounds of cutout- repair-cutout cycle.
Genoautotomy (Genome 'Self-Injury') in Eukaryotic Cells: A Cellular Defence Response to Genotoxic Stress  [PDF]
Gao-De Li
Open Access Library Journal (OALib Journal) , 2016, DOI: 10.4236/oalib.1102946
Abstract:
This paper proposes that eukaryotic cells, under severe genotoxic stress, can commit genoautotomy (genome “self-injury”) that involves cutting and releasing single-stranded DNA (ssDNA) fragments from double-stranded DNA and leaving ssDNA gaps in the genome. The ssDNA gaps could be easily and precisely repaired later. The released ssDNA fragments may play some role in the regulation of cell cycle progression. Taken together, genoautotomy causes limited nonlethal DNA damage, but prevents the whole genome from lethal damage, and thus should be deemed as a eukaryotic cellular defence response to genotoxic stress.
Certain Amplified Genomic-DNA Fragments (AGFs) May Be Involved in Cell Cycle Progression and Chloroquine Is Found to Induce the Production of Cell-Cycle-Associated AGFs (CAGFs) in Plasmodium falciparum  [PDF]
Gao-De Li
Open Access Library Journal (OALib Journal) , 2016, DOI: 10.4236/oalib.1102447
Abstract: It is well known that cyclins are a family of proteins that control cell-cycle progression by activating cyclin-dependent kinase. Based on our experimental results, we propose here a novel hypothesis that certain amplified genomic-DNA fragments (AGFs) may also be required for the cell cycle progression of eukaryotic cells and thus can be named as cell-cycle-associated AGFs (CAGFs). Like fluctuation in cyclin levels during cell cycle progression, these CAGFs are amplified and degraded at different points of the cell cycle. The functions of CAGFs are unknown, but we speculate that CAGFs may be involved in regulation of gene expression, genome protection, and formation of certain macromolecular complexes required for the dynamic genome architecture during cell cycle progression. Our experimental results also show that chloroquine induces the production of CAGFs in Plasmodium falciparum, suggesting that targeting cell cycle progression can be the primary mechanism of chloroquine’s antimalarial, anticancer, and immunomodulatory actions.
DNA to DNA Transcription Might Exist in Eukaryotic Cells  [PDF]
Gao-De Li
Open Access Library Journal (OALib Journal) , 2016, DOI: 10.4236/oalib.1102665
Abstract:
Till now, in biological sciences, the term, transcription, mainly refers to DNA to RNA transcription. But our recently published experimental findings obtained from Plasmodium falciparum strongly suggest the existence of DNA to DNA transcription in the genome of eukaryotic cells, which could shed some light on the functions of certain noncoding DNA in the human and other eukaryotic genomes.
Cell-Cycle-Associated Amplified Genomic-DNA Fragments (CAGFs) Might Be Involved in Chloroquine Action and Resistance in Plasmodium falciparum  [PDF]
Gao-De Li
Open Access Library Journal (OALib Journal) , 2017, DOI: 10.4236/oalib.1103451
Abstract:
As a cheap and safe antimalarial agent, chloroquine (CQ) has been used in the battle against malaria for more than half century. However, the mechanism of CQ action and resistance in Plasmodium falciparum remains elusive. Based on further analysis of our published experimental results, we propose that the mechanism of CQ action and resistance might be closely linked with cell-cycle-associated amplified genomic-DNA fragments (CAGFs, singular form = CAGF) as CQ induces CAGF production in P. falciparum, which could affect multiple biological processes of the parasite, and thus might contribute to parasite death and CQ resistance. Recently, we found that CQ induced one of CAGFs, UB1-CAGF, might downregulate a probable P. falciparum cystine transporter (Pfct) gene expression, which could be used to understand the mechanism of CQ action and resistance in P. falciparum.
Further Thoughts on Abnormal Chromatin Configuration and Oncogenesis  [PDF]
Gao-De Li
Open Access Library Journal (OALib Journal) , 2019, DOI: 10.4236/oalib.1105185
Abstract:
More than 30 years ago, we published a paper entitled as “Abnormal Chromatin Configuration and Oncogenesis”, which proposed the first hy-pothesis that links oncogenesis to abnormal three-dimensional (3D) genome structure. Recently, many studies have demonstrated that the 3D genome structure plays a major role in oncogenesis, which strongly supports our hypothesis. In this paper, further thoughts about our hypothesis are presented.
Hierarchical Scheduling of Large Scale Distributed Computation
大型分布式计算中的分级节能调度

QIN Gao-de,WEN Gao-jin,
秦高德
,文高进

计算机科学 , 2013,
Abstract: 随着云计算的快速发展,大型分布式计算被广泛应用。但是,其运行时的巨大能量消耗已经成为应用推广的难题。目前的节能研究主要提出通过调度来减少服务器的运行数量以节能,而没有考虑网络的能耗。提出的分级调度算法HAS(Hierarchical Scheduling Algorithm)针对各计算节点间可能出现任务调度的情况,以DMNS(Dynamic Maxi-mum Node Sorting)调度方法将这些应用尽量分配到连接到同一级交换机的服务器中,然后,将应用数量少的计算节点上的任务转移到还能增加任务的节点,从而减少节点的数量。同时,调度时选择的是较少的数据交换量和较短的交换路径,以节约网络能耗。HAS算法的复杂度较好,且其稳定性也通过计算仿真得到验证。通过仿真数据对比表明,HAS比目前的其它方法更优。
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