K. M. Lisowska, Joanna Rzeszowska-Wolny, Aleksander Sochanik
This essay is in memoriam of Professor Mieczysław Chorąży (1925 – 2021). Eminent Man, outstanding scientist, soldier of the Warsaw Uprising, moral authority for generations of fellow researchers and an exceptionally warm person. His character and life works are recalled here against the background of the times he lived in.
本文是对 Mieczysław Chorąży 教授（1925 - 2021 年）的悼念。他是一位杰出的人物、杰出的科学家、华沙起义的战士、几代研究人员的道德权威以及一位特别热情的人。这里以他所处的时代为背景，回顾了他的品格和生平事迹。
{"title":"Professor Mieczysław Chorąży and His Works","authors":"K. M. Lisowska, Joanna Rzeszowska-Wolny, Aleksander Sochanik","doi":"10.18388/pb.2021_525","DOIUrl":"https://doi.org/10.18388/pb.2021_525","url":null,"abstract":"This essay is in memoriam of Professor Mieczysław Chorąży (1925 – 2021). Eminent Man, outstanding scientist, soldier of the Warsaw Uprising, moral authority for generations of fellow researchers and an exceptionally warm person. His character and life works are recalled here against the background of the times he lived in.","PeriodicalId":20341,"journal":{"name":"Postępy Biochemii","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140660336","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. Gelléri, Michael Sterr, H. Strickfaden, Christoph Cremer, Thomas Cremer, Marion Cremer
Genome replication requires duplication of the complete set of DNA sequences together with nucleosomes and epigenetic signatures. Notwithstanding profound knowledge on mechanistic details of DNA replication, major problems of genome replication have remained unresolved. In this perspective article, we consider the accessibility of replication machines to all DNA sequences in due course, the maintenance of functionally important positional and structural features of chromatid domains during replication, and the rapid transition of CTs into prophase chromosomes with two chromatids. We illustrate this problem with EdU pulse-labeling (10 min) and chase experiments (80 min) performed with mouse myeloblast cells. Following light optical serial sectioning of nuclei with 3D structured illumination microscopy (SIM), seven DNA intensity classes were distinguished as proxies for increasing DNA compaction. In nuclei of cells fixed immediately after the pulse-label, we observed a relative under-representation of EdU-labeled DNA in low DNA density classes, representing the active nuclear compartment (ANC), and an over-representation in high density classes representing the inactive nuclear compartment (INC). Cells fixed after the chase revealed an even more pronounced shift to high DNA intensity classes. This finding contrasts with previous studies of the transcriptional topography demonstrating an under-representation of epigenetic signatures for active chromatin and RNAPII in high DNA intensity classes and their over-representation in low density classes. We discuss these findings in the light of current models viewing CDs either as structural chromatin frameworks or as phase-separated droplets, as well as methodological limitations that currently prevent an integration of this contrasting evidence for the spatial nuclear topography of replication and transcription into a common framework of the dynamic nuclear architecture.
基因组复制需要复制整套 DNA 序列以及核小体和表观遗传特征。尽管对 DNA 复制的机理细节有了深入了解，但基因组复制的主要问题仍未得到解决。在这篇透视文章中，我们考虑了复制机器在适当时候对所有 DNA 序列的可及性、复制过程中染色体结构域重要位置和结构特征的维持，以及 CT 快速转变为具有两条染色体的前期染色体等问题。我们用小鼠骨髓母细胞进行的 EdU 脉冲标记（10 分钟）和追逐实验（80 分钟）来说明这个问题。用三维结构照明显微镜（SIM）对细胞核进行光学连续切片后，可区分出七个DNA强度等级，作为DNA压实度增加的代用指标。在脉冲标记后立即固定的细胞核中，我们观察到代表活跃核区（ANC）的低DNA密度等级中EdU标记DNA的比例相对较低，而代表非活跃核区（INC）的高密度等级中EdU标记DNA的比例较高。追逐后固定的细胞显示出更明显的向高 DNA 密度级的转移。这一发现与之前的转录拓扑研究形成了鲜明对比，后者表明活性染色质和 RNAPII 的表观遗传特征在高 DNA 强度等级中的代表性不足，而在低密度等级中的代表性过高。我们将根据目前将 CD 视为染色质结构框架或相分离液滴的模型，以及目前阻碍将复制和转录的核空间拓扑的对比证据整合到动态核结构的共同框架中的方法学局限性来讨论这些发现。
{"title":"Perspective Article: Space-time dynamics of genome replication studied with super-resolved microscopy","authors":"M. Gelléri, Michael Sterr, H. Strickfaden, Christoph Cremer, Thomas Cremer, Marion Cremer","doi":"10.18388/pb.2021_523","DOIUrl":"https://doi.org/10.18388/pb.2021_523","url":null,"abstract":"Genome replication requires duplication of the complete set of DNA sequences together with nucleosomes and epigenetic signatures. Notwithstanding profound knowledge on mechanistic details of DNA replication, major problems of genome replication have remained unresolved. In this perspective article, we consider the accessibility of replication machines to all DNA sequences in due course, the maintenance of functionally important positional and structural features of chromatid domains during replication, and the rapid transition of CTs into prophase chromosomes with two chromatids. We illustrate this problem with EdU pulse-labeling (10 min) and chase experiments (80 min) performed with mouse myeloblast cells. Following light optical serial sectioning of nuclei with 3D structured illumination microscopy (SIM), seven DNA intensity classes were distinguished as proxies for increasing DNA compaction. In nuclei of cells fixed immediately after the pulse-label, we observed a relative under-representation of EdU-labeled DNA in low DNA density classes, representing the active nuclear compartment (ANC), and an over-representation in high density classes representing the inactive nuclear compartment (INC). Cells fixed after the chase revealed an even more pronounced shift to high DNA intensity classes. This finding contrasts with previous studies of the transcriptional topography demonstrating an under-representation of epigenetic signatures for active chromatin and RNAPII in high DNA intensity classes and their over-representation in low density classes. We discuss these findings in the light of current models viewing CDs either as structural chromatin frameworks or as phase-separated droplets, as well as methodological limitations that currently prevent an integration of this contrasting evidence for the spatial nuclear topography of replication and transcription into a common framework of the dynamic nuclear architecture.","PeriodicalId":20341,"journal":{"name":"Postępy Biochemii","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140670855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Wonderful World of Nucleic Acids","authors":"Joanna Rzeszowska-Wolny, Jan Barciszewski","doi":"10.18388/pb.2021_545","DOIUrl":"https://doi.org/10.18388/pb.2021_545","url":null,"abstract":"Wonderful World of Nucleic Acids","PeriodicalId":20341,"journal":{"name":"Postępy Biochemii","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140696998","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
70 Years - from DNA Double Helix via Approaching Systems Genomics to a Generalized Unified Evolution Theory
70 年--从 DNA 双螺旋到接近系统基因组再到广义统一进化论
{"title":"70 Years - from DNA Double Helix via Approaching Systems Genomics to a Generalized Unified Evolution Theory","authors":"Tobias A. Knoch","doi":"10.18388/pb.2021_544","DOIUrl":"https://doi.org/10.18388/pb.2021_544","url":null,"abstract":"70 Years \u0000-\u0000from\u0000DNA Double Helix\u0000via\u0000Approaching Systems Genomics\u0000to a\u0000Generalized Unified Evolution Theory","PeriodicalId":20341,"journal":{"name":"Postępy Biochemii","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140698081","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
This essay is in memoriam of Ronald Hancock (1933 – 2022).
这篇文章是为了纪念罗纳德-汉考克（1933 - 2022）。
{"title":"Memories of Ron Hancock","authors":"Olga Iarovaia","doi":"10.18388/pb.2021_541","DOIUrl":"https://doi.org/10.18388/pb.2021_541","url":null,"abstract":"This essay is in memoriam of Ronald Hancock (1933 – 2022). ","PeriodicalId":20341,"journal":{"name":"Postępy Biochemii","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140748713","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
This essay is in memoriam of Ronald Hancock (1933 – 2022).
这篇文章是为了纪念罗纳德-汉考克（1933 - 2022）。
{"title":"Ron Hancock – a passionate scientist and a Great Man","authors":"Sergey V. Razin","doi":"10.18388/pb.2021_540","DOIUrl":"https://doi.org/10.18388/pb.2021_540","url":null,"abstract":"This essay is in memoriam of Ronald Hancock (1933 – 2022). ","PeriodicalId":20341,"journal":{"name":"Postępy Biochemii","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140223337","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Host-pathogen interactions play an important role in understanding the dynamics of the insect immune system. The analysis of environmental modulators, both biotic and abiotic, directs our attention to the impact of the surroundings on the effectiveness of immunological responses. This knowledge is essential for the comprehensive understanding of insect’s immune reaction after infection with a pathogen. This article discusses the role of the immune system in insect, with a special emphasis on greater wax moth Galleria mellonella and highlights its adaptive capabilities. The processes are not only extremely interesting area of scientific research but also indicate potential practical applications in the context of plan protection, pest population control and medicine.
{"title":"Insect immunity - adaptive mechanisms and survival strategies","authors":"Jakub Kordaczuk","doi":"10.18388/pb.2021_519","DOIUrl":"https://doi.org/10.18388/pb.2021_519","url":null,"abstract":"Host-pathogen interactions play an important role in understanding the dynamics of the insect immune system. The analysis of environmental modulators, both biotic and abiotic, directs our attention to the impact of the surroundings on the effectiveness of immunological responses. This knowledge is essential for the comprehensive understanding of insect’s immune reaction after infection with a pathogen. This article discusses the role of the immune system in insect, with a special emphasis on greater wax moth Galleria mellonella and highlights its adaptive capabilities. The processes are not only extremely interesting area of scientific research but also indicate potential practical applications in the context of plan protection, pest population control and medicine.","PeriodicalId":20341,"journal":{"name":"Postępy Biochemii","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140222520","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"50th Anniversary of the Nucleosome Discovery: a Brief Essay","authors":"Ada L. Olins, D. Olins","doi":"10.18388/pb.2021_542","DOIUrl":"https://doi.org/10.18388/pb.2021_542","url":null,"abstract":"50th Anniversary of the Nucleosome Discovery","PeriodicalId":20341,"journal":{"name":"Postępy Biochemii","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140221601","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Elisabetta Scarfiello, Julian Eichlinger, Gunter Meister
MicroRNAs (miRNAs) are generated from stem-loop-structured double-stranded RNA precursors by the consecutive action of the two RNase III-type endoribonuclease Drosha and Dicer. However, such structures are very common on cellular transcripts and specific features have evolved that guide and regulate processing of stem-loop-structured hairpins into mature and functional miRNAs. These features include sequence motifs and local RNA structures but also trans-acting factors such as RNA binding proteins. The menu of features required for miRNA biogenesis is summarized in this review.
{"title":"The double-stranded microRNA precursor","authors":"Elisabetta Scarfiello, Julian Eichlinger, Gunter Meister","doi":"10.18388/pb.2021_522","DOIUrl":"https://doi.org/10.18388/pb.2021_522","url":null,"abstract":"MicroRNAs (miRNAs) are generated from stem-loop-structured double-stranded RNA precursors by the consecutive action of the two RNase III-type endoribonuclease Drosha and Dicer. However, such structures are very common on cellular transcripts and specific features have evolved that guide and regulate processing of stem-loop-structured hairpins into mature and functional miRNAs. These features include sequence motifs and local RNA structures but also trans-acting factors such as RNA binding proteins. The menu of features required for miRNA biogenesis is summarized in this review.","PeriodicalId":20341,"journal":{"name":"Postępy Biochemii","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140223919","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Information coded in DNA is replicated, modified and transmitted from the origins of protein-based life. Analogies of these processes to information processing, transmission and storage in computer systems is straightforward and can be utilized both in analysis of biological data and in development of biologically based technical systems. Transcription and translation processes are regulated by extremely complex regulatory networks, providing control of cell growth, cell cycle and cellular responses to stress. As such, they constitute engineering control systems exerting their actions at many levels of time scale and spatial organization. This work presents an engineering perspective on DNA-related information processing and biochemical process control in living cells, followed by a review of two-way crosstalk between engineering and biology.
从基于蛋白质的生命起源开始，DNA 中编码的信息就开始复制、修改和传输。将这些过程与计算机系统中的信息处理、传输和存储过程进行类比非常简单，既可用于分析生物数据，也可用于开发基于生物的技术系统。转录和翻译过程受极其复杂的调控网络调控，控制着细胞生长、细胞周期和细胞对压力的反应。因此，它们构成了工程控制系统，在时间尺度和空间组织的多个层面上发挥作用。本研究从工程学的角度介绍了活细胞中与 DNA 相关的信息处理和生化过程控制，随后回顾了工程学与生物学之间的双向串扰。
{"title":"An engineering perspective on transcription, translation and their regulation","authors":"Jaroslaw Smieja","doi":"10.18388/pb.2021_520","DOIUrl":"https://doi.org/10.18388/pb.2021_520","url":null,"abstract":"Information coded in DNA is replicated, modified and transmitted from the origins of protein-based life. Analogies of these processes to information processing, transmission and storage in computer systems is straightforward and can be utilized both in analysis of biological data and in development of biologically based technical systems. Transcription and translation processes are regulated by extremely complex regulatory networks, providing control of cell growth, cell cycle and cellular responses to stress. As such, they constitute engineering control systems exerting their actions at many levels of time scale and spatial organization. This work presents an engineering perspective on DNA-related information processing and biochemical process control in living cells, followed by a review of two-way crosstalk between engineering and biology.","PeriodicalId":20341,"journal":{"name":"Postępy Biochemii","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140234536","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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