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The role of the U1 snRNP complex in the regulation of gene expression: recent reports U1 snRNP 复合物在基因表达调控中的作用：最新报道
Postepy biochemii Pub Date : 2024-09-17 Print Date: 2024-09-30 DOI: 10.18388/pb.2021_566
Mikołaj Kiraga, Monika Zakrzewska-Płaczek
{"title":"The role of the U1 snRNP complex in the regulation of gene expression: recent reports","authors":"Mikołaj Kiraga, Monika Zakrzewska-Płaczek","doi":"10.18388/pb.2021_566","DOIUrl":"https://doi.org/10.18388/pb.2021_566","url":null,"abstract":"<p><p>U1 snRNP (U1 small nuclear ribonucleoprotein) is a nuclear ribonucleoprotein complex involved mainly in pre-mRNA splicing, which is a key regulatory process in the eukaryotic gene expression pathway, but also in the process of preventing premature transcription termination (telescripting). U1 snRNP interacts directly with RNA polymerase II, thereby influencing the synthesis and maturation of transcripts in the cell nucleus, including the formation of the 3' end of mRNA and polyadenylation. At the level of cell physiology, it regulates the functioning of mitochondria and energy metabolism. The core of the U1 snRNP complex is U1 snRNA, encoded by many copies of genes that differ in sequence and expression level, and the expression of some of them leads to the formation of defective products. According to current reports, U1 snRNA can be used for therapeutic purposes to regulate gene expression and improve mRNA splicing defects, which are the cause of many diseases. Here we present selected recent discoveries and achievements related to U1 snRNP.</p>","PeriodicalId":20335,"journal":{"name":"Postepy biochemii","volume":"70 3","pages":"348-357"},"PeriodicalIF":0.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142372666","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}
引用次数: 0
Characterization of KPC-type drug resistance in bacteria 细菌的 KPC 型耐药性特征
Postepy biochemii Pub Date : 2024-09-17 Print Date: 2024-09-30 DOI: 10.18388/pb.2021_555
Michalina Gniewosz, Sylwia Andrzejczak-Grządko
{"title":"Characterization of KPC-type drug resistance in bacteria","authors":"Michalina Gniewosz, Sylwia Andrzejczak-Grządko","doi":"10.18388/pb.2021_555","DOIUrl":"https://doi.org/10.18388/pb.2021_555","url":null,"abstract":"<p><p>One of the main problems of modern medicine is the phenomenon of drug resistance. Inappropriate use of antibiotics is considered to be the most important reason for the emergence of new resistance mechanisms in microorganisms. Carbapenems, which belong to the β-lactams, are considered the most effective group of antimicrobial agents. Unfortunately, as a result of prolonged exposure to the aforementioned drugs, bacteria have developed several mechanisms for survival. The most important of these is the production of hydrolytic enzymes (carbapenemases), which cleave the β-lactam ring and inactivate the antibiotics. The mentioned enzymes are encoded by blaKPC genes, which are located in so-called mobile genetic elements (i.e. plasmids and transposons). Such localization is associated with their ease of transfer between different bacterial species in the process of horizontal gene transfer.</p>","PeriodicalId":20335,"journal":{"name":"Postepy biochemii","volume":"70 3","pages":"315-324"},"PeriodicalIF":0.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142372662","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}
引用次数: 0
Heme-based aquareceptors 基于血红素的水生受体
Postepy biochemii Pub Date : 2024-09-17 Print Date: 2024-09-30 DOI: 10.18388/pb.2021_551
Savani Anbalagan
{"title":"Heme-based aquareceptors","authors":"Savani Anbalagan","doi":"10.18388/pb.2021_551","DOIUrl":"10.18388/pb.2021_551","url":null,"abstract":"<p><p>How cells sense water is of fundamental importance in biology. Hygrosensation has been demonstrated in specialized sensory cells that sense extracellular moisture. Even in microorganisms, osmosensors do not sense water per se. Water-sensing mechanisms would have been necessary for organisms to migrate and survive in water-poor conditions and to evolve into multicellular organisms. Due to the potential ability of water molecules to bind to gas-binding sites in the heme-based sensing domains of gasoreceptors, I suggest that some of them could have a parallel role as protein aquareceptors. Just as gasoreceptors function in almost every cell, aquareceptors must also function in almost every cell. I think that aquareceptors must be present in the cell membrane, cytoplasm, and every organelle. I also wonder if hemoglobin could also be considered a putative aquareceptor.</p>","PeriodicalId":20335,"journal":{"name":"Postepy biochemii","volume":"70 3","pages":"420-423"},"PeriodicalIF":0.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142372664","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}
引用次数: 0
Heavy metal tolerance in crop plants: an in silico comprehensive analysis of Metal- tolerance gene family in barley 作物对重金属的耐受性：对大麦耐金属基因家族的硅学综合分析
Postepy biochemii Pub Date : 2024-09-17 Print Date: 2024-09-30 DOI: 10.18388/pb.2021_559
Magda Grabsztunowicz, Ewelina Stolarska, Umesh Kumar Tanwar, Magdalena Arasimowicz-Jelonek, Ewa Sobieszczuk-Nowicka
{"title":"Heavy metal tolerance in crop plants: an in silico comprehensive analysis of Metal- tolerance gene family in barley","authors":"Magda Grabsztunowicz, Ewelina Stolarska, Umesh Kumar Tanwar, Magdalena Arasimowicz-Jelonek, Ewa Sobieszczuk-Nowicka","doi":"10.18388/pb.2021_559","DOIUrl":"https://doi.org/10.18388/pb.2021_559","url":null,"abstract":"<p><p>Heavy metal contamination in soil is a global concern due to its harmful effect to all living organisms. Phytoremediation is an emerging cost- effective technology, which utilizes different types of hyperaccumulator plants for the removal of heavy metal pollutants. Crop plants have been suggested as a good candidate for recultivation of agricultural soil in phytoremediation process, however the molecular mechanisms responsible for the crop tolerance to heavy metals is still unknown. Metal-tolerance proteins (MTPs) are divalent cation transporters that play critical roles in metal tolerance and ion homeostasis in plants. The current study identified 12 HvMTPs in the barley (Hordeum vulgare, Hv) genome; the majority of MTPs were hydrophobic proteins found in the vacuolar membrane. Gene expression profiling suggests that HvMTPs play an active role in maintaining barley nutrient homeostasis throughout its life cycle. The expression of barley HvMTP genes in the presence of heavy metals revealed that these MTPs were induced by at least one metal ion, implying their involvement in metal tolerance.</p>","PeriodicalId":20335,"journal":{"name":"Postepy biochemii","volume":"70 3","pages":"358-370"},"PeriodicalIF":0.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142372663","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}
引用次数: 0
Biosynthesis and metabolic inactivation of auxins 辅酶的生物合成和代谢失活
Postepy biochemii Pub Date : 2024-09-17 Print Date: 2024-09-30 DOI: 10.18388/pb.2021_549
Aleksandra Sobiech, Alicja Banasiak
{"title":"Biosynthesis and metabolic inactivation of auxins","authors":"Aleksandra Sobiech, Alicja Banasiak","doi":"10.18388/pb.2021_549","DOIUrl":"10.18388/pb.2021_549","url":null,"abstract":"<p><p>Auxins are a phytohormones that regulates of processes related to plant growth and morphogenesis, therefore their deficiency or excess results in severe developmental disorders. Plants have developed mechanisms aimed at regulating the level of the active form of these hormones, including their: directional transport, local biosynthesis, and degradation, as well as reversible and irreversible inactivation by binding to additional chemical groups. Despite almost a hundred years since the discovery of auxins, the functioning of these mechanisms, especially at the level of metabolism, is still not fully understood. In recent years, thanks to the development of new research methods, significant progress has been made in this field. This applies to both the identification of auxin biosynthetic pathways and the genes involved in them, as well as the detection of new auxin metabolites, their mutual connections and enzymes involved in their biosynthesis, transformation, and degradation. This work focuses on summarizing the current knowledge on this topic, considering the relationship of auxin metabolism with developmental processes and the response to changing environmental conditions.</p>","PeriodicalId":20335,"journal":{"name":"Postepy biochemii","volume":"70 3","pages":"297-306"},"PeriodicalIF":0.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142372661","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}
引用次数: 0
Polyploidy as an outcome of anticancer therapies and a contributing cause of their lack of efficacy 多倍体是抗癌疗法的一个结果，也是其缺乏疗效的一个原因
Postepy biochemii Pub Date : 2024-09-17 Print Date: 2024-09-30 DOI: 10.18388/pb.2021_557
Kinga Kołacz, Karolina Gronkowska, Magdalena Strachowska, Agnieszka Robaszkiewicz
{"title":"Polyploidy as an outcome of anticancer therapies and a contributing cause of their lack of efficacy","authors":"Kinga Kołacz, Karolina Gronkowska, Magdalena Strachowska, Agnieszka Robaszkiewicz","doi":"10.18388/pb.2021_557","DOIUrl":"10.18388/pb.2021_557","url":null,"abstract":"<p><p>In addition to innate and gained resistance poliploidy of cancer cells is described as a mechanism responsible for lack of response or cancer relapses after initial patient recovery. Formation of these cells is induced by cyto- and genotoxic agents, which trigger endoreduplication, cytokinesis failure, cell fusion or canibalism. These processes lead to amplification of DNA, cell cycle arrest and escape from death. Cancer reinitiation results from depolyploidization by neosis, amitotic and meiotic-like divisions. In this paper we review the known mechanisms, which drive cancer cell transition to poliploidy, major features of these cells and their role in cancer progression. We also depict the current approaches, which target metabolic and signaling pathways that are crucial for survival and functioning of polyploid cells. The combination of chemotherapy and radiotherapy with agents capable of inhibiting or eliminating polyploid cells could substantially improve the success rate and efficacy of anticancer therapies.</p>","PeriodicalId":20335,"journal":{"name":"Postepy biochemii","volume":"70 3","pages":"325-335"},"PeriodicalIF":0.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142372665","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}
引用次数: 0
Can the laws of physics be circumvented? On methods of super-resolution fluorescence microscopy 物理定律可以规避吗？关于超分辨率荧光显微镜的方法
Postepy biochemii Pub Date : 2024-07-01 DOI: 10.18388/pb.2021_527
Adrian Rüfli
{"title":"Can the laws of physics be circumvented? On methods of super-resolution fluorescence microscopy","authors":"Adrian Rüfli","doi":"10.18388/pb.2021_527","DOIUrl":"https://doi.org/10.18388/pb.2021_527","url":null,"abstract":"<p><p>Biological sciences are increasingly uncovering the foundations of life in greater detail, made possible by the development of research methods enabling exploration at the nanometer scale. Optical microscopy, a field with a significant contribution to current knowledge, is inherently limited by the Abbe limit, stemming from the fundamental wave properties of light. Through the efforts of scientists, this limit can be circumvented, as evidenced by STED and MINFLUX techniques. STED allows imaging with a resolution down to 40 nm, while MINFLUX enables resolution as fine as 2 nm. Both techniques require labelling of biological molecular targets with fluorescent markers and enable imaging in living cells, facilitating the study of dynamic biological processes. This article provides an introduction to super-resolution techniques STED and MINFLUX, demonstrating their utility through the example of studying kinesin movement along microtubules using the MINFLUX technique.</p>","PeriodicalId":20335,"journal":{"name":"Postepy biochemii","volume":"70 2","pages":"139-149"},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141860684","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}
引用次数: 0
Advancements in Structural Biology – How to See Molecules of Life? 结构生物学的进步--如何观察生命分子？
Postepy biochemii Pub Date : 2024-07-01 DOI: 10.18388/pb.2021_533
Wojciech Witek, Wiktoria Ragin, Ha Linh Tran, Ewa Połomska, Mikołaj Podlewski, Aleksandra Pawłowicz, Aleksandra Cioch-Biniaś, Amadeusz Woś, Witold Andrałojć, Marta Szachniuk, Miłosz Ruszkowski
{"title":"Advancements in Structural Biology – How to See Molecules of Life?","authors":"Wojciech Witek, Wiktoria Ragin, Ha Linh Tran, Ewa Połomska, Mikołaj Podlewski, Aleksandra Pawłowicz, Aleksandra Cioch-Biniaś, Amadeusz Woś, Witold Andrałojć, Marta Szachniuk, Miłosz Ruszkowski","doi":"10.18388/pb.2021_533","DOIUrl":"https://doi.org/10.18388/pb.2021_533","url":null,"abstract":"<p><p>Structural biology is focused on understanding the architecture of biomolecules, such as proteins and nucleic acids. Deciphering the structure helps to understand their function in the cell at a very precise – molecular level. This makes it possible to not only determine the basis of diseases but also to propose therapeutic strategies and tools. Such a strong motivation for the development of structural biology has led to the development of a number of methods, which enable determination of the structures of the molecules of life. The continuous progress has been enabled by the integration of biology, chemistry, physics, and computer science, making structural biology extremely interdisciplinary. In its 35-year history, the Institute of Bioorganic Chemistry of the Polish Academy of Sciences in Poznan has become one of the key Polish institutions conducting research in the field of structural biology. On one hand, the research has brought international recognition, and on the other hand, it has forced the implementation and development of cutting-edge methods. This review discusses the methods used in structural biology at the Institute.</p>","PeriodicalId":20335,"journal":{"name":"Postepy biochemii","volume":"70 2","pages":"128-138"},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141860682","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}
引用次数: 0
Chemical simulations of quantum systems using quantum computers - review of algorithms and their experimental verification 利用量子计算机对量子系统进行化学模拟 - 算法及其实验验证综述
Postepy biochemii Pub Date : 2024-07-01 DOI: 10.18388/pb.2021_536
Konrad Wojciechowski, Krzysztof Kurowski, Cezary Mazurek
{"title":"Chemical simulations of quantum systems using quantum computers - review of algorithms and their experimental verification","authors":"Konrad Wojciechowski, Krzysztof Kurowski, Cezary Mazurek","doi":"10.18388/pb.2021_536","DOIUrl":"https://doi.org/10.18388/pb.2021_536","url":null,"abstract":"<p><p>Computer simulations using ever-increasing computing power and machine learning techniques allow advanced molecular modelling, molecular dynamics simulations and studies of intermolecular interactions. However, due to the complexity of biological systems and chemical processes at the molecular level, their accurate representation using classical computer models and techniques has faced a number of significant limitations for many years. A new and promising direction for the development of computational science and its potential applications in biochemistry is quantum computing and its integration with classical high-performance supercomputing systems. This article responds to the growing interest in the use of available quantum computers in exemplary applications. In this paper, we aim to provide an overview of the basic notions involved in the development of quantum algorithms and simulations related to issues at the interface of quantum chemistry and biochemistry. In addition, the article introduces the basic principles of performing simulations using the state-of-the-art quantum computers in the era of Noisy Intermediate-Scale Quantum (NISQ). Experimental results of the classical-quantum algorithm Variational Quantum Eigensolver (VQE) for example molecules H2 and CH+ are also presented. Despite the many shortcomings of currently available quantum computers, the analysed VQE algorithm proved to be effective in approximating the ground state of molecules using a minimal functional basis.</p>","PeriodicalId":20335,"journal":{"name":"Postepy biochemii","volume":"70 2","pages":"257-265"},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141860685","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}
引用次数: 0
From Sanger to genome sequencing - an overview of DNA sequencing technologies 从桑格到基因组测序--DNA 测序技术概览
Postepy biochemii Pub Date : 2024-07-01 DOI: 10.18388/pb.2021_534
Małgorzata Marcinkowska-Swojak, Magdalena Rakoczy, Jan Podkowiński, Jurand Handschuh, Paweł Wojciechowski, Luiza Handschuh
{"title":"From Sanger to genome sequencing - an overview of DNA sequencing technologies","authors":"Małgorzata Marcinkowska-Swojak, Magdalena Rakoczy, Jan Podkowiński, Jurand Handschuh, Paweł Wojciechowski, Luiza Handschuh","doi":"10.18388/pb.2021_534","DOIUrl":"https://doi.org/10.18388/pb.2021_534","url":null,"abstract":"<p><p>There is no technique that would make a greater contribution to the development of genetics, molecular biology and medicine than DNA sequencing. For many years, the method based on enzymatic DNA synthesis developed by Frederic Sanger was the gold standard in this area. At the end of the 20th century, there was a dynamic development of next-generation sequencing (NGS) technologies, which ended the era of single gene analysis and initiated the era of genome sequencing. Despite fierce competition, one NGS technology has practically completely dominated the global market. In the article, we present our own review of DNA sequencing methods, starting from the Sanger method to high-throughput second- and third-generation sequencing technologies, with particular emphasis on those that have achieved commercial success. We present their short history, principles of operation, technical possibilities, applications and limitations. In the summary, we reveal how much human genome sequencing costs at the current stage of the genomic revolution and outline the prospects for further development of genomics.</p>","PeriodicalId":20335,"journal":{"name":"Postepy biochemii","volume":"70 2","pages":"173-189"},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141860686","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}
引用次数: 0
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