Postepy biochemii最新文献

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.

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.

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.

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.

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.

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.

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.

Chemical compounds of natural origin, the so-called natural products and their derivatives, constitute the basis of medicines. They are widely used, among others, in the agricultural, veterinary, food and cosmetics industries. The article presents the division of natural products, with particular emphasis on bioactive secondary metabolites, and progress in the development of synthetic biology tools for their bioproduction.

Human myeloid leukemia cells (HL-60/S4) exposed to hyperosmotic stress with sucrose undergo dehydration and cell shrinkage. Interphase chromatin and mitotic chromosomes congeal, exhibiting altered phase separation (demixing) of chromatin proteins. To investigate changes in the transcriptome, we exposed HL-60/S4 cells to hyperosmotic sucrose stress (~600 milliOsmolar) for 30 and 60 minutes. We employed RNA-Seq of polyA mRNA to identify genes with increased or decreased transcript levels relative to untreated control cells (i.e., differential gene expression). These genes were examined for over-representation of Gene Ontology (GO) terms.  In stressed cells, multiple GO terms associated with transcription, translation, mitochondrial function and proteosome activity, as well as "replication-dependent histones", were over-represented among genes with increased transcript levels; whereas, genes with decreased transcript levels were over-represented with transcription repressors. The transcriptome profiles of hyperosmotically-stressed cells suggest acquisition of cellular rebuilding, a futile homeostatic response, as these cells are ultimately doomed to a dehydrated death.

Environmental carcinogens exert their carcinogenic effects by forming DNA adducts. This type of DNA damage can also be formed endogenously as a result of, e.g., oxidative damage. Unrepaired  DNA adducts may induce mutations in critical genes, leading to the initiation of chemical carcinogenesis. Therefore,  detection, identification, and quantification of DNA adducts is essential for cancer risk assessment. Over the last 50 years, the major DNA adducts formed by different classes of environmental carcinogens were characterized. With the development of techniques such as 32P-postlabeling, their measurement was implemented into molecular epidemiology. Advances in liquid chromatography-tandem mass spectrometry (LC-MS ) made the measurement of adducts more precise  and allowed to gain knowledge about their identity and structures. Therefore,  opened the way to  DNA adductomics, the  "omics" approach investigating DNA adducts comprehensively, similarly to proteomics. This review presents the historical perspective of DNA adducts research and the emerging field of adductomics.