Article
Oncology
Martin K. Bakht, Yasutaka Yamada, Sheng-Yu Ku, Varadha Balaji Venkadakrishnan, Joshua A. Korsen, Teja M. Kalidindi, Kei Mizuno, Shin Hye Ahn, Ji-Heui Seo, Maria Mica Garcia, Francesca Khani, Olivier Elemento, Henry W. W. Long, Alain Chaglassian, Nagavarakishore Pillarsetty, Jason S. Lewis, Matthew Freedman, Anthony P. Belanger, Quang-De Nguyen, Himisha Beltran
Summary: Beltran and colleagues explore the regulatory roles of HOXB13 and AR in the heterogeneous expression of PSMA in castration-resistant prostate cancer. They found that PSMA expression is lost in a subset of CRPC patients and is influenced by the microenvironment. The study also identifies HOXB13 as an upstream regulator of PSMA, independent of AR expression. These findings provide insights for the development of PSMA-targeted therapies and complementary biomarkers.
Article
Biochemistry & Molecular Biology
Qiangwei Zhou, Pengpeng Guan, Zhixian Zhu, Sheng Cheng, Cong Zhou, Huanhuan Wang, Qian Xu, Wing-kin Sung, Guoliang Li
Summary: DNA methylation is a stable epigenetic modification that plays crucial roles in cell differentiation, development, X chromosome inactivation, and disease. Allele-specific DNA methylation (ASM) is an established mechanism in genomic imprinting, closely related to tumorigenesis and plant development. The establishment of a comprehensive ASM database and in-depth analysis across multiple species revealed potential ASM-related genes in cancer and provided valuable insights into the functions of ASM in diseases and development.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Bryan A. Ramirez-Corona, Stephanie Fruth, Oluchi Ofoegbu, Zeba Wunderlich
Summary: The study found that the mode of expression divergence varies between conditions within the Drosophila fat body. Trans-acting effects dominate in response to Gram-negative infection, while cis-acting effects dominate in Gram-positive and preinfection conditions. Before infection, compensatory effects in the fat body due to metabolic activity lead to changes in cis and trans that counteract each other.
Article
Cell Biology
Long Wang, Mu-Chun Wan, Ren-Yu Liao, Jie Xu, Zhou-Geng Xu, Hao-Chen Xue, Yan-Xia Mai, Jia-Wei Wang
Summary: Using time-resolved single-cell RNA sequencing, the cellular taxonomy of Marchantia polymorpha during asexual reproduction phases is defined. Two maturation and aging trajectories of the main plant body are identified: gradual maturation of tissues and organs along the tip-to-base axis of the midvein and progressive decline of meristem activities in the tip along the chronological axis. The observed aging trajectory is temporally correlated with the formation of clonal propagules, suggesting an ancient strategy to optimize resource allocation for producing offspring.
DEVELOPMENTAL CELL
(2023)
Review
Biochemistry & Molecular Biology
Wenjie Wang, Yuchao Yu, Nancy P. Keller, Pinmei Wang
Summary: Fungal secondary metabolites are both toxic and valuable sources of drugs, regulated by pathway specific transcription factors (PSTFs) in biosynthetic gene clusters (BGCs). The size of BGCs can predict the presence of PSTFs, and the number and relative location of PSTFs can affect their regulation of gene clusters.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Hongye Sun, Kangdi Hu, Shuwei Wei, Gaifang Yao, Hua Zhang
Summary: PYERF4.1 and PYERF4.2 were found to inhibit anthocyanin biosynthesis in red-skinned pears, revealing a feedback regulatory loop mechanism to balance the excessive accumulation of anthocyanins.
Article
Plant Sciences
Alejandro Aragon-Raygoza, Luis Herrera-Estrella, Alfredo Cruz-Ramirez
Summary: Gene expression analysis in Ceratopteris richardii revealed enriched functional categories related to histogenesis and cell division in the root tip transcriptional program, and conserved expression in the root meristem. However, divergence was observed in genes involved in root cap development.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Medicine, Research & Experimental
Hyun-Soo Kim, Yoon Jeon, Yoon Ok Jang, Ho Lee, Yong Shin, Chang-Woo Lee
Summary: This study reveals that mammalian Ssu72 plays a crucial role in the transcriptional regulation of various genes through transcriptional elongation rather than polyadenylation or RNA processing. Depletion of Ssu72 leads to Pol II pausing and elongation defects, and reduced transcriptional elongation efficiency primarily affects the expression levels of actively transcribed genes.
Article
Multidisciplinary Sciences
Mahashweta Basu, Kun Wang, Eytan Ruppin, Sridhar Hannenhalli
Summary: This study demonstrates that an individual's whole blood transcriptome can predict tissue-specific expression levels for around 60% of genes across various tissues, with particularly high accuracy in skeletal muscle. Predictions based on blood transcriptome are almost as effective as actual tissue expression in identifying disease states for six different complex disorders, surpassing the traditional blood transcriptome approach. The development of TEEBoT provides a valuable tool for further research in other medical conditions.
Article
Biochemistry & Molecular Biology
Muhammad Aamir Manzoor, Irfan Ali Sabir, Iftikhar Hussain Shah, Han Wang, Zhao Yu, Faiz Rasool, Muhammad Zaid Mazhar, Shoaib Younas, Muhammad Abdullah, Yongping Cai
Summary: The GATA gene family was identified and analyzed in four Rosaceae genomes, revealing the structural characteristics and properties of the gene family through comparative analysis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Fan Qi, Fu Wang, Chunxiao Xiaoyang, Zhenhui Wang, Yujie Lin, Zhanwu Peng, Jun Zhang, Ningning Wang, Jian Zhang
Summary: This study conducted transcriptome analysis to analyze the gene expression profiles of different organs in flax. The results identified differentially expressed genes and organ-specific expression patterns. Gene ontology enrichment analysis revealed the biological processes and molecular functions associated with organ growth. The study also investigated the role of AP2 transcription factors in regulating flax organ development and stress response. Overall, this research provides valuable insights into the molecular mechanisms of flax organ development and has implications for genetic improvement of flax crops.
Article
Biotechnology & Applied Microbiology
Irene M. Kaplow, Daniel E. Schaffer, Morgan E. Wirthlin, Alyssa J. Lawler, Ashley R. Brown, Michael Kleyman, Andreas R. Pfenning
Summary: This study proposes a machine learning-based approach to evaluate enhancer conservation, which leverages the combinatorial sequence code of enhancer activity instead of relying on individual nucleotide alignment. The researchers use a convolutional neural network model to predict tissue-specific open chromatin in mammals and demonstrate the model's high accuracy in predicting enhancer conservation and divergence. This framework provides a mechanism to annotate tissue-specific regulatory function across genomes and study enhancer evolution using predicted regulatory differences.
Article
Biochemistry & Molecular Biology
Xin-Wei Zhao, Jiaqi Wu, Hirohisa Kishino, Ling Chen
Summary: The study found that there was a peak of TF loss in placental mammals around 100 million years ago and after the massive extinction of dinosaurs, which led to a deceleration in the molecular evolutionary rates of their target genes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Mengyuan Wang, Qian Li, Lingbo Liu
Summary: Gene expression regulation involves multiple processes and various regulatory factors. This review provides an overview of key factors involved in gene expression regulation, such as transcription factors, chromatin accessibility, histone modifications, DNA methylation, and RNA modifications. Additionally, methods for detecting these regulatory factors are also described.
Article
Biochemistry & Molecular Biology
Olga Rosspopoff, Emmanuel Cazottes, Christophe Huret, Agnese Loda, Amanda J. Collier, Miguel Casanova, Peter J. Rugg-Gunn, Edith Heard, Jean-Francois Ouimette, Claire Rougeulle
Summary: XCI is a crucial process with remarkable diversity among mammalian species. Through analysis of single-cell RNA-seq data and functional assays, we find that FTX shows functional inconsistency in humans, while JPX acts as a major regulator of XIST expression in both species. However, we reveal that different forms of JPX control the production of XIST at different steps depending on the species. Overall, this study highlights the functional versatility of LRGs and suggests diversified mechanisms of action for functionally conserved orthologous LRGs.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Spectroscopy
M. P. Ivanov, Yu. A. Tolmachev
JOURNAL OF APPLIED SPECTROSCOPY
(2018)
Editorial Material
Biochemistry & Molecular Biology
M. P. Ivanov, Yu. A. Tolmachev, A. A. Tulub, L. E. Leonova, E. V. Romanovskaya
JOURNAL OF EVOLUTIONARY BIOCHEMISTRY AND PHYSIOLOGY
(2018)
Article
Biochemistry & Molecular Biology
Alena Soboleva, Gregory Mavropulo-Stolyarenko, Tatiana Karonova, Domenika Thieme, Wolfgang Hoehenwarter, Christian Ihling, Vasily Stefanov, Tatiana Grishina, Andrej Frolov
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2019)
Article
Acoustics
M. P. Ivanov, S. N. Butov, L. E. Leonova, E. Romanovskaya, V. E. Stefanov
ACOUSTICAL PHYSICS
(2019)
Article
Biochemistry & Molecular Biology
Tatiana Leonova, Veronika Popova, Alexander Tsarev, Christian Henning, Kristina Antonova, Nadezhda Rogovskaya, Maria Vikhnina, Tim Baldensperger, Alena Soboleva, Ekaterina Dinastia, Mandy Dorn, Olga Shiroglasova, Tatiana Grishina, Gerd U. Balcke, Christian Ihling, Galina Smolikova, Sergei Medvedev, Vladimir A. Zhukov, Vladimir Babakov, Igor A. Tikhonovich, Marcus A. Glomb, Tatiana Bilova, Andrej Frolov
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Plant Sciences
Anastasia Orlova, Elana Kysil, Elena Tsvetkova, Darya Meshalkina, Andrei Whaley, Anastasiia O. Whaley, Annegret Laub, Antonio Francioso, Olga Babich, Ludger A. Wessjohann, Luciana Mosca, Andrej Frolov, Maria Povydysh
Summary: Water avens is a widely distributed Rosaceae plant with potential pharmaceutical properties. In this study, the polyphenolic composition of the plant was comprehensively characterized, and several phenolic acid derivatives, flavonoids, and tannins were identified for the first time. The aerial parts of water avens exhibited significant antioxidant and antibacterial activities.
Article
Biochemistry & Molecular Biology
Darya Meshalkina, Elena Tsvetkova, Anastasia Orlova, Renata Islamova, Maria Grashina, Daria Gorbach, Vladimir Babakov, Antonio Francioso, Claudia Birkemeyer, Luciana Mosca, Elena Tarakhovskaya, Andrej Frolov
Summary: Phaeophyceae, or brown algae, play a significant role in cold and temperate seas as they are rich in biologically active natural products, particularly phlorotannins. These phlorotannins are complex polyphenols with diverse structures, known for their strong antioxidant properties and broad range of biological activities. While the biological activities of extractable intracellular phlorotannins have been well-studied, the properties of cell wall-bound polyphenol fraction are still largely unknown. In this study, the antioxidant, cytotoxic, neuroprotective, and antibacterial properties of the cell wall-bound phlorotannin fractions from two representatives of the order Fucales, Fucus vesiculosus and Pelvetia canaliculata, were investigated. The cell wall-bound phlorotannins exhibited softer antioxidant activity, stronger antibacterial properties, and lower cytotoxicity compared to the intracellular fraction. However, both sub-cellular phlorotannin fractions of F. vesiculosus and P. canaliculata showed similar neuroprotective effects. Therefore, due to their lower cytotoxicity, cell wall-bound phlorotannins hold promise as antioxidants and neuroprotectors.
Article
Plant Sciences
Elena Sharova, Tatiana Bilova, Elena Tsvetkova, Galina Smolikova, Andrej Frolov, Sergei Medvedev
Summary: Light is crucial for plant growth and development, serving as an energy source and sensory cue. The study focused on red light regulation of maize seedling growth, finding that exposure to red light inhibited mesocotyl growth. By using untargeted metabolomics, the study identified and characterized 44 metabolites in the apoplastic fluid of maize mesocotyls, which were dominated by sugars, acids, amino acids, and nitrogen-containing compounds. Red light irradiation increased the contents of beta-alanine, putrescine, and trans-aconitate, while decreasing the total ascorbate content. The role of apoplastic metabolites in the red light-induced inhibition of maize mesocotyl elongation is discussed.
FUNCTIONAL PLANT BIOLOGY
(2023)
Article
Plant Sciences
Maria V. Titova, Dmitry V. Kochkin, Elena S. Sukhanova, Elena N. Gorshkova, Tatiana M. Tyurina, Igor M. Ivanov, Maria K. Lunkova, Elena V. Tsvetkova, Anastasia Orlova, Elena V. Popova, Alexander M. Nosov
Summary: Polyscias fruticosa, a medicinal plant of the Araliaceae family, has various pharmaceutical properties and can be efficiently cultivated in bioreactors for biomass production.
Meeting Abstract
Biochemistry & Molecular Biology
A. Baklanova, T. Grishina, I. Krasovskaya, E. Romanovskaya, E. Tsvetkova, V. Stefanov, L. Leonova
Article
Infectious Diseases
I. A. Sychev, P. M. Kopeikin, E. Tsvetkova, K. Cheredova, B. L. Milman, O. Shamova, I. N. Isakova-Sivak, Y. A. Desheva
Summary: The study identified eight conserved linear B-cell epitopes around the active site of neuraminidase, with three of them synthesized and used for mouse immunization. Results showed specific antibodies produced in immunized mice bound to various influenza A viruses containing different NA subtypes. While immunization with NA peptides did not prevent substantial weight loss in mice infected with H1N1 virus, all immunized mice survived during the observation period.
INFEKTSIYA I IMMUNITET
(2021)
Article
Biochemical Research Methods
Aleksey Gladchuk, Julia Shumilina, Alena Kusnetsova, Ksenia Bureiko, Susan Billig, Alexander Tsarev, Irina Alexandrova, Larisa Leonova, Vladimir A. Zhukov, Igor A. Tikhonovich, Claudia Birkemeyer, Ekaterina Podolskaya, Andrej Frolov
METHODS AND PROTOCOLS
(2020)
