Article
Biochemistry & Molecular Biology
Yennifer Mata-Sucre, William Matzenauer, Natalia Castro, Bruno Huettel, Andrea Pedrosa-Harand, Andre Marques, Gustavo Souza
Summary: This study reassesses the systematics of the genus Juncus using genomic data and demonstrates the potential of comparative genomic analyses for understanding plant systematics and evolution. The results reveal the importance of repeat sequences in clarifying plant systematics and suggest an ancient hybridization event in the divergence of Juncus. The study also confirms the monocentricity of Juncus and identifies specific repeatome trends correlated with ancient origin.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Plant Sciences
Nadezhda L. Bolsheva, Nataliya V. Melnikova, Ekaterina M. Dvorianinova, Liudmila N. Mironova, Olga Y. Yurkevich, Alexandra V. Amosova, George S. Krasnov, Alexey A. Dmitriev, Olga V. Muravenko
Summary: The phylogenetic relationship between Linum stelleroides and other blue-flowered flax species in the Linaceae family has been controversial. Using genetic sequencing data, this study clarified the issue and found that Linum stelleroides forms a basal branch in the blue-flowered flax clade.
Article
Food Science & Technology
Ewa Tomaszewska-Ciosk, Ewa Zdybel
Summary: The study found that adding flax pomace affected the expansion ratio, color lightness, and mechanical properties of extruded snacks. Sensory analysis showed no significant differences between snacks with 5% flax pomace and those without. However, adding more than 10% flax pomace made the product unacceptable to the panelists. There was also no significant difference between common flax and golden flax pomace in most traits, except for color.
INTERNATIONAL JOURNAL OF FOOD SCIENCE AND TECHNOLOGY
(2021)
Article
Genetics & Heredity
Ekaterina M. Dvorianinova, Elena N. Pushkova, Nadezhda L. Bolsheva, Elena V. Borkhert, Tatiana A. Rozhmina, Daiana A. Zhernova, Roman O. Novakovskiy, Anastasia A. Turba, Elizaveta A. Sigova, Nataliya V. Melnikova, Alexey A. Dmitriev
Summary: Sequencing the genome of flax provides valuable genetic information for studying its evolution, domestication, and genome regulation. In this study, we obtained a high-quality genome assembly of Linum usitatissimum convar. crepitans using the Canu-Racon x2-medaka-POLCA approach.
FRONTIERS IN GENETICS
(2023)
Article
Agricultural Engineering
Yaning Bao, Yifei Zou, Ruifeng Tian, Xing Huang, Lijun Liu, Bo Wang, Dingxiang Peng
Summary: In recent years, frequent extreme climates, especially high temperatures, have posed a growing threat to crop production. Flax, a crop suitable for cool environments, is greatly impacted by temperature in terms of fiber formation. However, our understanding of the regulatory effect of high-temperature (HT) stress on flax fiber development at the RNA level is limited. In this study, we investigated the molecular-level impact of HT stress (30 degrees Celsius) on flax fiber development by selecting three stages of fiber development and utilizing transcriptome sequencing. We observed different effects of HT stress on fiber cell development in each stage and identified a key gene, Lus10007349 (XTH), involved in fiber cell expansion and cell wall thickening, as a candidate gene for future research.
INDUSTRIAL CROPS AND PRODUCTS
(2023)
Article
Plant Sciences
Zuzana Chumova, Alexander Belyayev, Terezie Mandakova, Vojtech Zeisek, Eva Hodkova, Kristyna Semberova, Douglas Euston-Brown, Pavel Travnicek
Summary: Non-coding repetitive DNA, dominated by transposable elements (TEs) and satellite DNA, plays an active role in the structure, evolution, and function of the nuclear genome. This study explores the relationship between changes in repetitive DNA and responses to a harsh environment in plants from the Cape Floristic hotspot. The findings suggest that the transition from Succulent Karoo to Fynbos environments is accompanied by a burst of TEs, which may contribute to phylogenetic divergence. The analysis of rapidly evolving repeatome could serve as an important proxy for understanding lineage divergence in rapidly radiating groups.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Shuhei Yasumoto, Toshiya Muranaka
Summary: Genome editing is a powerful breeding technique that introduces mutations into specific gene sequences in genomes. However, there is still no widely authorized method for detecting foreign genes in genome-edited crops.
SCIENTIFIC REPORTS
(2023)
Article
Genetics & Heredity
Dave J. Baker, Alp Aydin, Thanh Le-Viet, Gemma L. Kay, Steven Rudder, Leonardo de Oliveira Martins, Ana P. Tedim, Anastasia Kolyva, Maria Diaz, Nabil-Fareed Alikhan, Lizzie Meadows, Andrew Bell, Ana Victoria Gutierrez, Alexander J. Trotter, Nicholas M. Thomson, Rachel Gilroy, Luke Griffith, Evelien M. Adriaenssens, Rachael Stanley, Ian G. Charles, Ngozi Elumogo, John Wain, Reenesh Prakash, Emma Meader, Alison E. Mather, Mark A. Webber, Samir Dervisevic, Andrew J. Page, Justin O'Grady
Summary: CoronaHiT is a flexible sequencing method for SARS-CoV-2 genomes, suitable for rapid expansion of global sequencing efforts. In experiments, CoronaHiT demonstrated good performance on both nanopore and Illumina platforms.
Article
Agricultural Engineering
Dongliang Guo, Haixia Jiang, Jiali Ye, Aiqin Zhang, Yue Wang, Yanfang Gao, Qingcheng Yan, Jiaxun Chen, Lepeng Duan, Huiqing Liu, Xiao Li, Gongze Li, Min Xue, Liqiong Xie
Summary: In this study, a total of 1593 genes were identified as potentially associated with plant height in flax through homologous alignment and transcriptome analysis. Through population level validation, 30 genes were consistently linked to plant height across different environments. These findings offer a new strategy to rapidly identify candidate genes related to agronomic traits and provide valuable genomic resources for improving high yield flax varieties through genomics-assisted breeding.
INDUSTRIAL CROPS AND PRODUCTS
(2021)
Article
Biotechnology & Applied Microbiology
Michael Alonge, Ludivine Lebeigle, Melanie Kirsche, Katie Jenike, Shujun Ou, Sergey Aganezov, Xingang Wang, Zachary B. Lippman, Michael C. Schatz, Sebastian Soyk
Summary: This study introduces RagTag, a toolset for automating assembly scaffolding and patching, and establishes chromosome-scale reference genomes for tomato genotypes M82 and Sweet-100. This provides convenience for functional genomics and genome editing in tomato.
Article
Plant Sciences
Pavel Yu. Kroupin, Ekaterina D. Badaeva, Victoria M. Sokolova, Nadezhda N. Chikida, Maria Kh. Belousova, Sergei A. Surzhikov, Ekaterina A. Nikitina, Alina A. Kocheshkova, Daniil S. Ulyanov, Aleksey S. Ermolaev, Thi Mai Luong Khuat, Olga V. Razumova, Anna I. Yurkina, Gennady I. Karlov, Mikhail G. Divashuk
Summary: This study sequenced the genomes of Aegilops crassa and related species and analyzed their repetitive sequences, leading to the identification of several satellite repeats. Comparative analysis and fluorescence in situ hybridization (FISH) were used to assess the copy number and affinity of satellite repeats in different species and subgenomes.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Haixia Jiang, Dongliang Guo, Yuanyuan Liu, Leilei Zhu, Fang Xie, Liqiong Xie
Summary: Seed size is a crucial factor in determining crop yields. A study on flax revealed multiple genes that regulate seed size through phytohormone pathways and transcription factors. Additionally, 54 differentially expressed genes associated with seed size and weight were identified. Nucleotide diversity analysis showed that some seed size-related genes were selected during flax acclimation.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Kai Sun, Yan Liang, Xueting Zhong, Xuenan Hu, Pengjun Zhang, Xiaoping Yu
Summary: A novel geminivirus, provisionally designated nightshade curly top virus (NCTV), was identified in Zhejiang Province, China, causing virus-like symptoms on nightshade plants. The virus is widely distributed and highly infectious to various plant species, suggesting it belongs to the genus Topocuvirus.
Article
Immunology
Cristina Galli, Erika Ebranati, Laura Pellegrinelli, Martina Airoldi, Carla Veo, Carla Della Ventura, Arlinda Seiti, Sandro Binda, Massimo Galli, Gianguglielmo Zehender, Elena Pariani
Summary: The study successfully validated a rapid and reliable high-throughput sequencing protocol for obtaining the complete genome sequence of A(H3N2) influenza viruses directly from clinical specimens, providing important reference for influenza surveillance and outbreak investigation.
Article
Plant Sciences
Olga Muravenko, Olga Yu Yurkevich, Julia Kalnyuk, Tatiana E. Samatadze, Svyatoslav A. Zoshchuk, Alexandra Amosova
Summary: This study conducted a comparative analysis of the genome organization and chromosome structure of the important species Salvia officinalis and Salvia sclarea. The results revealed interspecific variations in repetitive DNA and identified potential chromosome markers. This research provides valuable insights into the taxonomy and genetic diversity of these two Salvia species.
Article
Biochemistry & Molecular Biology
Anastasiya Snezhkina, Maria Fedorova, Anastasiya Kobelyatskaya, Daria Markova, Margarita Lantsova, Anna Ikonnikova, Marina Emelyanova, Dmitry Kalinin, Elena Pudova, Nataliya Melnikova, Alexey Dmitriev, George Krasnov, Vladislav Pavlov, Anna Kudryavtseva
Summary: In this study, a high frequency missense variant p.H102R in the SDHD gene was found in an extended cohort of Russian HNPGL patients using whole-exome sequencing. The variant was associated with somatic loss of the gene wild-type allele and evident LOH at the 11p15.5 region and potential loss of the whole of chromosome 11. These findings help with understanding the mechanism of tumorigenesis and are important for the development of cost-effective genetic screening programs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Liubov V. V. Povkhova, Elena N. N. Pushkova, Tatiana A. A. Rozhmina, Alexander A. A. Zhuchenko, Roman I. I. Frykin, Roman O. O. Novakovskiy, Ekaterina M. M. Dvorianinova, Aleksey A. A. Gryzunov, Elena V. V. Borkhert, Elizaveta A. A. Sigova, Gleb N. N. Vladimirov, Anastasiya V. V. Snezhkina, Anna V. V. Kudryavtseva, George S. S. Krasnov, Alexey A. A. Dmitriev, Nataliya V. V. Melnikova
Summary: Flax is globally cultivated for its seeds and fiber. Varieties of linseed are used in various fields depending on their composition of linolenic and linoleic fatty acids. Three different approaches were proposed to identify low-LIN mutations in flax varieties, and they showed promising results in testing. These approaches can be utilized in marker-assisted selection for breeding and basic research on the molecular mechanisms of fatty acid synthesis in flax seeds.
Article
Biochemistry & Molecular Biology
Anastasiya Snezhkina, Vladislav Pavlov, Maria Fedorova, Dmitry Kalinin, Elena Pudova, Anastasiya Kobelyatskaya, Ildar Bakhtogarimov, George Krasnov, Anna Kudryavtseva
Summary: Malignant middle ear paraganglioma (MEPGL) is a rare neuroendocrine tumor. A case of malignant MEPGL was studied using comprehensive genetic analysis. A germline pathogenic mutation in the SDHB gene was identified, along with five novel somatic variants. The analysis showed the presence of specific mutation signatures and revealed the importance of SDHB mutation combined with loss of heterozygosity in tumor initiation and progression. These findings enhance our understanding of the molecular genetic mechanisms associated with this rare tumor.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Yulia S. Vershinina, George S. Krasnov, David G. Garbuz, Mikhail V. Shaposhnikov, Maria S. Fedorova, Elena A. Pudova, Irina V. Katunina, Alexey B. Kornev, Nadezhda V. Zemskaya, Alexander A. Kudryavtsev, Elizaveta V. Bulavkina, Anna A. Matveeva, Natalia S. Ulyasheva, Zulfiya G. Guvatova, Artemiy A. Anurov, Alexey A. Moskalev, Anna V. Kudryavtseva
Summary: Torin-2 is a highly selective inhibitor of TORC1 and TORC2 complexes, which can be used as an alternative to rapamycin. It has lower concentrations and fewer side effects than rapamycin. Our study evaluated the transcriptomic changes induced by Torin-2 in the heads of fruit flies and suggested possible neuroprotective mechanisms. Torin-2 had a slight positive effect on the lifespan of male flies but no positive effect on females.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Olga N. Ivanova, George S. Krasnov, Anastasiya V. Snezhkina, Anna V. Kudryavtseva, Vyacheslav S. Fedorov, Natalia F. Zakirova, Michail V. Golikov, Sergey N. Kochetkov, Birke Bartosch, Vladimir T. Valuev-Elliston, Alexander V. Ivanov
Summary: ROS play a major role in cell regulation, and their increase is associated with the development of various pathologies. This study analyzed gene expression of redox systems and related metabolic processes in hepatoma cells and liver progenitor cell lines, shedding light on the redox biology of viral hepatitis and the influence of laboratory models.
Article
Microbiology
Elizaveta A. Sigova, Elena N. Pushkova, Tatiana A. Rozhmina, Ludmila P. Kudryavtseva, Alexander A. Zhuchenko, Roman O. Novakovskiy, Daiana A. Zhernova, Liubov V. Povkhova, Anastasia A. Turba, Elena V. Borkhert, Nataliya V. Melnikova, Alexey A. Dmitriev, Ekaterina M. Dvorianinova
Summary: This article discusses the methods of assembling high-quality fungal genomes from Oxford Nanopore Technologies data. The researchers sequenced the genomes of three fungal pathogens attacking flax and obtained different volumes of sequencing data. They studied the impact of data quality and genome coverage on assembly statistics and tested different assembling and polishing software. The obtained results provide guidance for de novo genome assembly of fungi and can assist in genomic studies and management of flax diseases.
Article
Microbiology
Irina Efremova, Roman Maslennikov, Elena Poluektova, Maria Zharkova, Anna Kudryavtseva, George Krasnov, Maria Fedorova, Elena Shirokova, Evgenii Kozlov, Anna Levshina, Vladimir Ivashkin
Summary: This study aimed to evaluate the relationship between gut dysbiosis and hemodynamic changes in cirrhosis, as well as the relationship between hemodynamic changes and complications of this disease. The results showed that patients with hyperdynamic circulation had more severe cirrhosis and a higher incidence of complications compared to patients with normodynamic circulation.
Article
Plant Sciences
Elena N. Pushkova, Elena V. Borkhert, Roman O. Novakovskiy, Ekaterina M. Dvorianinova, Tatiana A. Rozhmina, Alexander A. Zhuchenko, Daiana A. Zhernova, Anastasia A. Turba, Arthur G. Yablokov, Elizaveta A. Sigova, George S. Krasnov, Nadezhda L. Bolsheva, Nataliya V. Melnikova, Alexey A. Dmitriev
Summary: Flax, a versatile plant, is widely used in various industries. This study developed a method based on transcriptome libraries to assess the genetic relationship of flax samples for pan-genomic analysis, and successfully selected representative genotypes for comprehensive genetic diversity.
Article
Gastroenterology & Hepatology
Aleksandra Kovaleva, Elena Poluektova, Roman Maslennikov, Oxana Zolnikova, Oleg Shifrin, Anna Kudryavtseva, George Krasnov, Maria Fedorova, Anna Karchevskaya, Vladimir Ivashkin
Summary: This study investigated the composition and metabolic activity of the gut microbiota in patients with diarrhea-predominant irritable bowel syndrome combined with functional dyspepsia (I + D). The study found significant differences in the abundance of certain gut bacteria as well as higher levels of short-chain fatty acids (SCFAs) in the feces of patients compared to healthy controls. Additionally, the levels of certain fatty acids in the feces correlated with the severity of the symptoms.
GASTROINTESTINAL DISORDERS
(2023)
Article
Biochemistry & Molecular Biology
Elena A. Pudova, Anastasiya A. Kobelyatskaya, Irina V. Katunina, Anastasiya V. Snezhkina, Maria S. Fedorova, Vladislav S. Pavlov, Ildar R. Bakhtogarimov, Margarita S. Lantsova, Sergey P. Kokin, Kirill M. Nyushko, Boris Ya. Alekseev, Dmitry V. Kalinin, Nataliya V. Melnikova, Alexey A. Dmitriev, George S. Krasnov, Anna V. Kudryavtseva
Summary: Radical prostatectomy is the gold standard treatment for prostate cancer, but complete cure is not always achieved and recurrence is common. The current methods for assessing prognosis and choosing treatment strategies in PCa patients are not sufficient and new markers are needed. This study used RNA-Seq to identify potential prognostic markers at the gene expression and miRNA levels associated with cancer aggressiveness. The expression of candidate markers was validated and the predictive value of different marker combinations was analyzed using machine learning algorithms, with the CST2 + OCLN + pT model showing the highest potential (AUC = 0.863) based on CatBoost Classifier algorithm.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Zulfiya G. Guvatova, Anastasiya A. Kobelyatskaya, Elena A. Pudova, Irina V. Tarasova, Anna V. Kudryavtseva, Olga N. Tkacheva, Irina D. Strazhesko, Alexey A. Moskalev
Summary: This study estimated the epigenetic age of long-lived individuals and found that their epigenetic age was significantly lower than their chronological age, indicating a slowing of aging. However, there were no significant differences in epigenetic age between healthy long-lived individuals and those with frailty, and no differences in epigenetic age were observed based on sex. The study emphasizes the need for further research on the epigenetic status of centenarians.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
