Article
Multidisciplinary Sciences
Hua-Jun Wu, Alexandro Landshammer, Elena K. Stamenova, Adriano Bolondi, Helene Kretzmer, Alexander Meissner, Franziska Michor
Summary: The disruption of a SOX17 boundary in human pluripotent stem cells interferes with proper differentiation, and germline variations affecting such boundaries are selectively retained, leading to underrepresentation in the human population.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Mayank N. K. Choudhary, Kara Quaid, Xiaoyun Xing, Heather Schmidt, Ting Wang
Summary: Transposable elements (TEs), previously considered as junk DNA, contribute to species-specific 3D-genome structure by providing binding sites for CTCF protein. These elements play a role in gene regulation during mammalian evolution.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
George Tsitsiridis, Ralph Steinkamp, Madalina Giurgiu, Barbara Brauner, Gisela Fobo, Goar Frishman, Corinna Montrone, Andreas Ruepp
Summary: The CORUM database provides comprehensive reference information about mammalian protein complexes and their properties, including 5204 manually curated complexes, covering 26% of human protein coding genes.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Cell Biology
Xuwen Li, Zijian Zhang, Xinlong Luo, Jacob Schrier, Andrew D. Yang, Tao P. Wu
Summary: N-6-methyladenine (N-6-mA, m(6)dA, or 6mA) is a prevalent DNA modification in prokaryotes and has been recently identified in higher eukaryotes, such as mammals. It can serve as an epigenetic mark and play critical roles in various biological processes, but the function and regulatory mechanism of 6mA in eukaryotes, especially mammals, are still poorly understood and require further research.
Article
Multidisciplinary Sciences
Yang Zhou, Linda Shearwin-Whyatt, Jing Li, Zhenzhen Song, Takashi Hayakawa, David Stevens, Jane C. Fenelon, Emma Peel, Yuanyuan Cheng, Filip Pajpach, Natasha Bradley, Hikoyu Suzuki, Masato Nikaido, Joana Damas, Tasman Daish, Tahlia Perry, Zexian Zhu, Yuncong Geng, Arang Rhie, Ying Sims, Jonathan Wood, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, Qiye Li, Huanming Yang, Jian Wang, Stephen D. Johnston, Adam M. Phillippy, Kerstin Howe, Erich D. Jarvis, Oliver A. Ryder, Henrik Kaessmann, Peter Donnelly, Jonas Korlach, Harris A. Lewin, Jennifer Graves, Katherine Belov, Marilyn B. Renfree, Frank Grutzner, Qi Zhou, Guojie Zhang
Summary: The study of egg-laying mammals' genomes offers insights into mammalian evolution, highlighting ancestral and lineage-specific genomic changes in monotremes and mammals. Unique chromosome complex in monotremes may have originated from ancestral chromosome configuration, and differences in specific genes underlie ecological adaptations of monotremes compared to therians.
Article
Biochemistry & Molecular Biology
Yongbing Zhao
Summary: TFSyntax is a database focusing on the arrangement of transcription factor binding sites, providing detailed TF binding maps and syntax information. It contains a large amount of data mapping transcription factor binding motifs, which is valuable for studying the mechanism of transcriptional regulation and the mechanism of regulatory DNA variants causing diseases.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Koichi Kitao, Hiyori Shoji, Takayuki Miyazawa, So Nakagawa
Summary: Independently acquired envelope (env) genes from endogenous retroviruses have contributed to the placental trophoblast cell-cell fusion in therian mammals. In this study, the env genes in the genomes of two monotremes, platypus and echidna, were investigated. The results showed that the echidna genome contained more env-derived open reading frames (env-ORFs) than the platypus genome. The env-Tac1 group in the echidna genome, which showed high similarity to RD114/simian type D retroviruses, was found to utilize echidna sodium-dependent neutral amino acid transporter type 1 and 2 (ASCT1 and ASCT2) as entry receptors.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Review
Biochemical Research Methods
Zhaoqian Liu, Jingtong Feng, Bin Yu, Qin Ma, Bingqiang Liu
Summary: Bacterial genomes are recognized to closely interact with cellular processes. Researchers focus on uncovering organizational mechanisms of bacterial genomes to reveal potential cellular activities. Advances in experimental techniques and computational models provide opportunities for understanding these mechanisms, including local structures such as operons/transcription units and global constraints shaping bacterial genomes.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Yongbing Zhao, Supriya V. Vartak, Andrea Conte, Xiang Wang, David A. Garcia, Evan Stevens, Seol Kyoung Jung, Kyong-Rim Kieffer-Kwon, Laura Vian, Timothy Stodola, Francisco Moris, Laura Chopp, Silvia Preite, Pamela L. Schwartzberg, Joseph M. Kulinski, Ana Olivera, Christelle Harly, Avinash Bhandoola, Elisabeth F. Heuston, David M. Bodine, Raul Urrutia, Arpita Upadhyaya, Matthew T. Weirauch, Gordon Hager, Rafael Casellas
Summary: This study analyzes 500 mouse and human primary cells and reveals two groups of co-localized transcription factors, one involved in tissue-specific transcription and the other functioning universally in all tissues. The study also uncovers how the universal stripe factors enhance accessibility and residence time of co-localized partners.
Article
Multidisciplinary Sciences
Sergey Ulianov, Vlada V. Zakharova, Aleksandra A. Galitsyna, Pavel Kos, Kirill E. Polovnikov, Ilya M. Flyamer, Elena A. Mikhaleva, Ekaterina E. Khrameeva, Diego Germini, Mariya D. Logacheva, Alexey A. Gavrilov, Alexander S. Gorsky, Sergey K. Nechaev, Mikhail S. Gelfand, Yegor S. Vassetzky, Alexander Chertovich, Yuri Y. Shevelyov, Sergey Razin
Summary: The study presents single-nucleus Hi-C maps in Drosophila at 10kb resolution, demonstrating the presence of chromatin compartments in individual nuclei and partitioning of the genome into non-hierarchical TADs at the scale of 100kb, resembling population TAD profiles.
NATURE COMMUNICATIONS
(2021)
Article
Cell Biology
Teerna Bhattacharyya, Ramanathan Sowdhamini
Summary: The age of genomics has provided us with valuable information and tools to study whole genomes, leading to genome-wide studies that uncover interesting evolutionary patterns and the crucial role of phosphorylation in various organisms.
CELLULAR SIGNALLING
(2021)
Article
Food Science & Technology
Monica Di Donato, Oscar Carpintero
Summary: The study discusses how increasing population challenges the global food system in terms of productivity and environmental pressures. It emphasizes the importance of innovative approaches to support effective policy efforts. By using household metabolism approach, the study illustrates the environmental pressures derived from household food consumption, especially during the 2008 crisis in Spanish regions. The study also highlights the impact of economic crisis on food consumption patterns and environmental performance, showing how it can drive change towards better sustainability.
Article
Chemistry, Multidisciplinary
Danye Qiu, Chunfang Gu, Guizhen Liu, Kevin Ritter, Verena B. Eisenbeis, Tamara Bittner, Artiom Gruzdev, Lea Seidel, Bertram Bengsch, Stephen B. Shears, Henning J. Jessen
Summary: This study used capillary electrophoresis mass spectrometry to investigate the levels of InsPs and PP-InsPs in mouse tissues. The results showed unusually high levels of InsPs and PP-InsPs in the mouse colon, and the PP-InsP profile was more complex than previously reported. Additionally, the study found that these molecules were not only present in the colon, but also in the heart and blood cells.
Article
Multidisciplinary Sciences
Sage Albright, Stilianos Louca
Summary: Common culturing techniques bias the discovery of microbial diversity. This study compares culture-independent metagenome-assembled genomes (MAGs) to the RefSeq genome database to examine these biases. The distribution of gene orthologs in MAGs and RefSeq genomes is compared, revealing significant biases. This systematic analysis provides a resource for addressing these biases in the future.
Article
Biochemical Research Methods
Caitlin Timmons, Quaid Morris, Caitlin F. Harrigan
Summary: This study presents regional profiles of mutational signature activities in cancer genomes, showcasing changes in these activities during tumor development. The research reveals shared changepoints across multiple tumor types and activity tradeoffs between signatures active in early and late cancer development.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Plant Sciences
Riccardo Aiese Cigliano, Riccardo Aversano, Antonio Di Matteo, Samuela Palombieri, Pasquale Termolino, Claudia Angelini, Hamed Bostan, Maria Cammareri, Federica Maria Consiglio, Floriana Della Ragione, Rosa Paparo, Vladimir Totev Valkov, Antonella Vitiello, Domenico Carputo, Maria Luisa Chiusano, Maurizio D'Esposito, Silvana Grandillo, Maria Rosaria Matarazzo, Luigi Frusciante, Nunzio D'Agostino, Clara Conicella
Summary: In this study, we investigated the changes in the transcriptome and epigenome of a long shelf-life tomato landrace during post-harvest. We discovered global changes in the transcriptome and epigenome, with increased DNA methylation and loss of a repressive histone mark. Thousands of genes showed differential expression, with a significant portion potentially being regulated by epigenetic mechanisms. Down-regulation of genes related to fruit ripening and softening was consistent with the prolonged shelf-life. Large-scale epigenome reprogramming during post-harvest likely contributes to delayed fruit senescence.
HORTICULTURE RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Grazia Maugeri, Agata Grazia D'Amico, Salvatore Giunta, Cesarina Giallongo, Daniele Tibullo, Claudio Bucolo, Salvatore Saccone, Concetta Federico, Davide Scollo, Antonio Longo, Teresio Avitabile, Giuseppe Musumeci, Velia D'Agata
Summary: The corneal epithelium acts as a barrier against harmful agents and is vulnerable to UV-B radiation damage. This study investigated the protective effects of ADNP and its derived peptide NAP in the corneal epithelium, demonstrating their ability to reduce cell death and signaling pathway activation caused by UV-B irradiation.
Article
Biochemistry & Molecular Biology
Girolamo Aurelio Vitello, Concetta Federico, Francesca Bruno, Mirella Vinci, Antonino Musumeci, Alda Ragalmuto, Valentina Sturiale, Desiree Brancato, Francesco Cali, Salvatore Saccone
Summary: During the first wave of COVID-19 infection in Italy, the number of cases and mortality rates were high. COVID-19 was found to be more severe in older individuals with comorbidities and male gender. However, some individuals in close contact with infected subjects showed resistance to virus infection. Besides genetic variability of the virus and other environmental factors, allelic variants of specific human genes related to the virus life cycle should be considered to understand the susceptibility to virus infection and COVID-19 progression.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Ketty Dugo, Francesca Bruno, Valentina Sturiale, Desiree Brancato, Salvatore Saccone, Concetta Federico
Summary: Point mutations of the TTR gene are associated with hATTR, requiring further investigation into their impact on expressivity, complexity, progression, and transmission. Emphasis should be placed on researching somatic mosaicism to explain the complexity of clinical features, estimate new case numbers, and focus on early personalized gene therapy.
Article
Biochemistry & Molecular Biology
Ambra Butera, Antonio Gennaro Nicotera, Gabriella Di Rosa, Sebastiano Antonino Musumeci, Girolamo Aurelio Vitello, Antonino Musumeci, Mirella Vinci, Angelo Gloria, Concetta Federico, Salvatore Saccone, Francesco Cali
Summary: The PHF21A gene is associated with Potocki-Shaffer Syndrome, characterized by multiple exostoses, biparietal foramina, intellectual disability, and craniofacial anomalies. However, there is limited description of the clinical phenotype of PHF21A-related disorders in the literature.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Varsha Poondi Krishnan, Barbara Morone, Shir Toubiana, Monika Krzak, Salvatore Fioriniello, Floriana Della Ragione, Maria Strazzullo, Claudia Angelini, Sara Selig, Maria R. Matarazzo
Summary: Researchers found that in ICF1 patients, different mutations in DNMT3B disrupt DNA methyltransferase activity and lead to widespread changes in the epigenome. While the majority of abnormal regions can be normalized, a small fraction remains resistant to correction, posing challenges for treatment.
Article
Biochemistry & Molecular Biology
Grazia Maugeri, Agata Grazia D'Amico, Benedetta Magri, Salvatore Giunta, Giuseppe Musumeci, Salvatore Saccone, Concetta Federico, Davide Scollo, Antonio Longo, Teresio Avitabile, Velia D'Agata
Summary: The corneal epithelium acts as a protective barrier against external insults and its disruption can lead to visual impairment. In this study, we investigated the role of NAP in counteracting the inflammatory response triggered by UV-B radiation, which can disrupt the corneal epithelial barrier. The results showed that NAP treatment can prevent UV-B-induced inflammation and maintain corneal epithelial barrier integrity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Materials Science, Multidisciplinary
Giuseppe Lazzara, Francesca Bruno, Desiree Brancato, Valentina Sturiale, Agata Grazia D'Amico, Stefana Miloto, Pooria Pasbakhsh, Velia D'Agata, Salvatore Saccone, Concetta Federico
Summary: The biocompatibility of four different halloysite clay nanotubes (HNT-N,-U,-P,-S) from various deposits was evaluated, indicating a generally high level of biocompatibility but with moderate toxicity at high concentrations and long times of exposition. Caution should be exercised in the future use of large amounts of HNTs due to their effects on living organisms.
Article
Oncology
Francesco Cecere, Laura Pignata, Bruno Hay Mele, Abu Saadat, Emilia D'Angelo, Orazio Palumbo, Pietro Palumbo, Massimo Carella, Gioacchino Scarano, Giovanni Battista Rossi, Claudia Angelini, Angela Sparago, Flavia Cerrato, Andrea Riccio
Summary: This study reports a case of early-onset colorectal cancer (EO-CRC) in a 27-year-old woman with Beckwith-Wiedemann syndrome (BWSp). Genetic and epigenetic analysis revealed the presence of genetic and epigenetic variations that may be associated with the development of EO-CRC.
Article
Biochemistry & Molecular Biology
Valentina Sturiale, Francesca Bruno, Desiree Brancato, Agata Grazia D'Amico, Grazia Maugeri, Velia D'Agata, Salvatore Saccone, Concetta Federico
Summary: A characteristic hallmark of Alzheimer's disease is the accumulation of hyperphosphorylated tau protein, which can trigger re-entry into the cell cycle in differentiated neurons and lead to neurodegeneration. Neuroblastoma cell lines prove to be a useful in vitro cellular model for studying the neuroprotective effects of natural molecules.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Genetics & Heredity
Desiree Brancato, Elvira Coniglio, Francesca Bruno, Vincenzo Agostini, Salvatore Saccone, Concetta Federico
Summary: The use of genetic polymorphisms related to specific phenotypes, such as eye color, has greatly contributed to the development of forensic DNA phenotyping and has enabled investigators of crime cases to reduce the number of suspects. The HERC2-OCA2 locus is the major contributor to eye color and shows a high level of evolutionary conservation. However, the exact role of genetic variants in eye color formation is still poorly understood, which limits the predictivity of current forensic DNA phenotyping assays.
Article
Medicine, General & Internal
Francesco Cali, Francesco Domenico Di Blasi, Emanuela Avola, Mirella Vinci, Antonino Musumeci, Angelo Gloria, Donatella Greco, Daniela Rita Raciti, Alessandro Zagami, Biagio Rizzo, Santina Citta, Concetta Federico, Luigi Vetri, Salvatore Saccone, Serafino Buono
Summary: In this study, genetic variants in the DGKI, DIP2A, KIAA0319, and PCNT genes were identified through genetic sequencing of 21 young individuals diagnosed with SLD from 9 families. Despite the limited sample size, this study is important for further research on the genetic basis of this disorder and its neuropsychological and social aspects.
MEDICINA-LITHUANIA
(2023)