Article
Biotechnology & Applied Microbiology
Tingting Jiang, Xiao-Ou Zhang, Zhiping Weng, Wen Xue
Summary: The study optimized prime editing tools for creating precise genomic deletions and direct replacement of a genomic fragment with a desired sequence without the need for an exogenous DNA template. By conjugating Cas9 nuclease to reverse transcriptase and using two PE guide RNAs targeting complementary DNA strands, the PEDAR method achieved precise and specific deletion and repair of target sequences.
NATURE BIOTECHNOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
Thays Duarte de Oliveira, Natasha Avila Bertocchi, Rafael Kretschmer, Edivaldo H. C. de Oliveira, Marcelo de Bello Cioffi, Thomas Liehr, Thales R. O. de Freitas
Summary: In this study, molecular cytogenetic analysis was used to investigate the genomic elements involved in the population variation observed in the Neotropical underground rodents of the genus Ctenomys. The results suggest that there is a correlation between repetitive genomic content and localization of evolutionary breakpoint regions, highlighting their direct impact on promoting chromosomal rearrangements.
Article
Biotechnology & Applied Microbiology
Meiqi Zhao, Guoping Shu, Yanhong Hu, Gangqiang Cao, Yibo Wang
Summary: This study used high-quality de novo-sequenced maize genomes to investigate the distribution and polymorphism of SSRs. The results showed that SSRs were more densely present in the telomeric region than the centromeric region, and were more abundant in genic sequences than intergenic sequences. The length and density of SSRs were found to be under the control of unknown evolutionary forces. The SSR polymorphism observed in different chromosome regions and motifs can be used as valuable genome resources for maize genetic research and molecular breeding.
Article
Multidisciplinary Sciences
Sung-Mo An, Bo-Yun Kim, Halam Kang, Ha-Rim Lee, Yoo-Bin Lee, Yoo-Jung Park, Kyeong-Sik Cheon, Kyung-Ah Kim
Summary: The phylogenetic relationships between Hylotelephium and Orostachys were evaluated by analyzing their complete chloroplast genomes. The study found that these two genera have similar genome structure and gene features, but the genus delimitation is not clear due to the paraphyly of Hylotelephium with subsect. Orostachys. The taxonomic position of Sedum taqeutii was also supported as an independent taxon.
Article
Plant Sciences
Shuang Wu, Jinyuan Chen, Ying Li, Ai Liu, Ao Li, Mou Yin, Nawal Shrestha, Jianquan Liu, Guangpeng Ren
Summary: Extensive genomic rearrangements and abundant repetitive elements were detected in plastomes of Medicago and its relatives. The repeat content was found to be positively correlated with the degree of genomic rearrangements, with repeat-mediated illegitimate recombination identified as the major mechanism leading to genome instability. The findings provide valuable genomic resources for further investigation into plastome evolution in legumes.
Review
Biochemistry & Molecular Biology
Terence Gall-Duncan, Nozomu Sato, Ryan K. C. Yuen, Christopher E. Pearson
Summary: Expansions of gene-specific DNA tandem repeats (TRs) have been found to cause more than 60 phenotypes, not just disease, and not only in humans. Technological advances in DNA sequencing and computational analyses have accelerated the discovery of disease-causing TR expansions. From 2019 to 2021, 17 new disease-causing TR expansions were reported, totaling over 69 diseases. Repeat diseases exhibit atypical clinical features, genetic anticipation, and multiple and partially penetrant phenotypes among family members.
Article
Biochemistry & Molecular Biology
Ni-Chen Chang, Quirze Rovira, Jonathan Wells, Cedric Feschotte, Juan M. Vaquerizas
Summary: This study describes the demography and genomic distribution of zebrafish transposable elements (TEs) and their expression during embryogenesis. The results reveal a highly dynamic genomic ecosystem comprising nearly 2000 distinct TE families, with longer retroelements being retained in intergenic regions and shorter elements more frequently found near or within genes. The study provides a valuable resource for using zebrafish as a model to study the impact of TEs on vertebrate development.
Article
Biotechnology & Applied Microbiology
Yingxin Zhang, Chengming Fan, Yuhong Chen, Richard R. C. Wang, Xiangqi Zhang, Fangpu Han, Zanmin Hu
Summary: The study revealed specific distribution patterns of SSRs in different chromosomes from different species, providing efficient visible markers for identification of individual chromosomes and tracing SSR sequence evolution from diploid progenitors to hexaploid wheat. The greatest changes in SSRs, including (AAC)(n), (AAG)(n), (AGC)(n), and (AG)(n), were observed in the B genome during wheat evolution, especially in centromeric and pericentromeric regions, suggesting that the B genome might be more sensitive to genome shock and more changeable during wheat polyploidization.
Article
Biochemistry & Molecular Biology
Jimin Yang, Guo Nan Yin, Do-Kyun Kim, Ah-reum Han, Dong Sun Lee, Kwang Wook Min, Yaoyao Fu, Jeongwon Yun, Jun-Kyu Suh, Ji-Kan Ryu, Ho Min Kim
Summary: The serum glycoprotein leucine-rich alpha-2-glycoprotein 1 (LRG1) is a multifunctional protein that modulates various signaling cascades. Its glycosylation alters LRG1's properties and functions, and aberrant glycosylation is recognized in diseases including diabetes. The crystal structure of LRG1 has been determined, and its deglycosylation at a specific site is essential for its interaction with LPHN2 and promotion of angiogenic and neurotrophic processes. In a diabetic mouse model, deglycosylated LRG1 alleviated vascular and neurological abnormalities.
EXPERIMENTAL AND MOLECULAR MEDICINE
(2023)
Review
Polymer Science
Marina P. Chang, Winnie Huang, Danielle J. Mai
Summary: Protein-based polymers with chemically defined sequences can encode diverse properties and functions into new biopolymeric materials. Identifying common sequences between proteins with similar functions can clarify sequence-function relationships. Consensus repeat sequences from repeat proteins are a convenient platform for investigating biopolymer sequence-property relationships systematically.
JOURNAL OF POLYMER SCIENCE
(2021)
Review
Genetics & Heredity
Isabel Costantino, Juliet Nicodemus, Jerold Chun
Summary: Over the past 20 years, studies have shown that the brain is a genomic mosaic made up of cells with different genomes, generated by DNA sequence-altering processes that occur somatically. These changes are not heritable and can affect normal brain functions as well as lead to dysfunction in neurodegenerative and other brain diseases. Further technological development is necessary for ongoing analysis of genomic mosaicism.
Article
Genetics & Heredity
Virali J. Parekh, Grzegorz Wegrzyn, Veronique Arluison, Richard R. Sinden
Summary: G-quadruplex formation promotes genetic instability in bacteria, and helicases play an important role in controlling this process in vivo.
Review
Ophthalmology
Murad Khan, Suleman Shah, Baixue Lv, Zhanjun Lv, Ning Ji, Zhixue Song, Peiyuan Wu, Xiufang Wang, Arshad Mehmood
Summary: This study explores the role of SINEs and LINE-1s in visual system dysfunction diseases. The results suggest that gene expression regulated by these repetitive sequences is one of the causes of these diseases, highlighting the potential implications of SINEs and LINE-1s in ophthalmology.
OCULAR IMMUNOLOGY AND INFLAMMATION
(2023)
Article
Biochemical Research Methods
Kathleen L. Morrissey, Dylan DeWitt, Nikhil Shah, William Fall, Hari Shah, Linda B. McGown
Summary: The study investigates a genome-inspired approach for aptamer discovery in cancer-related DNA-protein interactions, focusing on G-rich sequences that can form G-quadruplex structures. By using naturally occurring DNA sequences, the research aims to increase the chances of uncovering protein-DNA affinity binding interactions with biological significance and analytical utility, especially in oncogene promoters. The presence of a large diversity of G4-forming sequences throughout the human genome provides promising candidates for aptamers to regulatory proteins in cancer.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Biology
Kshitij Tandon, Francesco Ricci, Joana Costa, Monica Medina, Michael Kuhl, Linda L. Blackall, Heroen Verbruggen
Summary: Currently, our understanding of the coral holobiont microbiomes is biased towards the coral tissue, neglecting the diversity of the coral skeleton microbiome. Through genomic analysis of the coral skeletons of Porites lutea and Isopora palifera, we found a wide range of stress response genes and genes involved in maintaining host association in the skeleton microbiomes. The skeletal microbiome also plays important roles in metabolic processes such as nitrogen fixation and nitrate reduction.
Review
Genetics & Heredity
Sandra Louzada, Mariana Lopes, Daniela Ferreira, Filomena Adega, Ana Escudeiro, Margarida Gama-Carvalho, Raquel Chaves
Review
Biochemistry & Molecular Biology
Daniela Ferreira, Juliana Miranda, Paula Martins-Lopes, Filomena Adega, Raquel Chaves
Summary: Liquid biopsies are important for the early detection of gene alterations in NSCLC patients and disease management, highlighting the impact of NGS methods; however, their use in oncology is still limited.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Mariana Lopes, Sandra Louzada, Margarida Gama-Carvalho, Raquel Chaves
Summary: Studies have shown that satellite DNA sequences play an important role in the human genome, but there are differences in various features. Different satDNA families have been identified at different speeds, showing high sub-variability. Approaches combining multiple techniques have been successful in the field of human satDNA biology, promising integrated knowledge generation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
A. Escudeiro, F. Adega, T. J. Robinson, J. S. Heslop-Harrison, R. Chaves
Summary: The study reports a fine-scale molecular analysis of centromeric satDNA families in Robertsonian fusion chromosomes of domestic cattle and antelope species. It reveals that Rb fusions involve complex rearrangements of specific satDNA sequences, but do not affect their centromeric activity, suggesting a common mechanism for Rb fusions in bovids and mammals in general.
CHROMOSOME RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
C. Lino, S. Barrias, R. Chaves, F. Adega, P. Martins-Lopes, J. R. Fernandes
Summary: Nowadays, the development of new technological solutions in the medical field, especially biosensors, is a priority and a significant investment. Biomarkers combined with biosensors have the potential to revolutionize healthcare management, providing fast, cost-effective, reliable, and highly sensitive clinical diagnosis.
BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER
(2022)
Article
Biology
Albano Pinto, Catarina Cunha, Raquel Chaves, Matthew E. R. Butchbach, Filomena Adega
Summary: Transposable elements (TEs) are DNA sequences that can move throughout the genome and play important roles in gene regulation and function. In this study, we examined the presence of TEs in the genomes of SMA patients and healthy individuals and identified distinct TEs within the SMA genes that may impact gene expression by affecting promoter activity, transcriptional termination, and alternative splicing. Understanding the roles of TEs in SMA may provide valuable insights into other neurodegenerative diseases.
Article
Pharmacology & Pharmacy
Patricia Teixeira, Filomena Adega, Paula Martins-Lopes, Raul Machado, Carla M. M. Lopes, Marlene Lucio
Summary: By developing intelligent materials that respond to environmental stimuli, we have successfully optimized pH-triggered drug delivery nanoassemblies, which exhibit increased release of doxorubicin (DOX) in acidic conditions (pH 5.5) typical of cancer tissues, while exhibiting lower release in normal physiological conditions (pH 7.5), potentially reducing cytotoxicity in healthy cells.
Article
Biology
Mariana Lopes, Sandra Louzada, Daniela Ferreira, Gabriela Verissimo, Daniel Eleuterio, Margarida Gama-Carvalho, Raquel Chaves
Summary: This study aims to characterize and understand the biological relevance of HSat1A. Through in vitro isolation, gene cloning, and in vivo transcription analysis, the mapping and function of HSat1A in human chromosomes were identified. It was found that the polyadenylation status of HSat1A transcripts varies, suggesting a potential role in alternative polyadenylation regulation. This research is significant for understanding the transcriptional mechanism of HSat1A and its involvement in disease development.
Article
Chemistry, Analytical
Catarina Lino, Sara Barrias, Raquel Chaves, Filomena Adega, Jose Ramiro Fernandes, Paula Martins-Lopes
Summary: Lung cancer, with one of the lowest survival rates, is the main malignant cancer reported worldwide. Deletions in the Epidermal Growth Factor Receptor (EGFR) gene are often associated with non-small cell lung cancer (NSCLC), a common subtype of lung cancer. The development of a DNA-based biosensor, namely a quartz crystal microbalance (QCM), applied to the detection of NSCLC, was reported in this study. The biosensor was able to detect specific DNA sequences in both synthetic and real samples, and aspects such as reutilization and regeneration of the QCM electrode were also studied.
Article
Biotechnology & Applied Microbiology
Daniela Ferreira, Maria Soares, Jorge Correia, Filomena Adega, Fernando Ferreira, Raquel Chaves
Summary: The study investigates FA-SAT ncRNA in feline mammary tumors and finds associations between FA-SAT DNA and RNA levels and clinicopathological parameters, suggesting FA-SAT ncRNA as a potential biomarker for feline cancer.
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
(2022)