Review
Biochemistry & Molecular Biology
Xiao Tan, Justin H. Letendre, James J. Collins, Wilson W. Wong
Summary: Synthetic biology is a design-driven discipline focused on engineering novel biological functions through the discovery and repurposing of molecular parts. Applications in vaccine development, molecular diagnostics, and cell-based therapeutics are already in clinical use or active clinical trials, with ongoing innovations likely to have a significant impact on future biomedicine applications.
Article
Biochemistry & Molecular Biology
Pengyu Zhang, Hongming Zhang, Hao Wu
Summary: This study proposes a novel weighted average ensemble learning model, iPro-WAEL, for identifying promoters in multiple species, and demonstrates its optimal performance, cross-cell line prediction ability, and ability to distinguish between promoters and enhancers.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Biochemistry & Molecular Biology
Helen Ray-Jones, Mikhail Spivakov
Summary: Transcriptional enhancers play a key role in regulating gene expression in metazoa, particularly in initiating and maintaining gene expression programmes. Understanding how enhancers control their target genes in the right place and time is a crucial question in functional genomics, and modern approaches are beginning to unravel the complexity of enhancer-promoter relationships.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Article
Multidisciplinary Sciences
Travis La Fleur, Ayaan Hossain, Howard M. Salis
Summary: Transcription rates are regulated by interactions between RNA polymerase, sigma factor, and promoter DNA sequences. In this study, the authors developed a predictive biophysical model of transcription using massively parallel experiments and machine learning, which was validated across a large number of bacterial promoters with diverse sequences.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Sarah Cooper, Jeremy Schwartzentruber, Eve L. Coomber, Qianxin Wu, Andrew Bassett
Summary: Understanding the impact of genetic variation in gene regulatory elements is crucial for interpreting genome function. In this study, a new medium-throughput screening system called GenIE-ATAC was developed to measure the effect of individual variants on chromatin accessibility in their natural genomic and chromatin context. The method was validated in human induced pluripotent stem cells and demonstrated its ability to identify and prioritize causal variants for functional follow-up and understanding regulatory element function mechanisms.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Fisheries
Simon Baumgartner, Simon Creer, Charlie Jones, Jack James, Amy Ellison
Summary: One of the major challenges in sustainable global aquaculture is the threat of infectious diseases. To ensure fish health and reduce antibiotic use, preventative strategies such as health-promoting feed supplements like astaxanthin and probiotics are being explored. This study investigates the effects of probiotic blends on fish growth and gut microbial community, compared to astaxanthin supplementation, in two cyprinid species. The results reveal species-specific responses to probiotics and highlight the need for further research in understanding the mechanisms behind these responses.
Review
Agronomy
Ahamed Khan, Noohi Nasim, Baveesh Pudhuvai, Bhupendra Koul, Santosh Kumar Upadhyay, Lini Sethi, Nrisingha Dey
Summary: This review discusses the application of synthetic promoters in plants to overcome the limitations of native promoters in terms of size, distribution, and induction, which ultimately leads to insufficient transcriptional activity. It emphasizes the basic structure and function of the promoter, with a focus on the role of Cis-elements in gene expression regulation. The importance of synthetic promoters in the field of plant biology is highlighted, along with information on two major approaches: conventional methods and advancements in gene editing technology. The efficiency of synthetic promoters and the expression level of transgenes are crucial for successful plant genetic manipulation, making the development of synthetic promoters highly promising for genetic engineering-mediated crop improvement.
Article
Biochemistry & Molecular Biology
Ran Brosh, Camil Coedho, Andre M. Ribeiro-dos-Santos, Gwen Ellis, Megan S. Hogan, Hannah J. Ashe, Nicolette Somogyi, Raquel Ordonez, Raven D. Luther, Emily Huang, Jef D. Booke, Matthew T. Maurano
Summary: The expression of Sox2 gene in mouse embryonic stem cells (mESCs) relies on a cluster of distal DNase I hypersensitive sites (DHSs), but the individual contributions and the degree of interdependence between these DHSs are still unknown. Through the use of Big-IN technology, we found that two DHSs were sufficient to activate Sox2 gene expression over long distances, while three nearby DHSs were entirely context dependent and showed no activity alone, but significantly enhanced the activity of autonomous DHSs. Our study highlights the role of context in modulating genomic regulatory element function, and our synthetic regulatory genomics approach provides a roadmap for dissecting other genomic loci.
Article
Agriculture, Dairy & Animal Science
Nina Sandlund, Renate Johansen, Ingrid U. Fiksdal, Ann Cathrine B. Einen, Ingebjorg Modahl, Britt Gjerset, Oivind Bergh
Summary: Viral haemorrhagic septicaemia virus (VHSV) is a globally important group of viruses infecting a wide range of fish species, with recent initiatives to re-establish Atlantic cod as an aquaculture species. Studies show that Atlantic cod has limited ability to be infected by VHSV and has low susceptibility to the genotype III strain of this virus.
Article
Chemistry, Multidisciplinary
Melecio A. Perea, Brian Wang, Benjamin C. Wyler, Jin Su Ham, Nicholas R. O'Connor, Shota Nagasawa, Yuto Kimura, Carolin Manske, Maximilian Scherubl, Johny M. Nguyen, Richmond Sarpong
Summary: Chemical synthesis of natural products is often inspired by the structure and function of the target molecule, and this paper presents a unified enantiospecific approach to diverse taxane cores using (S)-carvone as the starting material, which involves skeletal remodeling and C-C bond cleavage strategies.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Multidisciplinary Sciences
Chirag Nepal, Jesper B. Andersen
Summary: The study investigates the regulatory mechanisms of alternative promoters in hepatocellular carcinoma and provides insights into their sequence and epigenetics landscape. The authors identify 4083 alternative promoters in 2926 multi-promoter genes, which are rarely detected in normal livers. These alternative promoters play a role in oncogenic processes and are associated with overall survival. The findings reveal the unique characteristics of alternative promoters, such as their narrow nucleosome depleted regions and enrichment of tissue-specific transcription factors.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Julan Kim, Ja Young Cho, Ju-Won Kim, Dong-Gyun Kim, Bo-Hye Nam, Bong-Seok Kim, Woo-Jin Kim, Young-Ok Kim, JaeHun Cheong, Hee Jeong Kong
Summary: PoMaf1 is a global suppressor of RNA polymerase III-dependent transcription, potentially playing a crucial role in the immune response to viral infections in fish. It is expressed in all tissues, with highest levels in eye and muscle tissues. The transcript levels of PoMaf1 decrease during VHSV infection, and its disruption leads to increased VHSV glycoprotein mRNA levels, indicating its involvement in the immune response to VSHV infection.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Max E. Distler, John P. Cavaliere, Michelle H. Teplensky, Michael Evangelopoulos, Chad A. Mirkin
Summary: A DNA dendron vaccine consisting of an adjuvant DNA strand that splits into multiple DNA branches with conjugated peptide antigens is reported. This vaccine demonstrated effective immune activation and potent cancer killing capabilities. The structure of the vaccine played a critical role in its efficacy in treating a mouse cancer model.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Tyler J. Hansen, Emily Hodges
Summary: This study reports an integrated approach using ATAC-STARR-seq to quantify the activities of gene regulatory elements, chromatin accessibility, and transcription factor occupancy. The researchers found that about 30% of accessible regions contain activators, silencers, or both. ATAC-STARR-seq has the capability to comprehensively investigate the regulatory landscape of the human genome at multiple layers.
Article
Plant Sciences
Lini Sethi, Debasish Deb, Badrinath Khadanga, Nrisingha Dey
Summary: Researchers analyzed the synthetic full-length transcript promoter of Blueberry red ringspot virus (BRRV) and developed two chimeric promoters (MBR3 and FBR3) with transcriptional activities equivalent to that of the CaMV35S(2) promoter. These chimeric promoters showed high antimicrobial activities against several pathogens, making them potential useful substitutes for the CaMV35S(2) promoter in plant genetic engineering.
Article
Fisheries
Melissa Bello-Perez, Regla Medina-Gali, Julio Coll, Luis Perez
Article
Fisheries
Regla Medina-Gali, Melissa Bello-Perez, Sergio Ciordia, Maria Carmen Mena, Julio Coll, Beatriz Novoa, Maria del Mar Ortega-Villaizan, Luis Perez
FISH & SHELLFISH IMMUNOLOGY
(2019)
Article
Cell Biology
Anastasia Selyutina, Mirjana Persaud, Lacy M. Simons, Angel Bulnes-Ramos, Cindy Buffone, Alicia Martinez-Lopez, Viviana Scoca, Francesca Di Nunzio, Joseph Hiatt, Alexander Marson, Nevan J. Krogan, Judd F. Hultquist, Felipe Diaz-Griffero
Article
Biology
Melissa Bello-Perez, Mikolaj Adamek, Julio Coll, Antonio Figueras, Beatriz Novoa, Alberto Falco
Summary: The study suggests that fish short pentraxins may serve as health biomarkers for bacterial and viral infections, with antiviral activity. Experiments in zebrafish show that skin is an important sampling source for the analysis of these short pentraxins' expression levels.
Article
Multidisciplinary Sciences
Corey H. Yu, Akash Bhattacharya, Mirjana Persaud, Alexander B. Taylor, Zhonghua Wang, Angel Bulnes-Ramos, Joella Xu, Anastasia Selyutina, Alicia Martinez-Lopez, Kristin Cano, Borries Demeler, Baek Kim, Stephen C. Hardies, Felipe Diaz-Griffero, Dmitri N. Ivanov
Summary: SAMHD1 is a protein that inhibits retrovirus infection by dephosphorylating deoxynucleotide triphosphates. Research shows that the allosteric binding sites of SAMHD1 are flexible and can accommodate oligonucleotides, with a preference for those containing phosphorothioate bonds. This discovery links nucleic acid binding to the antiretroviral activity of SAMHD1 and raises questions about the role of nucleic acid phosphorothioation in human innate immunity.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Blanca Chinchilla, Heran Getachew, Rosario Fernandez-Godino
Summary: Eye disorders impact millions globally, and mouse models provide insight into their pathophysiology. Changes in the retinal pigment epithelium are common in ocular diseases, but isolating and culturing primary mouse RPE cells is challenging. This new protocol offers a reproducible method for studying molecular and cellular mechanisms in eye diseases and testing therapeutic approaches.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
Article
Biochemistry & Molecular Biology
Blanca Chinchilla, Rosario Fernandez-Godino
Summary: Changes in the Bruch's membrane can lead to age-related macular degeneration, with abnormal ECM leading to epithelial mesenchymal transition in RPE cells. Understanding these processes may lead to the development of new therapies for AMD.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Oncology
Blanca Chinchilla, Parthena Foltopoulou, Rosario Fernandez-Godino
Summary: Despite multiple failed clinical trials for anti-complement drugs in treating age-related macular degeneration (AMD), the complement system has not been fully explored as a target to stop drusen growth in patients with dry AMD. A study combining gene editing tools with stem cell technology found that dysregulation of the tick-over in sub-RPE deposit formation may be prevented with therapies that downregulate C3 expression, indicating a potential new approach for treating AMD.
JOURNAL OF PATHOLOGY
(2021)
Article
Virology
Paloma Encinas, Gustavo del Real, Jayeeta Dutta, Zenab Khan, Harm van Bakel, M. Angeles Martin del Burgo, Adolfo Garcia-Sastre, Martha Nelson
Summary: Spain, as the largest swine producer in Europe, harbors genetically diverse influenza A viruses in both intensive and free-range pig production systems, showing different patterns of virus evolution and transmission. The interaction between intensive white pigs and free-range Iberian pigs contributes to the diversity and potential zoonotic risk of IAVs in swine populations.
Article
Fisheries
Noelia Nunez-Ortiz, Patricia Diaz-Rosales, Jose A. Garcia, Claudia R. Serra, Paula Enes, Carolina Tafalla, Eduardo Gomez-Casado
Summary: This study evaluated the immune-stimulating capacity of two recombinant flagellins and found that they can significantly increase the transcription of immune genes and limit viral replication in fish cells. Flagellins have the potential to be suitable adjuvants for fish vaccines in aquaculture.
FISH & SHELLFISH IMMUNOLOGY
(2022)
Editorial Material
Immunology
Maria del Mar Ortega-Villaizan, Julio Coll, Espen Rimstad
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Sylwia D. Tyrkalska, Alicia Martinez-Lopez, Ana B. Arroyo, Francisco J. Martinez-Morcillo, Sergio Candel, Diana Garcia-Moreno, Pablo Mesa-Del-Castillo, Maria L. Cayuela, Victoriano Mulero
Summary: The study reported the proinflammatory role of S proteins from different SARS-CoV-2 variants in zebrafish and identified differences in inflammatory responses and vascular endothelial function among different variants. Pharmacological inhibition of the inflammasome and the use of angiotensin (1-7) have positive effects on reducing inflammation and hemorrhages.
Article
Fisheries
Blanca Chinchilla, Esther Vazquez-Fernandez, Agustin Rebollada-Merino, Marta Perez-Sancho, Lucas Dominguez, Antonio Rodriguez-Bertos
Summary: In this study, Flavobacterium psychrophilum was identified as the causative agent of mortality in diseased juvenile Siberian sturgeons using MALDI-TOF MS and nested PCR. The infected sturgeons showed lethargy, dark skin pigmentation, increased mucus production, and skin ulcerations and haemorrhages. Histological examination revealed various pathological findings, including branchitis, dermatitis, myositis, lymphoid tissue atrophy, and organ degeneration. This is the first report of F. psychrophilum infection in Siberian sturgeons, and the findings contribute to understanding the bacterium's pathogenicity and susceptible fish species range.
JOURNAL OF FISH DISEASES
(2023)
Article
Immunology
Agustin Rebollada-Merino, Teresa Garcia-Seco, Blanca Chinchilla, Marta Perez-Sancho, Lucas Dominguez, Antonio Rodriguez-Bertos
Summary: Ovine brucellosis is an infectious disease that affects the reproductive tract in rams and leads to abortion in ewes. This study investigated the histopathological stages of rams infected with B. ovis and evaluated the expression of Brucella antigens, inflammatory cell markers, and cytokines. The results showed that early lesions had epithelial changes, interstitial inflammation, and mild fibrosis, while advanced lesions had caseous granulomas with macrophages, giant cells, lymphocytes, and plasma cells. The immune response against B. ovis was predominantly driven by T-cells, with a Th1 cell-mediated response observed in both early and advanced lesions. The expression of TNF-α and TGF-β1 played a role in the progression and chronicity of the lesions, respectively.
VETERINARY IMMUNOLOGY AND IMMUNOPATHOLOGY
(2023)
Meeting Abstract
Ophthalmology
Rosario Fernandez-Godino, Blanca Chinchilla Rodriguez
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2021)