Review
Biochemical Research Methods
Stefano Castellana, Tommaso Biagini, Luca Parca, Francesco Petrizzelli, Salvatore Daniele Bianco, Angelo Luigi Vescovi, Massimo Carella, Tommaso Mazza
Summary: This study found that hundreds of human proteins interact with degenerated DNA sequences, and identifying these motifs and genomic sites is a challenging research goal in modern molecular biology and bioinformatics. Over the past twenty years, there has been an explosion of computational tools for this task, and sixteen of them were evaluated for their ability to identify known motifs in simulated sequence datasets.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Biochemistry & Molecular Biology
Junyang Wang, Jens Nielsen, Zihe Liu
Summary: A wide range of bacteria, fungi, and plants can produce bioactive secondary metabolites known as natural products. Advances in synthetic biology have provided new opportunities for the discovery of natural products.
Review
Chemistry, Multidisciplinary
Marcelo D. T. Torres, Jicong Cao, Octavio L. Franco, Timothy K. Lu, Cesar de la Fuente-Nunez
Summary: Antibiotic resistance poses a significant global health challenge, with the need for innovative strategies becoming more urgent. Antimicrobial peptides (AMPs) offer a natural template for the discovery, design, and production of antibiotics, potentially leading the way for future advancements in peptide drug discovery through computational and synthetic biology approaches.
Review
Chemistry, Medicinal
Linda Sukmarini
Summary: This article focuses on the recent discovery of ribosomally synthesized and post-translationally modified peptides (RiPPs) from marine bacteria using genome mining and synthetic biology approaches. The biosynthetic studies are discussed, particularly the organization of targeted biosynthetic gene clusters associated with potential bioactivities of the encoded RiPPs.
Article
Biochemistry & Molecular Biology
Fatima Foflonker, Crysten E. Blaby-Haas
Summary: This study utilizes comparative genomics to identify evolutionarily conserved gene pairs in green algae and reveals novel functional clusters, indicating the potential existence of new biosynthetic pathways in green algae.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Review
Pharmacology & Pharmacy
Xiyan Wang, Nan Zhou, Baojun Wang
Summary: Bacterial synthetic biology provides powerful tools for drug discovery, including bioinformatic tools, CRISPR tools, engineered transcriptional regulators, and synthetic biosensors. Reprogramming bacteriophages as living drugs is also a recent advancement in this field.
EXPERT OPINION ON DRUG DISCOVERY
(2023)
Review
Biotechnology & Applied Microbiology
Tim Lueddecke, Anne Paas, Richard J. Harris, Lea Talmann, Kim N. Kirchhoff, Andre Billion, Kornelia Hardes, Antje Steinbrink, Doreen Gerlach, Bryan G. Fry, Andreas Vilcinskas
Summary: Venoms are complex chemical arsenals that have independently evolved in the animal kingdom. The application of systems biology and biotechnology has revolutionized venom research, providing methods to study venom systems at all levels of biological organization. This review explores the methods, insights, and potential future developments of biotechnological applications in venom research, arguing that combining various approaches and venomics technologies can answer urgent questions and further advance the field.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Kaiyue Zhou, Suzan Arslanturk, Douglas B. Craig, Elisabeth Heath, Sorin Draghici
Summary: Prostate cancer is the second leading cause of cancer death in American men, and over-diagnosis and over-treatment of low-risk patients can have significant long-term effects on quality of life. Cross-cancer disease learning helps discover important biomarkers, enriches study populations, and identifies important commonalities across diseases.
SCIENTIFIC REPORTS
(2021)
News Item
Multidisciplinary Sciences
Philip Ball
Summary: A pair of studies highlight ethical and legal concerns surrounding the status of lab-grown human embryo models.
Article
Biotechnology & Applied Microbiology
Stephanie LaHaye, James R. Fitch, Kyle J. Voytovich, Adam C. Herman, Benjamin J. Kelly, Grant E. Lammi, Jeremy A. Arbesfeld, Saranga Wijeratne, Samuel J. Franklin, Kathleen M. Schieffer, Natalie Bir, Sean D. McGrath, Anthony R. Miller, Amy Wetzel, Katherine E. Miller, Tracy A. Bedrosian, Kristen Leraas, Elizabeth A. Varga, Kristy Lee, Ajay Gupta, Bhuvana Setty, Daniel R. Boue, Jeffrey R. Leonard, Jonathan L. Finlay, Mohamed S. Abdelbaki, Diana S. Osorio, Selene C. Koo, Daniel C. Koboldt, Alex H. Wagner, Ann-Kathrin Eisfeld, Krzysztof Mrozek, Vincent Magrini, Catherine E. Cottrell, Elaine R. Mardis, Richard K. Wilson, Peter White
Summary: The EnFusion pipeline utilizes seven fusion calling algorithms to increase the accuracy of identifying clinically relevant fusions in pediatric cancer. By combining ensemble fusion-calling pipeline with a knowledge-based filtering strategy, it accurately identifies driver fusions in pediatric cancer, contributing evidence to diagnosis and guiding targeted therapies where appropriate.
Article
Multidisciplinary Sciences
Haitham A. Elmarakeby, Justin Hwang, Rand Arafeh, Jett Crowdis, Sydney Gang, David Liu, Saud H. AlDubayan, Keyan Salari, Steven Kregel, Camden Richter, Taylor E. Arnoff, Jihye Park, William C. Hahn, Eliezer M. Van Allen
Summary: The development of a biologically informed deep learning model P-NET enables stratification of prostate cancer patients by treatment-resistance state and evaluation of molecular drivers of treatment resistance for therapeutic targeting with complete model interpretability. This approach shows superior performance in cancer state prediction using molecular data compared to other modeling approaches.
Review
Developmental Biology
David Oriola, Francesca M. Spagnoli
Summary: The second EMBO-EMBL Symposium on Synthetic Morphogenesis was held virtually in March 2021, drawing participants from around the world to discuss the topic. Leading scientists from various disciplines covered a wide range of topics, from cell and tissue organization to synthetic approaches for exploring evolutionary and developmental biology principles.
Article
Biochemistry & Molecular Biology
Xinbin Dai, Zhaohong Zhuang, Clarissa Boschiero, Yibo Dong, Patrick X. Zhao
Summary: Legumes have been contributing to human health and sustainable food production for centuries. The study of model legumes is important for deciphering key genes and pathways. The LegumeIP V3 database provides valuable data and tools for identifying important genes in non-model legume crops.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Microbiology
Tanim Arpit Singh, Ajit Kumar Passari, Anjana Jajoo, Sheetal Bhasin, Vijai Kumar Gupta, Abeer Hashem, Abdulaziz A. Alqarawi, Elsayed Fathi Abd-Allah
Summary: Advancements in genome sequencing, metabolomics, and bioinformatics have provided a plethora of information about actinobacterial physiology and genetic regulation, enhancing our understanding of their ability to synthesize bioactive molecules. Developments in genomic approaches have opened new opportunities to discover and manipulate novel antibiotic gene clusters.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Chemistry, Multidisciplinary
Anthony Berdis
Summary: DNA, known as the molecule of life, contains the genetic blueprint for all forms of life. Nucleobase-modified nucleotides have various applications in biomedical fields, such as mechanistic probes for DNA polymerase activity, synthetic biology, and potential therapeutic agents against diseases.
FRONTIERS IN CHEMISTRY
(2022)
Article
Biochemical Research Methods
Russel M. Vincent, Bradley W. Wright, Paul R. Jaschke
ACS SYNTHETIC BIOLOGY
(2019)
Article
Virology
Dominic Y. Logel, Paul R. Jaschke
Article
Biochemical Research Methods
Bradley W. Wright, Juanfang Ruan, Mark P. Molloy, Paul R. Jaschke
ACS SYNTHETIC BIOLOGY
(2020)
Article
Oncology
Markus A. Brown, Gabrielle A. Dotson, Scott Ronquist, Georg Emons, Indika Rajapakse, Thomas Ried
Summary: Canonical Wnt signaling, mediated by TCF4, plays a crucial role in intestinal homeostasis by maintaining stem cell phenotype. Reduction of TCF4 leads to disproportionate up-regulation of gene expression and loss of TAD boundaries, with over-expression of CEACAM gene cluster. EMT and E2F pathways are most deregulated upon TCF4 depletion, with LUM, TMPO, and AURKA identified as highly influential genes in these networks.
Article
Microbiology
Bradley W. Wright, Dominic Y. Logel, Mehdi Mirzai, Dana Pascovici, Mark P. Molloy, Paul R. Jaschke
Summary: By studying the proteomic and transcriptomic responses of Escherichia coli to Microviridae infections, this research provides insights into the host response mechanisms, such as membrane damage and remodeling, cellular chaperone activity, and lipoprotein processing. The upregulation of small heat shock proteins IbpA/B during infection and their potential role in viral infections are also highlighted.
Article
Virology
Ellina Trofimova, Paul R. Jaschke
Summary: PST is an automated command-line application that can detect and measure bacteriophage plaque sizes of different morphologies. It has shown compatibility with manual measurements and can be applied to a variety of lytic bacteriophages, making it valuable for the advancement of laboratory automation.
Review
Genetics & Heredity
Bradley W. Wright, Mark P. Molloy, Paul R. Jaschke
Summary: The modern genome-scale methods have shown that gene overlap is widespread and functionally integrated in prokaryotic, eukaryotic, and viral genomes. This overlap can be utilized in bioengineering for building more robust synthetic strains. The authors focus on overlapping protein-coding and RNA-coding genes, highlighting their potential in controlling translation, compressing genetic constructs, and protecting against mutation in synthetic biology approaches.
NATURE REVIEWS GENETICS
(2022)
Article
Microbiology
Kelly L. Sovacool, Sarah L. Westcott, M. Brodie Mumphrey, Gabrielle A. Dotson, Patrick D. Schloss
Summary: Advancements in DNA sequencing technology have allowed researchers to generate millions of sequence reads from microorganisms. Efficient software tools are needed to assign microbial sequences into taxonomic groups. Existing methods either produce inconsistent results or have reduced quality. To address this, we developed OptiFit, a new algorithm that allows for consistent and high-quality assignments, making it easier to compare different studies or add new data to existing studies.
Article
Multidisciplinary Sciences
Stephen Lindsly, Wenlong Jia, Haiming Chen, Sijia Liu, Scott Ronquist, Can Chen, Xingzhao Wen, Cooper Stansbury, Gabrielle A. Dotson, Charles Ryan, Alnawaz Rehemtulla, Gilbert S. Omenn, Max Wicha, Shuai Cheng Li, Lindsey Muir, Indika Rajapakse
Summary: This study investigates the allele-specific relationship between gene expression and genome structure through the cell cycle using haplotype-resolved genome-wide chromosome conformation capture, mRNA, and protein binding data. The analysis reveals significant coordination between allelic expression biases and local genome conformation, with notably absent expression bias in certain essential genes, suggesting a prioritized preservation of essential gene sets. The study proposes a model in which coordinated biallelic expression reflects this prioritization.
Article
Multidisciplinary Sciences
Yaping Sun, Gabrielle A. Dotson, Lindsey A. Muir, Scott Ronquist, Katherine Oravecz-Wilson, Daniel Peltier, Keisuke Seike, Lu Li, Walter Meixner, Indika Rajapake, Pavan Reddy
Summary: This study reveals that WAPL deficiency affects the 3D structure and function of the genome in mature T cells, with implications for their biological and clinical characteristics.
Article
Multidisciplinary Sciences
Gabrielle A. Dotson, Can Chen, Stephen Lindsly, Anthony Cicalo, Sam Dilworth, Charles Ryan, Sivakumar Jeyarajan, Walter Meixner, Cooper Stansbury, Joshua Pickard, Nicholas Beckloff, Amit Surana, Max Wicha, Lindsey A. Muir, Indika Rajapakse
Summary: Mapping higher order chromatin architecture using long sequencing reads and hypergraph theory is effective in investigating chromatin organization and identifying cell type-specific transcription clusters. This study provides insights into the functional building blocks for cell identity and offers a global signature for different cell types.
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Akshay J. J. Maheshwari, Alp M. M. Sunol, Emma Gonzalez, Drew Endy, Roseanna N. N. Zia
Summary: Faster-growing cells need to synthesize proteins more quickly, and the increased abundance of ribosomes alone cannot explain the increase in total protein synthesis rates. The productivity of individual ribosomes must also increase, almost doubling by an unknown mechanism. Physical crowding, transport, and stoichiometry together provide a more nuanced explanation.
Review
Medicine, Research & Experimental
Gabrielle A. Dotson, Charles W. Ryan, Can Chen, Lindsey Muir, Indika Rajapakse
Summary: Cellular reprogramming is a promising strategy for tissue function restoration using transcription factors. Successful grafting of autologous reprogrammed cells has been achieved, but identifying appropriate transcription factors for specific transformation remains challenging. Computational methods leveraging gene expression data for predicting relevant transcription factors, based on mathematical frameworks, are highlighted for their utility and impact in the field of cellular reprogramming.
WIRES MECHANISMS OF DISEASE
(2021)