Editorial Material
Plant Sciences
Rodrigo S. Reis
Summary: There is a significant gap in our understanding of thermomorphogenesis regulation, specifically in processes involving RNA. This gap presents opportunities for exciting new discoveries in post-transcriptional regulation, while also posing manageable challenges.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Review
Biochemistry & Molecular Biology
Weijin Xu, Jeetayu Biswas, Robert H. Singer, Michael Rosbash
Summary: RNA binding proteins (RBPs) regulate post-transcriptional processes in cells, and it is crucial to identify their in vivo targets for understanding their function. Standard techniques for profiling RBP targets have limitations in certain situations, but new genetic approaches have been developed for such circumstances. These approaches, including TRIBE, RNA tagging, and STAMP, provide useful tools for studying post-transcriptional regulation and RBP identification, with potential therapeutic implications.
Article
Biochemical Research Methods
Simone Marini, Rodrigo A. Mora, Christina Boucher, Noelle Robertson Noyes, Mattia Prosperi
Summary: Antimicrobial resistance (AMR) poses a growing threat to public health and farming. High-throughput sequencing offers a promising option for AMR determination, but different algorithms show inconsistent performance in AMR classification, indicating challenges of sampling bias and unknown AMR genes.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Cell Biology
Matthew A. Reyer, Shriram Chennakesavalu, Emily M. Heideman, Xiangqian Ma, Magda Bujnowska, Lu Hong, Aaron R. Dinner, Carin K. Vanderpool, Jingyi Fei
Summary: Small RNAs (sRNAs) are important gene regulators in bacteria, acting post-transcriptionally by affecting translation and degradation of target mRNAs. Some sRNAs can regulate targets co-transcriptionally early in an mRNA's lifetime, potentially mediated by Rho-dependent termination. Data also reveals that certain kinetic steps and sRNA binding to target mRNA may dictate the regulation hierarchy within sRNA regulons.
Review
Biology
Katarina Gresova, Panagiotis Alexiou, Ilektra-Chara Giassa
Summary: MicroRNAs (miRNAs) are a type of small RNA that regulate gene expression. They target messenger RNAs (mRNA) for degradation or repression. Other types of small RNAs, such as tRFs, have also been found to be involved in gene regulation. Computational techniques play a crucial role in exploring RNA-RNA interactions.
Article
Agronomy
Maude Quinio, Marie-Helene Jeuffroy, Laurence Guichard, Paola Salazar, Francoise Detienne
Summary: This study aims to explore the reasoning and knowledge displayed and used by designers and facilitators throughout the agroecological cropping system design process, providing operational guidelines for the development of design-support tools.
AGRONOMY FOR SUSTAINABLE DEVELOPMENT
(2022)
Article
Genetics & Heredity
Judith Perez-Granado, Janet Pinero, Laura Furlong
Summary: Our understanding of complex disorders has been advanced by genome-wide association studies (GWAS) that have identified genetic variants significantly associated with disease phenotypes. However, we still lack knowledge on how these variants functionally impact disease pathogenesis or their underlying biological mechanisms. Fine-mapping and colocalization methods are commonly used post-GWAS approaches to identify causal variants and understand their functional effects. Despite the availability of various post-GWAS tools, there is no guideline for their eligibility or validity, and benchmarking of these tools is lacking. In this study, we compared two different fine-mapping and colocalization methods using the same GWAS datasets for major depression and expression quantitative trait loci (eQTL). We found that fine-mapping is a crucial step for subsequent analysis, as colocalizing variants, altered genes, and targeted tissues differed between methods with varying biological implications. This highlights the importance of post-GWAS analysis in elucidating disease pathobiology, prioritizing drug targets, and discovering biomarkers.
FRONTIERS IN GENETICS
(2022)
Review
Biochemistry & Molecular Biology
Chandramohan Muthu Lakshmi Bavithra, Marimuthu Murugan, Shanmugasundaram Pavithran, Kathirvel Naveena
Summary: Insecticide resistance in insects is a major threat to human health and agriculture, leading to pest management failures, increased costs, decreased crop yields, and public health disasters. The resistance is caused by factors such as indiscriminate insecticide usage and selection pressure on insect populations. Insects respond to insecticide stress at the cellular level through genetic propagations, transcriptional and post-transcriptional regulatory signals, and physiological changes. Understanding these cellular intricacies can help develop alternative pest control methods targeting insect vulnerabilities and using technologies like RNA interference to manage resistance-related genes.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Oscar Garcia-Blay, Pieter G. A. Verhagen, Benjamin Martin, Maike M. K. Hansen
Summary: Co-expression of two or more genes at the single-cell level is associated with functional co-regulation. Positive co-expression requires promoter coordination and similar mRNA half-lives, while negative co-expression emerges from differences in mRNA half-lives. There is a compensatory relationship between promoter coordination and mRNA half-lives, potentially shaping co-expression patterns.
Article
Education & Educational Research
Jarkko Suhonen, Erkki Sutinen
Summary: Identifying potential threats to the continuation of online study programs is crucial. This study analyzed the critical events of a Finnish online doctoral study program and found that key factors in each sustainability pillar have significant effects on the program's sustainability. Resilience and shared commitment within the community are crucial for the program's sustainability.
ETR&D-EDUCATIONAL TECHNOLOGY RESEARCH AND DEVELOPMENT
(2022)
Article
Cardiac & Cardiovascular Systems
Sara Ballouz, Melissa M. Mangala, Matthew D. Perry, Stewart Heitmann, Jesse A. Gillis, Adam P. Hill, Jamie Vandenberg
Summary: The study identified a strong correlation between the expression of CACNA1C and KCNH2 ion channel genes in human heart tissue, which can limit variability in action potential duration and reduce susceptibility to early afterdepolarizations. In addition, there is a correlation between the levels of KCNH2 and CACNA1C expression in human-induced pluripotent stem cell-derived cardiac myocytes, and their expression levels are inversely correlated with changes in repolarization duration following inhibition of I-Kr. Meta-analytic approaches of multiple gene expression datasets can help identify gene modules important for regulating heart function and the co-expression of CACNA1C and KCNH2 can increase the robustness of cardiac electrical activity.
CARDIOVASCULAR RESEARCH
(2021)
Article
Cardiac & Cardiovascular Systems
Sara Ballouz, Melissa M. Mangala, Matthew D. Perry, Stewart Heitmann, Jesse A. Gillis, Adam P. Hill, Jamie Vandenberg
Summary: The study identified a strong correlation between CACNA1C (L-type calcium current) and KCNH2 (rapid delayed rectifier K+ current) expression in human hearts, which could limit variability in action potential duration and reduce susceptibility to arrhythmia. This co-expression also increased the robustness of cardiac electrical activity.
CARDIOVASCULAR RESEARCH
(2021)
Article
Chemistry, Medicinal
Valentina Sala, Sophie Julie Cnudde, Alessandra Murabito, Alberto Massarotti, Emilio Hirsch, Alessandra Ghigo
Summary: Cystic fibrosis (CF) is a common rare genetic disease affecting over 70,000 people worldwide, characterized by lung blockage and chronic infections. Peptides hold promise as therapeutics for respiratory diseases like CF due to their high specificity, efficacy, and low toxicity, but face challenges like retention within mucus, proteolysis, immunogenicity, and aggregation in the development process. Solutions to overcome these issues and advancements in peptide design are being explored.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Environmental Studies
Gerardo Martinez, Nicole M. Smith, Aaron Malone
Summary: Efforts to formalize artisanal and small-scale gold mining activities in Peru have shown some progress, but there are still challenges such as obtaining technical support and accessing funding. Establishing a solid postformalization strategy focused on educating and supporting formal ASGM operations would benefit both governments and miners.
Review
Biotechnology & Applied Microbiology
Ilias Georgakopoulos-Soares, Candace S. Y. Chan, Nadav Ahituv, Martin Hemberg
Summary: The canonical right-handed double helix structure of DNA, known as B DNA, is the most stable form. However, non-canonical secondary structures can also form under specific environments and sequence motifs. The roles of these secondary structures in transcriptional regulation are not fully understood, but recent advancements in high-throughput assays have allowed for genome-wide characterization of some secondary structures. This article discusses their regulatory functions in promoters and 3'UTRs, their implications in human disease, and the potential insights that can be gained through molecular technologies and high-throughput experimental methods.
Article
Oncology
Adam Kosti, Rodrigo Barreiro, Gabriela D. A. Guardia, Shiva Ostadrahimi, Erzsebet Kokovay, Alexander Pertsemlidis, Pedro A. F. Galante, Luiz O. F. Penalva
Summary: miRNAs act as key regulators of gene expression, contributing to cancer phenotypes as oncogenes or tumor suppressors. Cooperative action of miRNAs regulates biological processes and pathways, suggesting that miRNA combinations could be more effective in targeting cancer stem cells. Using combinations of tumor suppressor miRNAs may offer new routes to disrupt cancer phenotypes and growth of cancer-initiating cell populations.
Article
Oncology
Carla Frau, Catherine Jamard, Gaspard Delpouve, Gabriela D. A. Guardia, Christelle Machon, Camilla Pilati, Clementine Le Neve, Pierre Laurent-Puig, Jerome Guitton, Pedro A. F. Galante, Luiz O. Penalva, Jean-Noel Freund, Christelle de la Fouchardiere, Michelina Plateroti
Summary: The study reveals paradoxical roles of MSI1 in both facilitating intestinal regeneration after injury and promoting drug-resistant colorectal cancer stem cells. Increased levels of MSI1 contribute to the reprogramming of progenitor cells into drug-resistant phenotypes, highlighting its importance in chemotherapy resistance and tumor grading in colorectal cancer patients. These findings shed light on the biology and plasticity of normal and cancer cell populations, presenting potential new targets for improving chemotherapy outcomes.
Article
Oncology
Mirella Baroni, Caihong Yi, Saket Choudhary, Xiufen Lei, Adam Kosti, Denise Grieshober, Mitzli Velasco, Mei Qiao, Suzanne S. Burns, Patricia R. Araujo, Talia DeLambre, Mi Young Son, Michelina Plateroti, Marco A. R. Ferreira, E. Paul Hasty, Luiz O. F. Penalva
Summary: RNA binding protein Msi1 plays a crucial role in glioblastoma by regulating cell cycle and DNA replication genes, impacting tumor growth and response to therapy. High levels of Msi1 are associated with poor prognosis and tumor growth in multiple cancers.
Article
Neurosciences
Sajina Shakya, Anthony D. Gromovsky, James S. Hale, Arnon M. Knudsen, Briana Prager, Lisa C. Wallace, Luiz O. F. Penalva, H. Alex Brown, Bjarne W. Kristensen, Jeremy N. Rich, Justin D. Lathia, J. Mark Brown, Christopher G. Hubert
Summary: Glioblastoma displays significant cellular and metabolic heterogeneity, with striking differences in lipid metabolism across different microenvironments, and cancer stem cells (CSCs) also show altered lipid metabolism. The differences in lipid metabolism may not only be a product of the microenvironment, but also a reflection of cellular state, providing new insights into therapeutic targets for GBM.
ACTA NEUROPATHOLOGICA COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Antoine Baudin, Alma K. Moreno-Romero, Xiaoping Xu, Emily E. Selig, Luiz O. F. Penalva, David S. Libich
Summary: RNA binding proteins (RBPs) such as SERBP1 play crucial roles in mRNA processing and translation regulation, with implications in diseases like cancer and neurodegeneration. Despite being initially identified as a hyaluronic acid binding protein, SERBP1 is now recognized for its central roles in brain function and development, including neurogenesis and synaptogenesis. Studies have shown that SERBP1 regulates One-carbon metabolism and epigenetic modification of histones, with increased expression in various cancers correlating with poor patient outcomes. Further research on SERBP1's structural and dynamic properties, as well as its interaction mechanisms with RNA, contribute to the understanding of its functions in physiological and pathological processes.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Radiology, Nuclear Medicine & Medical Imaging
Lin Ma, Weicheng Chi, Howard E. Morgan, Mu-Han Lin, Mingli Chen, David Sher, Dominic Moon, Dat T. Vo, Vladimir Avkshtol, Weiguo Lu, Xuejun Gu
Summary: In this study, a registration-guided DL segmentation framework for online cone beam computed tomography (CBCT) image was proposed. By integrating image registration algorithms and DL segmentation models, this framework overcame the issues of low image quality and limited training data, resulting in more accurate segmentation.
Article
Oncology
David J. Sher, Sepeadeh Radpour, Jennifer L. Shah, Nhat-Long Pham, Steve Jiang, Dat Vo, Baran D. Sumer, Andrew T. Day
Summary: In this pilot study, although the compliance goal was not met, the majority of patients did use the wearable biometric device. Step count reduction may predict significant decline in quality of life before it occurs, while heart rate showed no association with any endpoints.
JCO CLINICAL CANCER INFORMATICS
(2022)
Article
Oncology
Eric J. Hsu, Jameson T. Mendel, Kristin A. Ward, Mariam El-Ashmawy, Minjae Lee, Hak Choy, Kenneth D. Westover, Dat T. Vo, Robert D. Timmerman, David J. Sher, Puneeth Iyengar
Summary: This study analyzed the treatment outcomes of 90 patients with T1-2 non-small cell lung cancer who received five-fraction stereotactic ablative radiotherapy (SABR). The results identified the clinical parameters predictive of treatment failures with these regimens, providing guidance for treatment selection.
ADVANCES IN RADIATION ONCOLOGY
(2022)
Article
Oncology
Eric J. Hsu, Jamie Thomas, Elizabeth A. Maher, Michael Youssef, Robert D. Timmerman, Zabi Wardak, Minjae Lee, Tu D. Dan, Toral R. Patel, Dat T. Vo
Summary: This study found that neutrophilia before radiation, pre-radiation NLR, and post-radiation thrombocytopenia were predictors of poor survival in glioma patients.
FRONTIERS IN ONCOLOGY
(2022)
Article
Clinical Neurology
Eric J. J. Hsu, Jamie Thomas, Robert D. D. Timmerman, Zabi Wardak, Tu D. D. Dan, Toral R. R. Patel, Nina N. N. Sanford, Dat T. T. Vo
Summary: The study identified age and total resection surgery as predictors of overall survival in glioblastoma patients, while increased radiation fractions and history of depressive disorder were associated with decreased progression. Patients with depressive disorder history had more neuro-oncology office visits.
FRONTIERS IN NEUROLOGY
(2022)
Editorial Material
Oncology
Young Suk Kwon, Michael Dohopolski, Howard Morgan, Aurelie Garant, David Sher, Asal Rahimi, Nina N. Sanford, Dat T. Vo, Kevin Albuquerque, Kiran Kumar, Robert Timmerman, Steve B. Jiang
PRACTICAL RADIATION ONCOLOGY
(2023)
Article
Oncology
Eric J. Hsu, Jamie Thomas, Elizabeth A. Maher, Michael Youssef, Robert D. Timmerman, Zabi Wardak, Tu D. Dan, Toral R. Patel, Dat T. Vo
Summary: CDKN2A, CDKN2B, and MTAP predict poor prognosis in IDHwt glioblastomas. TERT and CDKN2A mutations are associated with worse survival only when treated with lower radiation doses.
Article
Oncology
Maryam Mashayekhi, Rafe McBeth, Dan Nguyen, Allen Yen, Zipalkumar Trivedi, Dominic Moon, Vlad Avkshtol, Dat Vo, David Sher, Steve Jiang, Mu-Han Lin
CLINICAL AND TRANSLATIONAL RADIATION ONCOLOGY
(2023)
Article
Oncology
David J. Sher, Dominic H. Moon, Dat Vo, Jing Wang, Liyuan Chen, Michael Dohopolski, Randall Hughes, Baran D. Sumer, Chul Ahn, Vladimir Avkshtol
Summary: This prospective phase II study indicates that elective neck irradiation is no longer mandatory for head and neck squamous cell carcinoma treatment, and radiation therapy can effectively reduce tumor recurrence and improve patients' quality of life.
CLINICAL CANCER RESEARCH
(2023)
Article
Radiology, Nuclear Medicine & Medical Imaging
Eric J. Hsu, David Parsons, Tsuicheng Chiu, Andrew R. Godley, David J. Sher, Dat T. Vo
Summary: We utilized a custom 3D-printed integrated bolus and headrest to irradiate malignancies involving the posterior scalp, and found that it allowed for comfortable, consistent, and reproducible treatment setup while minimizing the risk of creating air gaps.
3D PRINTING IN MEDICINE
(2022)
