Article
Chemistry, Multidisciplinary
Yi Fang, Amogh Changavi, Manyun Yang, Luo Sun, Aihua Zhang, Daniel Sun, Zhiyi Sun, Boce Zhang, Ming-Qun Xu
Summary: The study introduces a novel solid-phase catalysis strategy for RNA library preparation, enabling low sample loss, reduced processing time, and higher sequencing throughput in Nanopore direct RNA-seq.
Article
Biochemistry & Molecular Biology
Yiming Zhu, Lingtao Duan, Chengqi Zhu, Li Wang, Zhenrui He, Mei Yang, Erxun Zhou
Summary: This study investigated the molecular mechanism of anthracnose resistance in cruciferous plants using dual transcriptome analysis. The results showed that gene expression differences were mainly associated with fungal development, secondary metabolite biosynthesis, plant-fungal interactions, and phytohormone signaling. Real-time quantitative PCR confirmed the results, enriching the research resources for understanding the role of the ChATG8 gene during C. higginsianum infection in A. thaliana.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Xu Shi, Xiao Wang, Andrew F. Neuwald, Leena Halakivi-Clarke, Robert Clarke, Jianhua Xuan
Summary: BayesDenovo addresses the challenge of de novo transcriptome assembly by accurately reconstructing splicing graphs using a read-guided and Bayesian strategy, achieving higher accuracy and reducing false positives, especially for alternatively spliced genes and highly/lowly expressed transcripts. Additionally, it is more robust on multiple replicates and can identify phenotype-specific transcripts associated with breast cancer recurrence.
SCIENTIFIC REPORTS
(2021)
Article
Microbiology
Bo Jiang, Jing Wang, Wenxiao Liu, Jing Cheng, Jian Xu, Mengyao Cao, Yongqing Li
Summary: This study demonstrates that pre-treatment with bovine interferon gamma can reduce bovine herpesvirus production and alleviate its cytopathic effect. RNA sequencing analysis reveals that pre-treatment with bovine interferon gamma reduces lipid metabolism disorder and DNA damage caused by bovine herpesvirus infection. Additionally, bovine interferon gamma treatment can regulate the immune response and cellular metabolism of host cells.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Tianmin Wang, Ping Shen, Ruochen Chai, Yihui He, Jintao Liu
Summary: In this study, researchers developed a new method called miniBac-seq for constructing high-quality bacterial RNA-seq libraries with ultra-low amounts of RNA. The method is 100-fold lower than the current benchmark kit and reduces preparation cost significantly. By applying miniBac-seq, the researchers were able to profile the transcriptome of growth-arrested bacteria, providing insights into bacterial physiology and regulation in their native contexts.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Microbiology
Parnika Mukherjee, Gaetan Burgio, Emanuel Heitlinger
Summary: Through dual RNA sequencing and meta-analysis, this study identified common interactions between hosts and parasites, such as host immune response to the Plasmodium protein degradation system. Coexpression networks revealed known processes and individual protein associations between hosts and parasites, providing a foundation for prioritizing research in human malaria experiments.
Article
Biochemical Research Methods
Laura Puente-Santamaria, Lucia Sanchez-Gonzalez, Ricardo Ramos-Ruiz, Luis del Peso
Summary: This study focuses on the transcriptional response to hypoxia and generates widely applicable classifiers that can accurately identify hypoxic samples and regions, and can be applied to a variety of gene expression datasets and formats.
BMC BIOINFORMATICS
(2022)
Article
Genetics & Heredity
Mojdeh Dinarvand, Forrest C. Koch, Daniel Al Mouiee, Kaylee Vuong, Abhishek Vijayan, Afia Fariha Tanzim, A. K. M. Azad, Anahit Penesyan, Natalia Castallo-Rodriguez, Fatemeh Vafaee
Summary: Infection leads to complex interactions between host and pathogen, resulting in significant changes in gene expression. The dual RNA-seq technique is a powerful tool to study molecular interactions between host and pathogen. To effectively analyze dual RNA-seq data, we developed a computational pipeline called dRNASb, which allows for comprehensive, systems-level, and temporal analysis. Through analyzing dual RNA-seq data of Salmonella-infected human cells, we were able to identify key genes and potential functions related to the infection process.
MICROBIAL GENOMICS
(2022)
Article
Biotechnology & Applied Microbiology
Hongyu Liu, N. M. Prashant, Liam F. Spurr, Pavlos Bousounis, Nawaf Alomran, Helen Ibeawuchi, Justin Sein, Piotr Slowinski, Krasimira Tsaneva-Atanasova, Anelia Horvath
Summary: ScReQTL is a QTL-related approach for transcribed SNV loci from scRNA-seq data, which can be used to assess the effects of SNVs in a single sample or individual. It captures RNA-mediated genetic interactions with cell-specific and transient effects in the context of identical genotypes.
Article
Microbiology
Yu Zhang, Lina Song, Lie Hou, Zhengfeng Cao, Wanwipa Vongsangnak, Guoqiang Zhu, Qi Xu, Guohong Chen
Summary: This study investigated the host-pathogen interactions between Salmonella enteritidis (SE) and ducks using dual RNA-sequencing analyses of SE infection in duck granulosa cells. The results revealed enrichment of cytokine-cytokine receptor interaction pathway in host dGCs and pathways related to bacterial secretion system and metabolism of pathogen factors in SE during infection. Pathogenic factors and regulators of systemic infection were upregulated in SE, providing new insights for antimicrobial drug development.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Arnar K. S. Sandholt, Eva Wattrang, Tobias Lilja, Harri Ahola, Anna Lunden, Karin Troell, Staffan G. Svard, Robert Soderlund
Summary: The study found that the chicken immune system is activated from day 3 after infection and peaks on day 10, while the gene expression of E. tenella during infection also changes, showing an increase in protein synthesis and metabolism, as well as a decrease in DNA and RNA processing genes.
Article
Immunology
Yibin Yang, Xia Zhu, Haixin Zhang, Yuhua Chen, Yi Song, Xiaohui Ai
Summary: The study on the host-pathogen interaction between channel catfish and Yersinia ruckeri revealed the dynamic regulation of the transcriptome during infection, with significant upregulation of immune-related pathways. Specifically, the infection was found to be closely related to metabolic pathways, and the pathogenesis promoted by Y. ruckeri in channel catfish was mainly through the flagellum gene fliC. This research contributes to understanding how catfish respond to infection and develop enteric red mouth disease (ERM) through a transcriptional perspective.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Agronomy
Zheng-Liang Wang, Hai-Bo Pan, Mu-Yu Li, Wei Wu, Xiao-Ping Yu
Summary: This study provides a comprehensive understanding of the molecular mechanisms of host-pathogen interaction between BPH and M. anisopliae. The results show that BPH and the fungal entomopathogen can both induce specific genes to defend against or infect the other, highlighting potential targets for biocontrol strategies. Synergistic effects were observed when combining RNAi and fungal infection, leading to enhanced mortality rates of BPH.
PEST MANAGEMENT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Roksana Rakoczy-Lelek, Malgorzata Czernicka, Magdalena Ptaszek, Anna Jarecka-Boncela, Ewa M. Furmanczyk, Kinga Keska-Izworska, Marlena Grzanka, Lukasz Skoczylas, Nikodem Kuznik, Sylwester Smolen, Alicja Macko-Podgorni, Klaudia Gaska, Aneta Chalanska, Krzysztof Ambroziak, Hubert Kardasz
Summary: The induction of natural defense mechanisms in plants is an important strategy in integrated pest management. Plant immune inducers like Planticine((R)) can reduce the use of chemicals and their harmful impacts on the environment. This study found that foliar application of Planticine((R)) activated various defense-related genes and effectively reduced damage by a pathogen and insect herbivores in greenhouse conditions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Miaomiao Yang, Qiang Fan, Tom K. Hei, Guodong Chen, Wei Cao, Gang Meng, Wei Han
Summary: In this study, we used scRNA-seq to reveal the changes in cell subtype abundance in RP lung tissue of mice and identified markers and transcriptional states associated with inflammatory response and fibrosis formation in RP lung tissue.
Review
Clinical Neurology
Michael J. Strong, Julianne Santarosa, Timothy P. Sullivan, Noojan Kazemi, Jacob R. Joseph, Osama N. Kashlan, Mark E. Oppenlander, Nicholas J. Szerlip, Paul Park, Clay M. Elswick
Summary: This review assesses and describes thoracic spine localization techniques. The study found that while there are multiple methods available for accurately localizing lesions in the thoracic spine, each method has its own advantages and disadvantages. The choice of localization technique ultimately depends on the specific patient and the preference of the spine surgeon.
JOURNAL OF NEUROSURGERY-SPINE
(2022)
Article
Nutrition & Dietetics
Ali Boolani, Karyn M. Gallivan, Kristin S. Ondrak, Courtney J. Christopher, Hector F. Castro, Shawn R. Campagna, Christopher M. Taylor, Meng Luo, Scot E. Dowd, Matthew Lee Smith, Lauri O. Byerley
Summary: Recent research suggests that traits of energy and fatigue are two distinct moods with unique mental and physical components. A study investigated the correlation between mental and physical energy and fatigue and gut microbiome. The results show that certain bacteria, such as Anaerostipes, are associated with mental energy while processed meat consumption is associated with all moods. The findings suggest that energy and fatigue traits can be defined by specific bacterial communities and are not solely driven by diet. Larger studies are needed to confirm these findings.
Article
Nutrition & Dietetics
Lauri O. Byerley, Karyn M. Gallivan, Courtney J. Christopher, Christopher M. Taylor, Meng Luo, Scot E. Dowd, Gregory M. Davis, Hector F. Castro, Shawn R. Campagna, Kristin S. Ondrak
Summary: This study compared the gut microbiome and metabolome of muscle builders who consumed protein supplements or not. The results showed that protein supplement users consumed more protein and had a different gut microbiome. Protein supplement intake impacted nitrogen metabolism, especially nucleotide degradation.
Review
Oncology
Michael J. Strong, Sravanthi Koduri, Jodi A. Allison, Cecilia M. Pesavento, Sebele Ogunsola, Oludotun Ogunsola, Timothy J. Yee, Siri Sahib S. Khalsa, Yamaan S. Saadeh, Jacob R. Joseph, Osama N. Kashlan, Paul Park, Mark E. Oppenlander, Nicholas J. Szerlip
Summary: This article provides a systematic literature review on osseous metastases of GBM, highlighting the high incidence of metastasis to the vertebral column. The authors suggest that workup for metastatic disease, especially involving the spinal column, should be considered in symptomatic patients. They also propose a management algorithm for GBM vertebral column metastases based on the International Spine Oncology Consortium guidelines.
JOURNAL OF NEURO-ONCOLOGY
(2022)
Article
Multidisciplinary Sciences
Aqila A. Ahmed, Michael J. Strong, Xiaofeng Zhou, Tyler Robinson, Sabrina Rocco, Geoffrey W. Siegel, Gregory A. Clines, Bethany B. Moore, Evan T. Keller, Nicholas J. Szerlip
Summary: Approximately 400,000 people in the U.S. have bone metastases, mostly occurring in the spine. The preference for cancer to metastasize to the bone is seen across various types of cancer, with prostate, breast, and lung cancer having the highest incidence. Immune cells play a significant role in tumor growth and progression in bone disease, and studying the immune landscape differences between axial and appendicular bones in a noncancerous setting could provide insights into the distribution and growth of bone metastases.
Article
Clinical Neurology
Dimitri Benner, Benjamin K. Hendricks, Cyrus Elahi, Michael D. White, Gary Kocharian, Leonardo E. Albertini Sanchez, Kyle E. Zappi, Andrew L. A. Garton, Joseph A. Carnevale, Theodore H. Schwartz, Ehsan Dowlati, Daniel R. Felbaum, Kenneth D. Sack, Walter C. Jean, Andrew K. Chan, John F. Burke, Praveen Mummaneni, Michael J. Strong, Timothy J. Yee, Mark E. Oppenlander, Mariam Ishaque, Mark E. Shaffrey, Hasan R. Syed, Michael T. Lawton
Summary: During the COVID-19 surge, operative volume in neurosurgery decreased significantly by 58.5% compared to the previous year. The infection rates within the departments' counties were associated with decreased operative volume and increased patient acuity. Different subspecialties experienced distinct changes in surgical volume and proportions.
WORLD NEUROSURGERY
(2022)
Review
Clinical Neurology
Michael J. J. Strong, Michael Swash
Summary: Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are two seemingly disparate syndromes, but they share common molecular vulnerabilities. The relationship between ALS and FTD is not based on unique neuroanatomic correlations, but rather on shared underlying mechanisms.
Editorial Material
Clinical Neurology
Hunter R. Kiesling, Michael J. Strong, Yamaan S. Saadeh, Paul Park
OPERATIVE NEUROSURGERY
(2022)
Article
Biology
Callie E. Scull, Meng Luo, Scott Jennings, Christopher M. Taylor, Guoshun Wang
Summary: The function of the cftr gene in epithelial and immune cells affects gut microbiome in mice differently, with immune defect playing a major role in dysbiosis in the small intestine and epithelial defect largely influencing dysbiosis in the large intestine.
COMMUNICATIONS BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Michael J. Strong
Summary: As the world continues to battle the COVID-19 pandemic, there is growing evidence suggesting that the long-term neurological sequelae of the viral infection will be significant and enduring. This pandemic is unique due to its impact on an aging population, putting survivors at increased risk of developing neurodegenerative conditions. The SARS-CoV-2 virus itself, as well as its key proteins, have been implicated in potential neurodegenerative processes.
JOURNAL OF NEUROCHEMISTRY
(2023)
Article
Agriculture, Dairy & Animal Science
Hannah B. B. Gafen, Chin-Chi Liu, Nikole E. E. Ineck, Clare M. M. Scully, Melanie A. A. Mironovich, Lauren Guarneri, Christopher M. M. Taylor, Meng Luo, Marina L. L. Leis, Erin M. M. Scott, Renee T. T. Carter, Andrew C. C. Lewin
Summary: This study aimed to characterize the ocular surface microbiome of cattle with and without ocular squamous cell carcinoma (OSCC) using real-time polymerase chain reaction (RT-PCR) and 16S ribosomal RNA (rRNA) gene sequencing. Significant differences in quantitative and relative abundance of bacterial microbiome were identified based on disease status and geographic location. Quadratic discriminant analysis (DA) was capable of accurately categorizing samples, which can be valuable for differentiating between normal and OSCC-affected cattle.
Meeting Abstract
Oncology
Michael Strong, Varun Kathawate, Peyton Goethe, Lila Tudrick, Joseph Linzey, Ayobami Ward, Mark Zaki, Rushikesh Joshi, William Jackson, Nicholas Szerlip
Review
Clinical Neurology
Sravanthi Koduri, Michael J. Strong, Yamaan S. Saadeh, Whitney E. Muhlestein, Paul Park
OPERATIVE NEUROSURGERY
(2022)
Article
Clinical Neurology
Ibrahim Youssef, Yamaan S. Saadeh, Michael J. Strong, Paul Park
OPERATIVE NEUROSURGERY
(2022)