Review
Neurosciences
Zhigang Jiao, Zhengyi He, Nanhai Liu, Yanwei Lai, Tianyu Zhong
Summary: Neuropathy is a growing public health concern, especially among older adults, adolescents, and athletes. The causes of neuropathy include aging, violence, and conflicts related to sports. The understanding of the signaling pathways involved in neuronal aging and damage is incomplete, and evidence-based treatments for neuropathy are lacking. This review focuses on the role of extracellular vesicles (EVs) in disease progression, specifically in neuronal damage. The challenges and obstacles in isolating and analyzing neuronal EVs are discussed, with an emphasis on the application of EVs in translational medicine.
FRONTIERS IN CELLULAR NEUROSCIENCE
(2022)
Article
Cell Biology
Alin Rai, Haoyun Fang, Bethany Claridge, Richard J. Simpson, David W. Greening
Summary: The surface proteome of extracellular vesicles plays a crucial role in mediating interactions with their environment and serves as a potential source of disease biomarkers and therapeutic targets. This study reveals the surface protein composition of large EVs and highlights the diversity and heterogeneity between different EV subtypes, providing important insights into their functions and molecular complexity.
JOURNAL OF EXTRACELLULAR VESICLES
(2021)
Article
Multidisciplinary Sciences
John P. McGee, Pei Su, Kenneth R. Durbin, Michael A. R. Hollas, Nicholas W. Bateman, G. Larry Maxwell, Thomas P. Conrads, Ryan T. Fellers, Rafael D. Melani, Jeannie M. Camarillo, Jared O. Kafader, Neil L. Kelleher
Summary: This study introduces a semi-automated single-ion mass spectrometry workflow for top-down tandem mass spectrometry analysis directly from tissue microenvironments. The results demonstrate that this method can identify multiple proteoforms in tumor samples within a short period of time, and effectively identify proteoform signatures in tumor and stromal regions.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Ana Sofia Carvalho, Henrique Baeta, Andreia F. A. Henriques, Mostafa Ejtehadifar, Erin M. Tranfield, Ana Laura Sousa, Ana Farinho, Bruno Costa Silva, Jose Cabecadas, Paula Gameiro, Maria Gomes da Silva, Hans Christian Beck, Rune Matthiesen
Summary: The study analyzed the proteome of EVs in DLBCL subtypes and found that they can effectively separate cells into GCB and ABC categories. Through functional and enrichment analysis, it was discovered that DEPs are significantly enriched in immune response pathways, suggesting the potential of using EVs as diagnostic and therapeutic tools.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Letter
Oncology
Shrikant B. Mali
Summary: In-depth transcriptomic and proteomic analyses are crucial for understanding normal and pathological biology. Next-generation sequencing technology (NGS) is used for assessing gene expression, but there is a lack of methods to scale up protein abundance. This poses a major obstacle to single-cell proteomics, as protein expression determines cell state. Single-cell proteomics is a promising field that provides direct and comprehensive insights into cellular functions without averaging effects. However, protein adsorption loss (PAL) has been a technical challenge, and current mitigations have not been specific to individual proteins.
Review
Biochemistry & Molecular Biology
Anna Meyfour, Sara Pahlavan, Mehdi Mirzaei, Jeroen Krijgsveld, Hossein Baharvand, Ghasem Hosseini Salekdeh
Summary: Stem cells and their derivatives hold promise for tissue replacement therapy, but their heterogeneous characteristics pose challenges. Targeting specific cell surface markers with antibodies has proven efficient in isolating cell populations, with proteomics playing a key role in identifying these markers. Single cell proteomics and surface markers associated with progenitor stages show potential for use in regenerative medicine.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Brett Vahkal, Jamie Kraft, Emanuela Ferretti, Minyoung Chung, Jean-Francois Beaulieu, Illimar Altosaar
Summary: Proteomics can map extracellular vesicles (EVs), such as exosomes, across disease states and cell types, but careful consideration must be given to avoid the impact of contaminants in samples. Human milk EVs and exosomes are increasingly important in health and disease research, yet experimental characterization and functional assays still need further refinement.
Article
Chemistry, Analytical
Fenglong Jiao, Fangyuan Gao, Yuanyuan Liu, Zhiya Fan, Xiaochao Xiang, Chaoshuang Xia, Yayao Lv, Yuping Xie, Haihong Bai, Wanjun Zhang, Weijie Qin, Xiaohong Qian
Summary: Small extracellular vesicles (SEVs) are cell-derived nanometer-sized vesicles that play vital roles in diseases and biomarker research. Current techniques for SEVs isolation face challenges, but Ti4+-modified magnetic graphene-oxide composites may offer a new approach for phosphoproteome studies of SEVs.
Article
Oncology
Juliana Mueller Bark, Lucas Trevisan Franca de Lima, Xi Zhang, Daniel Broszczak, Paul J. Leo, Rosalind L. Jeffree, Benjamin Chua, Bryan W. Day, Chamindie Punyadeera
Summary: This study demonstrates the feasibility of isolating and characterizing small extracellular vesicles (EVs) from pre- and postoperative saliva samples from glioblastoma (GBM) patients for the first time. Preliminary findings encourage further large cohort validation studies on salivary small EVs to evaluate prognosis in GBM.
Article
Biochemistry & Molecular Biology
Pei Jiang, Xiangyu Ma, Shanying Han, Leyao Ma, Jingru Ai, Leilei Wu, Yuan Zhang, Hairong Xiao, Mengyao Tian, W. Andy Tao, Shasha Zhang, Renjie Chai
Summary: This study discovers the existence of sEVs in the cochlea and reveals their importance in the normal development of the auditory system.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Kaizhe Wang, Yuhan Wei, Xiaodong Xie, Qian Li, Xiaoguo Liu, Lihua Wang, Jiang Li, Ji Wu, Chunhai Fan
Summary: This study presents a method for encoding the heterogeneous interfaces of extracellular vesicles (EVs) and cells using DNA, enabling interspecies EV-cell communications in complex environments. The use of cholesterol-modified DNA strands and tetrahedral DNA frameworks allows specific and efficient cellular internalization of EVs via base pairing. The system demonstrates orthogonal EV-cell communications and efficient delivery of bioactive contents derived from feeder cells to target cells.
ADVANCED MATERIALS
(2023)
Article
Chemistry, Physical
Jessica L. Symons, Kwang-Jin Cho, Jeffrey T. Chang, Guangwei Du, M. Neal Waxham, John F. Hancock, Ilya Levental, Kandice R. Levental
Summary: Lipid membranes are essential for the structural and functional compartmentalization of cells and sub-cellular organelles. This study used shotgun lipidomics to analyze the lipidomes of various cultured and primary mammalian membrane preparations, identifying clear differences between cultured and primary cells, as well as distinct lipidomic signatures of individual cell lines and tissue types. These findings contribute to a comprehensive understanding of mammalian lipidomes and their regulation in various contexts.
Review
Biochemical Research Methods
Vivian Weiwen Xue, Chenxi Yang, Sze Chuen Cesar Wong, William Chi Shing Cho
Summary: Extracellular vesicles (EVs) play essential roles in cancer development through influencing cells in the tumor microenvironment. Specific proteins expressed in tumor-derived EVs can be utilized for cancer diagnosis and monitoring.
Article
Biochemical Research Methods
Ai Nguyen, Illarion V. Turko
Summary: This study evaluated the efficiency of chromatographic isolation of extracellular vesicles (EVs) using a multiple reaction monitoring assay. The results showed that non-EV mitochondrial content in samples after initial ultracentrifugation could not be separated from EVs using size exclusion chromatography, but could be efficiently separated on the column with immobilized heparin.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Cell Biology
Yael Hirschberg, Natalia Valle-Tamayo, Oriol Dols-Icardo, Sebastiaan Engelborghs, Bart Buelens, Roosmarijn E. Vandenbroucke, Yannick Vermeiren, Kurt Boonen, Inge Mertens
Summary: Dementia is a leading cause of death worldwide, and this study focused on analyzing the proteome of cerebrospinal fluid (CSF) and CSF-derived extracellular vesicles (EVs) from patients with Alzheimer's disease, dementia with Lewy bodies, and Parkinson's disease dementia. The analysis identified differentially expressed proteins that can be helpful for differential diagnosis and offer new avenues for research into disease-specific pharmacological therapeutics.
JOURNAL OF EXTRACELLULAR VESICLES
(2023)
Article
Biochemistry & Molecular Biology
Alexander J. Hart, Samuel Ginzburg, Muyang (Sam) Xu, Cera R. Fisher, Nasim Rahmatpour, Jeffry B. Mitton, Robin Paul, Jill L. Wegrzyn
MOLECULAR ECOLOGY RESOURCES
(2020)
Article
Plant Sciences
Alexander J. Trouern-Trend, Taylor Falk, Sumaira Zaman, Madison Caballero, David B. Neale, Charles H. Langley, Abhaya M. Dandekar, Kristian A. Stevens, Jill L. Wegrzyn
Article
Ecology
Cera R. Fisher, Jill L. Wegrzyn, Elizabeth L. Jockusch
NATURE ECOLOGY & EVOLUTION
(2020)
Article
Genetics & Heredity
Alison D. Scott, Aleksey V. Zimin, Daniela Puiu, Rachael Workman, Monica Britton, Sumaira Zaman, Madison Caballero, Andrew C. Read, Adam J. Bogdanove, Emily Burns, Jill Wegrzyn, Winston Timp, Steven L. Salzberg, David B. Neale
G3-GENES GENOMES GENETICS
(2020)
Article
Biochemistry & Molecular Biology
Nasim Rahmatpour, Neranjan Perera, Vijender Singh, Jill L. Wegrzyn, Bernard Goffinet
Summary: A new paradigm is emerging in the diversification of bryophytes, revealing the dynamic evolution of their genome with evidence of whole genome duplication events. Comparative transcriptome analysis of closely related species highlights significant gene sequence and gene number divergence, suggesting a strong genome evolution influenced by duplication events. The evolution of Funariaceae may be driven by the diversification of metabolic genes optimizing adaptations to environmental conditions, reflecting ecological patterns seen in seed plants.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Forestry
Laura Figueroa-Corona, Patricia Delgado Valerio, Jill Wegrzyn, Daniel Pinero
Summary: The study reconstructed the needle tissue transcriptome of P. pinceana and identified differential responses to biotic stress in different biogeographic regions. Phenotypic plasticity in physiological traits was found to be influenced by changes in mRNA expression levels. The research showed that P. pinceana exhibits differential responses to climate heterogeneity along its natural distribution, indicating different molecular phenotypes in adaptation to environmental stress.
TREES-STRUCTURE AND FUNCTION
(2021)
Article
Plant Sciences
Madison Caballero, Edwin Lauer, Jeremy Bennett, Sumaira Zaman, Susan McEvoy, Juan Acosta, Colin Jackson, Laura Townsend, Andrew Eckert, Ross W. Whetten, Carol Loopstra, Jason Holliday, Mihir Mandal, Jill L. Wegrzyn, Fikret Isik
Summary: This study introduces the construction of an Axiom genotyping array using an informatics approach from high-throughput sequence data to assess the complex genome of loblolly pine. The Axiom array, representing 46,439 high-confidence variants, was developed to provide a genome-wide resource for the forest tree breeding and genetics community.
APPLICATIONS IN PLANT SCIENCES
(2021)
Article
Genetics & Heredity
Jingjia Li, Jason B. West, Alexander Hart, Jill L. Wegrzyn, Matthew A. Smith, Jean-Christophe Domec, Carol A. Loopstra, Claudio Casola
Summary: The response to water limitation in drought-tolerant and -sensitive loblolly pine genotypes differs significantly at the gene level, although involving similar genetic networks. Upregulated transcripts under drought conditions represent the most diverging component between genotypes, which might depend on the activation and repression of substantially different groups of transcription factors.
FRONTIERS IN GENETICS
(2021)
Article
Plant Sciences
Susan L. McEvoy, U. Uzay Sezen, Alexander Trouern-Trend, Sean M. McMahon, Paul G. Schaberg, Jie Yang, Jill L. Wegrzyn, Nathan G. Swenson
Summary: The first chromosome-scale assemblies for sugar maple and boxelder, as well as transcriptomic evaluation of the abiotic stress response in sugar maple, were reported in this study. The integrated research provides insights into the contribution of different factors to tolerance in each species and utilizes knowledge from various areas of plant genome biology and Acer physiology to understand the genomic complexities underlying tolerance in broadleaf tree species.
Article
Multidisciplinary Sciences
W. John Kress, Douglas E. Soltis, Paul J. Kersey, Jill L. Wegrzyn, James H. Leebens-Mack, Morgan R. Gostel, Xin Liu, Pamela S. Soltis
Summary: Green plants are essential to ecosystems, human health, and agriculture, but generating and storing their genomes is a major challenge. Currently, there are fewer than 300 complete chromosome-scale genome assemblies for green plants, representing less than 900 species. Many species, especially those from extreme environments, still lack suitable tissue samples for genomic sequencing. The annotation of plant genomes also needs improvement.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Ecology
Cynthia Webster, Laura Figueroa-Corona, Ivan David Mendez-Gonzalez, Lluvia Alvarez-Soto, David B. Neale, Juan Pablo Jaramillo-Correa, Jill L. Wegrzyn, Alejandra Vazquez-Lobo
Summary: This study compared leaf heteroblastic development in Juniperus flaccida and Pinus cembroides and found differences in gene regulation and pathways between the two species. Juvenile leaves of P. cembroides showed a focus on cell division and development, while adult leaves of J. flaccida exhibited differential expression and gene interaction patterns related to photosynthesis and chloroplast biogenesis.
ECOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Daniel Ence, Katherine E. Smith, Shenghua Fan, Leandro Gomide Neves, Robin Paul, Jill Wegrzyn, Gary F. Peter, Matias Kirst, Jeremy Brawner, C. Dana Nelson, John M. Davis
Summary: This study investigates the diversity of NLR genes in loblolly pine and identifies SNPs associated with resistance, providing a resource to enhance breeding and deployment of resistant pine seedlings.
G3-GENES GENOMES GENETICS
(2022)
Article
Ecology
Laura Figueroa-Corona, Alejandra Moreno-Letelier, Diego Ortega-Del Vecchyo, Pablo Pelaez, David S. Gernandt, Luis E. Eguiarte, Jill Wegrzyn, Daniel Pinero
Summary: Climate changes and geographical barriers have influenced genetic diversity and distribution patterns of species in northern Mexico. The study on the genetic diversity of Pinus pinceana reveals that it diverged into two lineages and colonized the Sierra Madre Oriental and the Chihuahuan Desert.
ECOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Vera Marjorie Elauria Velasco, Alyssa Ferreira, Sumaira Zaman, Devin Noordermeer, Ingo Ensminger, Jill L. Wegrzyn
Summary: In this study, a highly accurate and complete reference transcriptome and genome annotation of Douglas-fir were generated. Deep sequencing of the transcriptome using long-read and short-read platforms was performed on Douglas-fir needles grown under nonstress control conditions or a combination of heat and drought stress conditions. Two computational approaches were used for transcriptome assembly, and the results showed that the de novo assembly approach identified more high-quality transcripts, complete genes, and functionally annotated genes compared to the genome-guided assembly approach. Additionally, a refined genome annotation was generated using an improved informatics approach.
G3-GENES GENOMES GENETICS
(2023)
Article
Mathematical & Computational Biology
Shawna Spoor, Connor Wytko, Brian Soto, Ming Chen, Abdullah Almsaeed, Bradford Condon, Nic Herndon, Heidi Hough, Sook Jung, Meg Staton, Jill Wegrzyn, Dorrie Main, F. Alex Feltus, Stephen P. Ficklin
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2020)