Article
Infectious Diseases
Zachary L. Nikolakis, Nicole R. Hales, Blair W. Perry, Drew R. Schield, Laura E. Timm, Yang Liu, Bo Zhong, Katerina J. Kechris, Elizabeth J. Carlton, David D. Pollock, Todd A. Castoe
Summary: Genomic approaches show potential in studying transmission patterns and responses to control efforts for diseases like schistosomiasis. This study demonstrates the use of whole genome amplification and sequencing to analyze individual archival schistosome larvae, providing insights into genetic diversity, relatedness, and transmission patterns. The results suggest that population-level WGS datasets for individual larvae could be valuable for disease control efforts, offering new avenues for understanding parasite biology and transmission pathways.
PLOS NEGLECTED TROPICAL DISEASES
(2021)
Article
Biochemistry & Molecular Biology
Stephanie J. Szarmach, Alan Brelsford, Christopher C. Witt, David P. L. Toews
Summary: Researchers studying genomic data for non-model organisms face trade-offs between reduced representation methods and whole genome resequencing, impacting marker density, sequencing depth, and multiplexing capabilities. This study compared GBS, ddRAD, and WGS sequencing data for the yellow-rumped warbler species complex, finding that WGS outperformed the other methods in identifying high levels of differentiation on a finer scale. WGS also allowed for the identification of small regions of elevated differentiation, highlighting its advantages over reduced representation methods.
Article
Biochemistry & Molecular Biology
Ying Ni, Xudong Liu, Zemenu Mengistie Simeneh, Mengsu Yang, Runsheng Li
Summary: This study evaluates the application of the recently released R10.4 flow cell from Oxford Nanopore Technologies in human cancer genomics and epigenomic research. The results show that R10.4 performs better than R9.4.1 in terms of read accuracy, variant detection, methylation calling, and genome recovery rate. In addition, the study proposes a promising method for high-yield single-cell whole-genome amplification sequencing and provides a possible solution for filtering false positive sites using R10.4 data.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Kun Yin, Shanqing Huang, Weidong Ruan, Haopai Wei, He Dong, Dianyi Liang, Meijuan Zhao, Wei Qi, Chaoyong Yang, Zhi Zhu
Summary: Iso-seq is a rapid and uniform single-cell whole-genome sequencing method that uses a specially designed dual-well structure and a capillary-based centrifugal-driven droplet generator to isolate single cells and compartmentalize their genomes in droplets within 3 minutes. Iso-seq achieves high mapping ratio, broad coverage of the genome, and low coefficient of variation, making it promising for a wide variety of biological applications.
Article
Multidisciplinary Sciences
Tamir Biezuner, Ofir Raz, Shiran Amir, Lilach Milo, Rivka Adar, Yael Fried, Elena Ainbinder, Ehud Shapiro
Summary: This study compared various commercially available scWGA kits based on targeted sequencing of a large cohort of human single cells, revealing that no single kit excels in all categories and emphasizing the importance of selecting a suitable kit according to experimental requirements.
SCIENTIFIC REPORTS
(2021)
Article
Immunology
Mark Itsko, Nadav Topaz, Sani Ousmane, Micheal Popoola, Rasmata Ouedraogo, Kadidja Gamougam, Adodo Yao Sadji, Abass Abdul-Karim, Christine Lascols, Xin Wang
Summary: Genomic surveillance for meningococcal meningitis can be significantly improved using culture-free methods to increase data representativeness and monitor changes in epidemiological landscape, especially for countries with low culture rate.
JOURNAL OF INFECTIOUS DISEASES
(2022)
Article
Parasitology
Mengtao Sun, Yuheng Cheng, Changzhe Gao, Hanqi Peng, Ning Wang, Weiling Gu, Dabing Lu
Summary: The goal of this study was to develop highly polymorphic genetic markers to monitor the transmission dynamics of rodent-associated Schistosoma japonicum. The whole genome of the schistosome was sequenced using next-generation sequencing technology, and 71 microsatellite markers were developed. Two multiplex reactions consisting of 10 loci were successfully applied to capture the genetic diversity of schistosome populations.
PARASITOLOGY RESEARCH
(2023)
Article
Multidisciplinary Sciences
Joanna Przybyl, Lien Spans, Kristen Ganjoo, Nam Bui, David Mohler, Jeffrey Norton, George Poultsides, Maria Debiec-Rychter, Matt van de Rijn
Summary: This study found that amplification of MDM2 and other genes in plasma cell-free DNA may be used for distinguishing liposarcomas and other retroperitoneal tumors as well as for early detection of disease recurrence. Tracking MDM2 amplification in cell-free DNA may also be useful for evaluating response to treatment. The results of this study have clinical implications for improved diagnosis and surveillance of patients with retroperitoneal tumors.
Article
Parasitology
Qunfeng Wu, Zheng Feng, Wei Hu
Summary: Different chemical reagents were tested to reduce autofluorescence in Schistosomes, with Sudan black B, trypan blue, and copper sulfate showing the most promising results. Optimized conditions were applied to the immunofluorescence of SjCRT protein, successfully reducing autofluorescence interference and providing a clearer signal. This method could be useful for immunofluorescence assays in other flukes with autofluorescence.
PARASITES & VECTORS
(2021)
Review
Biochemistry & Molecular Biology
Ludmila Volozonoka, Anna Miskova, Linda Gailite
Summary: This review provides insight into the performance and drawbacks of WGA techniques such as DOP-PCR, MDA, MALBAC, and hybrid techniques in PGT. The advantages of MDA-based solutions for comprehensive genome coverage and PCR-based solutions for uniformity of coverage are highlighted. The choice of WGA technique should take into consideration the influence of MPS parameters.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Immunology
Yu Zhang, Junhui Li, Hao Li, Jie Jiang, Chen Guo, Chen Zhou, Zhaoqin Zhou, Yingzi Ming
Summary: Our study used single-cell sequencing to explore the mechanism of hepatic fibrosis in murine schistosomiasis japonica. We found that NKT cells and Th2 cells were increased, and there was close communication between NKT cells and the FASLG signaling pathway. Additionally, flow cytometry analysis showed that the expression of Fasl in NKT cells, CD8+ T cells, and NK cells was higher in the schistosomiasis group. Marker genes of alternatively activated macrophages (M2) were mainly expressed in mononuclear phagocyte (MP(1)), suggesting M2-like polarization of Kupffer cells might occur in the fibrotic liver of schistosomiasis. Analysis of CXCL and CCL signaling pathways showed prominent interactions between T cells and mononuclear phagocytes.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Zhe Xu, Si Cheng, Xin Qiu, Xiaoqi Wang, Qiuwen Hu, Yanfeng Shi, Yang Liu, Jinxi Lin, Jichao Tian, Yongfei Peng, Yong Jiang, Yadong Yang, Jianwei Ye, Yilong Wang, Xia Meng, Zixiao Li, Hao Li, Yongjun Wang
Summary: This study constructed an optimized pipeline and identified applicable fingerprint panels to address the sample tagging problem in whole genome bisulfite sequencing (WGBS) data. By using autosome-wide A/T polymorphic single nucleotide variants (SNVs), a fingerprint panel was designed and genotypes were called from the WGBS data. The capability to tag WGBS data was validated and the lower boundary for the number of fingerprint genetic variants needed for correct sample tagging was determined.
Article
Parasitology
Bikash R. Giri, Chuantao Fang, Guofeng Cheng
Summary: This study identified hundreds of gender-associated circRNAs in the blood fluke Schistosoma japonicum, and suggested their potential regulatory roles in gene expression through binding with microRNAs.
INTERNATIONAL JOURNAL FOR PARASITOLOGY
(2022)
Article
Microbiology
Masayasu Misu, Tomoki Yoshikawa, Satoko Sugimoto, Yuki Takamatsu, Takeshi Kurosu, Yukiteru Ouji, Masahide Yoshikawa, Masayuki Shimojima, Hideki Ebihara, Masayuki Saijo
Summary: RNA viruses are the cause of many infectious diseases, and there is a need for rapid, accurate, and cost-effective whole genome sequencing of these viruses. Next-generation sequencing techniques have high-throughput capacity but require significant sample preparation burden.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Sungmi Choi, Kwan Woo Kim, Keun Bon Ku, Seong-Jun Kim, Changwoo Park, Dongju Park, Seil Kim, Hana Yi
Summary: In this study, a universal primer set (AC primer set) was developed for rapid and accurate sequencing of the entire genome of all known human alphacoronaviruses. The AC primer set produced PCR products of the expected size from both HCoV-229E and HCoV-NL63 strains. Various sequencing platforms were used to evaluate the sequencing accuracy, with all methods showing a sequencing error of less than 0.01%. The AC primer set and experimental procedure optimized in this study could enable fast and accurate diagnosis of mutant alphacoronaviruses in future epidemics.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biology
Nazila Koochekian, Alfredo Ascanio, Keaka Farleigh, Daren C. Card, Drew R. Schield, Todd A. Castoe, Tereza Jezkova
Summary: This study investigates the chromosomal structure and composition of the desert horned lizard genome and compares it to genomes of other reptiles. The results indicate dynamic karyotypic evolution across reptiles, with frequent splits, fusions, and rearrangements of chromosomal blocks between macrochromosomes and microchromosomes. The study also provides evidence for distinct gene content and chromosomal structure between microchromosomes and macrochromosomes within reptiles.
Article
Parasitology
Elise Grover, Sara Paull, Katerina Kechris, Andrea Buchwald, Katherine James, Yang Liu, Elizabeth J. Carlton
Summary: This study investigates the physical and environmental predictors of bovine Schistosoma japonicum infection in rural areas of China using a machine learning approach. The results highlight the importance of factors such as bovine density, agricultural practices, and human infection prevalence in predicting bovine infection.
INTERNATIONAL JOURNAL FOR PARASITOLOGY
(2022)
Article
Entomology
Elizabeth A. Freeman, Elizabeth J. Carlton, Sara Paull, Samuel Dadzie, Andrea Buchwald
Summary: In the rapidly urbanizing region of West Africa, Aedes mosquitoes pose an emerging threat of infectious disease that is compounded by limited vector surveillance. Citizen science has been proposed as a way to fill surveillance gaps by training local residents to collect and share information on disease vectors. Combining citizen science data with literature-derived observations can improve our understanding of Ae. aegypti distribution in West Africa.
JOURNAL OF VECTOR ECOLOGY
(2022)
Editorial Material
Parasitology
Zachary L. Nikolakis, Elizabeth J. Carlton, David D. Pollock, Todd A. Castoe
Summary: Luo et al. identified genes associated with host-switching in Schistosoma japonicum, providing a guide for studying selected chromosomal genes using population genetics.
TRENDS IN PARASITOLOGY
(2022)
Article
Multidisciplinary Sciences
Gianluca Bianchin, Emiliano Dall'Anese, Jorge Poveda, David Jacobson, Elizabeth J. Carlton, Andrea G. Buchwald
Summary: This study developed a mathematical model to investigate the impact of risk tolerance and vaccination rates on the speed at which a population can return to pre-pandemic contact behavior. The results suggest that coordination in decision-making across regions is crucial and increasing risk tolerance can shorten the time required to discontinue non-pharmaceutical interventions (NPIs), but at the expense of increased deaths. If vaccination uptake is less than 70%, returning to pre-pandemic contact behaviors may pose a new threat to the healthcare system. Achieving a population-level vaccination rate of over 70% as soon as possible is necessary to safely resume pre-pandemic behaviors.
SCIENTIFIC REPORTS
(2022)
Article
Evolutionary Biology
Drew R. Schield, Blair W. Perry, Daren C. Card, Giulia I. M. Pasquesi, Aundrea K. Westfall, Stephen P. Mackessy, Todd A. Castoe
Summary: After recombination suppression, sex chromosomes diverge and develop differential sex-linkage, resulting in the presence of degenerated Y and W chromosomes in one sex. This study characterizes the structure and gene content of the female-specific W chromosome in the prairie rattlesnake, revealing a high degree of repetition and enrichment of retroviral sequences. The W chromosome is specialized for reproductive and developmental functions since recombination suppression.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Environmental Sciences
Andrea G. Buchwald, Evan Thomas, Kristopher B. Karnauskas, Elise Grover, Karen Kotloff, Elizabeth J. Carlton
Summary: Climate change can affect access to safe drinking water, impacting health. Higher temperatures are associated with decreased use of basic drinking water, while increased rainfall is associated with increased use. Lower income populations may be more sensitive to weather-driven changes in water access.
Article
Genetics & Heredity
Daren C. Card, Andrew G. Van Camp, Trenten Santonastaso, Michael I. Jensen-Seaman, Nicola M. Anthony, Scott V. Edwards
Summary: The study identified the core MHC genomic region in two squamate species and revealed similarities and differences in the genomic structure and composition of MHC regions between squamates and mammals. The investigation also highlighted unique features of the anole MHC, such as higher proportions of DNA transposons and larger MHC region size. Evolutionary analyses of MHC homologs in squamates and other amniotes demonstrated species-specific relationships and functional relevance of certain codons under diversifying selection.
FRONTIERS IN GENETICS
(2022)
Review
Agriculture, Dairy & Animal Science
Daren C. Card, W. Bryan Jennings, Scott V. Edwards
Summary: Non-avian reptiles, especially squamate reptiles (lizards and snakes), have become the most species-rich group among tetrapods, surpassing birds. However, genomic resources in non-avian reptiles have been accumulating at a slower pace compared to mammals and birds. This review highlights the importance of studying the natural history, physical traits, genomic characteristics, and sequence compositional patterns of non-avian reptiles, as well as the need for high-quality genomic resources and methods to extract different markers from genome assemblies. The development of a comprehensive phylogenomic tree of life for non-avian reptiles and amniotes will contribute to a better understanding of biodiversity.
Article
Ecology
Kenji Fukushima, David D. Pollock
Summary: To address the problem of convergent evolution on macroevolutionary timescales, we developed a new metric called omega(C) that measures error-corrected convergence rate of protein evolution. Using gene expression data, we explored over 20 million branch combinations in vertebrate genes and identified the joint convergence of expression patterns and protein sequences with amino acid substitutions in functionally important sites, providing hypotheses on undiscovered phenotypes.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Kathleen J. Kirsch, Corey Nagel, Chantal Iribagiza, John Ecklu, Ghislaine Akonkwa Zawadi, Pacifique Mugaruka Ntabaza, Christina Barstow, Andrea Lund, James Harper, Elizabeth Carlton, Amy Javernick-Will, Karl Linden, Evan Thomas
Summary: This study aims to evaluate the impact of interventions on peri-urban water access, security, and quality in Kasai Oriental province of the Democratic Republic of the Congo. The study will utilize various monitoring and impact evaluation methods to provide feedback at multiple points during the intervention. Long-term evaluation will focus on the combination of factors that lead to improved water access, security, and quality.
Article
Public, Environmental & Occupational Health
Elise N. Grover, William B. Allshouse, Andrea J. Lund, Yang Liu, Sara H. Paull, Katherine A. James, James L. Crooks, Elizabeth J. Carlton
Summary: In this study, open-source environmental data was used to predict the presence of human Schistosoma japonicum infections, and the results showed that leveraging open-source environmental data can more accurately identify pockets of human infection compared to snail surveys, especially in low-transmission environments. The study also identified aspects of the local environment, such as distance from roads and presence of surface water, that may indicate increased risk of schistosomiasis.
INTERNATIONAL JOURNAL OF HEALTH GEOGRAPHICS
(2023)
Article
Biochemistry & Molecular Biology
Keaka Farleigh, Alfredo Ascanio, Mackenzie E. Farleigh, Drew R. Schield, Daren C. Card, Manuel Leal, Todd A. Castoe, Tereza Jezkova, Javier A. Rodriguez-Robles
Summary: The study found different patterns of differential introgression in hybrids of Caribbean anoles, with pulchellus-derived alleles dominating in the hybrids. A. krugi loci in hybrids exhibited a signal of non-random differential introgression, which was linked to genes involved in development and immune function.
Correction
Evolutionary Biology
Drew R. Schield, Blair W. Perry, Daren C. Card, Giulia I. M. Pasquesi, Aundrea K. Westfall, Stephen P. Mackessy, Todd A. Castoe
GENOME BIOLOGY AND EVOLUTION
(2022)