Review
Microbiology
Alexander S. F. Berry, Camila Farias Amorim, Corbett L. Berry, Camille M. Syrett, Elise D. English, Daniel P. Beiting
Summary: With the increasing accessibility to high-throughput sequencing technology, the bottleneck in biomedical research has shifted to data analysis. This study describes a modular framework for teaching bioinformatics using publicly available RNA sequencing data sets from infectious disease studies, focusing on host-parasite interactions. Lessons learned from adapting the course for virtual learners during the COVID-19 pandemic are highlighted.
Article
Microbiology
Tatiana Dvorkina, Anton Bankevich, Alexei Sorokin, Fan Yang, Boahemaa Adu-Oppong, Ryan Williams, Keith Turner, Pavel A. Pevzner
Summary: The study introduces a gene prediction tool called ORFograph that can predict IPGs in assembly graphs and has discovered numerous novel IPGs from (meta)genomic datasets. Analysis of assembly graphs reveals potential candidate IPGs, including known genes hidden in assembly graphs and potential new IPGs. ORFograph is a fast tool that could potentially identify even more novel IPGs for phenotypic testing from (meta)genomic assembly graphs than traditional gene-finding methods.
Article
Microbiology
Zhongyou Li, Katja Koeppen, Victoria I. Holden, Samuel L. Neff, Liviu Cengher, Elora G. Demers, Dallas L. Mould, Bruce A. Stanton, Thomas H. Hampton
Summary: Researchers developed an algorithm called GAUGE, which automatically annotates GEO microbial data sets, increasing the percentage of analyzable data sets from 4% to 33%. The annotations provide valuable insights and facilitate the identification of consistent patterns of differential gene expression. Additionally, they created a web interface called GAPE for reanalyzing P. aeruginosa and E. coli transcriptomic data.
Article
Biochemistry & Molecular Biology
Robert Literman, Rachel Schwartz
Summary: Despite whole-genome sequencing data, evolutionary relationships remain controversial due to challenges in accurately modeling complex phylogenetic signals. Noncoding sequence sites provide more data and proportionally more concordant sites compared to coding sequences, which are also predominant drivers of tree incongruence.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Review
Biotechnology & Applied Microbiology
Kristin Bornstein, Gary Gryan, E. Sally Chang, Aron Marchler-Bauer, Valerie A. Schneider
Summary: Comparative genomics involves comparing genetic information to understand the evolution, structure, and function of genes, proteins, and non-coding regions. This analysis can aid in understanding biological relationships, gene structure and function, and disease and drug targets. Despite challenges, new tools and approaches are needed to meet research needs.
Article
Microbiology
Xuefang Zhao, Qi Liang, Xuemei Song, Yan Zhang
Summary: This study analyzed the genomic characteristics of Lactiplantibacillus plantarum MC5 and its exopolysaccharide (EPS) biosynthesis mechanism. The results showed that MC5 can metabolize seven sugars and produce a significant amount of EPS. These findings can be used to enhance EPS production through genetic engineering.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Arthur Rand, Philip Zimny, Roland Nagel, Chaitra Telang, Justin Mollison, Aaron Bruns, Emily Leff, Walter W. Reisner, William B. Dunbar
Summary: In this study, an electronic mapping of a bacterial genome using solid-state nanopore technology was presented. The method involves a dual-nano-pore architecture and active control logic to produce single-molecule data and estimate distances between physical tags on double-stranded DNA. Custom analysis methods were developed to generate consensus alignments from multiple scans, and this approach was applied to map the E. coli chromosome. The results showed a significant increase in alignment length with the recapture method, and the intertag resolution was determined to be around 150-166 bp.
Article
Public, Environmental & Occupational Health
Nathan A. Ruprecht, Sonalika Singhal, Kalli Schaefer, Jappreet S. Gill, Benu Bansal, Donald Sens, Sandeep K. Singhal
Summary: One way to quantify the response or damage from ionizing radiation is to estimate the accelerated biological age of individuals after exposure. This study aims to establish a correlation between radiation exposure and biological age using genomics. Two datasets were combined to determine the age cutoff between young and old patients, and the interaction between radiation and age was tested using two other datasets. Pathway and disease analysis highlighted significant pathways and genes associated with cell proliferation diseases and lung carcinoma.
FRONTIERS IN PUBLIC HEALTH
(2023)
Review
Biochemistry & Molecular Biology
Andres Rincon-Riveros, Duvan Morales, Josefa Antonia Rodriguez, Victoria E. Villegas, Liliana Lopez-Kleine
Summary: Noncoding RNAs play key roles in gene expression regulation by interacting with other biological molecules, and computational biology can enhance our understanding of these interactions. Experimental findings drive advancements in computational methods, which in turn provide new insights for experimental validation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biology
Leila Fattel, Dennis Psaroudakis, Colleen F. Yanarella, Kevin O. Chiteri, Haley A. Dostalik, Parnal Joshi, Dollye C. Starr, Ha Vu, Kokulapalan Wimalanathan, Carolyn J. Lawrence-Dill
Summary: Genome-wide functional annotations are crucial for studying gene function and traits in plants. By comparing functional annotation data from different species, similarities and differences can be identified, leading to the generation of novel hypotheses about gene function and evolutionary relationships.
Article
Computer Science, Information Systems
Nephi A. Walton, Radha Nagarajan, Chen Wang, Murat Sincan, Robert R. Freimuth, David B. Everman, Derek C. Walton, Scott P. Mcgrath, Dominick J. Lemas, Panayiotis Benos, Alexander Alekseyenko, Qianqian Song, Ece Gamsiz Uzun, Casey Overby Taylor, Alper Uzun, Thomas Nate Person, Nadav Rappoport, Zhongming Zhao, Marc S. Williams
Summary: Substantial informatics research and development are needed to fully realize the clinical potential of AI in genomics. Developing larger datasets is crucial for emulating the success of AI in other domains. It is important to ensure that AI methods do not worsen existing socio-economic, racial, and ethnic disparities. Genomic data standards are critical for effectively scaling such technologies across institutions. The current focus should be on using these technologies in collaboration with clinicians, highlighting their value in clinical decision-making.
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
(2023)
Article
Biochemistry & Molecular Biology
Andrew Webb, Jared Knoblauch, Nitesh Sabankar, Apeksha Sukesh Kallur, Jody Hey, Arun Sethuraman
Summary: The Pop-Gen Pipeline Platform (PPP) is an open-source software platform designed for population genomic analyses in a consistent and standardized Python environment. The platform encompasses entire workflows for input preparation, file format conversion, various population genomic analyses, and output generation, with reproducibility and extensibility in mind. Users can download and use PPP at https://ppp.readthedocs.io/en/latest/PPP_pages/install.html.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biotechnology & Applied Microbiology
Kapudeep Karmakar, Saurabh Kumar, Dipankar Roy, Mohini Singh, Vaishnavi Kolte, Ashok Choudhury, Gaurav Sharma
Summary: This study analyzed the CRISPR-Cas diversity in the genomes of common free-living nitrogen-fixing Azotobacter spp. The results showed that strains of Azotobacter vinelandii and Azotobacter chroococcum harbor a large number of spacers. The stability of the repeat sequence structure may be correlated with the number of spacers acquired by the CRISPR loci.
LETTERS IN APPLIED MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Mary E. Warren, Brett E. Pickett, Byron J. Adams, Crystal Villalva, Alyssa Applegate, Richard A. Robison
Summary: This study sequenced and analyzed the genomes of 22 novel strains of Yersinia pestis from New Mexico in order to gain a better understanding of its evolutionary patterns in the southwestern United States. The results revealed a single introduction event of Y. pestis into the United States from California, followed by two independent movements into New Mexico. Analysis also identified three genes that displayed significant variations associated with metadata of the strains.
Article
Plant Sciences
Aynhoa Gomez-Olle, Amanda Bullones, Jose I. Hormaza, Lukas A. Mueller, Noe Fernandez-Pozo
Summary: MangoBase is a web portal dedicated to mango genomics, providing various interactive bioinformatics tools, sequences, and annotations to analyze, visualize, and download omics data related to mango. It also includes a gene expression atlas with multiple datasets and experiments that study mango fruit ripening, postharvest treatment, infection, and organ tissues.
Article
Biology
Marie-Emilie A. Gauthier, Ruvini V. Lelwala, Candace E. Elliott, Craig Windell, Sonia Fiorito, Adrian Dinsdale, Mark Whattam, Julie Pattemore, Roberto A. Barrero
Summary: The increase in global trade presents both new opportunities and challenges to the biosecurity system. This study explores the use of high throughput sequencing technologies to improve quarantine testing and detect viruses and viroids in imported plants. The researchers developed a new pipeline, VirusReport, which can analyze sRNA datasets to identify regulated exotic viruses in a single assay.
Article
Immunology
Shingo Suzuki, Satoko Morishima, Makoto Murata, Masafumi Tanaka, Atsuko Shigenari, Sayaka Ito, Uma Kanga, Jerzy K. Kulski, Yasuo Morishima, Takashi Shiina
Summary: Acute graft-versus-host disease (aGVHD) is an immune response syndrome that occurs early after allogeneic hematopoietic stem cell transplantation. This study found that the mismatch between HLA-F-AS1 and HLA-DPB1 is strongly associated with aGVHD, independently of each other. This provides new insights into the molecular mechanism of aGVHD caused by HLA-matched UR-BMT.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Wenying Zhang, Cong Tan, Haifei Hu, Rui Pan, Yuhui Xiao, Kai Ouyang, Gaofeng Zhou, Yong Jia, Xiao-Qi Zhang, Camilla Beate Hill, Penghao Wang, Brett Chapman, Yong Han, Le Xu, Yanhao Xu, Tefera Angessa, Hao Luo, Sharon Westcott, Darshan Sharma, Eviatar Nevo, Roberto A. Barrero, Matthew Bellgard, Tianhua He, Xiaohai Tian, Chengdao Li
Summary: Divergent selection in different environments leads to functional genomic divergence. This study examined the genomic differentiation and gene expression patterns in two populations of wild barley under abiotic stress. The researchers identified structural variants and single nucleotide polymorphisms (SNPs) that may be associated with well-differentiated phenotypes and local adaptation. The findings provide new insights into the genomic basis of local adaptation and have implications for the genetic improvement of cultivated barley.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Education, Special
G. Leader, S. Whelan, N. N. Chonaill, R. Coyne, M. Tones, H. Heussler, M. Bellgard, A. Mannion
Summary: Angelman syndrome is a neurogenetic disorder that causes severe intellectual disability and GI symptoms. This study explored the relationship between early and current GI symptoms and co-morbidity in children and adolescents with AS, finding that constipation and gastroesophageal reflux were common issues.
JOURNAL OF INTELLECTUAL DISABILITY RESEARCH
(2022)
Article
Education, Special
Laura Roche, Megan Tones, Meagan Cross, Mathew Bellgard, Helen Heussler
Summary: This study analyzed parent reports to explore the adaptive behavior profile of 204 young children with Angelman syndrome (AS). The results showed that while many adaptive behaviors were determined by age, children with a non-deletion etiology exhibited advantages in communication skills, which may have influenced subsequent adaptive skills.
ADVANCES IN NEURODEVELOPMENTAL DISORDERS
(2022)
Article
Biochemistry & Molecular Biology
Ziheng Zhou, Cong Tan, Matthew Hoi Kin Chau, Xiaosen Jiang, Ziyuan Ke, Xiaoyan Chen, Ye Cao, Yvonne K. Kwok, Matthew Bellgard, Tak Yeung Leung, Kwong Wai Choy, Zirui Dong
Summary: In this study, we curated and analyzed sequencing data from multiple developmental periods of humans and various model organisms, providing insights into gene expression, chromatin accessibility, and gene-gene regulation interactions. The findings contribute to our understanding of the roles of genes in tissue/organ development and disease mechanisms.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Orthopedics
X. Wu, C. Liyanage, M. Plan, T. Stark, T. McCubbin, R. A. Barrero, J. Batra, R. Crawford, Y. Xiao, I. Prasadam
Summary: This study aims to identify the changes in energy metabolism in osteoarthritis (OA) cartilage. Metabolomics, proteomics, and transcriptomics analyses were conducted to investigate the global alterations in OA metabolism. The results showed increased lactate production and decreased mitochondrial respiratory rates in OA chondrocytes. This study provides a basis for targeting metabolism as a therapeutic approach for OA.
OSTEOARTHRITIS AND CARTILAGE
(2023)
Article
Cell Biology
Yuko Ohnuki, Shigeaki Suzuki, Akinori Uruha, Munenori Oyama, Shingo Suzuki, Jerzy K. Kulski, Ichizo Nishino, Takashi Shiina
Summary: Immune-mediated necrotizing myopathy (IMNM) is an autoimmune myositis characterized by muscle weakness, elevated creatine kinase levels, myofiber necrosis, and the presence of certain autoantibodies. This study investigated the association between IMNM and specific HLA alleles, and found that DRB1*08:03 was strongly associated with IMNM in adult patients. Subgroup analysis also identified higher risk alleles for collagen disease in adult patients (C*03:04) and for juvenile patients with anti-HMGCR antibody-positive IMNM (B*13:01 and C*03:04). These findings contribute to a better understanding of the HLA genetic background and features of IMNM.
Article
Plant Sciences
Paula Moolhuijzen, Lilian M. V. P. Sanglard, David J. Paterson, Sean Gray, Karina Khambatta, Mark J. Hackett, Ayalsew Zerihun, Mark R. Gibberd, Fatima Naim
Summary: In susceptible wheat cultivars infected with Pyrenophora tritici-repentis, calcium oscillations are modified, resulting in frozen host defence signals and silencing of recognition and defence mechanisms. In contrast, resistant cultivars show heightened defence response and calcium accumulation at later stages of disease development. By using gene expression data and high-resolution elemental imaging, the study provides insights into spatial and temporal changes in the asymptomatic green region, highlighting the benefits of spatially resolved molecular analysis and nutrient mapping in understanding complex plant-pathogen interactions.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Biochemical Research Methods
Selvam Paramasivan, Janna L. Morrison, Mitchell C. Lock, Jack R. T. Darby, Roberto A. Barrero, Paul C. Mills, Pawel Sadowski
Summary: Sequential window acquisition of all theoretical mass spectra-mass spectrometry, supported by advanced bioinformatics, provides a comprehensive framework for proteome analysis and biomarker discovery. However, the lack of a generic sample preparation platform for heterogeneous materials from different sources limits its broad application. We developed universal and fully automated workflows using a robotic sample preparation platform, enabling in-depth and reproducible proteome coverage of bovine and ovine specimens. The high correlation between sheep proteomics and transcriptomics datasets validates this development and suggests the potential for various clinical applications across different animal species and disease models.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Agronomy
Paula Moolhuijzen, Cynthia Ge, Elzette Palmiero, Simon R. R. Ellwood
Summary: Gene expression analysis revealed that RBgh2 plays a role in cAMP/G-protein-coupled signalling and innate immunity in barley powdery mildew adult plant resistance. RBgh2 is a major effect adult plant resistance gene in barley powdery mildew, showing different underlying genetic factors compared to conventional resistance genes. The resistance mechanism of RBgh2 involves temporary genome-wide gene expression changes and constitutive changes, especially at the RBgh2 locus, inducing defence-related genes associated with innate immunity and pathogen recognition.
THEORETICAL AND APPLIED GENETICS
(2023)
Article
Oncology
Chameera Ekanayake Weeramange, Kai Dun Tang, Roberto A. Barrero, Gunter Hartel, Zhen Liu, Rahul Ladwa, Julian Langton-Lockton, Ian Frazer, Lizbeth Kenny, Sarju Vasani, Chamindie Punyadeera
Summary: This study found that salivary microRNAs could be used for early detection and prognosis of oropharyngeal cancer, specifically the HPV-associated fraction. A panel of nine microRNAs was identified to effectively distinguish HPV-positive oropharyngeal cancer from HPV-positive controls, and a panel of six microRNAs was identified to distinguish oropharyngeal cancer from controls regardless of HPV status. Additionally, downregulation of hsa-miR-7-5p was associated with poor overall survival of oropharyngeal cancer patients, and a panel of nine microRNAs was identified to predict overall survival.
Article
Cell Biology
Jiro Miyamae, Masaharu Okano, Fumihiko Katakura, Jerzy K. Kulski, Tadaaki Moritomo, Takashi Shiina
Summary: Polymorphisms and genetic diversity of DLA-88, DLA-12/88L, and DLA-DRB1 loci were examined in 829 dogs of 59 breeds in Japan. Multiple alleles and various 88-12/88L-DRB1 haplotypes were detected. The findings suggest that high DLA homozygosity rate and low DLA diversity within a breed are beneficial for transplantation therapy but may affect biological fitness as homozygosity progresses.
Article
Medicine, Research & Experimental
Jerzy K. Kulski, Abigail L. Pfaff, Luke D. Marney, Alexander Froehlich, Vivien J. Bubb, John P. Quinn, Sulev Koks
Summary: Genomic and transcriptomic studies have shown that SVA retrotransposon insertion polymorphisms (RIPs) within human genomes significantly affect the co-expression of coding and noncoding genes. This study explored the role of polymorphic SVA in modulating gene co-expression within the major histocompatibility complex (MHC) genomic region, which is involved in immune responses. The findings indicate that SVA within the MHC region act as important regulators of gene co-expression and may contribute to genetic diversity, health, and disease.
EXPERIMENTAL BIOLOGY AND MEDICINE
(2023)
