Article
Microbiology
Brianna Atto, Dale Kunde, David A. Gell, Stephen Tristram
Summary: This study demonstrates the potential therapeutic effect of using Haemophilus haemolyticus strains with haem-binding proteins to inhibit Nontypeable Haemophilus influenzae infections by preventing their invasion of respiratory epithelium.
Article
Microbiology
Antoine Zboralski, Adrien Biessy, Marie Ciotola, Melanie Cadieux, Daphne Albert, Jochen Blom, Martin Filion
Summary: Lettuce, a major vegetable crop worldwide, is affected by various bacterial pathogens. In a study to develop new methods to control these pathogens, researchers screened over 1,200 plant-associated Pseudomonas strains and identified 35 strains that showed significant antagonistic capabilities against the three bacterial pathogens under study.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Veterinary Sciences
John P. Bannantine, Judith R. Stabel, Darrell O. Bayles, Cyril Conde, Franck Biet
Summary: This study identified over 250 subspecies defining genes in M. avium using pan genomic comparison tools, with the majority arranged in genomic islands. Through bioinformatics and PCR testing, 86 Map-specific genes, 7 Maa-specific genes, and 3 Mah-specific genes were confirmed. A single-tube PCR reaction was conducted as a proof of concept method for quickly distinguishing M. avium subspecies strains.
FRONTIERS IN VETERINARY SCIENCE
(2021)
Article
Immunology
Jian Guo, Jianbo Jian, Lili Wang, Lijuan Xiong, Huiping Lin, Ziyi Zhou, Eva C. Sonnenschein, Wenjuan Wu
Summary: This study sequenced the genomes of two strains of P. wickerhamii to gain insight into the genetic basis for its pathogenicity and provide a basis for future prevention and treatment strategies. The analysis revealed the evolutionary relationship of Prototheca and identified enriched genes in metabolic pathways.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Seong-Wan Kim, Min Jee Kim, Seong-Ryul Kim, Jeong Sun Park, Kee-Young Kim, Ki Hwan Kim, Woori Kwak, Iksoo Kim
Summary: This study reports the whole-genome sequences of 37 breeding line Bombyx mori strains established over the past 60 years, along with the description of their phenotypic characteristics. These data are valuable resources for studying B. mori and other insects.
Article
Genetics & Heredity
Hendor N. R. Jesus, Juliana N. N. Ramos, Danilo J. P. G. Rocha, Daniele A. A. Alves, Carolina S. S. Silva, Joao V. O. Cruz, Veronica V. Vieira, Cassius Souza, Louisy S. S. Santos, Jesus Navas, Rommel T. J. Ramos, Vasco Azevedo, Eric R. G. R. Aguiar, Ana L. L. Mattos-Guaraldi, Luis G. C. Pacheco
Summary: This study analyzed the genomes of C. striatum isolates and identified genomic characteristics that contribute to its pathogenicity and multidrug resistance. The research sheds light on the transition of C. striatum from a normal skin microbiome constituent to a multidrug-resistant and invasive pathogen.
FUNCTIONAL & INTEGRATIVE GENOMICS
(2023)
Article
Biochemistry & Molecular Biology
Lin-Feng Li, Zhi-Bin Zhang, Zhen-Hui Wang, Ning Li, Yan Sha, Xin-Feng Wang, Ning Ding, Yang Li, Jing Zhao, Ying Wu, Lei Gong, Fabrizio Mafessoni, Avraham A. Levy, Bao Liu
Summary: The study identified the donor of the common wheat B subgenome as a distinct and most likely extinct diploid species, differing from the still existing Aegilops species. It also found interspecific genetic introgressions during the evolution of the Triticum/Aegilops species complex. These newly assembled genome resources offer a new avenue for wheat improvement.
Article
Biology
Van Schepler-Luu, Coline Sciallano, Melissa Stiebner, Chonghui Ji, Gabriel Boulard, Amadou Diallo, Florence Auguy, Si Nian Char, Yugander Arra, Kyrylo Schenstnyi, Marcel Buchholzer, Eliza P. I. Loo, Atugonza L. Bilaro, David Lihepanyama, Mohammed Mkuya, Rosemary Murori, Ricardo Oliva, Sebastien Cunnac, Bing Yang, Boris Szurek, Wolf B. Frommer
Summary: Bacterial leaf blight (BB) of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), poses a threat to global food security and the livelihood of small-scale rice producers. Despite robust global rice trade, Xoo strains from different regions show complete continental segregation. Unprecedented BB outbreaks were discovered in Tanzania, caused by Xoo strains carrying Asian-type TAL effectors and iTAL effectors, unlike endemic African Xoo strains. In order to protect African rice production from this emerging threat, a hybrid CRISPR-Cas9/Cpf1 system was developed to edit TALe-binding elements in SWEET promoters. The edited lines displayed broad-spectrum resistance against Asian and African Xoo strains.
Article
Agricultural Engineering
Jiajing Sheng, Mi Yan, Jia Wang, Lingling Zhao, Fasong Zhou, Zhongli Hu, Surong Jin, Ying Diao
Summary: The chloroplast genomes of five Miscanthus species were sequenced using Illumina technology, revealing conservation in gene content and order but also identifying variation hotspots. Comparisons with other grass chloroplast genomes showed polymorphism hotspots, while phylogenetic analysis suggested a sister relationship between certain clades. This comprehensive analysis provides valuable genetic information for phylogeography, population genetics, and plastid genetic engineering research in Miscanthus.
INDUSTRIAL CROPS AND PRODUCTS
(2021)
Article
Evolutionary Biology
Hugo Devillers, Veronique Sarilar, Cecile Grondin, Lieven Sterck, Diego Segond, Noemie Jacques, Delphine Sicard, Serge Casaregola, Colin Tinsley
Summary: This study sequenced, assembled, and annotated the complete genomes of two Kazachstania barnettii strains, and compared the genomes in terms of structure and gene content. The findings revealed minimal differences between the two strains. The proposed genome assemblies will serve as valuable references for future comparative genomic, population genomic, or transcriptomic studies of the K. barnettii species.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Horticulture
Jianmin Tang, Rong Zou, Xiao Wei, Dianpeng Li
Summary: In this study, the complete chloroplast genomes of five species of Ormosia were sequenced and compared. Ten hypervariable regions were identified, with petN-psbM showing the highest variation. Phylogenetic analysis revealed the evolutionary relationships within the genus Ormosia and provided valuable insights for future studies.
Article
Biotechnology & Applied Microbiology
Peter Rugbjerg, Anne Sofie Brask Dyerberg, Scott Quainoo, Christian Munck, Morten Otto Alexander Sommer
Summary: This study used second and third generation deep sequencing technologies to analyze the genetic heterogeneity modes of five common E. coli host strains, revealing specific mutational patterns such as single nucleotide polymorphisms and inversions. The results suggest that organism engineers should avoid using chassis strains with active insertion sequences and monitor for increased mutagenicity in pathway transcription initiation regions and recombinogenic repeats.
METABOLIC ENGINEERING
(2021)
Article
Infectious Diseases
Willian Klassen Oliveira, Hugo Leonardo Avila, Michelle Zibeti Tadra, Rodrigo Luiz Cardoso, Cyntia Maria Teles Fadel-Pichet, Emanuel Maltempi de Souza, Fabio de Oliveira Pedrosa, Helisson Faoro
Summary: The genus Herbaspirillum is known for its ability to associate with grasses and participate in biological nitrogen fixation, but can also be isolated from clinical samples. The genome analysis of H. frisingense AU14559 revealed unique metabolic characteristics that allow it to infect and colonize human hosts, along with shared antibiotic resistance genes with other strains. These findings suggest potential for monitoring emerging pathogens and predicting outbreaks.
Article
Microbiology
Ahmed M. Abdel-Hamid, Corina N. D'Alessandro-Gabazza, Taro Yasuma, Kimberly K. O. Walden, Christopher J. Fields, Esteban C. Gabazza, Isaac Cann
Summary: We report the complete genome sequences of three Staphylococcus haemolyticus strains isolated from a mouse fibrotic lung tissue, which exhibit proapoptotic activity on human lung alveolar epithelial cells. The genomes were obtained using a combination of Illumina MiSeq and Oxford Nanopore MinION sequencing.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Article
Microbiology
Dustin A. Therrien, Kranti Konganti, Jason J. Gill, Brian W. Davis, Andrew E. Hillhouse, Jordyn Michalik, H. Russell Cross, Gary C. Smith, Thomas M. Taylor, Penny K. Riggs
Summary: This study involved sequencing the genomes of E. coli surrogates using two different platforms and found that combining long-read, short-read, and combined sequences can yield more accurate completed genomes. These data provide valuable insights for the adoption of WGS in the food industry and offer guidance for researchers and regulators in implementing related workflows.
Article
Oncology
Taylor R. Cushman, Bernard Jones, David Akhavan, Chad G. Rusthoven, Vivek Verma, Ravi Salgia, Mina Sedrak, Erminia Massarelli, James W. Welsh, Arya Amini
Summary: The study aimed to investigate the impact of time from diagnosis to initial treatment on survival in patients with non-small cell lung cancer. Delayed treatment was associated with poorer survival outcomes and disparities based on race, ethnicity, and socioeconomic status in non-metastatic non-small cell lung cancer.
CLINICAL LUNG CANCER
(2021)
Article
Chemistry, Multidisciplinary
Steve D. Knutson, Robert A. Arthur, H. Richard Johnston, Jennifer M. Heemstra
Summary: The study presents an EndoV-linked immunosorbency assay (EndoVLISA) for rapid measurement of global A-to-I editing signatures in cellular RNA. The method is cost-effective, straightforward, and suitable for disease detection and drug development applications.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Geriatrics & Gerontology
Irene Yang, Robert Adam Arthur, Liping Zhao, Jasmine Clark, Yijuan Hu, Elizabeth J. Corwin, James Lah
Summary: The study revealed a link between the oral microbiome and mild cognitive impairment (MCI), aiding in the diagnosis of MCI. Two taxa, Pasteurellacae and Lautropia mirabilis, were identified to be differentially abundant in the two groups. Although systemic inflammatory markers did not differentiate the groups, differences in cerebrospinal fluid inflammatory mediators were associated with MCI.
EXPERIMENTAL GERONTOLOGY
(2021)
Article
Immunology
Mary Elizabeth Sexton, Jesse J. Waggoner, Ludy R. Carmola, Phuong-Vi Nguyen, Ethan Wang, Dara Khosravi, Azmain Taz, Robert A. Arthur, Mit Patel, Venkata-Viswanadh Edara, Stephanie L. Foster, Kathryn M. Moore, Matthew Gagne, Jesmine Roberts-Torres, Amy R. Henry, Sucheta Godbole, Daniel C. Douek, Nadine Rouphael, Mehul S. Suthar, Anne Piantadosi
Summary: This article describes the rapid detection of the SARS-CoV-2 Omicron variant through targeted spike single-nucleotide polymorphism polymerase chain reaction and viral genome sequencing. The case occurred in a fully vaccinated and boosted traveler with mild symptoms, and was identified through community surveillance rather than clinical care.
CLINICAL INFECTIOUS DISEASES
(2022)
Article
Public, Environmental & Occupational Health
Charles E. Marvil, Ahmed Babiker, Aaron Preston, Andrew S. Webster, Jeannette Guarner, Kari Love, Elham Ghonim, Paulina A. Rebolledo, Yun F. Wang, Robert A. Arthur, H. Richard Johnston, Jesse J. Waggoner, Anne Piantadosi, Jesse T. Jacob
Summary: In this study, an epidemiological investigation and genome sequencing were performed to determine the source and scope of an outbreak of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) in a cluster of hospitalized patients. Lack of appropriate respiratory hygiene during a single hemodialysis session resulted in transmission of SARS-CoV-2 to patients and healthcare workers, highlighting the importance of infection prevention precautions.
INFECTION CONTROL AND HOSPITAL EPIDEMIOLOGY
(2023)
Article
Ecology
Karen L. Bell, Robert A. Petit, Anya Cutler, Emily K. Dobbs, J. Michael Macpherson, Timothy D. Read, Kevin S. Burgess, Berry J. Brosi
Summary: In this study, the performance of whole-genome shotgun (WGS) sequencing for species identification and quantitative analysis of pollen was evaluated. WGS showed near 100% accuracy in species identification in mixtures but generated higher rates of false positives compared to rbcL and ITS2 amplicon sequencing. WGS data provided a stronger correlation between pollen grain proportion and sequence read proportion for relative species abundance quantification, but diverged more from a 1:1 relationship.
ECOLOGY AND EVOLUTION
(2021)
Article
Microbiology
Vishnu Raghuram, Ashley M. Alexander, Hui Qi Loo, Robert A. Petit, Joanna B. Goldberg, Timothy D. Read
Summary: This study investigates the mutations in the agr operon of Staphylococcus aureus and their impact on strain characteristics. The study shows a close association between agr type and S. aureus clonal complex, and a strong linkage between agrBDC alleles. More than 5% of the genomes analyzed have frameshift mutations in the agr operon. The recurring mutations in different clonal lineages suggest that strains with agr frameshifts are short-lived in evolution.
MICROBIOLOGY SPECTRUM
(2022)
Article
Immunology
Irene Yang, Henry Claussen, Robert Adam Arthur, Vicki Stover Hertzberg, Nicolaas Geurs, Elizabeth J. Corwin, Anne L. Dunlop
Summary: This study aims to understand the structure and diversity of the subgingival microbiome in pregnant Black women and explore its relationship with preterm birth. The study found that although the composition of the subgingival microbiome shifted, the diversity remained stable throughout pregnancy. Additionally, several bacteria were found to be associated with spontaneous early term birth.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Oncology
Jay C. Shiao, Douglas Holt, Colton Ladbury, Dexiang Gao, Bernard Jones, Sana D. Karam, Arya Amini
Summary: CCRT showed improved OS for HPV-positive and HPV-negative T3N0 OPSCC. RT alone demonstrated similar OS to CCRT for both HPV-negative and HPV-positive T1-T2N0 OPSCC.
Article
Immunology
Cassie G. Ackerley, S. Abigail Smith, Phillip M. Murray, Praveen K. Amancha, Robert A. Arthur, Zhengyi Zhu, Ann Chahroudi, Rama R. Amara, Yi-Juan Hu, Colleen F. Kelley
Summary: Young men who have sex with men (YMSM) in the US are at a particularly high risk for HIV acquisition. This could be attributed to differences in the rectal mucosal immune environment associated with earlier sexual debut and less lifetime exposure to receptive anal intercourse. Additionally, the microbiome composition of YMSM is enriched for anaerobic bacteria associated with HIV acquisition risk.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Microbiology
Vanessa M. Van Doren, S. Abigail R. Smith, Yi-Juan K. Hu, Gregory A. Tharp, Steven Bosinger, Cassie F. Ackerley, Phillip R. Murray, Rama C. Amara, Praveen R. Amancha, Robert C. Arthur, H. Richard R. Johnston, Colleen C. Kelley
Summary: Young men who have sex with men (YMSM) are disproportionately affected by HIV and asymptomatic bacterial sexually transmitted infections (STI) including gonorrhea, chlamydia, and syphilis. This study examined the immunologic effects of these infections on the rectal mucosa among YMSM, and found that HIV was associated with differences in the cellular make-up of the rectal tissues, while STI was associated with an increase in the detection of potentially dangerous bacteria in the rectum. Asymptomatic bacterial STI may contribute to inflammation particularly among YMSM with HIV, and further research should examine potential harms and interventions to reduce the health impact of these syndemic infections.
Article
Oncology
Nader Ghassemi, Richard Castillo, Edward Castillo, Bernard L. Jones, Moyed Miften, Brian Kavanagh, Maria Werner-Wasik, Ryan Miller, Julie A. Barta, Inga Grills, Benjamin E. Leiby, Thomas Guerrero, Chad G. Rusthoven, Yevgeniy Vinogradskiy
Summary: This study evaluated the factors predicting pulmonary function changes in patients receiving functional avoidance radiotherapy. The data showed that lung dose-function metrics can predict pulmonary function changes, proving the importance of reducing dose to functional lung regions and providing guidance for future clinical trials.
RADIOTHERAPY AND ONCOLOGY
(2023)
Article
Genetics & Heredity
Kevin G. Libuit, Emma L. Doughty, James R. Otieno, Frank Ambrosio, Curtis J. Kapsak, Emily A. Smith, Sage M. Wright, Michelle R. Scribner, Robert A. Petit, Catarina Ines Mendes, Marcela Huergo, Gregory Legacki, Christine Loreth, Daniel J. Park, Joel R. Sevinsky
Summary: We have adopted an open bioinformatics ecosystem to address the challenges of bioinformatics implementation in public health laboratories. By using the Terra data analysis platform and specific bioinformatics workflows, we are able to perform standardized analysis and generate reproducible, validated, and auditable results that meet the needs of public health practitioners.
MICROBIAL GENOMICS
(2023)
Article
Microbiology
Abraham G. Moller, Robert A. Petit, Timothy D. Read
Summary: Phage therapy is a potential alternative treatment for Staphylococcus aureus infections. The study found that phage adsorption genes are highly conserved in the S. aureus species, but horizontal gene transfer may play an important role in the strain-specific evolution of host range patterns.
Article
Engineering, Biomedical
A. M. Amanso, T. C. Turner, A. Kamalakar, S. A. Ballestas, L. A. Hymel, J. Randall, R. Johnston, R. A. Arthur, N. J. Willett, E. A. Botchwey, S. L. Goudy
Summary: This study aimed to investigate the effects of local biomaterial-based FTY720 delivery in a murine ONF model on early bulk gene expression and neutrophil phenotypic response within the regenerating tissue. Results showed that FTY720 significantly influenced immune cell recruitment and modulation during ONF healing, leading to distinct neutrophil subpopulations in oral mucosal defect tissue.
REGENERATIVE ENGINEERING AND TRANSLATIONAL MEDICINE
(2021)
