Article
Agriculture, Dairy & Animal Science
Cory Schwarz, Jacques Mathieu, Jenny Laverde Gomez, Megan R. Miller, Marina Tikhonova, Tiruvoor. G. Nagaraja, Pedro J. J. Alvarez
Summary: The commonly used method to prevent liver abscess in feedlot cattle is in-feed use of tylosin, but our investigation revealed that Fusobacterium varium, a different species from Fusobacterium necrophorum, is abundant in the ruminal compartment. F. varium, which is an emerging pathogen in humans, showed resistance to commonly fed antibiotics and had genes linked to pathogenicity. This finding suggests that F. varium may play a more significant role in liver abscesses than previously thought and calls for further research and interventions.
JOURNAL OF ANIMAL SCIENCE
(2023)
Article
Multidisciplinary Sciences
Jorge Luis Galeano Nino, Hanrui Wu, Kaitlyn D. LaCourse, Andrew G. Kempchinsky, Alexander Baryiames, Brittany Barber, Neal Futran, Jeffrey Houlton, Cassie Sather, Ewa Sicinska, Alison Taylor, Samuel S. Minot, Christopher D. Johnston, Susan Bullman
Summary: The study investigates the interactions between tumor-associated microbiota and host cells in oral squamous cell carcinoma and colorectal cancer using in situ spatial-profiling technologies and single-cell RNA sequencing. The results show that the distribution of microbiota within the tumor is highly organized in microniches with immune and epithelial cell functions, promoting cancer progression.
Article
Microbiology
Jessica Queen, Jada C. Domingue, James Robert White, Courtney Stevens, Barath Udayasuryan, Tam T. D. Nguyen, Shaoguang Wu, Hua Ding, Hongni Fan, Madison McMann, Alina Corona, Tatianna C. Larman, Scott S. Verbridge, Franck Housseau, Daniel J. Slade, Julia L. Drewes, Cynthia L. Sears
Summary: This study investigated the inflammatory and tumorigenic potential of several clinical isolates of F. nucleatum using multiple murine models, in vitro assays with a human colon cancer cell line, and whole-genome sequencing analysis. The results showed that F. nucleatum subspecies did not induce tumorigenesis in murine models, but did induce greater cytokine responses in a human colorectal cell line.
Review
Neurosciences
Mark L. Mayer
Summary: The research by Watkins and colleagues has played a crucial role in our understanding of excitatory synaptic transmission in the central nervous system of animals; recent studies have revealed unexpected ligand binding profiles for newly identified glutamate receptors; structural studies indicate that the biology of glutamate receptors is more complex than initially anticipated.
JOURNAL OF PHYSIOLOGY-LONDON
(2021)
Article
Microbiology
Jessica Queen, Jada C. Domingue, James Robert White, Courtney Stevens, Barath Udayasuryan, Tam T. D. Nguyen, Shaoguang Wu, Hua Ding, Hongni Fan, Madison McMann, Alina Corona, Tatianna C. Larman, Scott S. Verbridge, Franck Housseau, Daniel J. Slade, Julia L. Drewes, Cynthia L. Sears
Summary: This study aimed to establish a stable murine model for the colonization of Fusobacterium nucleatum and to understand its inflammatory potential and virulence genes. The results showed that F. nucleatum subspecies did not induce tumorigenesis in mice and the level of inflammation varied among different subspecies. No distinct virulence genes associated with human colorectal cancer strains were identified. The study suggests that the difference in biology between humans and mice, as well as a synergistic role of F. nucleatum with other bacteria, may contribute to the lack of tumorigenesis in the model.
Review
Pharmacology & Pharmacy
Sian Chen, Chenbin Chen, Yuanbo Hu, Gendi Song, Xian Shen
Summary: Pancreatic cancer is a type of malignant tumor with poor prognosis, and the molecular mechanisms behind its development are not fully understood. In addition to key signaling pathways, noncoding RNAs like circRNAs have been found to be involved in pancreatic cancer progression. Compounds that regulate circRNA expression could potentially be beneficial in treating pancreatic cancer.
PHARMACOLOGY & THERAPEUTICS
(2021)
Article
Multidisciplinary Sciences
Edita Ritmejeryte, Berin A. Boughton, Michael J. Bayly, Rebecca E. Miller
Summary: Floral chemical defence strategies have been insufficiently studied, despite their importance to plant fitness. This study investigated the allocation of cyanogenic glycosides (CNglycs) within flowers and found extremely high CNglyc content in floral tissues of certain species, as well as diverse and specific within-flower distributions. The study also identified four patterns of within-flower CNglyc allocation and demonstrated the importance of visualizing metabolite localization.
Article
Forestry
Ramiro R. Ripa, Julissa Roncal, Yan B. Linhart, Jorgelina Franzese, Estela Raffaele, Andrea C. Premoli
Summary: Evolutionary forces such as genetic drift and natural selection play a crucial role in biological invasion. The gene pool of invasive fire-adapted species may differ from the native and originally planted species due to selective forces and founder effects. Genetic differentiation is influenced by both neutral and adaptive drivers, and fire acts as a rapid selection factor promoting the adaptive divergence of cohorts recruited after fires in fire-prone ecosystems.
FOREST ECOLOGY AND MANAGEMENT
(2023)
Article
Plant Sciences
Nikolai Friesen, Lisa Grutzmacher, Mikhail Skaptsov, Polina Vesselova, Vladimir Dorofeyev, Alexander N. Luferov, Nazgul Turdumatova, Georgii Lazkov, Sergei Smirnov, Alexander Shmakov, Herbert Hurka
Summary: The polymorph Allium pallasii s.l. from monotypic A. sect. Pallasia was studied using various methods, and it was found to be divided into two distinct species based on morphology, geography, cytology, and genetics. A. pallasii s. str. is found in North-East Kazakhstan, Western Siberia, and the Altai Mountains, while A. caricifolium is found in Kyrgyzstan, Northwest China, South-East Kazakhstan, and Zaysan Lake. Despite significant genetic differences, both species are sisters and are related to species of the A. sect. Codonoprasum (Subg. Allium). Allium caricifolium differs from A. pallasii s. str. in terms of taller stems, dense inflorescence, and longer filaments. The possible phylogenetic reasons for the separation of these species are discussed, and a nomenclature analysis of synonyms was conducted.
Article
Multidisciplinary Sciences
Falk Ponath, Yan Zhu, Valentina Cosi, Jorg Vogel
Summary: Fusobacterium nucleatum, a common oral microbe, has been found to colonize tissues and tumors in the human body and is associated with several major cancer types. However, little is known about gene regulation in F. nucleatum. This study characterizes a global stress-response network governed by the sigma(E) factor and develops genetic tools to study regulatory networks in this bacteria.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biotechnology & Applied Microbiology
Sonia Rey, Xingkun Jin, Borge Damsgard, Marie-Laure Begout, Simon Mackenzie
Summary: The study investigated the transferability of personality-specific mRNA transcripts across distantly-related fish species and the conservation of a proactive transcriptome signature across three different species. Results showed that differential mRNA transcript abundance in the brain appears to be partially conserved across species relative to personality type, suggesting functional conservation of cross-species molecular signatures related to proactive behavior.
Article
Multidisciplinary Sciences
Lachlan Pettit, Mathew S. Crowther, Georgia Ward-Fear, Richard Shine
Summary: This study found that the invasion of cane toads had different effects on the population of giant monitor lizards in Australia, possibly due to differences in food resource availability in different regions. Additionally, anthropogenically-induced changes to natural ecosystems may produce synergistic effects, intensifying their impacts.
Article
Microbiology
Zhenzhi Han, Jinbo Xiao, Yang Song, Xiaonan Zhao, Qiang Sun, Huanhuan Lu, Keyi Zhang, Jichen Li, Junhan Li, Fenfen Si, Guoyan Zhang, Hehe Zhao, Senquan Jia, Jienan Zhou, Dongyan Wang, Shuangli Zhu, Dongmei Yan, Wenbo Xu, Xiaoqing Fu, Yong Zhang
Summary: This study used metagenomic next-generation sequencing to investigate the viral diversity in different host species in Yunnan province, China. Multiple RNA viruses were identified and analyzed for their genome organization, genetic divergence, and phylogenetic relationships. The newly discovered viruses showed significant variations and evidence of recombination events, suggesting the emergence of new species or even genera. The study also estimated the evolutionary characteristics of the viruses among different hosts, highlighting the close association between emerging viruses and infectious diseases, and emphasizing the importance of more comprehensive surveys.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Microbiology
Jinjin Zhu, Yang Wang, Yuanyuan Cao, Jilong Shen, Li Yu
Summary: Research on Toxoplasma gondii microneme proteins (MICs) has shown their important role in host cell attachment, invasion, motility, and pathogenesis. Specifically focusing on the TgMIC1/4/6 complex can help improve understanding of T. gondii infection and provide a basis for effective control strategies.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biodiversity Conservation
Ernesto Azzurro, Sonia Smeraldo, Manuela D'Amen
Summary: With over a thousand introduced species, the Mediterranean is the most heavily invaded marine region in the world. The study reconstructed the invasion and dynamics of exotic fish species, calculated introduction and spread rates, and investigated time correlates since introduction using a comprehensive dataset of georeferenced observations. The findings revealed an exponential increase in the arrival rate of introduced species and highlighted temporal and geographical patterns in the invasion process.
GLOBAL CHANGE BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Madison M. Mann, James D. Tang, Bryan W. Berger
Summary: PFAS are synthetic fluorinated chemicals with surface active and water-repellent properties that accumulate significantly in humans due to widespread use. A fluorescence-based biosensor designed using hLFABP allows for rapid detection of PFAS, demonstrating its usefulness in environmental water samples.
BIOTECHNOLOGY AND BIOENGINEERING
(2022)
Article
Multidisciplinary Sciences
Erica J. Zheng, Ian W. Andrews, Alexandra T. Grote, Abigail L. Manson, Miguel A. Alcantar, Ashlee M. Earl, James J. Collins
Summary: The evolution of antibiotic tolerance is closely related to the dependency of antibiotics on bacterial metabolism. Antibiotics that have minimal effect on metabolism are less likely to lead to tolerance. The cycling of antibiotics with different metabolic dependencies can interrupt the evolution of tolerance and increase the effectiveness of treatment.
NATURE COMMUNICATIONS
(2022)
Article
Engineering, Environmental
David Calderon-Franco, Roel Sarelse, Stella Christou, Mario Pronk, Mark C. M. van Loosdrecht, Thomas Abeel, David G. Weissbrodt
Summary: In the context of One Health, wastewater treatment plants play a crucial role in preventing the dissemination of antimicrobial resistance. However, current surveillance studies focus mainly on monitoring intracellular DNA, while the role of extracellular free DNA is often overlooked. This study found that in the process of wastewater treatment, the exDNA fractions containing resistance determinants and mobile genetic elements need to be considered for AMR surveillance and risk assessment.
Article
Biochemical Research Methods
Ramin Shirali Hossein Zade, Aysun Urhan, Alvaro Assis de Souza, Akash Singh, Thomas Abeel
Summary: This study introduces a new tool called HAT for haplotype assembly, which utilizes short and long reads along with a reference genome to obtain higher-quality continuous haplotypes.
Correction
Biochemistry & Molecular Biology
Elizabeth Bloch, Eden L. Sikorski, David Pontoriero, Evan K. Day, Bryan W. Berger, Matthew J. Lazzara, Damien Thevenin
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Felix Wong, Aarti Krishnan, Erica J. Zheng, Hannes Stark, Abigail L. Manson, Ashlee M. Earl, Tommi Jaakkola, James J. Collins
Summary: Efficient identification of drug mechanisms of action remains a challenge. In this study, AlphaFold2 combined with molecular docking simulations was used to predict protein-ligand interactions and revealed widespread compound and protein promiscuity. Rescoring docking poses using machine learning-based approaches improved model performance. This work highlights the need for further development of protein-ligand interaction modeling, particularly using machine learning-based approaches, to better harness AlphaFold2 for drug discovery.
MOLECULAR SYSTEMS BIOLOGY
(2022)
Review
Biochemical Research Methods
Sosie Yorki, Terrance Shea, Christina A. Cuomo, Bruce J. Walker, Regina C. LaRocque, Abigail L. Manson, Ashlee M. Earl, Colin J. Worby
Summary: Recent advances in technology and computation have made metagenomic assembly a viable method for studying complex microbial communities. Previous benchmarking has shown that short-read (SR) assemblers are more accurate, long-read (LR) assemblers provide more contiguous sequences, and hybrid (HY) assemblers balance accuracy and length. However, there has been no specific assessment of these assemblers on low-abundance species, including clinically relevant organisms in the gut. Our study examined the performance of different assemblers on low-abundance species, specifically looking at the assembly of Escherichia coli contigs and antibiotic resistance genes (ARGs). We found that each assembler type has its own strengths and trade-offs, and the optimal approach depends on the specific goal of the study.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Shubhant Pandey, Bryan W. Berger, Rudresh Acharya
Summary: Anionic polysaccharides found in nature and the corresponding polysaccharide lyases (PLs) exhibit functional and structural convergence. pH affects substrate binding and catalytic activity, and specific groups of substrates are cleaved in different pH ranges regardless of the PL fold, supporting the concept of functional convergence. This study reveals the structural determinants of conserved substrate-pH activity pairing within and between PL families.
Article
Biochemical Research Methods
Paul van Lent, Joep Schmitz, Thomas Abeel
Summary: Combinatorial pathway optimization is important in metabolic flux optimization. Strain optimization is often performed using iterative design-build-test-learn (DBTL) cycles, but evaluating the effectiveness of machine learning methods over multiple DBTL cycles remains a challenge. In this work, a kinetic model-based framework is proposed to test and optimize machine learning for iterative combinatorial pathway optimization. Gradient boosting and random forest models outperformed other tested methods in the low-data regime, and an algorithm for recommending new designs using machine learning predictions was introduced.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Microbiology
Rauf Salamzade, Christi L. McElheny, Abigail L. Manson, Ashlee M. Earl, Nader Shaikh, Yohei Doi
Summary: Escherichia coli is the most common cause of urinary tract infections (UTIs) in children. However, the mechanisms of virulence and antibiotic resistance, as well as the population structure of this species, are poorly understood in this age group. This study examined the genetic markers and population structure of uropathogenic E. coli (UPEC) in children with UTIs. The results revealed similarities between UPEC populations in children and adults, with certain genetic markers being more common in pediatric pyelonephritis cases. Additionally, antibiotic resistance was correlated with known genetic markers, and a fimbrial gene allele was found to confer a selective advantage for UPEC.
Article
Materials Science, Multidisciplinary
Toriana N. Vigil, Mary-Jean C. Rowson, Abigail J. Frost, Bryan W. Berger
Summary: Silicatein is an enzyme that mineralizes environmental precursors for the formation of nanomaterials in marine sponges. Solubility of the enzyme has been studied using fusion proteins, and it was found that the solubility does not significantly affect the enzyme's activity. The results also suggest that the biomineralization activity of silicatein is inherent to the enzyme itself, and future studies should focus on understanding its kinetic mechanisms.
MATERIALS ADVANCES
(2023)
Article
Biochemical Research Methods
Marco Teixeira, Stephanie Pillay, Aysun Urhan, Thomas Abeel
Summary: This study developed a novel method to accurately identify the transfer of antimicrobial resistance (AMR) genes across plasmids and discovered the mechanisms and pathways of gene transfer, providing new insights into the spread of AMR.
Article
Biology
Bianca-Maria Cosma, Ramin Shirali Hossein Zade, Erin Noel Jordan, Paul van Lent, Chengyao Peng, Stephanie Pillay, Thomas Abeel
Summary: Our study benchmarks the latest long-read de novo assemblers to help readers make informed choices for eukaryotic genome assembly. We evaluated 12 real and 64 simulated datasets from different eukaryotic genomes, imitating PacBio CLR, PacBio HiFi, and ONT sequencing. We included 5 commonly used long-read assemblers for ONT and PacBio CLR reads, as well as 5 state-of-the-art HiFi assemblers for PacBio HiFi reads. Evaluation metrics included reference-based metrics, assembly statistics, misassembly count, BUSCO completeness, runtime, and RAM usage. Our benchmark concluded that there is no single assembler that performs the best in all evaluation categories. However, we found that Flye is the best-performing assembler for PacBio CLR and ONT reads, while Hifiasm and LJA are the best-performing assemblers for PacBio HiFi reads. We also observed that increased read length can improve assembly quality, but the extent of improvement depends on the size and complexity of the reference genome.