Article
Microbiology
M. H. Y. Leung, X. Tong, K. O. Boifot, D. Bezdan, D. J. Butler, D. C. Danko, J. Gohli, D. C. Green, M. T. Hernandez, F. J. Kelly, S. Levy, G. Mason-Buck, M. Nieto-Caballero, D. Syndercombe-Court, K. Udekwu, B. G. Young, C. E. Mason, M. Dybwad, P. K. H. Lee
Summary: The study found that city was the main factor influencing differences in the public transit air microbiome, with diverse taxa driving geography-specific functional potentials. Bacterial strains in different cities showed variations in genes related to resistance and other functions. Human skin, soil, and wastewater were identified as major presumptive sources of resistome in the public transit air, with a significant presence of resistance genes co-located with mobile genetic elements like plasmids. Geographical specificity played a key role in shaping the public transit air microbiome, highlighting the need for global efforts to better understand this built environment.
Article
Microbiology
Chian Teng Ong, Gry Boe-Hansen, Elizabeth M. Ross, Patrick J. Blackall, Conny Turni, Ben J. Hayes, Ala E. Tabor
Summary: This study compared the effectiveness of different host depletion and DNA extraction methods for bovine vaginal metagenomic samples. The findings indicated that Soft-spin and QIAamp were the most effective methods in reducing host DNA contamination and increasing sequencing depth for microbial reads. Thus, a combination of these methods provided the most robust representation of the vaginal microbial community in cattle.
MICROBIOLOGY SPECTRUM
(2022)
Article
Environmental Sciences
Md Aminul Islam, Atsuo Ikeguchi, Takanori Naide
Summary: There is increasing pressure to find solutions to reduce emissions of pollutants from occupational settings. In this study, an air cleaner device was tested and showed significant reduction in aerosol numbers and airborne bacteria. However, after stopping the device, there was an increase in these indicators.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2022)
Article
Environmental Sciences
Andres Nunez, Ana M. Garcia, Diego A. Moreno, Raul Guantes
Summary: Compared to soil or aquatic ecosystems, the atmosphere remains relatively unexplored in terms of microbial diversity. This study surveyed microbes in the near surface atmosphere of a highly populated area around Madrid, finding a stable ecosystem with a core of abundant bacterial genera across space and time, modulated by climatic variations. The microbial communities exhibited clear seasonal patterns driven by environmental factors, contributing to our understanding of long-term changes in human exposure in highly populated urban areas.
ENVIRONMENT INTERNATIONAL
(2021)
Article
Veterinary Sciences
Shuli Yang, Jieyi Zheng, Shichun He, Zaimei Yuan, Rongjiao Wang, Dongwang Wu
Summary: The diversity and abundance of rumen microorganisms can reflect the host's digestive and metabolic capacity as well as its health status. In this study, we analyzed the variations in rumen microorganisms among cattle at different altitudes in Yunnan, China. The results showed that altitude had a significant impact on the diversity and richness of the rumen microbiota.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Article
Microbiology
Alexa M. Nicolas, Alexander L. Jaffe, Erin E. Nuccio, Michiko E. Taga, Mary K. Firestone, Jillian F. Banfield
Summary: This study focused on Candidate Phyla Radiation (CPR) bacteria and DPANN archaea in soil, which are often overlooked. By concentrating small particles from soil, the researchers were able to identify these organisms as part of the rare soil biosphere with unique metabolic platforms. Some of these predicted symbionts have acquired aerobic capacity through lateral transfer, enabling them to adapt to oxic soil environments.
Article
Veterinary Sciences
Shuli Yang, Guangrong Zhang, Zaimei Yuan, Shichun He, Rongjiao Wang, Jieyi Zheng, Huaming Mao, Jianmin Chai, Dongwang Wu
Summary: In this study, the bacterial and fungal communities in the rumen of pastured yaks of different ages were analyzed using full-length sequencing. The results showed that the rumen microflora of Zhongdian yaks changed gradually from 5 to 180 days after birth and tended to stabilize at 2 years of age. The rumen of adult yaks was the most suitable for the growth and reproduction of most bacteria. At 90 days of age, the yak rumen was the most suitable for the growth and reproduction of most fungi, and 90 days of age could be a cut-off point for the distribution of fungal communities. The study provided insights into the dynamic changes of dominant microflora with yak growth.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Article
Chemistry, Analytical
Youngung Seok, Joonseok Lee, Min-Gon Kim
Summary: The paper-based airborne bacteria collection and DNA extraction kit developed in this study offers a simple, rapid, and cost-effective method for monitoring airborne pathogens. With the integration of 3D printing technology and an air pump, the entire operation process can be completed within 20 minutes, making it suitable for use in resource-limited settings. The effectiveness of the paper kit was demonstrated under specific conditions, showing potential for widespread application in monitoring airborne pathogens efficiently.
Article
Ecology
Brian K. Trevelline, Andrew H. Moeller
Summary: This study analyzed gut microbiota profiles from wild and captive hosts in seven mammalian families, finding that captive mammals tend to have gut microbiota composition similar to that of humans, with the exception of giraffes and bovids.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Luis Pedro Coelho, Renato Alves, Alvaro Rodriguez del Rio, Pernille Neve Myers, Carlos P. Cantalapiedra, Joaquin Giner-Lamia, Thomas Sebastian Schmidt, Daniel R. Mende, Askarbek Orakov, Ivica Letunic, Falk Hildebrand, Thea Van Rossum, Sofia K. Forslund, Supriya Khedkar, Oleksandr M. Maistrenko, Shaojun Pan, Longhao Jia, Pamela Ferretti, Shinichi Sunagawa, Xing-Ming Zhao, Henrik Bjorn Nielsen, Jaime Huerta-Cepas, Peer Bork
Summary: The majority of microbial genes are specific to a single habitat, with a small fraction found in multiple habitats enriched in antibiotic-resistance genes and markers for mobile genetic elements. A small fraction of protein families contain the majority of genes, with most genetic variability observed within the families being neutral or nearly neutral.
Article
Multidisciplinary Sciences
Jue Zhao, Ling Jin, Dong Wu, Jia-wen Xie, Jun Li, Xue-wu Fu, Zhi-yuan Cong, Ping-qing Fu, Yang Zhang, Xiao-san Luo, Xin-bin Feng, Gan Zhang, James M. Tiedje, Xiang-dong Li
Summary: This study analyzed the bacterial communities in airborne particulate samples from around the world and found that they have a biogeographic pattern and interact with surface environments. While the total abundance of airborne bacteria is lower than other habitats, the number of bacterial taxa is comparable to the hydrosphere and is highest in midlatitude regions. The structure of the airborne bacterial community is easily perturbed and influenced by surface microbiomes and atmospheric conditions, particularly in urban areas. These findings provide valuable insights for predicting microbial responses and health impacts in different environments.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Yeonhwa Jo, Chang-Gi Back, Kook-Hyung Kim, Hyosub Chu, Jeong Hun Lee, Sang Hyun Moh, Won Kyong Cho
Summary: In this study, in silico analysis was conducted on garlic RNA-sequencing data to identify microorganisms in different tissues. The microbial community varied depending on the tissue types, with dominant microorganisms observed in each tissue. Kraken2 was found to be a powerful tool for bacteria analysis but had some limitations for virome study.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Yeonhwa Jo, Chang-Gi Back, Kook-Hyung Kim, Hyosub Chu, Jeong Hun Lee, Sang Hyun Moh, Won Kyong Cho
Summary: Red pepper is an important spice plant in Korea, and overwintering pepper fruits can harbor various microbial diseases. Metagenomics and metatranscriptomics were used to analyze microbial communities in overwintering pepper fruits, with DNA sequencing proving useful for identifying bacteria and DNA viruses, while mRNA sequencing was beneficial for identifying fungi and RNA viruses. Among the analytical methods, KRAKEN2 with raw data reads was found to be superior for identifying microbial species, but had limitations in accurately assigning some species with low read numbers. Additionally, it was noted that databases for bacteria and viruses were more established compared to the fungal database. Overall, it is recommended to use different library types and analytical methods with appropriate databases for microbiome studies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
C. Ogawa, R. Inoue, Y. Yonejima, K. Hisa, Y. Yamamoto, T. Suzuki
Summary: The study demonstrates that Leuconostoc mesenteroides NTM048 strain can alleviate IMQ-induced psoriasis in mice by modulating the gut microbiota composition and increasing plasma deoxycholic acid levels, which in turn leads to the reduction of IL-17 levels, a key effector cytokine in psoriasis. These findings suggest a potential novel approach for psoriasis treatment and highlight the crosstalk between the skin and intestine in psoriasis.
JOURNAL OF APPLIED MICROBIOLOGY
(2021)
Article
Environmental Sciences
A. Torres-Agullo, A. Karanasiou, T. Moreno, S. Lacorte
Summary: Airborne microplastics have become a concern in recent years due to their potential risks to human health. This study evaluated the concentrations of microplastics in indoor environments and found that public transport had the highest levels. The most common polymers identified were polyamide, polyester, and polypropylene, which are commonly used in personal care products and synthetic textiles.
ENVIRONMENTAL POLLUTION
(2022)
Article
Ecology
Elena Kozlova, Shivanand Hegde, Christopher M. Roundy, George Golovko, Miguel A. Saldana, Charles E. Hart, Enyia R. Anderson, Emily A. Hornett, Kamil Khanipov, Vsevolod L. Popov, Maria Pimenova, Yiyang Zhou, Yuriy Fovanov, Scott C. Weaver, Andrew L. Routh, Eva Heinz, Grant L. Hughes
Summary: The interactions between microbes in the mosquito gut are complex and can influence mosquito behavior and the parasitic habits of the microbes.
Article
Cardiac & Cardiovascular Systems
Lorraine S. Evangelista, Mini M. Jose, Hanaa Sallam, Hani Serag, George Golovko, Kamil Khanipov, Michele A. Hamilton, Gregg C. Fonarow
Summary: The study compared the effects of two calorie-restricted diets on cardiometabolic risk factors in overweight and obese patients, showing that a high-protein diet can effectively reduce glycosylated hemoglobin levels, cholesterol, and triglycerides, and significantly improve blood pressure.
Review
Biochemical Research Methods
Fangfang Xia, Jonathan Allen, Prasanna Balaprakash, Thomas Brettin, Cristina Garcia-Cardona, Austin Clyde, Judith Cohn, James Doroshow, Xiaotian Duan, Veronika Dubinkina, Yvonne Evrard, Ya Ju Fan, Jason Gans, Stewart He, Pinyi Lu, Sergei Maslov, Alexander Partin, Maulik Shukla, Eric Stahlberg, Justin M. Wozniak, Hyunseung Yoo, George Zaki, Yitan Zhu, Rick Stevens
Summary: To enable personalized cancer treatment, machine learning models have been developed to predict drug response based on tumor and drug features. This study used machine learning to analyze five publicly available cell line-based data sets and rigorously evaluated the model generalizability between different studies. The results showed that a multitasking deep neural network achieved the best cross-study generalizability, with models trained on the CTRP data set providing the most accurate predictions on testing data, and the gCSI data set being the most predictable among the cell line data sets.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Surgery
Andrew Ko, Juquan Song, George Golovko, Amina El Ayadi, Deepak K. Ozhathil, Kendall Wermine, Robert E. Africa, Sunny Gotewal, Sandy Reynolds, Steven E. Wolf
Summary: Severely burned patients with rhabdomyolysis have a significantly higher risk of acute kidney injury and mortality.
Article
Chemistry, Medicinal
Heesung Shim, Hyojin Kim, Jonathan E. Allen, Heike Wulff
Summary: The article introduces a machine learning approach to identify correct docking poses from docking screening results, enhancing the effectiveness of virtual high-throughput screening.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Multidisciplinary Sciences
Luke A. Bourner, Israel Muro, Amy M. Cooper, Barun K. Choudhury, Aaron O. Bailey, William K. Russell, Kamil Khanipov, George Golovko, Casey W. Wright
Summary: Research has shown that the ratio of ARNT isoforms 1:3 in human T cell lymphoma cells determines the regulation of AhR target genes. Modulating this ratio can enhance or abrogate AhR responsiveness, leading to either inflammation or immunosuppression. The phosphorylation of ARNT isoform 1 by CK2 is essential for optimal AhR target gene regulation. These findings highlight the importance of ARNT in modulating AhR activity and suggest potential ARNT-based therapies for immune disorders.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Medicinal
Vincent Blay, Tijana Radivojevic, Jonathan E. Allen, Corey M. Hudson, Hector Garcia Martin
Summary: MACAW is a tool that generates molecules predicted to meet desired property specifications by embedding them into a multidimensional numerical space. It demonstrates high computational efficiency and accuracy, showcasing superior performance in virtual screening for small- to medium-sized datasets commonly used in biosciences.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Physical
Derek Jones, Jonathan E. Allen, Yue Yang, William F. Drew Bennett, Maya Gokhale, Niema Moshiri, Tajana S. Rosing
Summary: In this article, the fundamental algorithms used in Atomistic Molecular Dynamics (MD) simulations are summarized, and the challenges in implementing accelerators are discussed. By comparing different categories of accelerators, the current state of the art in this field is provided. Finally, insights into the potential of emerging hardware platforms and algorithms for MD are given.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Virology
Jenna McGowan, Monica Borucki, Hicham Omairi, Merina Varghese, Shahnaz Vellani, Sukanya Chakravarty, Shumin Fan, Srestha Chattopadhyay, Mashuk Siddiquee, James B. Thissen, Nisha Mulakken, Joseph Moon, Jeffrey Kimbrel, Amit K. Tiwari, Roger Travis Taylor, Dae-Wook Kang, Crystal Jaing, Ritu Chakravarti, Saurabh Chattopadhyay
Summary: Wastewater-based epidemiology (WBE) is an effective tool for predicting the community spread of infectious diseases, especially during the COVID-19 pandemic. Through analyzing the correlation between viral gene copies and clinical cases, as well as sequencing RNA from wastewater to identify viral mutants, WBE can be used to predict the spread of COVID-19 and the emergence of new variants of concern. Furthermore, significant changes in the microbial community of wastewater, particularly in bacterial genera belonging to the families of Lachnospiraceae and Actinomycetaceae, show a strong correlation with the presence of SARS-CoV-2. These microbial biomarkers could serve as prediction tools for future infectious disease surveillance and outbreak responses.
Article
Multidisciplinary Sciences
James B. Thissen, Michael D. Morrison, Nisha Mulakken, William C. Nelson, Chris Daum, Sharon Messenger, Debra A. Wadford, Crystal Jaing
Summary: Co-infections or secondary infections with SARS-CoV-2 can affect disease severity and morbidity. The influence of nasal microbiome on COVID-19 illness is not well understood. In this study, researchers analyzed 203 samples and found the presence of opportunistic bacteria or viral pathogens with the potential to cause co-infections in some samples.
Article
Virology
Jeffrey Kimbrel, Joseph Moon, Aram Avila-Herrera, Jose Manuel Marti, James Thissen, Nisha Mulakken, Sarah H. Sandholtz, Tyshawn Ferrell, Chris Daum, Sara Hall, Brent Segelke, Kathryn T. Arrildt, Sharon Messenger, Debra A. Wadford, Crystal Jaing, Jonathan E. Allen, Monica K. Borucki
Summary: Genetic analysis of SARS-CoV-2 positive clinical samples collected in California during the early months of the pandemic revealed insights into the emergence and spread of viral mutations. Many mutations associated with global variants were present at varying frequencies even in samples collected during the initial detection of the virus in the US. Subconsensus mutations emerged later in the consensus sequences. Spike protein mutations and mutations in the furin cleavage site, nucleocapsid, and envelope genes were detected prior to their emergence in variant genotypes. A bioinformatics pipeline enabled detection of low-frequency variants, including a spike protein deletion associated with a variant of concern.
Article
Biology
George Golovko, Kamil Khanipov, Victor Reyes, Irina Pinchuk, Yuriy Fofanov
Summary: Identifying complex relations in biological systems requires searching for patterns among variables/features. Traditional methods are limited to two-dimensional patterns, while complex systems require multidimensional patterns. This study introduces a novel type of multivariable Boolean pattern associations and proposes a pattern classification method, along with a new definition of pattern strength. Analysis of microbial genomics and microbiomics data reveals the common occurrence of statistically significant multivariable patterns.
Article
Chemistry, Medicinal
Garrett A. Stevenson, Dan Kirshner, Brian J. Bennion, Yue Yang, Xiaohua Zhang, Adam Zemla, Marisa W. Torres, Aidan Epstein, Derek Jones, Hyojin Kim, W. F. Drew Bennett, Sergio E. Wong, Jonathan E. Allen, Felice C. Lightstone
Summary: Protein-ligand interactions are crucial for drug discovery and development. This study introduces a novel ligand-based featurization and mapping method to identify related protein targets and predict protein interactions of drugs.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Genetics & Heredity
Adam T. Zemla, Jonathan E. Allen, Dan Kirshner, Felice C. Lightstone
Summary: We present a structure-based method for finding and evaluating structural similarities in protein regions relevant to ligand binding. This method uses the LGA structure alignment algorithm to detect structural similarities and assess confidence in structural matches by considering side chain placement.
NAR GENOMICS AND BIOINFORMATICS
(2022)
Article
Geriatrics & Gerontology
Andrea Dimet-Wiley, George Golovko, Stanley J. Watowich
Summary: Hip fracture in older adults is associated with increased mortality risk, and dementia may exacerbate this risk.
