Article
Mathematics
Jie Ma, Tianchi Yang
Summary: The research proves that the maximum number of edges in a 2-connected graph without repeated cycle lengths can be conceptually reduced to the classic problem of finding the maximum Sidon sequences in number theory, as shown by the proof and the lower bound construction.
ISRAEL JOURNAL OF MATHEMATICS
(2021)
Article
Plant Sciences
G. F. (Ciska) Veen, Freddy C. ten Hooven, Carolin Weser, S. Emilia Hannula
Summary: Repeated litter additions can lead to directional shifts in fungal community composition, while 9 months of litter addition did not alter bacterial community composition and the functioning and specialisation of microbial communities. Testing further how repeated litter inputs affect microbial functioning is essential for optimizing soil carbon and nutrient cycling.
JOURNAL OF ECOLOGY
(2021)
Article
Environmental Sciences
Jiumei Long, Dongsheng Zhou, Jing Wang, Binyan Huang, Yuanlai Luo, Guocheng Zhang, Zui Liu, Ming Lei
Summary: Applying beneficial bacteria in rice rhizosphere to manage heavy metal behaviour in soil-plant system is promising strategy. However, colonization/domination of exogenous bacteria in rhizosphere soils remains challenge.
Article
Multidisciplinary Sciences
Teresa Faddetta, Alberto Vassallo, Sara Del Duca, Giuseppe Gallo, Renato Fani, Anna Maria Puglia
Summary: Membrane vesicles (MVs) are nanoscale spherical particles that carry diverse cargos. Bacterial MVs, including those from Streptomyces coelicolor, have been identified as a fourth mechanism of horizontal gene transfer. This study demonstrates for the first time that MVs from S. coelicolor carry both DNA and RNA, with the DNA content representing the entire chromosome of the bacterium. These findings highlight the potential significance of MVs in the evolution of Streptomyces genomes and strain engineering strategies.
SCIENTIFIC REPORTS
(2022)
Article
Biology
Shufang Wu, Zhencheng Fang, Jie Tan, Mo Li, Chunhui Wang, Qian Guo, Congmin Xu, Xiaoqing Jiang, Huaiqiu Zhu
Summary: DeePhage is a novel computational tool that can rapidly and efficiently identify two types of phage fragments, especially suitable for metagenomics analysis.
Article
Biochemistry & Molecular Biology
Xia Wang, Guanqi Wu, Shuo Han, Jingjing Yang, Xiangwei He, Haifang Li
Summary: Plant endophytic bacteria play important roles in plant growth and stress resistance. This study identified and classified endophytic bacteria in Populus based on MALDI-TOF MS data and 16S rRNA gene sequencing, and verified the classification capacity of protein mass fingerprints. The results provide a valuable reference for differentiating and identifying endophytic bacteria.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
Hana Barak, Naomi Fuchs, Michal Liddor-Naim, Irit Nir, Alex Sivan, Ariel Kushmaro
Summary: Microbial dark matter (MDM), representing uncultured microorganisms, plays an important role in the diversity of microbial ecosystems. By analyzing 16S rRNA gene sequences, potential unknown bacteria were identified and a comprehensive phylogenetic tree was constructed to reveal new candidate phyla and other lineages. This study highlights the significant importance of MDM in environmental metataxonomic analyses and provides a simple method for the examination of MDM hidden behind amplicon sequencing results.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemical Research Methods
Bennett J. Kapili, Anne E. Dekas
Summary: This study introduces an R package called PPIT that infers microbial taxonomy from nifH amplicons using both phylogenetic and sequence identity approaches. By placing query sequences on a reference nifH gene tree, PPIT searches the phylogenetic neighborhood of each query sequence and attempts to draw microbial taxonomy inferences. The results show that PPIT returns a higher proportion of correct taxonomic inferences compared to BLAST-based approaches.
Article
Immunology
Danilo Donnarumma, Fabiola Giusti, Carine Ysebaert, Philippe Hermand, Nathalie Devos, Ilaria Ferlenghi, Immaculada Margarit, Silvia Rossi Paccani, Maria Scarselli, Nathalie Norais
Summary: Moraxella catarrhalis is an important respiratory pathogen associated with various respiratory diseases. Its surface protein A2 (UspA2) plays a role in the early stage of infection and contributes to bacterial serum resistance. The study provides insights into the structure and function of UspA2 and identifies key amino acids involved in its binding, highlighting its potential as a vaccine candidate against M. catarrhalis.
Article
Infectious Diseases
Lucie Galiot, Xavier C. Monger, Antony T. Vincent
Summary: Antibiotic resistance is a widespread issue that challenges the study and control of bacterial communities due to the mobility of resistance genes. This study investigates the relationship between insertion sequences and antibiotic resistance genes in microbiomes using two datasets. Statistically significant correlations were found in both datasets, but further research is needed to fully understand the contribution of insertion sequences to gene mobility.
Article
Microbiology
Ju-Hyeong Park, Angela R. Lemons, Jerry Roseman, Brett J. Green, Jean M. Cox-Ganser
Summary: Characterizing indoor microbial communities in 50 elementary schools revealed that classroom floor dust had a characteristic bacterial community different from house dust. Factors such as school location, degree of water damage, and building condition influenced bacterial richness and composition, but the classroom microbiome showed relative stability.
Article
Physics, Multidisciplinary
Eugene Korotkov, Konstantin Zaytsev, Alexey Fedorov
Summary: This paper examines the irregularity of 6-base occurrences in bacterial genomes using a probabilistic mathematical method, and reveals that bacterial genomes can be divided into two groups, with the coding sequences in the second group being less susceptible to evolutionary changes than those in the first group.
Article
Biotechnology & Applied Microbiology
Kathryn Whitehead, Lisa I. Pilkington, Anthony J. Slate, Fabien Saubade, Mohsin Amin, Adrian Lutey, Laura Gemini, Rainer Kling, Luca Romoli
Summary: Biofouling is a significant issue in the food industry, and the use of topographically patterned surfaces is an effective method to control biofouling. This study utilized a laser surface texturing process to create six different topographies and examined their impact on biofouling and cleaning.
FOOD AND BIOPRODUCTS PROCESSING
(2022)
Article
Biochemistry & Molecular Biology
Jui-Tse Ko, Ying-Yang Li, Pa-Yu Chen, Po-Yu Liu, Ming-Yang Ho
Summary: This article introduces a new method, far-red cyanobacteria identification (FRCI), based on 16S rRNA gene sequences to identify far-red light-utilizing cyanobacteria (FRLCyano). Experimental results demonstrate that FRCI can detect FRLCyano more sensitively than pigment analysis during far-red light enrichments and can also resolve their composition at the genus level. Additionally, the method is applied to published datasets and reveals potential FRLCyano in diverse environments.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemical Research Methods
De Xing, Shangjia Li, Mei Shang, Wenwen Wang, Qin Zhang, Jinhai Wang, Tasnuba Hasin, Darshika Hettiarachchi, Veronica Alston, Logan Bern, Abel Paladines Parrales, Cuiyu Lu, Michael Coogan, Andrew Johnson, Zhenkui Qin, Baofeng Su, Rex Dunham
Summary: CRISPR/Cas9-mediated knock-in is widely used in gene therapy, gene function study, and transgenic breeding programs. Researchers have developed a new strategy to improve knock-in efficiency and achieve multiple gene knock-ins simultaneously by targeting long repeated sequences in the genome.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Ekaterina Avershina, Knut Rudi
ANNALS OF MICROBIOLOGY
(2016)
Article
Genetics & Heredity
Eirik Nataas Hanssen, Ekaterina Avershina, Knut Rudi, Peter Gill, Lars Snipen
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2017)
Letter
Allergy
Ekaterina Avershina, Raul Cabrera Rubio, Krister Lundgard, Gaspar Perez Martinez, Maria Carmen Collado, Ola Storro, Torbjorn Oien, Christian Kvikne Dotterud, Roar Johnsen, Knut Rudi
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2017)
Article
Microbiology
Kasper Schei, Ekaterina Avershina, Torbjorn Oien, Knut Rudi, Turid Follestad, Saideh Salamati, Ronnaug Astri Odegard
Article
Agriculture, Dairy & Animal Science
Melanie Rae Simpson, Ekaterina Avershina, Ola Storro, Roar Johnsen, Knut Rudi, Torbjorn Oien
JOURNAL OF DAIRY SCIENCE
(2018)
Article
Biochemical Research Methods
Anuradha Ravi, Ekaterina Avershina, Inga Leena Angell, Jane Ludvigsen, Prasanth Manohar, Sumathi Padmanaban, Ramesh Nachimuthu, Lars Snipen, Knut Rudi
JOURNAL OF MICROBIOLOGICAL METHODS
(2018)
Article
Genetics & Heredity
Ekaterina Avershina, Inga Leena Angell, Melanie Simpson, Ola Storro, Torbjorn Oien, Roar Johnsen, Knut Rudi
Article
Multidisciplinary Sciences
Ekaterina Avershina, Silje Slangsvold, Melanie Rae Simpson, Ola Storro, Roar Johnsen, Torbjorn Oien, Knut Rudi
SCIENTIFIC REPORTS
(2017)
Article
Multidisciplinary Sciences
Ekaterina Avershina, Marte Gro Larsen, Marina Aspholm, Toril Lindback, Ola Storro, Torbjorn Oien, Roar Johnsen, Knut Rudi
SCIENTIFIC REPORTS
(2020)
Article
Multidisciplinary Sciences
Arne M. Taxt, Ekaterina Avershina, Stephan A. Frye, Umaer Naseer, Rafi Ahmad
SCIENTIFIC REPORTS
(2020)
Article
Microbiology
Abdolrahman Khezri, Ekaterina Avershina, Rafi Ahmad
Summary: This study analyzed strains from Norwegian patients and found the IncFIB plasmid to be the most prevalent in both E. coli and K. pneumoniae isolates, along with identifying certain plasmid-mediated antibiotic resistance genes. Hybrid assembly was used to more confidently locate plasmids and predict antibiotic resistance genes.
Review
Infectious Diseases
Ekaterina Avershina, Abdolrahman Khezri, Rafi Ahmad
Summary: Antimicrobial resistance (AMR) causes millions of deaths annually and its rapid spread requires changes in healthcare routines. The lack of rapid diagnostic tools for pathogen identification and AMR detection is a major issue. DNA sequencing technologies offer potential for rapid diagnostics, but currently require advanced bioinformatics knowledge and are not suitable for routine use.
Article
Biochemistry & Molecular Biology
Ekaterina Avershina, Priyanka Sharma, Arne M. Taxt, Harpreet Singh, Stephan A. Frye, Kolin Paul, Arti Kapil, Umaer Naseer, Punit Kaur, Rafi Ahmad
Summary: This study utilizes neural networks and sequencing technologies to predict antibiotic susceptibility in Escherichia coli and Klebsiella pneumoniae, reducing the time needed for susceptibility prediction. Through cross-checking and ensemble networks, the accuracy of cross-dataset prediction is improved.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Pediatrics
Kasper Schei, Melanie Rae Simpson, Ekaterina Avershina, Knut Rudi, Torbjorn Oien, Petur Benedikt Juliusson, David Underhill, Saideh Salamati, Ronnaug Astri Odegard
FRONTIERS IN PEDIATRICS
(2020)
Article
Food Science & Technology
Guro Alette Bjerke, Knut Rudi, Ekaterina Avershina, Birgitte Moen, Hans Blom, Lars Axelsson
Article
Biotechnology & Applied Microbiology
Zutan Li, Bingbing Jin, Jingya Fang
Summary: In this study, we propose MetaAc4C, an advanced deep learning model for accurate identification of N4-acetylcytidine (ac4C) sites using pre-trained BERT and various optimization techniques. By adapting generative adversarial networks to address data imbalance and augmenting training RNA samples, our model outperforms existing methods in terms of ACC, MCC, and AUROC.