Article
Multidisciplinary Sciences
Paschalis Natsidis, Paschalia Kapli, Philipp H. Schiffer, Maximilian J. Telford
Summary: The availability of complete gene sets from different organisms allows for identification of unique or lost genes in specific clades. Through simulation, it has been shown that errors in predicting orthologs increase with higher rates of evolution. Empirical data findings are closely replicated by simulated data with errors, suggesting downstream analyses should consider the impact of orthology prediction errors on gene evolution patterns.
Article
Biochemistry & Molecular Biology
Douglas Chesters, Rafael R. Ferrari, Xiaolong Lin, Michael C. Orr, Michael Staab, Chao-Dong Zhu
Summary: The Holy Grail of an Insect Tree of Life can only be 'discovered' through extensive collaboration among taxon specialists, phylogeneticists, and centralized frameworks such as Open Tree of Life, but so far insufficient effort from stakeholders has hampered this promising approach. To address this issue, we establish a new online hub that centralizes the collation of relevant phylogenetic data and provides synthesis molecular phylogenies. The functionality of the framework is demonstrated by constructing a highly supported, species-comprehensive phylogeny of Diptera, which is publicly available at insectphylo.org.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Plant Sciences
Catherine Damerval, Carmine Claudot, Martine Le Guilloux, Natalia Conde e Silva, Veronique Brunaud, Ludivine Soubigou-Taconnat, Jose Caius, Etienne Delannoy, Sophie Nadot, Florian Jabbour, Yves Deveaux
Summary: TCP transcription factors are important in developmental processes and hormonal pathways. We studied the TCP genes in the plant species Nigella damascena and found that they are orthologs of TCP genes in Aquilegia coerulea. Phylogenetic analysis and amino acid motif identification suggest that six paralogous genes of class I TCP transcription factors were present in the common ancestor of angiosperms. There have been independent duplications in core eudicots and Ranunculales, resulting in different numbers of paralogs within TCP gene subclasses.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Yi Li, Zihao Li, Furui Zhang, Song Li, Yongbing Gu, Weijun Tian, Weirong Tian, Jianbo Wang, Jun Wen, Jiaru Li
Summary: Steroidal saponins are specialized metabolites essential for plants' response to stresses and for industrial production of steroid drugs. The origin and evolution of steroidal saponins in plants remain poorly understood. By studying the evolutionary history of steroidal saponin-associated module in plants, this study reveals their origin in Asparagus and Dioscorea and multiple origins in angiosperms. Understanding the distribution and diversity of steroidal saponins contributes to our knowledge of plant resistance to stresses and helps facilitate their industrial production and pharmacological applications.
Article
Plant Sciences
Xiangyu Tian, Jia Guo, Xiaojiao Zhou, Ke Ma, Yonggui Ma, Tuansheng Shi, Yuhua Shi
Summary: Many species of the genus Kalanchoe have evolved the Crassulacean acid metabolism (CAM) photosynthetic pathway for better adaptation to dry environments, although the monophyly of Kalanchoe is still debated. Plastomes of five Kalanchoe species were sequenced and analyzed, revealing similarities in size, GC contents, and gene numbers. Identification of SSRs, long repeats, and highly divergent regions could aid in future phylogenetic studies, while genomic analyses suggest potential roles of certain genes in the adaptive evolution of Kalanchoe to dry environments.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Euki Yazaki, Akinori Yabuki, Ayaka Imaizumi, Keitaro Kume, Tetsuo Hashimoto, Yuji Inagaki
Summary: By clarifying the phylogenetic positions of 'orphan' protists, this study reveals the novel affiliation between major lineages in eukaryotes. The analysis of a 319-gene alignment demonstrates that M. maris represents a basal lineage of Cryptista and proposes a new clade name 'Pancryptista'. Additionally, M. maris is found to be a key taxon for recovering the monophyly of Archaeplastida and the sister relationship between Archaeplastida and Pancryptista.
Article
Biochemistry & Molecular Biology
Fang Yan, Lotanna M. Nneji, Jie-qiong Jin, Zhi-yong Yuan, Jin-min Chen, Xue Mi, Hong-man Chen, Robert W. Murphy, Jing Che
Summary: The study identified the distribution of Quasipaa frogs in southern China to Southeast Asia, revealing two new species and significant environmental differences between regions. Genetic data showed the evolutionary history of Quasipaa species in South China, with divergence dating back to 15.3-16.56 million years ago, influenced by different topographic terrains.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Plant Sciences
Tian Wan, Bai-xue Qiao, Jing Zhou, Ke-sen Shao, Liu-yi Pan, Feng An, Xu-sheng He, Tao Liu, Ping-ke Li, Yu-liang Cai
Summary: This study reports the chloroplast genome sequences of 11 Cerasus species to investigate the evolution of their plastome. The results reveal the typical quadripartite circular structure of Cerasus chloroplast genomes and the presence of 115 unique genes. Several genes were found to have high nucleotide diversity and more polymorphic sites, including matK, rps16, and rbcL. The phylogenetic analysis sheds light on the relationships between different Cerasus species, providing insights for further research on their phylogenetics and phylogeography.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Genetics & Heredity
Min Li, Min Liu, Shi-Yun Hu, Fang-Zhen Luo, Ming-Long Yuan
Summary: This study analyzed the mitogenomes of ten spider species and found that nucleotide composition and codon usage were conserved within the RTA clade, but there was diversity in sequence length and structure in the control region. Most protein-coding genes were undergoing purifying selection.
FRONTIERS IN GENETICS
(2022)
Article
Plant Sciences
Lorhenn Bryanda Lemes Maia, Humberto D'Muniz Pereira, Richard Charles Garratt, Jose Brandao-Neto, Flavio Henrique-Silva, Danyelle Toyama, Renata O. Dias, Jose Fernando Ruggiero Bachega, Julia Vasconcellos Peixoto, Marcio C. Silva-Filho
Summary: SUGARWINs are PR-4 proteins associated with sugarcane defense against phytopathogens, particularly fungal pathogens. While SUGARWIN1 exhibits ribonuclease, chitosanase, and chitinase activities, SUGARWIN2 only displays chitosanase activity. Structural analysis reveals that SUGARWIN1's structure and presence of the catalytic histidine at position 42 make it competent as a ribonuclease.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Microbiology
Yue Liu, Amina Nawal Bahoussi, Pei-Hua Wang, Changxin Wu, Li Xing
Summary: This study reclassified and analyzed 203 complete genomic sequences of CSFVs collected worldwide, revealing a new lineage, GI-2.2b, and identifying 10 potential natural recombination events. The involvement of vaccine strains and highly virulent strains in recombination events presents additional challenges for vaccine development.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Agricultural Engineering
Wuqin Xu, Ruisen Lu, Junyou Li, Maoqin Xia, Guangyong Chen, Pan Li
Summary: In this study, we sequenced the complete plastomes of 21 species and cultivars in the Atractylodes genus, revealing the typical quadripartite structure and highly variable regions of the plastomes. Our phylogenetic analysis based on plastid and RAD datasets provides strong support for studying the phylogeography and population genetics of Atractylodes, and the genomic resources accumulated in this study will also be valuable for genetic engineering and germplasm exploration of this important genus.
INDUSTRIAL CROPS AND PRODUCTS
(2023)
Article
Environmental Sciences
Ning Huang, Shuai Chen, Ming He, Qi Song, Lina Hou, Yan Zhao, Shuo Zhao, Miao Miao
Summary: Ciliates, the most complex unicellular eukaryotic organisms, play essential roles in various ecosystems. The research on Euplotes mitochondrial genomes revealed gene rearrangements and codon usage differences among species, indicating salinity as a potential barrier for species distribution. Mitochondrial genes were recommended for distinguishing closely related Euplotes species.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
William R. Conner, Emily K. Delaney, Michael J. Bronski, Paul S. Ginsberg, Timothy B. Wheeler, Kelly M. Richardson, Brooke Peckenpaugh, Kevin J. Kim, Masayoshi Watada, Ary A. Hoffmann, Michael B. Eisen, Artyom Kopp, Brandon S. Cooper, Michael Turelli
Summary: The Drosophila montium species group consists of 94 named species closely related to D. melanogaster, distributed widely across Asia, Africa, and Australasia. Genomic data from 42 species were used to estimate phylogeny, relative divergence times, and support monophyly within the group. However, age estimates for the montium crown group compared to D. melanogaster remain uncertain.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Virology
Semmannan Kalaiyarasu, Niranjan Mishra, Saravanan Subramaniam, Dashprakash Moorthy, Shashi Bhusan Sudhakar, Vijendra Pal Singh, Aniket Sanyal
Summary: This study determined the full-genome sequences of three new clades (c, d, and e) of HoBiPeV and performed genetic and evolutionary analyses. It revealed the existence of four main clades (a, c, d, and e) globally, with genetic divergence ranging from 13.0% to 18.2%. The study suggested that HoBiPeV most likely originated in India in 1938, providing new insights into its origin and evolution.
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.
Article
Geriatrics & Gerontology
Knut Sindre Molmen, Daniel Hammarstrom, Karianne Pedersen, Anne Cecilie Lian Lie, Ragnvald B. Steile, Havard Nygaard, Yusuf Khan, Havard Hamarsland, Lise Koll, Marita Hanestadhaugen, Atle Lie Eriksen, Eirik Grindaker, Jon Elling Whist, Daniel Buck, Rafi Ahmad, Tor A. Strand, Bent R. Ronnestad, Stian Ellefsen
Summary: The study findings suggest that vitamin D-3 supplementation does not significantly affect muscular responses to resistance training in older adults with or without COPD.
JOURNAL OF CACHEXIA SARCOPENIA AND MUSCLE
(2021)
Editorial Material
Biology
Maria Vittoria Modica, Rafi Ahmad, Stuart Ainsworth, Gregor Anderluh, Agostinho Antunes, Dimitris Beis, Figen Caliskan, Mauro Dalla Serra, Sebastien Dutertre, Yehu Moran, Ayse Nalbantsoy, Naoual Oukkache, Stano Pekar, Maido Remm, Bjoern Marcus von Reumont, Yiannis Sarigiannis, Andrea Tarallo, Jan Tytgat, Eivind Andreas Baste Undheim, Yuri Utkin, Aida Verdes, Aude Violette, Giulia Zancolli
Summary: Venom research is a highly multidisciplinary field involving various subfields of biology, informatics, pharmacology, medicine, and other areas. However, lack of coordination among different research teams hampers the full development of venom investigation and applications. The recently launched European Venom Network aims to promote synergistic interactions among stakeholders and foster venom research at the European level.
Article
Medicine, Research & Experimental
Knut Sindre Molmen, Daniel Hammarstrom, Gunnar Slettalokken Falch, Morten Grundtvig, Lise Koll, Marita Hanestadhaugen, Yusuf Khan, Rafi Ahmad, Bente Malerbakken, Tore Jorgen Rodolen, Roger Lien, Bent R. Ronnestad, Truls Raastad, Stian Ellefsen
Summary: Despite the well-known pathophysiologies associated with COPD, resistance training led to improvements in lower-limb muscle strength, muscle mass, muscle quality, and endurance performance in COPD subjects, resembling or exceeding responses seen in healthy controls. These findings highlight the largely unrecognized responsiveness of COPD patients to resistance training and suggest it as a potent measure to relieve disease-related impairments.
JOURNAL OF TRANSLATIONAL MEDICINE
(2021)
Article
Genetics & Heredity
Cecilie Baekkedal Sonnenberg, Peik Haugen
Summary: This study investigates the genome of Pseudoalteromonadaceae and finds that core/softcore genes are significantly overrepresented in late replicating sectors of the chromid. Gene expression trends downward with increasing distance from the chromosomal oriC. The data strongly suggest that the chromid originates from a plasmid acquired in a relatively recent event.
G3-GENES GENOMES GENETICS
(2021)
Article
Microbiology
Abdolrahman Khezri, Ekaterina Avershina, Rafi Ahmad
Summary: This study utilized different sequencing platforms to sequence bacteria from clinical samples and tested multiple genome assembly methods. The results indicated that hybrid assembly performed better in predicting factors related to microbial pathogenicity.
Article
Microbiology
Ekaterina Avershina, Stephan A. Frye, Jawad Ali, Arne M. Taxt, Rafi Ahmad
Summary: This study investigates the suitability of the Oxford Nanopore Technology's Flongle sequencing platform for real-time sequencing of bacteria and detection of antibiotic resistance genes directly from blood cultures. The results show that Flongle data allows rapid bacterial identification and detection of resistance genes, although the identification of ARG variants may not always correspond with other sequencing methods.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Genetics & Heredity
Betty M. N. Furulund, Bard O. Karlsen, Igor Babiak, Peik Haugen, Steinar D. Johansen
Summary: Group I introns in myxomycetes, a distinct protist phylum, exhibit dynamic structures and complex inheritance patterns. The consensus secondary structure reveals a conserved core and RNA sequence complexity in the peripheral regions. These introns possess various structural organizations, including twintron organization and direct repeat arrays. Phylogenetic analyses indicate both vertical and horizontal transfers. The evolutionary history involves the insertion of mobile-type introns, degradation of homing endonuclease genes, and ultimately complete loss of the introns.
Article
Biochemical Research Methods
Yusuf Khan, Daniel Hammarstrom, Stian Ellefsen, Rafi Ahmad
Summary: The choice of data normalization method is crucial for interpreting gene expression data, especially in studies involving cellular plasticity. This study analyzed RNA-seq data from human skeletal muscle undergoing exercise training and found that different normalization modes led to different conclusions. Scientists should be explicit with their normalization strategies and interpret gene expression analyses with caution.
BMC BIOINFORMATICS
(2022)
Article
Genetics & Heredity
Kjersti Lian, Betty M. N. Furulund, Anders A. Tveita, Peik Haugen, Steinar D. Johansen
Summary: The study analyzed nuclear L2066 group I introns from myxomycetes and ascomycetes, revealing the presence of mobile-type introns with homing endonuclease genes. In vitro and in vivo experiments demonstrated the mechanism of double-strand break at the DNA insertion site by these introns.
Article
Microbiology
Asal Ahmadi, Abdolrahman Khezri, Havard Norstebo, Rafi Ahmad
Summary: In this study, a method for efficient removal of host DNA and enrichment of bacterial DNA directly from mastitis milk samples was developed. This method utilized nanopore-based metagenomic sequencing and allowed for real-time detection of the pathogen and antimicrobial resistance genes, offering a potential adaptable approach for clinical management of mastitis.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Nanoscience & Nanotechnology
Sathi Das, Kanchan Saxena, Jean-Claude Tinguely, Arijit Pal, Nima L. Wickramasinghe, Abdolrahman Khezri, Vishesh Dubey, Azeem Ahmad, Vivekanandan Perumal, Rafi Ahmad, Dushan N. Wadduwage, Balpreet Singh Ahluwalia, Dalip Singh Mehta
Summary: Antimicrobial resistance (AMR) is a global health threat. Surface-enhanced Raman spectroscopy (SERS) can be used for real-time and sensitive detection of bacteria, providing a promising solution for culture-free bacterial detection.
ACS APPLIED MATERIALS & INTERFACES
(2023)
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.
Proceedings Paper
Nanoscience & Nanotechnology
Niall Hanrahan, Adam Lister, Callum Highmore, Leena Rajith, Ekaterina Avershina, Jawad Ali, Rafi Ahmad, Jeremy Webb, Sumeet Mahajan
Summary: This paper describes the application of multi-excitation surface enhanced Raman spectroscopy (MX-SERS) in robust strain-level bacteria identification. Compared to the previous multi-excitation Raman spectroscopy (MX-Raman), MX-SERS has faster data acquisition speed and lower laser power. The researchers also fabricated a simple and low-cost SERS-active substrate, which shows potential in clinical diagnostics and pathogen detection.
ENHANCED SPECTROSCOPIES AND NANOIMAGING 2022
(2022)
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)