Article
Genetics & Heredity
Yanjie Shang, Lipin Ren, Xiangyan Zhang, Yi Li, Changquan Zhang, Yadong Guo
Summary: The Calliphoridae (blowflies) are important for forensic science, veterinary management, medical science, and economic issues. This study presents a comparative analysis of mitochondrial genomes among the Calliphoridae and reconstructs the phylogenetic relationship of this family within the larger context of the other Oestroidea. The results indicate that the gene arrangement, codon usage, and base composition are conserved within the Calliphoridae, and the Chrysomyinae are sister taxon to Luciliinae + Calliphorinae.
FRONTIERS IN GENETICS
(2022)
Article
Biochemical Research Methods
Mandy Ibene, Audrey Legendre, Guillaume Postic, Eric Angel, Fariza Tahi
Summary: RNAs can interact with other molecules to form complexes and predicting the structure of these complexes is important but challenging. This study focuses on RNA complexes composed of multiple interacting RNAs and shows how existing knowledge and probing data can help predict their secondary structure. The researchers developed an interactive tool called C-RCPRed, based on a multi-objective optimization algorithm, and demonstrated its efficiency and the positive impact of considering user knowledge and probing data through extensive benchmarking. C-RCPRed is freely available as an open-source program and web server on the EvryRNA website.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biodiversity Conservation
Arianna Thomas-Cabianca, Martin H. Villet, Anabel Martinez-Sanchez, Santos Rojo
Summary: This study developed an annotated checklist of 73 species of Rhiniinae in South Africa, based on entomological collections from Africa, Europe, and North America. It identified nine new species records and provided novel biological and seasonality information, historical occurrence maps, and high-definition photographs for each species.
BIODIVERSITY DATA JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Tzu-Hsien Yang, Yu-Cian Lin, Min Hsia, Zhan-Yi Liao
Summary: This research implemented a web service called SSRTool for ranking and evaluating predicted structures of a given sequence. Based on computed species-specific interpretability significance, SSRTool provides functions for ranking user-generated predictions, automated prediction and ranking for a given sequence, and inferring the functional aspects of a given structure.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemical Research Methods
Tzu-Hsien Yang
Summary: A novel method was proposed in this research to identify the functionally interpretable structure ensemble of a given RNA sequence and provide the meta-stable structure based on the ensemble. The method outperformed existing tools in predicting meta-stable structures and showed resistance to sequence length-dependent performance deterioration. The study demonstrated the importance of considering RNA structure ensembles for functional hypotheses.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Article
Virology
Simon Poblete, Horacio V. Guzman
Summary: Studying the three-dimensional reconstruction of RNA is crucial for understanding the functions of proteinaceus capsids, but RNA self-association remains an open question. Recent chemical probing reports provide reliable secondary structures of diverse RNA ensembles. The proposed method combines a coarse-grained model with a subdomain composition scheme to reconstruct the complete 3D structure of RNA genomes based on experimental techniques.
Article
Entomology
Jose Orlando de Almeida Silva, Fernando da Silva Carvalho-Filho, Leandro Juen, Maria Cristina Esposito
Summary: This research describes the process of ecological succession by studying the decomposition of pig carcasses and its association with flies from the Calliphoridae family. The findings suggest that different species of flies are associated with different stages of decomposition and can be used as indicators in forensic investigations.
JOURNAL OF MEDICAL ENTOMOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Margherita A. G. Matarrese, Alessandro Loppini, Martina Nicoletti, Simonetta Filippi, Letizia Chiodo
Summary: The study of RNA structure is crucial in understanding RNA molecular functioning. With the flexibility of RNA, the large number of expressed RNAs, and the diverse functions they have, it is difficult to obtain structural information on the same scale as is available for proteins. In silico prediction of RNA 3D structures is particularly important to understand the relationship between structure and function, as the 3D structure plays a significant role in molecular interactions with DNA or protein complexes. The accuracy of RNA 3D structure prediction relies on a properly predicted or measured secondary structure. This paper comparatively evaluates computational tools for modeling RNA secondary structure, focusing on freely available web-server versions for more accessible use. The evaluation focuses on the performance for long sequences and aims to select the best methods for investigating long non-coding RNAs (lncRNAs), which are of special relevance due to their involvement in regulatory mechanisms.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemical Research Methods
Thomas Binet, Berangere Avalle, Miraine Davila Felipe, Irene Maffucci
Summary: AptaMat, a simple and sensitive algorithm, has been developed for comparing the secondary structures of single-stranded nucleic acids (ssNAs). It outperforms other commonly used metrics in discriminating similar structures and correctly classifying RFAM families during clustering.
Review
Biochemical Research Methods
Kengo Sato, Michiaki Hamada
Summary: Computational analysis of RNA sequences plays a crucial role in RNA biology. In recent years, the incorporation of artificial intelligence and machine learning techniques into RNA sequence analysis has gained significant traction. Machine learning-based approaches have shown remarkable advancements, enhancing the precision of sequence analysis related to RNA secondary structures. Furthermore, artificial intelligence and machine learning innovations are also applied in the analysis of RNA-small molecule interactions, RNA drug discovery, and the design of RNA aptamers.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Kengo Sato, Yuki Kato
Summary: Pseudoknots are important RNA structural elements involved in various biological phenomena. Current methods for secondary structure prediction considering pseudoknots are not widely available. We propose an improved version of IPknot that enables linear time calculation and automatic selection of optimal threshold parameters.
BRIEFINGS IN BIOINFORMATICS
(2022)
Review
Pharmacology & Pharmacy
Christopher L. Haga, Donald G. Phinney
Summary: Traditionally, therapeutic treatment of disease has focused on targeting proteins, with RNA largely ignored as a druggable target. Recent studies suggest that only a small percentage of disease-associated proteins can be targeted with drugs.
EXPERT OPINION ON DRUG DISCOVERY
(2023)
Review
Virology
Siwy Ling Yang, Riccardo Delli Ponti, Yue Wan, Roland G. Huber
Summary: This review article summarizes the importance of RNA viruses and their impact on society and the economy. It presents the significance of studying genome folding and the use of computational and high-throughput RNA structure-mapping approaches. The focus is on the genome structures of dengue, Zika, and SARS-CoV-2 viruses.
Article
Biochemistry & Molecular Biology
Barbara Szutkowska, Klaudia Wieczorek, Ryszard Kierzek, Pawel Zmora, Jake M. Peterson, Walter N. Moss, David H. Mathews, Elzbieta Kierzek
Summary: This study proposes a secondary structure for segment 8 vRNA of A/California/04/2009 (H1N1) for the first time and highlights the location of conserved structural motifs within IAV strains. The research has implications for understanding the functionality of viral RNA structures and developing inhibition methods against influenza A virus.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemical Research Methods
L. A. Bugnon, A. A. Edera, S. Prochetto, M. Gerard, J. Raad, E. Fenoy, M. Rubiolo, U. Chorostecki, T. Gabaldon, F. Ariel, L. E. Di Persia, D. H. Milone, G. Stegmayer
Summary: This study compares the performance of classical methods and recently proposed approaches for predicting RNA secondary structure, and introduces a new metric based on chemical probing data to assess their predictive performance. The results provide a comprehensive assessment and a benchmark resource for future approaches.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Gastroenterology & Hepatology
Balakrishnan N. V. Premkrishnan, Cassie E. Heinle, Akira Uchida, Rikky W. Purbojati, Kavita K. Kushwaha, Alexander Putra, Puramadathil Sasi Santhi, Benjamin W. Y. Khoo, Anthony Wong, Vineeth Kodengil Vettath, Daniela I. Drautz-Moses, Ana Carolina M. Junqueira, Stephan C. Schuster
Summary: Bacillus cereus is commonly found in nature and can cause foodborne illnesses. Analysis of whole-genome sequences from two strains isolated from air showed a diarrheal potential, with resistance to ampicillin and fosfomycin but susceptibility to ciprofloxacin, tetracycline, and vancomycin.
Article
Zoology
Arianna Thomas-Cabianca, Anabel Martinez-Sanchez, Martin H. Villet, Santos Rojo
Summary: This study revised the taxonomy of the exclusive Afrotropical genus Fainia, recognizing three valid species and providing identification tools and updated distribution records.
Article
Biotechnology & Applied Microbiology
Irvan Luhung, Akira Uchida, Serene B. Y. Lim, Nicolas E. Gaultier, Carmon Kee, Kenny J. X. Lau, Elena S. Gusareva, Cassie E. Heinle, Anthony Wong, Balakrishnan N. Premkrishnan, Rikky W. Purbojati, Enzo Acerbi, Hie Lim Kim, Ana C. M. Junqueira, Sharon Longford, Sachin R. Lohar, Zhei Hwee Yap, Deepa Panicker, Yanqing Koh, Kavita K. Kushwaha, Poh Nee Ang, Alexander Putra, Daniela Drautz-Moses, Stephan C. Schuster
Summary: The study focuses on the microbial ecology of terrestrial, aquatic, and atmospheric ecosystems, with a particular emphasis on analyzing ultra-low biomass air samples. By developing an ultra-low biomass pipeline, researchers are able to significantly reduce sampling times while still maintaining species-level identification through metagenomic sequencing. The pipeline is robust across various climatic settings and can be adapted to analyze ultra-low biomass samples from environments like dust and surfaces.
NPJ BIOFILMS AND MICROBIOMES
(2021)
Article
Entomology
Martin H. Villet, Shelley Edwards
Summary: The cicada genus Tugelana Distant, 1912 is monotypic and endemic to south-eastern Africa, closely related to the Platypleura genus. The species Tugelana butleri and Platypleura zuluensis show a close relationship within the African clade of Platypleura.
AFRICAN INVERTEBRATES
(2021)
Article
Multidisciplinary Sciences
Daniel F. Paulo, Ana C. M. Junqueira, Alex P. Arp, Andre S. Vieira, Jorge Ceballos, Steven R. Skoda, Adalberto A. Perez-de-Leon, Agustin Sagel, William O. McMillan, Maxwell J. Scott, Carolina Concha, Ana M. L. Azeredo-Espin
Summary: The genetics behind obligate ectoparasitism in blowflies has been largely unknown. A study found that a specific gene mutation can affect foraging and host-seeking behaviors in blowflies. This suggests that olfaction plays a central role in niche specialization within this group.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Dalton de Souza Amorim, Brian Brown, Danilo Boscolo, Rosaly Ale-Rocha, Deivys Moises Alvarez-Garcia, Maria Isabel P. A. Balbi, Alan de Marco Barbosa, Renato Soares Capellari, Claudio Jose Barros de Carvalho, Marcia Souto Couri, Rodrigo de Vilhena Perez Dios, Diego Aguilar Fachin, Gustavo B. Ferro, Heloisa Fernandes Flores, Livia Maria Frare, Filipe Macedo Gudin, Martin Hauser, Carlos Jose Einicker Lamas, Kate G. Lindsay, Marco Antonio Tonus Marinho, Dayse Willkenia Almeida Marques, Stephen A. Marshall, Catia Mello-Patiu, Marco Antonio Menezes, Mirian Nunes Morales, Silvio S. Nihei, Sarah Siqueira Oliveira, Gabriela Pirani, Guilherme Cunha Ribeiro, Paula Raille Riccardi, Marcelo Domingos de Santis, Daubian Santos, Josenilson Rodrigues dos Santos, Vera Cristina Silva, Eric Matthew Wood, Jose Albertino Rafael
Summary: Tropical forests are known for their high biodiversity, but quantifying the abundance and species richness of insects in these forests is a challenge. This study examined the variability of insect fauna across a vertical canopy gradient in a tropical forest in the Amazon. The researchers collected insect samples using traps set at different heights and found that certain insect orders were more abundant at the ground level, while others were more abundant in the upper levels of the canopy. They also identified a large number of species that were not sampled at the ground level, suggesting the need for a more comprehensive understanding of the three-dimensional distribution of insect diversity in tropical forests for effective conservation strategies.
SCIENTIFIC REPORTS
(2022)
Article
Biodiversity Conservation
Benjamin Miller, Martin Villet, John Mark Midgley
Summary: This study reports the first record of intrusive fluid feeding on vertebrate carrion by Philoliche rondani, highlighting the rarity of such observations in nature.
BIODIVERSITY DATA JOURNAL
(2022)
Article
Entomology
Daniel F. Paulo, Alex Y. Cha, Angela N. Kauwe, Keena Curbelo, Renee L. Corpuz, Tyler J. Simmonds, Sheina B. Sim, Scott M. Geib
Summary: In recent years, many studies have utilized CRISPR/Cas9 technology to conduct gene editing research in fruit flies, creating new strains and proposing a unified candidate gene knockout protocol. High rates of somatic and germline mutagenesis were induced by microinjection of CRISPR/Cas9 components into fruit fly embryos, showcasing the efficiency of the method.
JOURNAL OF ECONOMIC ENTOMOLOGY
(2022)
Article
Biodiversity Conservation
Arianna Thomas-Cabianca, Martin H. Villet, Anabel Martinez-Sanchez, Santos Rojo
Summary: This study developed an annotated checklist of 73 species of Rhiniinae in South Africa, based on entomological collections from Africa, Europe, and North America. It identified nine new species records and provided novel biological and seasonality information, historical occurrence maps, and high-definition photographs for each species.
BIODIVERSITY DATA JOURNAL
(2023)
Article
Entomology
Martin H. Villet
Summary: Jason G.H. Londt contributed a significant portion of Cicadidae specimens to the KwaZulu-Natal Museum, including a notable collection of female specimens and the most comprehensive collection of African records of predation on cicadas by robber flies to date. The collection reveals that robber flies primarily target male cicadas, potentially due to a higher failure rate in attacking the heavier-bodied females. The metadata obtained from these specimens also serve as a small gazetteer of Londt's collecting sites.
AFRICAN INVERTEBRATES
(2023)
Article
Biochemistry & Molecular Biology
Alexandre Pedro Selvatti, Filipe Romero Rebello Moreira, Daniel Cardoso Carvalho, Francisco Prosdocimi, Claudia Augusta de Moraes Russo, Ana Carolina Martins Junqueira
Summary: This study used mitochondrial genomes and nuclear orthologs to investigate the divergence time of turtles. The findings suggest that the split of Testudines occurred in the Early Jurassic, associated with the fragmentation of Pangaea and the formation of saltwater barriers. The divergence of Pleurodira coincided with Late Jurassic and Early Cretaceous geologic events, while Cryptodira remained in Laurasia and diversified during the Cenozoic. The study also provides a detailed hypothesis of Cryptodira evolution in the Southern Hemisphere correlated with landmass contacts derived from Gondwana and Laurasia.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Kenny J. X. Lau, Elena S. Gusareva, Irvan Luhung, Balakrishnan N. V. Premkrishnan, Anthony Wong, Tuang Yeow Poh, Akira Uchida, Elaine L. Oliveira, Daniela I. Drautz-Moses, Ana Carolina M. Junqueira, Stephan C. Schuster
Summary: The analysis of phyllosphere microbiomes traditionally relied on DNA extracted from whole leaves. Swabs collected from the adaxial and abaxial leaf surfaces of two garden plants, Rhapis excelsa and Cordyline fruticosa, showed that the abaxial surface had fewer bacteria compared to the adaxial surface. Our co-occurrence network analysis revealed that bacteria were predominantly found on the adaxial surface, while only a small group of leaf blotch fungi thrived on the abaxial surface. This suggests that the abaxial leaf surface has distinct characteristics and reduced microbial diversity, likely due to plant-microbe interactions.
Article
Zoology
Luis Gustavo Moreli Tauhyl, Marco Antonio Tonus Marinho, Maria Virginia Urso-Guimaraes
Summary: Toxotarsinae is a subfamily of Calliphoridae with controversial classification. We conducted the first study to understand the transformation series of controversial characters and establish a valid classification system. Our results suggest that genera like Sarconesia and Neta do not accurately reflect the evolutionary lineages in the subfamily and should not be considered as valid. Toxotarsus, on the other hand, was consistently recovered as monophyletic and should include all known species of Toxotarsinae.
Article
Medicine, Legal
John Mark Midgley, Martin Herrer Villet
Summary: Accurate age estimates of immature necrophagous insects associated with a human or animal body can provide evidence of how long the body has been dead. Many professionals who produce or use identified organisms as forensic evidence have little training in taxonomy or metrology, and appreciate the availability of formalized principles and standards for biological identification. Relevant criteria for good characters include high repeatability (including low scope for ambiguity or parallax effects), pronounced discreteness, and small relative error in measurements.
FORENSIC SCIENCES RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Markus Osaland Fjelde, Einar Timdal, Reidar Haugan, Mika Bendiksby
Summary: This study investigated the taxonomy of the crustose lichen genus Calvitimela using molecular phylogenetics and morphological observations. The results revealed evolutionarily old and deeply divergent lineages within Calvitimela, with overlapping morphological characters between different subgenera. Chemical characters were informative at the level of subgenera but often homoplastic at the species level. A practical taxonomy of Calvitimela was proposed based on these findings.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Bo-Yang Shi, Da Pan, Kang-Qin Zhang, Tian-Yu Gu, Darren C. J. Yeo, Peter K. L. Ng, Neil Cumberlidge, Hong-Ying Sun
Summary: This study investigates the evolutionary history and speciation mechanisms of montane potamids in the Hengduan Mountains Region. The results suggest that the vicariance events of these crabs are correlated with the emergence of sky islands due to the uplift of the mountains. The mountain ridges provided corridors for their dispersal and past climatic conditions played a crucial role in their evolutionary history. The mechanisms isolating sky islands are reinforced by the climatic features of dry-hot valleys and continue to affect local diversification.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Attila Nemeth, Edvard Mizsei, Levente Laczko, David Czaban, Zsolt Hegyeli, Szabolcs Lengyel, Gabor Csorba, Gabor Sramko
Summary: Species delimitation of European blind mole rats is challenging due to their small morphological differences and complex chromosomal evolution. This study provides a comprehensive framework to improve understanding of their evolutionary history and revise their taxonomy. The results reveal the presence of multiple superspecies and species, with distinct geographic patterns and rapid chromosomal evolution.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Ying Qi, Zhaoyan Zhong, Xu Liu, Xing He, Yadong Zhou, Lili Zhang, Chong Chen, Katrin Linse, Jian-Wen Qiu, Jin Sun
Summary: This study investigates the phylogenetic relationships among patellogastropod families using mitochondrial and phylogenomic data. The results show that the mitochondrial phylogeny recovers monophyly of most families, but the relationships among families are still contentious. However, a more robust family-level topology consistent with morphology is achieved by phylogenomics. Additionally, the mainly deep-water families are found to be monophyletic, suggesting a single colonization of the deep water during the Jurassic.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Yu-Jie Shi, Jin -Liang Huang, Jia-Xuan Mi, Jing Li, Fan-Yu Meng, Yu Zhong, Fang He, Fei -Fei Tian, Fan Zhang, Liang-Hua Chen, Han-Bo Yang, Hong-Lin Hu, Xue-Qin Wan
Summary: Despite numerous studies on hybrid speciation, our understanding of this process remains limited. In this study, we conducted an 18-year systematic investigation on Populus taxa on the Qinghai-Tibet Plateau and discovered three new taxa that originated from distant hybridization between two different sections. These hybrid taxa demonstrate greater ecological adaptability than their ancestral species due to heterosis. We propose a hybrid speciation process model that can explain important evolutionary concerns.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Anna Cho, Denis Tikhonenkov, Gordon Lax, Kristina I. Prokina, Patrick J. Keeling
Summary: Unlike conspicuous ochrophytes, many small and overlooked flagellates belonging to basally branching stramenopiles remain poorly characterized at the cellular or genomic level. This study describes four new species, including two new genera, of sediment-dwelling MAST-6 and provides updated phylogenomic tree of stramenopiles. The characterization of these flagellates is important due to their phylogenetic diversity and abundance in various environments.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Tian-Tian Xue, Steven B. Janssens, Bin-Bin Liu, Sheng-Xiang Yu
Summary: Phylogenomic conflicts are widespread among genomic data, with most previous studies primarily focusing on nuclear datasets instead of organellar genomes. In this study, we investigated the phylogenetic conflicts within and between plastid and mitochondrial genomes using Potentilla as a case study. We found that both plastid and mitochondrial genomes divided Potentilla into eight highly supported clades, with two newly identified clades. Our results demonstrate that mitochondrial genes can fully resolve phylogenetic relationships among major clades of Potentilla and are not always linked with plastomes in evolutionary history.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Alexandra A. Grossi, Chunpo Tian, Mengjiao Ren, Fasheng Zou, Daniel R. Gustafsson
Summary: This study suggests that the coevolutionary relationships between chewing lice, endosymbiotic bacteria, and birds are not independent, but the patterns vary depending on the analysis method used. Additionally, louse host-switching does not seem to affect bacterial strains.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Ingrid Olivares, Sergio Tusso, Maria Jose Sanin, Marylaure de La Harpe, Oriane Loiseau, Jonathan Rolland, Nicolas Salamin, Michael Kessler, Kentaro K. Shimizu, Margot Paris
Summary: Traditionally, differences between species have been associated with morphological variation. However, the discovery of cryptic diversity suggests that the evolution of distinct lineages can occur without morphological differences. Through genetic analysis, we found that a tropical montane plant lineage is composed of numerous unrecognized genetic groups that are not morphologically distinct. Geographic distance and topography play a crucial role in determining the genetic divergence of these groups.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)