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JOURNAL ARTICLE
M J N Thomas, M A Brockhurst, K Z Coyte
UNLABELLED: Temperate bacteriophages (phages) are common features of bacterial genomes and can act as self-amplifying biological weapons, killing susceptible competitors and thus increasing the fitness of their bacterial hosts (lysogens). Despite their prevalence, however, the key characteristics of an effective temperate phage weapon remain unclear. Here, we use systematic mathematical analyses coupled with experimental tests to understand what makes an effective temperate phage weapon...
May 10, 2024: MSystems
#2
JOURNAL ARTICLE
Zilong Yang, Zili Chai, Xia Wang, Zehan Zhang, Fengwei Zhang, Fuqiang Kang, Wenting Liu, Hongguang Ren, Yuan Jin, Junjie Yue
Some Brucella spp. are important pathogens. According to the latest prokaryotic taxonomy, the Brucella genus consists of facultative intracellular parasitic Brucella species and extracellular opportunistic or environmental Brucella species. Intracellular Brucella species include classical and nonclassical types, with different species generally exhibiting host preferences. Some classical intracellular Brucella species can cause zoonotic brucellosis, including B. melitensis , B. abortus , B. suis , and B. canis ...
2024: Frontiers in Microbiology
#3
JOURNAL ARTICLE
Alíz T Y Owolabi, Petra Schneider, Sarah E Reece
Most malaria ( Plasmodium spp.) parasite species undergo asexual replication synchronously within the red blood cells of their vertebrate host. Rhythmicity in this intraerythrocytic developmental cycle (IDC) enables parasites to maximise exploitation of the host and align transmission activities with the time of day that mosquito vectors blood feed. The IDC is also responsible for the major pathologies associated with malaria, and plasticity in the parasite's rhythm can confer tolerance to antimalarial drugs...
May 2024: Evolutionary Applications
#4
JOURNAL ARTICLE
An Zhou, Wei Zhang, Xueling Ge, Qi Liu, Fang Luo, Shuhua Xu, Wei Hu, Yan Lu
BACKGROUND: Schistosomiasis is a neglected tropical disease that afflicts millions of people worldwide; it is caused by Schistosoma, the only dioecious flukes with ZW systems. Schistosoma japonicum is endemic to Asia; the Z chromosome of S. japonicum comprises one-quarter of the entire genome. Detection of positive selection using resequencing data to understand adaptive evolution has been applied to a variety of pathogens, including S. japonicum. However, the contribution of the Z chromosome to evolution and adaptation is often neglected...
May 8, 2024: Parasites & Vectors
#5
JOURNAL ARTICLE
Shuchen Feng, Gail E Reid, Nina M Clark, Amanda Harrington, Susan L Uprichard, Susan C Baker
BACKGROUND: The factors contributing to the accelerated convergent evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are not fully understood. Unraveling the contribution of viral replication in immunocompromised patients is important for the early detection of novel mutations and developing approaches to limit COVID-19. METHODS: We deep sequenced SARS-CoV-2 RNA from 192 patients (64% hospitalized, 39% immunosuppressed) and compared the viral genetic diversity within the patient groups of different immunity and hospitalization status...
May 7, 2024: Virology Journal
#6
JOURNAL ARTICLE
Elena Radaelli, Giorgia Palladino, Enrico Nanetti, Daniel Scicchitano, Simone Rampelli, Sabina Airoldi, Marco Candela, Marianna Marangi
Despite their critical roles in marine ecosystems, only few studies have addressed the gut microbiome (GM) of cetaceans in a comprehensive way. Being long-living apex predators with a carnivorous diet but evolved from herbivorous ancestors, cetaceans are an ideal model for studying GM-host evolutionary drivers of symbiosis and represent a valuable proxy of overall marine ecosystem health. Here, we investigated the GM of eight different cetacean species, including both Odontocetes (toothed whales) and Mysticetes (baleen whales), by means of 16S rRNA-targeted amplicon sequencing...
May 5, 2024: Science of the Total Environment
#7
JOURNAL ARTICLE
Zhen Wang, Lars Vilhelmsen, Alexandr P Rasnitsyn, Alexandra Viertler, Chungkun Shih, Shanshan Wen, Hongru Yang, Qiong Wu, Yanjie Zhang, Dong Ren, Taiping Gao
Insects have evolved complex sensory systems that are important for feeding, defence and reproduction. Parasitoid wasps often spend much time and effort in searching for concealed hosts with the help of specialized sensilla. However, the early evolution of such behaviour and sensilla is poorly known. We describe two fossil female wasps, †Tichostephanus kachinensis sp. nov. and †Tichostephanus longus sp. nov., from mid-Cretaceous Kachin amber. Phylogenetic analyses based on morphological data retrieved †Tichostephanus as deeply nested within Evanioidea and closely related to extant Gasteruptiidae and Evaniidae...
May 7, 2024: Cladistics
#8
Khavong Pha, Katherine Mirrashidi, Jessica Sherry, Cuong Joseph Tran, Clara M Herrera, Eleanor McMahon, Cherilyn A Elwell, Joanne N Engel
Chlamydia trachomatis, a leading cause of bacteria sexually transmitted infections, creates a specialized intracellular replicative niche by translocation and insertion of a diverse array of effectors (Incs) into the inclusion membrane. Here, we characterize IncE, a multi-functional Inc that encodes two non-overlapping short linear motifs (SLiMs) within its short cytosolic C-terminus. The proximal SLiM mimics an R-SNARE motif to recruit syntaxin (STX) 7 and 12-containing vesicles to the inclusion. The distal SLiM mimics the Sorting Nexin (SNX) 5 and 6 cargo binding site to recruit SNX6-containing vesicles to the inclusion...
April 24, 2024: bioRxiv
#9
JOURNAL ARTICLE
Samsuddin Ahmad Syazwan, Ahmad Mohd-Farid, Shiou Yih Lee, Rozi Mohamed
The decline ofAcacia mangiumWilld. in Malaysia, especially in Sabah since 2010, is primarily due toCeratocystiswilt and canker disease (CWCD) caused by theCeratocystis fimbriataEllis & Halst. complex. This study was aimed to investigate the mitochondrial genome architecture of two differentC. fimbriatacomplex isolates from Malaysia: one fromA. mangiumin Pahang (FRIM1162) and another fromEucalyptus pellitain Sarawak (FRIM1441). This research employed Next- Generation Sequencing (NGS) to contrast genomes from diverse hosts with nine additional mitochondrial sequences, identifying significant genetic diversity and mutational hotspots in the mitochondrial genome alignment...
May 4, 2024: Gene
#10
JOURNAL ARTICLE
Yachao Zuo, Jiawen Yang, Hao Zhang, Lu Li, Jing Luo, Yanrong Lv, Meijin Yuan, Kai Yang
Cnaphalocrocis medinalis granulovirus (CnmeGV), belonging to Betabaculovirus cnamedinalis, can infect the rice pest, the rice leaf roller. In 1979, a CnmeGV isolate, CnmeGV-EP, was collected from Enping County, China. In 2014, we collected another CnmeGV isolate, CnmeGV-EPDH3, at the same location and obtained the complete virus genome sequence using Illumina and ONT sequencing technologies. By combining these two virus isolates, we updated the genome annotation of CnmeGV and conducted an in-depth analysis of its genome features...
May 4, 2024: Virus Research
#11
REVIEW
Niloofar Faraji, Tahereh Zeinali, Farahnaz Joukar, Maryam Sadat Aleali, Narges Eslami, Mohammad Shenagari, Fariborz Mansour-Ghanaei
The rapid emergence of multiple strains of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has sparked profound concerns regarding the ongoing evolution of the virus and its potential impact on global health. Classified by the World Health Organization (WHO) as variants of concern (VOC), these strains exhibit heightened transmissibility and pathogenicity, posing significant challenges to existing vaccine strategies. Despite widespread vaccination efforts, the continual evolution of SARS-CoV-2 variants presents a formidable obstacle to achieving herd immunity...
May 15, 2024: Heliyon
#12
JOURNAL ARTICLE
Saba Kobakhidze, Stylianos Koulouris, Nata Kakabadze, Mamuka Kotetishvili
BACKGROUND: The in-depth understanding of the role of lateral genetic transfer (LGT) in phage-prophage interactions is essential to rationalizing phage applications for human and animal therapy, as well as for food and environmental safety. This in silico study aimed to detect LGT between phages of potential industrial importance and their hosts. METHODS: A large array of genetic recombination detection algorithms, implemented in SplitsTree and RDP4, was applied to detect LGT between various Escherichia, Listeria, Salmonella, Campylobacter, Staphylococcus, Pseudomonas, and Vibrio phages and their hosts...
May 4, 2024: BMC Microbiology
#13
JOURNAL ARTICLE
Aruljothi Ambalavanan, Mallana Gowdra Mallikarjuna, Shilpi Bansal, Bishnu Maya Bashyal, Sabtharishi Subramanian, Aundy Kumar, Ganesan Prakash
The investigation is the first report on genome-wide identification and characterization of NBLRR genes in pearl millet. We have shown the role of gene loss and purifying selection in the divergence of NBLRRs in Poaceae lineage and candidate CaNBLRR genes for resistance to Magnaporthe grisea infection. Plants have evolved multiple integral mechanisms to counteract the pathogens' infection, among which plant immunity through NBLRR (nucleotide-binding site, leucine-rich repeat) genes is at the forefront. The genome-wide mining in pearl millet (Cenchrus americanus (L...
May 4, 2024: Planta
#14
JOURNAL ARTICLE
Raghunath Singha, Pankaj Maity, Dipak Samanta
The dynamic interplay of coordination bonds within metal-organic cages offers a unique avenue for structural evolution in response to external stimuli, presenting a promising strategy for the construction of chiral assemblies. This adaptability is crucial for the selective synthesis of homochiral assemblies and advancement of asymmetric catalysis. In this study, we report the self-assembly of an achiral square-planar Pd(II) acceptor with a C2-symmetric tetrapyridyl donor resulted in the formation of a racemic mixture of the chiral octahedral cage Pd4L2...
May 3, 2024: Chemistry: a European Journal
#15
JOURNAL ARTICLE
Alice Fusaro, Bianca Zecchin, Edoardo Giussani, Elisa Palumbo, Montserrat Agüero-García, Claudia Bachofen, Ádám Bálint, Fereshteh Banihashem, Ashley C Banyard, Nancy Beerens, Manon Bourg, Francois-Xavier Briand, Caroline Bröjer, Ian H Brown, Brigitte Brugger, Alexander M P Byrne, Armend Cana, Vasiliki Christodoulou, Zuzana Dirbakova, Teresa Fagulha, Ron A M Fouchier, Laura Garza-Cuartero, George Georgiades, Britt Gjerset, Beatrice Grasland, Oxana Groza, Timm Harder, Ana Margarida Henriques, Charlotte Kristiane Hjulsager, Emiliya Ivanova, Zygimantas Janeliunas, Laura Krivko, Ken Lemon, Yuan Liang, Aldin Lika, Péter Malik, Michael J McMenamy, Alexander Nagy, Imbi Nurmoja, Iuliana Onita, Anne Pohlmann, Sandra Revilla-Fernández, Azucena Sánchez-Sánchez, Vladimir Savic, Brigita Slavec, Krzysztof Smietanka, Chantal J Snoeck, Mieke Steensels, Vilhjálmur Svansson, Edyta Swieton, Niina Tammiranta, Martin Tinak, Steven Van Borm, Siamak Zohari, Cornelia Adlhoch, Francesca Baldinelli, Calogero Terregino, Isabella Monne
Since 2016, A(H5Nx) high pathogenic avian influenza (HPAI) virus of clade 2.3.4.4b has become one of the most serious global threats not only to wild and domestic birds, but also to public health. In recent years, important changes in the ecology, epidemiology, and evolution of this virus have been reported, with an unprecedented global diffusion and variety of affected birds and mammalian species. After the two consecutive and devastating epidemic waves in Europe in 2020-2021 and 2021-2022, with the second one recognized as one of the largest epidemics recorded so far, this clade has begun to circulate endemically in European wild bird populations...
2024: Virus Evolution
#16
JOURNAL ARTICLE
Joel E Brame, Craig Liddicoat, Catherine A Abbott, Robert A Edwards, Jake M Robinson, Nicolas E Gauthier, Martin F Breed
Butyrate-producing bacteria are found in many outdoor ecosystems and host organisms, including humans, and are vital to ecosystem functionality and human health. These bacteria ferment organic matter, producing the short-chain fatty acid butyrate. However, the macroecological influences on their biogeographical distribution remain poorly resolved. Here we aimed to characterise their global distribution together with key explanatory climatic, geographical and physicochemical variables. We developed new normalised butyrate production capacity (BPC) indices derived from global metagenomic ( n = 13,078) and Australia-wide soil 16S rRNA ( n = 1331) data, using Geographic Information System (GIS) and modelling techniques to detail their ecological and biogeographical associations...
May 2024: Ecology and Evolution
#17
JOURNAL ARTICLE
Laura Solarte-Murillo, Humberto Reyes, Loreto Ojeda, Juan G Cárcamo, Juan Pablo Pontigo, Carlos A Loncoman
Piscine orthoreovirus (PRV) is a pathogen that causes heart and skeletal muscle inflammation in Salmo salar and has also been linked to circulatory disorders in other farmed salmonids, such as Oncorhynchus kisutch and Oncorhynchus mykiss . The virus has a segmented, double-stranded RNA genome, which makes it possible to undergo genetic reassortment and increase its genomic diversity through point mutations. In this study, genetic reassortment in PRV was assessed using the full genome sequences available in public databases...
April 2, 2024: Viruses
#18
JOURNAL ARTICLE
Maria E S Monteiro, Guilherme C Lechuga, Paloma Napoleão-Pêgo, João P R S Carvalho, Larissa R Gomes, Carlos M Morel, David W Provance, Salvatore G De-Simone
The worldwide spread of SARS-CoV-2 has led to a significant economic and social burden on a global scale. Even though the pandemic has concluded, apprehension remains regarding the emergence of highly transmissible variants capable of evading immunity induced by either vaccination or prior infection. The success of viral penetration is due to the specific amino acid residues of the receptor-binding motif (RBM) involved in viral attachment. This region interacts with the cellular receptor ACE2, triggering a neutralizing antibody (nAb) response...
March 22, 2024: Vaccines
#19
JOURNAL ARTICLE
Mingyue Zhang, Yanan Zhou, Xinyuan Cui, Lifeng Zhu
Bacteria and phages are two of the most abundant biological entities in the gut microbiome, and diet and host phylogeny are two of the most critical factors influencing the gut microbiome. A stable gut bacterial community plays a pivotal role in the host's physiological development and immune health. A phage is a virus that directly infects bacteria, and phages' close associations and interactions with bacteria are essential for maintaining the stability of the gut bacterial community and the entire microbial ecosystem...
March 31, 2024: Microorganisms
#20
JOURNAL ARTICLE
Ergin Sahin, Gulce Edis, Emre Keskin, Ilgaz Akata
Advancements in high-throughput sequencing and the development of new bioinformatics tools for large-scale data analysis play a crucial role in uncovering virus diversity and enhancing our understanding of virus evolution. The discovery of the ormycovirus clades, a group of RNA viruses that are phylogenetically distinct from all known Riboviria members and are found in fungi, highlights the value of these tools for the discovery of novel viruses. The aim of this study was to examine viral populations in fungal hosts to gain insights into the diversity, evolution, and classification of these viruses...
April 25, 2024: Archives of Virology
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