Chloroviruses (family
) are large double-stranded DNA (dsDNA) viruses that infect unicellular green algae present in inland waters. These viruses have been isolated using three main chlorella-like ...green algal host cells, traditionally called NC64A, SAG, and Pbi, revealing extensive genetic diversity. In this study, we performed a functional genomic analysis on 36 chloroviruses that infected the three different hosts. Phylogenetic reconstruction based on the DNA polymerase B family gene clustered the chloroviruses into three distinct clades. The viral pan-genome consists of 1,345 clusters of orthologous groups of genes (COGs), with 126 COGs conserved in all viruses. Totals of 368, 268, and 265 COGs are found exclusively in viruses that infect NC64A, SAG, and Pbi algal hosts, respectively. Two-thirds of the COGs have no known function, constituting the "dark pan-genome" of chloroviruses, and further studies focusing on these genes may identify important novelties. The proportions of functionally characterized COGs composing the pan-genome and the core-genome are similar, but those related to transcription and RNA processing, protein metabolism, and virion morphogenesis are at least 4-fold more represented in the core genome. Bipartite network construction evidencing the COG sharing among host-specific viruses identified 270 COGs shared by at least one virus from each of the different host groups. Finally, our results reveal an open pan-genome for chloroviruses and a well-established core genome, indicating that the isolation of new chloroviruses can be a valuable source of genetic discovery.
Chloroviruses are large dsDNA viruses that infect unicellular green algae distributed worldwide in freshwater environments. They comprise a genetically diverse group of viruses; however, a comprehensive investigation of the genomic evolution of these viruses is still missing. Here, we performed a functional pan-genome analysis comprising 36 chloroviruses associated with three different algal hosts in the family
, referred to as zoochlorellae because of their endosymbiotic lifestyle. We identified a set of 126 highly conserved genes, most of which are related to essential functions in the viral replicative cycle. Several genes are unique to distinct isolates, resulting in an open pan-genome for chloroviruses. This profile is associated with generalist organisms, and new insights into the evolution and ecology of chloroviruses are presented. Ultimately, our results highlight the potential for genetic diversity in new isolates.
Abstract
The phylum Nucleocytoviricota includes the largest and most complex viruses known. These “giant viruses” have a long evolutionary history that dates back to the early diversification of ...eukaryotes, and over time they have evolved elaborate strategies for manipulating the physiology of their hosts during infection. One of the most captivating of these mechanisms involves the use of genes acquired from the host—referred to here as viral homologs or “virologs”—as a means of promoting viral propagation. The best-known examples of these are involved in mimicry, in which viral machinery “imitates” immunomodulatory elements in the vertebrate defense system. But recent findings have highlighted a vast and rapidly expanding array of other virologs that include many genes not typically found in viruses, such as those involved in translation, central carbon metabolism, cytoskeletal structure, nutrient transport, vesicular trafficking, and light harvesting. Unraveling the roles of virologs during infection as well as the evolutionary pathways through which complex functional repertoires are acquired by viruses are important frontiers at the forefront of giant virus research.
The authors discuss recent research into the complex functions encoded in the genomes of giant viruses.
Orpheoviruses, cedratviruses, and pithoviruses are large DNA viruses that cluster together taxonomically within the order
Pimascovirales
of the phylum
Nucleocytoviricota
. However, they were not ...classified previously by the International Committee on Taxonomy of Viruses (ICTV). Here, we present a comprehensive analysis of the gene content, morphology, and phylogenomics of these viruses, providing data that underpinned the recent proposal to establish new taxa for their initial classification. The new taxonomy, which has now been ratified by the ICTV, includes the family
Orpheoviridae
and genus
Alphaorpheovirus
, the family
Pithoviridae
and genus
Alphapithovirus
, and the family
Cedratviridae
and genus
Alphacedratvirus
, aiming to formally catalogue the isolates covered in this study. Additionally, as per the newly adopted rules, we applied standardized binomial names for the virus species created to classify isolates with complete genome sequences available in public databases at the time of the proposal. The specific epithet of each virus species was chosen as a reference to the location where the exemplar virus was isolated.
Background
Despite the overwhelming evidence showing the influence of sex or obesity in the development of respiratory diseases in humans and animals, the mechanisms by which these combined two ...factors influence allergic asthma are not well understood.
Objective
We have investigated the interaction between sex and weight gain in an experimental model of lung allergic inflammation induced by chicken egg ovalbumin (OVA) in mice.
Methods
Animals were fed a high‐fat diet for 8 weeks and then sensitized and challenged with OVA.
Results
Our results demonstrate that in comparison with males, high‐fat diet (HFD) allergic female mice exhibit a reduction in the number of leucocytes in the lung lumen when challenged with OVA and, in contrast, an accumulation of these cells in the lung tissue. In addition, we also observed that allergic HFD female mice presented a robust lung remodelling in comparison with HFD males, evidenced by higher deposition of collagen in the airways and TGF‐β in lung fluid. Measuring epithelial adhesion molecule expression, we observed that female mice presented a significantly lower expression of CD103 than males in BAL cells, regardless of the diet. Similarly, HFD female mice express lower levels of EpCAM in lung tissue in comparison with males and lean females. Levels of A20/TNFAIP3 expression in lung tissue demonstrated that HFD female mice express lower levels of these regulatory factors than all the other groups. However, this reduction was not accompanied by an increase in activated NF‐κB.
Conclusions
Our results present evidence that the interaction between sex and weight gain alters the progression of allergic asthma in mice with females developing airway remodelling at a much earlier stage than males.
Clinical Relevance
These data may contribute to a better understanding of the clinical differences in the development and severity of allergic asthma observed between men and women of reproductive age.
Concerns have been raised regarding the potential negative effects on human health of water disinfectants used in swimming pools. Among the disinfection options, the approaches using chlorine‐based ...products have been typically preferred. Chlorine readily reacts with natural organic matter that are introduced in the water mainly through the bathers, leading to the formation of potentially harmful chlorination by‐products (CBPs). The formation of CBPs is of particular concern since some have been epidemiologically associated with the development of various clinical manifestations. The higher the concentration of volatile CBPs in the water, the higher their concentration in the air above the pool, and different routes of exposure to chemicals in swimming pools (water ingestion, skin absorption, and inhalation) contribute to the individual exposome. Some CBPs may affect the respiratory and skin health of those who stay indoor for long periods, such as swimming instructors, pool staff, and competitive swimmers. Whether those who use chlorinated pools as customers, particularly children, may also be affected has been a matter of debate. In this article, we discuss the current evidence regarding the health effects of both acute and chronic exposures in different populations (work‐related exposures, intensive sports, and recreational attendance) and identify the main recommendations and unmet needs for research in this area.
The
family is comprised of double-stranded DNA viruses belonging to nucleocytoplasmic large DNA viruses (NCLDV). Among the NCLDV, poxviruses exhibit the widest known host range, which is likely ...observed because this viral family has been more heavily investigated. However, relative to each member of the
family, the spectrum of the host is variable, where certain viruses can infect a large range of hosts, while others are restricted to only one host species. It has been suggested that the variability in host spectrum among poxviruses is linked with the presence or absence of some host range genes. Would it be possible to extrapolate the restriction of viral replication in a specific cell lineage to an animal, a far more complex organism? In this study, we compare and discuss the relationship between the host range of poxvirus species and the abundance/diversity of host range genes. We analyzed the sequences of 38 previously identified and putative homologs of poxvirus host range genes, and updated these data with deposited sequences of new poxvirus genomes. Overall, the term host range genes might not be the most appropriate for these genes, since no correlation between them and the viruses' host spectrum was observed, and a change in nomenclature should be considered. Finally, we analyzed the evolutionary history of these genes, and reaffirmed the occurrence of horizontal gene transfer (HGT) for certain elements, as previously suggested. Considering the data presented in this study, it is not possible to associate the diversity of host range factors with the amount of hosts of known poxviruses, and this traditional nomenclature creates misunderstandings.
The customization of polymeric prototypes is available to meet the specific needs of individual patients, considering tissue location and patient‐specific characteristics. Poly (butylene ...adipate‐co‐terephthalate) (PBAT) has shown great promise among various polymers in this scenario due to its biodegradability and processability properties. However, the effect of geometry changes on the mechanical properties of PBAT 3D scaffolds and their mechanical stability after in vitro degradation are crucial to determining the final application. This study focuses on the structural, morphological, and mechanical characterization of PBAT prototypes with different architectures and evaluating their mechanical properties before and after in vitro degradation. Three‐dimensional structures were 3D printed with rectilinear deposition angles of 15°, 30°, 45°, 60°, 75°, and 90°. Mechanical tests revealed that the prototype architecture influenced the stiffness, elongation, and maximum tension, where a greater resistance was observed for filaments containing the lowest angles. The thermal stability of PBAT remained unaffected either by reprocessing or hydrolytic degradation; however, in vitro degradation affected the mechanical behavior by increasing the stiffness and decreasing the elongation of the scaffold. Biological assays have demonstrated the nontoxic nature of PBAT and its potential to promote cell viability at a rate of 95%. These findings underscore the possibility of optimizing the PBAT design and structure to tune the mechanical properties and contribute to advancing tissue engineering strategies.
FDM/3D printing of PBAT with different filament orientations.
Here we report the discovery of two Tupanvirus strains, the longest tailed Mimiviridae members isolated in amoebae. Their genomes are 1.44-1.51 Mb linear double-strand DNA coding for 1276-1425 ...predicted proteins. Tupanviruses share the same ancestors with mimivirus lineages and these giant viruses present the largest translational apparatus within the known virosphere, with up to 70 tRNA, 20 aaRS, 11 factors for all translation steps, and factors related to tRNA/mRNA maturation and ribosome protein modification. Moreover, two sequences with significant similarity to intronic regions of 18 S rRNA genes are encoded by the tupanviruses and highly expressed. In this translation-associated gene set, only the ribosome is lacking. At high multiplicity of infections, tupanvirus is also cytotoxic and causes a severe shutdown of ribosomal RNA and a progressive degradation of the nucleus in host and non-host cells. The analysis of tupanviruses constitutes a new step toward understanding the evolution of giant viruses.
Purpose: To explore enhanced recovery after surgery (ERAS) components and their current application to major urologic surgeries, barriers to implementation and maintenance of the associated quality ...improvement. Data Identification: An English language literature search was done using PubMed. Study Selection: After independent review, 55 of the original 214 articles were selected to specifically address the stated purpose. Data Extraction: Clinical trials were included, randomized trials were prioritized, but robust observational studies were also included. Results of Data Synthesis: Many ERAS components have good data to support usage in radical cystectomy (RC) patients. Most ERAS programs include multidisciplinary teams carrying out multimodal pathways to hasten recovery after a major operation. ERAS components generally include preoperative counseling and medical optimization, venous thromboembolism prophylaxis, ileus prevention, avoidance of fluid overload, normothermia maintenance, early mobilization, pain control and early feeding, all leading to early discharge without increased complications or readmissions. Although there may not be specific data pertaining to other major urologic operations, the principles remain similar and ERAS is easily applicable. Conclusion: The benefits of ERAS programs are well established for RC and principles are easily applicable to other major urology operations. Barriers to implantation and maintenance of ERAS must be recognized to continue to maintain the benefits of these programs.
New representatives of the phylum
have been rapidly described in the last decade. Despite this, not all viruses of this phylum are allocated to recognized taxonomic families, as is the case for ...orpheovirus, pithovirus, and cedratvirus, which form the proposed family Pithoviridae. In this study, we performed comprehensive comparative genomic analyses of 8 pithovirus-like isolates, aiming to understand their common traits and evolutionary history. Structural and functional genome annotation was performed
for all the viruses, which served as a reference for pangenome construction. The synteny analysis showed substantial differences in genome organization between these viruses, with very few and short syntenic blocks shared between orpheovirus and its relatives. It was possible to observe an open pangenome with a significant increase in the slope when orpheovirus was added, alongside a decrease in the core genome. Network analysis placed orpheovirus as a distant and major hub with a large fraction of unique clusters of orthologs, indicating a distant relationship between this virus and its relatives, with only a few shared genes. Additionally, phylogenetic analyses of strict core genes shared with other viruses of the phylum reinforced the divergence of orpheovirus from pithoviruses and cedratviruses. Altogether, our results indicate that although pithovirus-like isolates share common features, this group of ovoid-shaped giant viruses presents substantial differences in gene contents, genomic architectures, and the phylogenetic history of several core genes. Our data indicate that orpheovirus is an evolutionarily divergent viral entity, suggesting its allocation to a different viral family, Orpheoviridae.
Giant viruses that infect amoebae form a monophyletic group named the phylum
. Despite being genomically and morphologically very diverse, the taxonomic categories of some clades that form this phylum are not yet well established. With advances in isolation techniques, the speed at which new giant viruses are described has increased, escalating the need to establish criteria to define the emerging viral taxa. In this work, we performed a comparative genomic analysis of representatives of the putative family Pithoviridae. Based on the dissimilarity of orpheovirus from the other viruses of this putative family, we propose that orpheovirus be considered a member of an independent family, Orpheoviridae, and suggest criteria to demarcate families consisting of ovoid-shaped giant viruses.
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