Multiple Host Research Articles

CWL-PLAS: Task Workflows Assisted by Data Science Cloud Platforms

The Common Workflow Language (CWL) is a platform-independent description language for the representation of data science workflows consisting of a set of tasks that interact with each other to perform scientific analysis. The tasks can be packaged as Linux containers. On the one hand, using containers ensures the reproducibility and portability of workflows. Still, on the other hand, it limits each task to exploiting, at most, the resources of the host where its container runs. In this paper, we propose CWL-PLAS, an extension of CWL that allows a task to instantiate and temporarily use a supporting cloud platform for parallel computing, which is specialized for the task’s activity. In this way, tasks can leverage the resources of multiple hosts in parallel, reducing the duration of the workflow. We implemented an open-source workflow manager that supports CWL-PLAS workflows and exploits a Kubernetes back-end. We used this workflow manager to evaluate the performance of CWL-PLAS in a couple of machine learning workflows.

Host biomarker-based quantitative rapid tests for detection and treatment monitoring of tuberculosis and COVID-19

Diagnostic services for tuberculosis (TB) are not sufficiently accessible in low-resource settings, where most cases occur, which was aggravated by the COVID-19 pandemic. Early diagnosis of pulmonary TB can reduce transmission. Current TB-diagnostics rely on detection of Mycobacterium tuberculosis (Mtb) in sputum requiring costly, time-consuming methods, and trained staff. In this study, quantitative lateral flow (LF) assays were used to measure levels of seven host proteins in sera from pre-COVID-19 TB-patients diagnosed in Europe and latently Mtb-infected individuals (LTBI), and from COVID-19 patients and healthy controls. Analysis of host proteins showed significantly lower levels in LTBI versus TB (AUC:0·94) and discriminated healthy individuals from COVID-19 patients (0·99) and severe COVID-19 from TB. Importantly, these host proteins allowed treatment monitoring of both respiratory diseases. This study demonstrates the potential of non-sputum LF assays as adjunct diagnostics and treatment monitoring for COVID-19 and TB based on quantitative detection of multiple host biomarkers.

A novel narnavirus is widespread in Saccharomyces cerevisiae and impacts multiple host phenotypes.

RNA viruses are a widespread, biologically diverse group that includes the narnaviridiae, a family of unencapsidated RNA viruses containing a single ORF that encodes an RNA-dependent RNA polymerase. In the yeast Saccharomyces cerevisiae, the 20S and 23S RNA viruses are well-studied members of the narnaviridiae, which are present at low intracellular copy numbers, unless induced by stress or unfavorable growth conditions (Wickneret al. 2013), and are not known to affect host fitness. In this study, we describe a new Saccharomyces cerevisiae narnavirus that we designate as N1199. We show that N1199 is uniquely present as a double-stranded RNA at a high level relative to other known members of this family in one strain background, YJM1199, and is present as a single-stranded RNA at lower levels in 98 of the remaining 100-genomes strains. Further, we see a strong association between the presence of high level N1199 and host phenotype defects, including greatly reduced sporulation efficiency and growth on multiple carbon sources. Finally, we describe associations between N1199 abundance and host phenotype defects, including autophagy.

Aphelinus nigritus Howard (Hymenoptera: Aphelinidae) Preference for Sorghum Aphid, Melanaphis sorghi (Theobald, 1904) (Hemiptera: Aphididae), Honeydew Is Stronger in Johnson Grass, Sorghum halepense, Than in Grain Sorghum, Sorghum bicolor.

How aphid parasitoids of recent invasive species interact with their hosts can affect the feasibility of biological control. In this study, we focus on a recent invasive pest of US grain sorghum, Sorghum bicolor, the sorghum aphid (SA), Melanaphis sorghi. Understanding this pest's ecology in the grain sorghum agroecosystem is critical to develop effective control strategies. As parasitoids often use aphid honeydew as a sugar resource, and honeydew is known to mediate parasitoid-aphid interactions, we investigated the ability of SA honeydew to retain the parasitoid Aphelinus nigritus. Since SAs in the US have multiple plant hosts, and host-plant diet can modulate parasitoid retention (a major component in host foraging), we measured SA honeydew sugar, organic acid, and amino acid profiles, then assessed via retention time A. nigritus preference for honeydew produced on grain sorghum or Johnson grass, Sorghum halepense. Compared to a water control, A. nigritus spent more time on SA honeydew produced on either host plant. Despite similar honeydew profiles from both plant species, A. nigritus preferred honeydew produced on Johnson grass. Our results suggest the potential for SA honeydew to facilitate augmentation strategies aimed at maintaining A. nigritus on Johnson grass to suppress SAs before grain sorghum is planted.

PROMoting the use of studies within a trial (PROMETHEUS): Results and experiences from a large programme to evaluate the routine embedding of recruitment and retention strategies within randomised controlled trials routinely

Aim PROMoting THE USE of Studies Within A Trial (PROMETHEUS) aimed to improve the evidence base for recruiting and retaining participants in Randomised Controlled Trials (RCTs) by pump-priming and facilitating the start of at least 25 Studies Within A Trial (SWATs) testing recruitment or retention interventions. Methods Ten Clinical Trials Units (CTUs) and one Primary Care Research Centre formed a network to conduct randomised SWATs of recruitment and/or retention strategies. We identified promising recruitment and retention interventions from various sources, which were reviewed by patient and public (PPI) partners to generate an initial priority list of seven recruitment and eight retention interventions. Host trial teams could apply for funding of up to £5000 and receive support from the PROMETHEUS team to design, implement, and report SWATs. We additionally tested the feasibility of undertaking coordinated SWATs across multiple host trials simultaneously. Results PROMETHEUS funded 42 SWATs, embedded within 31 host trials, across 12 CTUs. The SWAT cost per SWAT was £3535. Of the 42 SWATs, 12 tested the same SWAT in multiple trials ( simultaneous SWAT design) and eight tested a factorial SWAT design. PROMETHEUS will add 18% and 79% more SWATs to the Cochrane systematic review of recruitment strategies and the Cochrane review of retention strategies respectively. Conclusion The PROMETHEUS programme substantially increased the evidence base for both recruitment and retention strategies within RCTs. Future research should adopt a systematic approach to identifying and targeting gaps in the evidence base and focus on translating SWAT evidence into recruitment and retention practice.

Determinants of Retroviral Integration and Implications for Gene Therapeutic MLV-Based Vectors and for a Cure for HIV-1 Infection.

To complete their replication cycle, retroviruses need to integrate a DNA copy of their RNA genome into a host chromosome. Integration site selection is not random and is driven by multiple viral and cellular host factors specific to different classes of retroviruses. Today, overwhelming evidence from cell culture, animal experiments and clinical data suggests that integration sites are important for retroviral replication, oncogenesis and/or latency. In this review, we will summarize the increasing knowledge of the mechanisms underlying the integration site selection of the gammaretrovirus MLV and the lentivirus HIV-1. We will discuss how host factors of the integration site selection of retroviruses may steer the development of safer viral vectors for gene therapy. Next, we will discuss how altering the integration site preference of HIV-1 using small molecules could lead to a cure for HIV-1 infection.

Evolutionary adaptation of bovine coronavirus (BCoV): Screening of natural recombinations across the complete genomes.

Bovine coronavirus (BCoV) is a member of pathogenic Betacoronaviruses that has been circulating for several decades in multiple host species. Given the similarity between BCoV and human coronaviruses, the current study aimed to review the complete genomes of 107 BCoV strains available on the GenBank database, collected between 1983 and 2017 from different countries. The maximum-likelihood based phylogenetic analysis revealed three main BCoV genogroups: GI, GII, and GIII. GI is further divided into nine subgenogroups: GI-a to GI-i. The GI-a to GI-d are restricted to Japan, and GI-e to GI-i to the USA. The evolutionary relationships were also inferred using phylogenetic network analysis, revealing two major distinct networks dominated by viruses identified in the USA and Japan, respectively. The USA strains-dominated Network Cluster includes two sub-branches: France/Germany and Japan/China in addition to the United States, while Japan strains-dominated Network Cluster is limited to Japan. Twelve recombination events were determined, including 11 intragenogroup (GI) and one intergenogroup (GII vs. GI-g). The breakpoints of the recombination events were mainly located in ORF1ab and the spike glycoprotein ORF. Interestingly, 10 of 12 recombination events occurred between Japan strains, one between the USA strains, and one from intercontinental recombination (Japan vs. USA). These findings suggest that geographical characteristics, and population density with closer contact, might significantly impact the BCoV infection and co-infection and boost the emergence of more complex virus lineages.

Conservation of Nematocida microsporidia gene expression and host response in Caenorhabditis nematodes.

Microsporidia are obligate intracellular parasites that are known to infect most types of animals. Many species of microsporidia can infect multiple related hosts, but it is not known if microsporidia express different genes depending upon which host species is infected or if the host response to infection is specific to each microsporidia species. To address these questions, we took advantage of two species of Nematocida microsporidia, N. parisii and N. ausubeli, that infect two species of Caenorhabditis nematodes, C. elegans and C. briggsae. We performed RNA-seq at several time points for each host infected with either microsporidia species. We observed that Nematocida transcription was largely independent of its host. We also observed that the host transcriptional response was similar when infected with either microsporidia species. Finally, we analyzed if the host response to microsporidia infection was conserved across host species. We observed that although many of the genes upregulated in response to infection are not direct orthologs, the same expanded gene families are upregulated in both Caenorhabditis hosts. Together our results describe the transcriptional interactions of Nematocida infection in Caenorhabditis hosts and demonstrate that these responses are evolutionarily conserved.

Macroevolutionary analyses point to a key role of hosts in diversification of the highly speciose eriophyoid mite superfamily

The superfamily Eriophyoidea includes >5000 named species of very small phytophagous mites. As for many groups of phytophagous invertebrates, factors responsible for diversification of eriophyoid mites are unclear. Here, we used an inferred phylogeny of 566 putative species of eriophyoid mites based on fragments of two mitochondrial genes and two nuclear genes to examine factors associated with their massive evolutionary diversification through time. Our dated phylogeny indicates a Carboniferous origin for gymnosperm-associated Eriophyoidea with subsequent diversification involving multiple host shifts to angiosperms—first to dicots, and then to monocots or shifts back to gymnosperms—beginning in the Cretaceous period when angiosperms diverged. Speciation rates increased more rapidly in the Eriophyidae + Diptilomiopidae (mostly infesting angiosperms) than in the Phytoptidae (mostly infesting gymnosperms). Phylogenetic signal, speciation rates, dispersal and vicariance results combined with inferred topologies show that hosts played a key role in the evolution of eriophyoid mites. Speciation constrained by hosts was probably the main driver behind eriophyoid mite diversification worldwide. We demonstrate monophyly of the Eriophyoidea, whereas all three families, most subfamilies, tribes, and most genera are not monophyletic. Our time-calibrated tree provides a framework for further evolutionary studies of eriophyoid mites and their interactions with host plants as well as taxonomic revisions above the species level.

How do multiple host plants and virus species challenge aphid molecular machinery?

A recommendation of: Quentin Chesnais, Victor Golyaev, Amandine Velt, Camille Rustenholz, Maxime Verdier, Véronique Brault, Mikhail M. Pooggin, Martin Drucker Transcriptome responses of the aphid vector Myzus persicae are shaped by identities of the host plant and the virus https://doi.org/10.1101/2022.07.18.500449

Coxiella burnetii in Dogs and Cats from Portugal: Serological and Molecular Analysis.

Dogs and cats are potential sources of infection for some zoonotic diseases such as Q fever, caused by Coxiella burnetii, a multiple host pathogen. Q fever outbreaks in dogs and cats have been related with parturition and abortion events, and ticks have a potential role in the transmission of this pathogen. This study aimed to screen for C. burnetii in dogs and cats, and in ticks collected from infested animals. An observational descriptive study was conducted in Portugal at two time points nine years apart, 2012 and 2021. Sera obtained from dogs and cats (total n = 294) were tested for C. burnetii antibodies using a commercial ELISA adapted for multi-species detection. C. burnetii DNA was screened by qPCR assay targeting IS1111 in uterine samples and in ticks. A decrease in the exposure to C. burnetii was observed in cats from 17.2% (95% CI: 5.8−35.8%) in 2012 to 0.0% in 2021, and in dogs from 12.6% (95% CI: 7.7−19.0%) in 2012 to 1.7% (95% CI: 0.3−9.1%) in 2021 (p < 0.05). Overall, and despite differences in the samples, rural habitat seems to favour the exposure to C. burnetii. The DNA of C. burnetii was not detected in ticks. The low seropositivity observed in 2021 and the absence of C. burnetii DNA in the tested samples, suggest that dogs and cats from Portugal are not often exposed to the pathogen. Nevertheless, the monitoring of C. burnetii infection in companion animals is an important tool to prevent human outbreaks, considering the zoonotic potential for owners and veterinarians contacting infected animals, mainly dogs and cats from rural areas which often come into contact with livestock.

Genetic Variants and Protective Immunity against SARS-CoV-2.

The novel coronavirus-19 (SARS-CoV-2), has infected numerous individuals worldwide, resulting in millions of fatalities. The pandemic spread with high mortality rates in multiple waves, leaving others with moderate to severe symptoms. Co-morbidity variables, including hypertension, diabetes, and immunosuppression, have exacerbated the severity of COVID-19. In addition, numerous efforts have been made to comprehend the pathogenic and host variables that contribute to COVID-19 susceptibility and pathogenesis. One of these endeavours is understanding the host genetic factors predisposing an individual to COVID-19. Genome-Wide Association Studies (GWAS) have demonstrated the host predisposition factors in different populations. These factors are involved in the appropriate immune response, their imbalance influences susceptibility or resistance to viral infection. This review investigated the host genetic components implicated at the various stages of viral pathogenesis, including viral entry, pathophysiological alterations, and immunological responses. In addition, the recent and most updated genetic variations associated with multiple host factors affecting COVID-19 pathogenesis are described in the study.

Linking integrative taxonomy and ecology: Diversity and population structure of two platyhelminth parasites (Digenea: Lepidapedidae) of sympatric deep-sea fishes in the Western Mediterranean

Current knowledge about deep-sea parasites is limited and the data shedding light on population differentiation at host, geographical or bathymetric scales are scarce. Here, we applied an integrative taxonomic approach to the identification of metazoan parasites in a large sample of deep-sea fish species from the Western Mediterranean and assessed the diversity of Lepidapedon spp. (Digenea) and the patterns of genetic and epidemiological variation of parasite populations in relation to host, geographical and bathymetric provenance. Fully censused infrapopulations of Lepidapedon spp. were analysed from five species of deep-sea fish (Coelorinchus mediterraneus (Mediterranean grenadier), Lepidion lepidion (Mediterranean codling), Phycis blennoides (greater forkbeard), Trachyrincus scabrus (roughsnout grenadier) and Mora moro (common mora)) collected by bottom trawling at depths of 400–2000 m. Partial fragments of the mitochondrial nad1 gene amplified for representative samples per morphotype were used to aid species delineation. After completion of the combined morphological and molecular characterisation of select samples, the total collected material was re-identified based on a suite of differentiating morphological features. Analyses revealed low species diversity and host specificity of Lepidapedon spp. Two species infecting multiple hosts were identified: Lepidapedon desclersae and L. guevarai. Genetic analyses showed lack of genetic differentiation for populations of the more abundantly sequenced species, whereas ecological analyses depicted significant differences in epidemiological parameters of both digenean species associated with host species, geographical area and bathymetric range. Overall, our results indicate that combining population genetics with ecological analyses holds a promise of gaining insights into the factors and possible mechanisms that determine the patterns of connectivity among parasite populations in the deep sea.

Evaluating coevolution in a horizontally transmitted mutualism.

Many interspecific interactions are shaped by coevolution. Transmission mode is thought to influence opportunities for coevolution within symbiotic interactions. Vertical transmission maintains partner fidelity, increasing opportunities for coevolution, but horizontal transmission may disrupt partner fidelity, potentially reducing opportunities for coevolution. Despite these predictions, the role of coevolution in the maintenance of horizontally transmitted symbioses is unclear. Leveraging a tractable insect-bacteria symbiosis, we tested for signatures of pairwise coevolution by assessing patterns of host-symbiont specialization. If pairwise coevolution defines the interaction, we expected to observe evidence of reciprocal specialization between hosts and their local symbionts. We found no evidence for local adaptation between sympatric lineages of Anasa tristis squash bugs and Caballeronia spp. symbionts across their native geographic range. We also found no evidence for specialization between three co-localized Anasa host species and their native Caballeronia symbionts. Our results demonstrate generalist dynamics underlie the interaction between Anasa insect hosts and their Caballeronia symbionts. We predict that selection from multiple host species may favor generalist symbiont traits through diffuse coevolution. Alternatively, selection for generalist traits may be a consequence of selection by hosts for fixed cooperative symbiont traits without coevolution.

News and perspectives for Annals of Applied Biology in 2023: Looking forward to more and more submissions

News and perspectives for <scp><i>Annals of Applied Biology</i></scp> in 2023: Looking forward to more and more submissions

Study within a review (SWAR).

Study within a review (SWAR).

Fatal mobbing and attack of the common cuckoo by its warbler hosts.

Nest defense is an effective strategy of hosts against parasites. Typically, hosts will aggressively attack brood parasites that approach or visit their nests, which can prevent the parasites from laying eggs or may even lead to the death of the parasites. Few previous studies have specifically reported such fatal cases involving brood parasites and have attributed the cause of death to either drowning or hypothermia after falling into the water following an attack from hosts. In this study, we recorded the process of multiple host individuals of the Oriental reed warbler (Acrocephalus orientalis) mobbing and attacking a female common cuckoo (Cuculus canorus) in the field. We discovered that the immediate cause of the cuckoo's death was the fatal physical damage resulting from the aggressive defense from the hosts, suggesting that frantic pecking and scratching by the hosts is the most proximate cause of mortality among egg-laying female cuckoos. This finding enhances our essential understanding of the effectiveness of host attacks.

Host specificity varies widely in dispersal-limited symbionts

A fundamental aspect of symbiotic relationships is host specificity, ranging from extreme specialists associated with only a single host species to generalists associated with many different species. Although symbionts with limited dispersal abilities are typically host specialists, some are known to associate with multiple hosts, but our understanding of the causes and consequences of this variation is limited.

A Novel XRE-Type Regulator Mediates Phage Lytic Development and Multiple Host Metabolic Processes in Pseudomonas aeruginosa.

Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen, the leading cause of acute and chronic infections in immunocompromised patients, frequently with high morbidity and mortality rates. The xenobiotic response element (XRE) family proteins are the second most common transcriptional regulators (TRs) in P. aeruginosa. However, only a few XRE-like TRs have been reported to regulate multiple bacterial cellular processes, encompassing virulence, metabolism, antibiotic synthesis or resistance, stress responses, and phage infection, etc. Our understanding of what roles these XRE-like small regulatory proteins play in P. aeruginosa remains limited. Here, we aimed to decipher the role of a putative XRE-type transcriptional regulator (designated LfsT) from a prophage region on the chromosome of a clinical P. aeruginosa isolate, P8W. Southern blot and reverse transcription quantitative PCR (RT-qPCR) assays demonstrated that LfsT controlled host sensitivity to the phage PP9W2 and was essential for efficient phage replication. In addition, electrophoretic mobility shift assays (EMSAs) and transcriptional lacZ fusion analyses indicated that LfsT repressed the lysogenic development and promoted the lytic cycle of phage PP9W2 by binding to the promoter regions of the gp71 gene (encoding a CI-like repressor) and several vital phage genes. Combined with RNA-seq and a series of phenotypic validation tests, our results showed that LfsT bound to the flexible palindromic sites within the promoters upstream of several genes in the bacterial genome, regulating fatty acid (FA) metabolism, spermidine (SPD) transport, as well as the type III secretion system (T3SS). Overall, this study reveals novel regulatory roles of LfsT in P. aeruginosa, improving our understanding of the molecular mechanisms behind bacterium-phage interactions. IMPORTANCE This work elucidates the novel roles of a putative XRE family TR, LfsT, in the intricate regulatory systems of P. aeruginosa. We found that LfsT bound directly to the core promoter regions upstream of the start codons of numerous genes involved in various processes, including phage infection, FA metabolism, SPD transport, and the T3SS, regulating as the repressor or activator. The identified partial palindromic motif NAACN(5,8)GTTN recognized by LfsT suggests extensive effects of LfsT on gene expression by maintaining preferential binding to nucleotide sites under evolutionary pressure. In summary, these findings indicate that LfsT enhances metabolic activity in P. aeruginosa, while it reduces host resistance to the phage. This study helps us better understand the coevolution of bacteria and phages (e.g., survival comes at a cost) and provides clues for designing novel antimicrobials against P. aeruginosa infections.

Seroprevalence of Specific Antibodies to Toxoplasma gondii, Neospora caninum, and Brucella spp. in Sheep and Goats in Egypt.

Toxoplasmosis, neosporosis, and brucellosis are devastating diseases causing infectious abortion and, therefore, substantial economic losses in farm animals. Toxoplasmosis and neosporosis are caused by the intracellular protozoan parasites Toxoplasma gondii (T. gondii) and Neospora caninum (N. caninum), respectively. Brucellosis is a bacterial disease caused by numerous Brucella species in multiple hosts. Toxoplasmosis and brucellosis are also considered foodborne zoonotic diseases. In the current study, specific antibodies to T. gondii and N. caninum, in addition to those to Brucella spp., were detected to gain a better understanding of the epidemiological situation for these three pathogens. Sheep and goat sera from Egypt (n = 360) of animals with and without a history of abortion were tested using commercial ELISAs. Seropositivity rates of 46.1%, 11.9%, and 8.6% for T. gondii, N. caninum, and Brucella spp., respectively, were revealed. Mixed infections with T. gondii and Brucella spp. (4.4%), T. gondii and N. caninum (4.2%), N. caninum and Brucella spp. (1.4%), and even some triple infections (0.6%) have been observed. Animals with a history of abortion had a significantly higher seroprevalence for Brucella spp. infection than those without abortion (12.6%; 28/222 vs. 2.2%; 3/138) (p = 0.0005; Odds ratio = 1.9-21.8), while none of the other pathogens showed a similar effect. This result suggests brucellosis as a possible cause of abortion in the study population. However, the high seroprevalence for T. gondii and N. caninum revealed in our study warrants further investigations.