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PubMed2026

Multilayered nucleotide organization reveals purifying selection and host-driven adaptation in CPV and FPV.

Since feline panleukopenia virus (FPV) is considered the most likely ancestor of canine parvovirus (CPV), comprehensive comparisons of nucleotide organization in corresponding viral genes between CPV and FPV may provide novel insights into the evolutionary dynamics underlying the divergence of these two viruses. Here, we characterize the evolutionary patterns of CPV and FPV genes across multiple levels of nucleotide organization. Both viruses exhibited highly conserved nucleotide usage at nonsynonymous sites, with Ka/Ks patterns consistent with strong purifying selection, whereas synonymous sites showed greater variability. CpG dinucleotides were markedly underrepresented across all four viral genes, suggesting host-associated selective pressure and/or intrinsic nucleotide compositional constraints. Extensive nonrandom biases in synonymous codon usage, codon neighboring nucleotide context, and codon pair usage further revealed fine-scale genomic optimization shaped by natural selection and nucleotide compositional constraints. Structural protein genes (VP1 and VP2) displayed stronger codon usage bias and higher tRNA adaptation than nonstructural genes. Moreover, CPV genes showed greater translational adaptation to feline hosts than to canine hosts. These findings highlight how closely related parvoviruses exploit flexible nucleotide organization to facilitate host adaptation while maintaining essential protein functions.

Animals↗
PubMed2001

Human cytomegalovirus and natural killer-mediated surveillance of HLA class I expression: a paradigm of host-pathogen adaptation.

Among various strategies to evade the host immune response, some viruses like human cytomegalovirus (HCMV) interfere with surface MHC class I expression and antigen presentation to T lymphocytes. The ability of natural killer (NK) cells to detect MHC class I molecules through inhibitory receptors can be envisaged as an adaptation of the immune system for responding to such pathological alterations. To fulfil that role, rodents use members of the Ly49 C-type lectin superfamily, whereas primates employ killer immunoglobulin-like receptors and the immunoglobulin-like transcript 2/leucocyte immunoglobulin-like receptor-1 receptor. CD94/NKG2 lectin-like heterodimers represent the most conserved receptor system for MHC class I molecules; by interacting with human HLA-E or murine Qa-1b, CD94/NKG2A inhibitory receptors broadly probe the biosynthesis pathway of other class I molecules. Reciprocally, HCMV has developed mechanisms to evade the NK response while modulating HLA class Ia expression. The ability of HCMV to maintain surface levels of HLA-E and to express an HLA class I surrogate (UL18) are herein discussed in the context of the interplay with human NKR systems.

Adaptation, Physiological↗
PubMed2000

Evidence for predominant clones in a cyclically parthenogenetic organism provided by combined demographic and genetic analyses.

Aphids are particularly interesting models in the study of genetic and demographic components of plant adaptation because of their breeding system which combines parthenogenesis and sexual reproduction (i.e. cyclical parthenogenesis), and the frequent emergence of host-adapted races reported in this group. In this paper, patterns of host adaptation were assessed on local populations of the aphid Sitobion avenae by following their demographic and genetic structure in a maize field for two consecutive years. The existence of putative generalist (polyphagous) or specialized (host-adapted) genotypes was also investigated by comparing the genotypic distribution of this aphid on maize and other cultivated host plants, using five microsatellite loci. Although population dynamics revealed strong variation in aphid abundance during the colonization period on maize, two genotypes identified at seven additional microsatellite loci were predominant and exhibited stable frequencies over cropping season and between years. Based on present and earlier studies, these two prevalent genotypes were shown to survive on different host plants other than maize, to colonize large geographical zones and to persist parthenogenetically for several years. All these data strongly suggest that these two genotypes are asexual generalist clones that could have been favoured by agricultural practices encountered in western Europe. Besides these two clones, a continual replacement of rare genotypes was observed on maize in both years. Hypotheses involving selection via aphid-plant interactions and natural enemies were proposed for explaining the disappearance of these genotypes on maize.

Alleles↗
PubMed2025

Predicting host tropism in influenza a viruses: insights from multi-segment nucleotide signatures.

BACKGROUND: Influenza A virus (IAV) poses a significant public health threat due to its cross-species transmission and complex host adaptation mechanisms. This study integrated whole-genome data from avian, human, swine, and bovine IAV strains, using machine learning to predict viral host tropism based on nucleotide site features and to identify key sites driving host adaptation along with their synergistic effects. METHODS: A total of 64,000 IAV sequences from avian, human, swine, and bovine hosts were analyzed to build host-prediction models. A four-class classification framework (avian, human, swine, bovine) was constructed using nucleotide site features from all eight genomic segments (PB2, PB1, PA, HA, NP, NA, MP, NS). Eight machine learning algorithms (logistic regression, decision tree, random forest, SVM, KNN, gradient boosting, XGBoost, LightGBM) were benchmarked via 10-fold stratified cross-validation. Model performance was evaluated using accuracy, precision, recall, F1-score, AUPRC, and AUC. SHAP (SHapley Additive exPlanations) analysis prioritized critical nucleotide sites, while bivariate association tests identified synergistic/antagonistic interactions between sites. Nucleotide composition profiles were compared across host groups using hierarchical clustering and heatmap visualization. RESULTS: The XGBoost algorithm demonstrated the best and most stable performance, achieving an AUC value of over 0.95 in distinguishing human-derived sequences from non-human ones. SHAP analysis identified the top 20 critical nucleotide sites for each gene segment, such as sites 46 and 698 in the NS segment. Nucleotide composition analysis revealed high similarity between human and swine sequences in the HA and PB2 segments, and between avian and bovine sequences. The HA segment was particularly challenging in differentiating human from swine strains. Bivariate site association analysis uncovered significant synergistic or antagonistic effects between key sites within gene segments, forming complex networks. For instance, in the NS segment, a positive prediction contribution was observed when sites 371, 698, and 419 were all G. CONCLUSIONS: This study advances our mechanistic understanding of IAV host adaptation, identifies molecular determinants for zoonotic risk stratification, and establishes a scalable machine learning framework for predicting viral host tropism through nucleotide signature analysis, thereby enhancing surveillance strategies and informing preventive measures against emerging viral threats.

Influenza A virus↗
PubMed2002

Outer membrane proteins: key players for bacterial adaptation in host niches.

Outer membrane proteins (OMPs) of Gram-negative bacteria have diverse functions and are directly involved in the interaction with various environments encountered by pathogenic organisms. Thus, OMPs represent important virulence factors and play essential roles in bacterial adaptation to host niches, which are usually hostile to invading pathogens. Understanding the structure and functions of bacterial OMPs will facilitate the design of antimicrobial drugs and vaccines. In this paper, we will present a brief review on OMPs that contribute to bacterial adaptive responses including iron uptake, antimicrobial peptide resistance, serum resistance, and drug/bile resistance.

Adaptation, Physiological↗
PubMed1975

Survival of salmonellae during pepperoni manufacture.

Survival of salmonellae in artificially contaminated beef-pork mixtures (approximately 10(4) salmonellae/g) was studied in pepperoni prepared by either a natural flora or lactic starter culture fermentation or in nonfermented sausages. The pepperoni did not become salmonellae free during the usual commercial 15 to 30-day drying period. Salmonella dublin was present in all products, fermented or unfermented, after 42 to 43 days of drying. At a lower level of contamination, 10(3)/g, S. dublin could not be recovered from starter culture-fermented pepperoni after 14 days of drying but persisted in the natural flora-fermented sausage. S. typhimurium (initial count, 10(4)/g) was absent after 42 days of drying when starter culture was used to ferment the pepperoni, but was still present in the natural flora-fermented and unfermented products. S. dublin, host adapted to cattle, or S. choleraesuis, host adapted to swine, had similar survival patterns in beef pork, or beef-pork pepperoni. Heating salmonellae contaminated beef-pork pepperoni (after fermantation but before drying) to an internal temperature of 60 C (trichinae inactivating) eliminated the food-borne pathogen from the sausage product.

Animals↗
PubMed2026

Evolutionary constraints and regulatory plasticity shape host specialization in the Magnaporthe oryzae species complex.

Rice blast caused by Magnaporthe oryzae threatens global rice production, and wheat blast emergence highlights the pathogen's capacity for host shifts. Although numerous studies have described M. oryzae genome organization and infection mechanisms, critical questions remain regarding the evolutionary drivers of stable host specialization. Importantly, the blast pathogen comprises a species complex of genetically differentiated, host-adapted lineages rather than single homogeneous species. To address this knowledge gap, we integrate evidence from evolutionary genomics, transcriptomics, and metabolomics to develop the "Constrained Plasticity" framework. We argue that host adaptation arises from three interacting layers: genomic scaffolding (including epigenetic and noncoding RNA regulation), regulatory networks (enabling transcriptional plasticity), and metabolic compatibility (determining physiological success). This systems-level perspective explains the long-term stability of host-adapted lineages and the rare breakdowns resulting in host shifts, such as wheat blast. This framework generates testable predictions for pathogen emergence and provides a roadmap for developing lineage-aware resistance strategies.

Oryza↗
PubMed1999

Identification of a putative Salmonella enterica serotype typhimurium host range factor with homology to IpaH and YopM by signature-tagged mutagenesis.

The genetic basis for the host adaptation of Salmonella serotypes is currently unknown. We have explored a new strategy to identify Salmonella enterica serotype Typhimurium (S. typhimurium) genes involved in host adaptation, by comparing the virulence of 260 randomly generated signature-tagged mutants during the oral infection of mice and calves. This screen identified four mutants, which were defective for colonization of only one of the two host species tested. One mutant, which only displayed a colonization defect during the infection of mice, was further characterized. During competitive infection experiments performed with the S. typhimurium wild type, the mutant was defective for colonization of murine Peyer's patches but colonized bovine Peyer's patches at the wild-type level. No difference in virulence between wild type and mutant was observed when calves were infected orally with 10(10) CFU/animal. In contrast, the mutant possessed a sixfold increase in 50% lethal morbidity dose when mice were infected orally. The transposon in this mutant was inserted in a 2.9-kb pathogenicity islet, which is located between uvrB and yphK on the S. typhimurium chromosome. This pathogenicity islet contained a single gene, termed slrP, with homology to ipaH of Shigella flexneri and yopM of Yersinia pestis. These data show that comparative screening of signature-tagged mutants in two animal species can be used for scanning the S. typhimurium genome for genes involved in host adaptation.

Amino Acid Sequence↗
PubMed1995

The temperature threshold for development of Elaphostrongylus rangiferi in the intermediate host: an adaptation to winter survival?

To test the hypothesis that the relatively high developmental temperature threshold of the parasitic nematode Elaphostrongylus rangiferi in the intermediate snail host is an adaptation to minimize larval mortality during winter, an experiment was set up in which snails of the species Arianta arbustorum were experimentally infected with the parasite. The snails were divided into 3 groups known to contain 1st, 2nd or 3rd-stage larvae, and incubated at 3 degrees C for an experimental period of 18 weeks. First-stage larvae showed a significantly higher survival rate within snails than 2nd or 3rd-stage larvae. We also found that snails carrying 1st-stage larvae survived better than snails with other larval stages. It is concluded that if the nematode has started development before the hibernation, this has a real and significant effect on the risk of dying. The high developmental threshold is therefore likely to be an adaptation to reduce the chance of hibernating as developing larvae during long periods of low temperatures.

Adaptation, Physiological↗
PubMed1999

Testing alternative hypotheses for variation in amphipod behaviour and life history in relation to parasitism.

We tested two hypotheses concerning changes in investment in current reproduction for parasitised hosts, using amphipods (Corophium volutator) which act as second intermediate hosts for trematodes (Gynaecoyla aduncta). One hypothesis requires that parasites exert control over their hosts (parasite manipulation), whereas the other predicts that hosts control decisions over investment (adaptive host response). Although these hypotheses are viewed as mutually exclusive, our various results support both hypotheses. For example, female amphipods infected by late-stage larvae were often found crawling at times when predation by sandpipers (Calidris pusilla), which are the final hosts for trematodes, was likely, while uninfected females typically remained in their burrows. Furthermore, old females that were newly-infected by trematodes often aborted and ate their young. Both of these responses seem inconsistent with female investment in current reproduction, but can be interpreted as adaptive parasite manipulation. In contrast, young non-ovigerous females that were newly-infected hastened the onset of their parturial moult and thus, time to becoming receptive. This response can be explained as a host adaptation to minimise the cost of parasites. We contend that differences between parasitised and unparasitised hosts in behaviour or investment can be explained as both parasite and host adaptations, expressed at different times in the host's life history. Such compromise will help explain the persistence of parasite-host associations in nature.

Adaptation, Physiological↗
PubMed2005

Iron chelator induces MIP-alpha/CCL20 in human intestinal epithelial cells: implication for triggering mucosal adaptive immunity.

A previous report by this laboratory demonstrated that bacterial iron chelator (siderophore) triggers inflammatory signals, including the production of CXC chemokine IL-8, in human intestinal epithelial cells (IECs). Microarray-based gene expression profiling revealed that iron chelator also induces macrophage inflammatory protein 3 alpha (MIP-3alpha)/CC chemokine-ligand 20 (CCL20). As CCL20 is chemotactic for the cells involved in host adaptive immunity, this suggests that iron chelator may stimulate IECs to have the capacity to link mucosal innate and adaptive immunity. The basal medium from iron chelator deferoxamine (DFO)-treated HT-29 monolayers was as chemotactic as recombinant human CCL20 at equivalent concentrations to attract CCR6(+) cells. The increase of CCL20 protein secretion appeared to correspond to that of CCL20 mRNA levels, as determined by real-time quantitative RT-PCR. The efficacy of DFO at inducing CCL20 mRNA was also observed in human PBMCs and in THP-1 cells, but not in human umbilical vein endothelial cells. Interestingly, unlike other proinflammatory cytokines, such as TNF-alpha and IL-1beta, a time-dependent experiment revealed that DFO slowly induces CCL20, suggesting a novel mechanism of action. A pharmacologic study also revealed that multiple signaling pathways are differentially involved in CCL20 production by DFO, while some of those pathways are not involved in TNF-alpha-induced CCL20 production. Collectively, these results demonstrate that, in addition to some bacterial products known to induce host adaptive immune responses, direct chelation of host iron by infected bacteria may also contribute to the initiation of host adaptive immunity in the intestinal mucosa.

Calcium↗
PubMed2005

Low survival of parasite chicks may result from their imperfect adaptation to hosts rather than expression of defenses against parasitism.

Host parents exhibit a variety of behaviors toward avian brood parasites, but not all of their actions have necessarily evolved in response to costs imposed by parasites. To investigate whether common waxbills (Estrilda astrild) have evolved defenses specifically against parasitic pin-tailed whydahs (Vidua macroura), I studied the specificity and flexibility of host behaviors toward nestlings at two sites that differed significantly in parasitism rates and intensities. I focused on documenting nestling survival because V. macroura young match the elaborate gape morphology of E. astrild nestlings, a pattern that suggests hosts may possess unique defenses against parasite chicks. Parasite young survived significantly worse than host young in mixed broods. However, this apparent discrimination was not associated with parasitism risk as would be expected if defenses had evolved specifically to counter parasitism. Parasite young may have survived poorly compared to host young because individual chicks were less able to stimulate sufficient care from foster parents or because they were more susceptible to nestling competition, disease, or reduced provisioning by hosts. Mortality may have also been exacerbated by poor timing of parasite egg laying. In nonparasitized and parasitized nests, rates of nestling survival were similar, further suggesting that parenting behaviors that result in chick mortality did not evolve solely in response to parasite young. In addition, orange-breasted waxbills (Amandava subflava) and zebra finches (Taeniopygia guttata), rarely parasitized and nonparasitized relatives of E. astrild, experience similar levels of nestling mortality presumably as a result of phylogenetically widespread parenting strategies. Despite the similarity of parasitic V. macroura nestlings and E. astrild nestlings, I found no evidence that E. astrild parents possess defenses that allow for specific discrimination against parasite chicks during the nestling period. Rather than being subject to host defenses evolved in an arms race, Vidua chicks may simply be imperfectly adapted to life in the nests of their hosts.

Adaptation, Biological↗
PubMed2003

Comparison of early ileal invasion by Salmonella enterica serovars Choleraesuis and Typhimurium.

The mechanisms of Salmonella serovar-host specificity are not well defined. Pig ileal loops were used to compare phenotypic differences in early cellular invasion between non-host-adapted Salmonella serovar Typhimurium (SsT) and host-adapted Salmonella serovar Choleraesuis (SsC). By 10 minutes postinoculation, both serovars invaded a small number of M cells, enterocytes, and goblet cells. Multiple SsC organisms (up to 6 per cell) simultaneously invaded M cells, whereas SsT often invaded as one to two organisms per M cell. Internalization of both serovars resulted in vacuoles containing a single bacterium. The follicle-associated epithelium (FAE) of SsC-inoculated loops responded with more filopodia and lamellipodia although exhibiting less cell swelling than SsT. Additionally, SsT showed an enhanced affinity for sites of cell extrusion compared with SsC at 60 minutes. These results suggest: 1) both SsC and SsT exhibit non-cell-specific invasion as early as 10 minutes postinoculation, 2) Salmonella serovars exhibit differences in early invasion of FAE and M cells, and 3) cells undergoing extrusion may provide a site for preferential adherence by SsT and SsC.

Animals↗
PubMed1997

Altered 3'-terminal RNA structure in phage Qbeta adapted to host factor-less Escherichia coli.

The RNA phage Qbeta requires for the replication of its genome an RNA binding protein called Qbeta host factor or Hfq protein. Our previous results suggested that this protein mediates the access of replicase to the 3'-end of the Qbeta plus strand RNA. Here we report the results of an evolutionary experiment in which phage Qbeta was adapted to an Escherichia coli Q13 host strain with an inactivated host factor (hfq) gene. This strain initially produced phage at a titer approximately 10,000-fold lower than the wild-type strain and with minute plaque morphology, but after 12 growth cycles, phage titer and plaque size had evolved to levels near those of the wild-type host. RNAs isolated from adapted Qbeta mutants were efficient templates for replicase without host factor in vitro. Electron microscopy showed that mutant RNAs, in contrast to wild-type RNA, efficiently interacted with replicase at the 3'-end in the absence of host factor. The same set of four mutations in the 3'-terminal third of the genome was found in several independently evolved phage clones. One mutation disrupts the base pairing of the 3'-terminal CCCOH sequence, suggesting that the host factor stimulates activity of the wild-type RNA template by melting out its 3'-end.

Base Sequence↗
PubMed2005

Dispersal in a parasitic worm and its two hosts: consequence for local adaptation.

Characterizing host and parasite population genetic structure and estimating gene flow among populations is essential for understanding coevolutionary interactions between hosts and parasites. We examined the population genetic structure of the trematode Schistosoma mansoni and its two host species (the definitive host Rattus rattus and the intermediate host Biomphalaria glabrata) using microsatellite markers. Parasites were sampled from rats. The study was conducted in five sites of the Guadeloupe Island, Lesser Antilles. Mollusks display a pattern of isolation by distance whereas such a pattern is not found neither in schistosomes nor in rats. The comparison of the distribution of genetic variability in S. mansoni and its two host species strongly suggests that migration of parasites is principally determined by that of the vertebrate host in the marshy focus of Guadeloupe. However, the comparison between genetic differentiation values in schistosomes and rats suggests that the efficacy of the schistosome rat-mediated dispersal between transmission sites is lower than expected given the prevalence, parasitic load and migration rate of rats among sites. This could notably suggest that rat migration rate could be negatively correlated to the age or the infection status of individuals. Models made about the evolution of local adaptation in function of the dispersal rates of hosts and parasites suggest that rats and mollusks should be locally adapted to their parasites.

Animals↗
PubMed1999

Zoite migration during infection: parasite adaptation to host defences.

The apicomplexan parasite Eimeria tenella has evolved a number of strategies for migration into different compartments of the intestinal tissue during its life cycle. These migration events are associated intricately with pathogenesis and are currently of great interest to coccidiologists. Using evidence from in vivo studies and recent work on the dynamics of gut cell turnover, Peter Daszak suggests that E. tenella zoite migration might be viewed as parasite evolutionary adaptation to evade the host innate immune responses (resistance) and deal with the complex, dynamic nature of gut epithelial tissue.

Adaptation, Physiological↗
PubMed2004

Toxicity and adaptive immune response to intracellular transgenes delivered by helper-dependent vs. first generation adenoviral vectors.

The host immune response to intracellular transgenes delivered by helper-dependent (HDV) vs. first generation (FGV) adenoviral vectors has been relatively unstudied. Previous studies showed short-term correction of bovine and murine argininosuccinate synthetase (ASS) deficiency after first generation adenoviral-mediated liver gene therapy. To determine whether the host adaptive immune response against the intracellular transgene human ASS (hASS) contributed to loss of gene expression in this setting, the same vector (FGV-CAG-hASS) was injected into Rag-/- (immunodeficient) mice. As in wild-type C57BL/6 (B6) mice, Rag-/- mice also showed significant loss of hASS expression and vector by week 4 post-injection, with concomitant elevation of liver enzymes and disruption of liver architecture. Therefore, direct toxicity due to vector rather than adaptive immune response against hASS primarily accounted for loss of expression with FGVs. In contrast to hASS, beta-galactosidase is strongly immunogenic and activates the host adaptive immune response. Loss of transgene expression was observed in B6 mice with either a FGV or a HDV expressing beta-galactosidase. However, the drop in gene expression observed with the HDV was primarily due to the adaptive immune response, since both beta-galactosidase expression and vector genome were sustained in immunodeficient mice treated with HDV. As expected, with weakly immunogenic hASS, vector genome and hASS expression were sustained with a HDV in spite of ubiquitous expression of the transgene. Therefore, viral gene expression is a primary determinant of intermediate and chronic toxicities at day 3 and week 4 post-injection. However, even in the absence of viral gene expression, strongly immunogenic intracellular transgenes can stimulate clearance of transduced hepatocytes.

Adaptation, Physiological↗