A comparative analysis of L1 retrotransposition activities in human genomes suggests an ongoing increase in L1 number despite an evolutionary trend towards lower activity.

BACKGROUND: LINE-1 (Long Interspersed Nuclear Elements, L1) retrotransposons are the only autonomously active transposable elements in the human genome. The evolution of L1 retrotransposition rates and its implications for L1 dynamics are poorly understood. Retrotransposition rates are commonly measured in cell culture-based assays, but it is unclear how well these measurements provide insight into L1 population dynamics. This study applied comparative methods to estimate parameters for the evolution of retrotransposition rates, and infer L1 dynamics from these estimates. RESULTS: Our results show that the rates at which new L1s emerge in the human population correlate positively to cell-culture based retrotransposition activities, that there is an evolutionary trend towards lower retrotransposition activity, and that this evolutionary trend is not sufficient to counter-balance the increase in active L1s resulting from continuing retrotransposition. CONCLUSIONS: Together, these findings support a model of the population-level L1 retrotransposition dynamics that is consistent with prior expectations and indicate the remaining gaps in the understanding of L1 dynamics in human genomes.

A risk progression breast epithelial 3D culture model reveals Cx43/hsa_circ_0077755/miR-182 as a biomarker axis for heightened risk of breast cancer initiation.

mRNA-circRNA-miRNAs axes have been characterized in breast cancer, but not as risk-assessment axes for tumor initiation in early-onset breast cancer that is increasing drastically worldwide. To address this gap, we performed circular RNA (circRNA) microarrays and microRNA (miRNA) sequencing on acini of HMT-3522 S1 (S1) breast epithelial risk-progression culture model in 3D and chose an early-stage population miRNome for a validation cohort. Nontumorigenic S1 cells form fully polarized epithelium while pretumorigenic counterparts silenced for gap junction Cx43 (Cx43-KO-S1) lose epithelial polarity, multilayer and mimic premalignant in vivo mammary epithelial morphology. Here, 121 circRNAs and 65 miRNAs were significantly dysregulated in response to Cx43 silencing in cultured epithelia and 15 miRNAs from the patient cohort were involved in epithelial polarity disruption. Focusing on the possible sponging activity of the validated circRNAs to their target miRNAs, we found all miRNAs to be highly enriched in cancer-related pathways and cross-compared their dysregulation to actual miRNA datasets from the cultured epithelia and the patient validation cohort. We present the involvement of gap junction in post-transcriptional axes and reveal Cx43/hsa_circ_0077755/miR-182 as a potential biomarker signature axis for heightened-risk of breast cancer initiation, and that its dysregulation patterns might predict prognosis along breast cancer initiation and progression.

The Route of Infection Influences the Contribution of Key Immunity Genes to Antibacterial Defense in Anopheles gambiae.

Insect systemic immune responses to bacterial infections have been mainly studied using microinjections, whereby the microbe is directly injected into the hemocoel. While this methodology has been instrumental in defining immune signaling pathways and enzymatic cascades in the hemolymph, it remains unclear whether and to what extent the contribution of systemic immune defenses to host microbial resistance varies if bacteria invade the hemolymph after crossing the midgut epithelium subsequent to an oral infection. Here, we address this question using the pathogenic Serratia marcescens (Sm) DB11 strain to establish systemic infections of the malaria vector Anopheles gambiae, either by septic Sm injections or by midgut crossing after feeding on Sm. Using functional genetic studies by RNAi, we report that the two humoral immune factors, thioester-containing protein 1 and C-type lectin 4, which play key roles in defense against Gram-negative bacterial infections, are essential for defense against systemic Sm infections established through injection, but they become dispensable when Sm infects the hemolymph following oral infection. Similar results were observed for the mosquito Rel2 pathway. Surprisingly, blocking phagocytosis by cytochalasin D treatment did not affect mosquito susceptibility to Sm infections established through either route. Transcriptomic analysis of mosquito midguts and abdomens by RNA-seq revealed that the transcriptional response in these tissues is more pronounced in response to feeding on Sm. Functional classification of differentially expressed transcripts identified metabolic genes as the most represented class in response to both routes of infection, while immune genes were poorly regulated in both routes. We also report that Sm oral infections are associated with significant downregulation of several immune genes belonging to different families, specifically the clip-domain serine protease family. In sum, our findings reveal that the route of infection not only alters the contribution of key immunity genes to host antimicrobial defense but is also associated with different transcriptional responses in midguts and abdomens, possibly reflecting different adaptive strategies of the host.

Habitat suitability, niche unfilling and the potential spread of Pterois miles in the Mediterranean Sea.

The common lionfish Pterois miles has rapidly spread across the eastern Mediterranean Sea. We compiled occurrence data from both native and invaded range under the framework of Species Distribution Modelling (SDM). Through a construction of an environmental suitability model and estimation of spread rates we investigated the lionfish climate niche in both its native and invaded domains, this latter represented by the Mediterranean region. Model projections allowed to identify suitable areas for lionfish establishment in the Mediterranean. Spread analysis suggested that a further geographical expansion in this basin could be completed within the next years. Our results did not provide evidence for niche expansion but highlighted a high degree of niche unfilling thus prospecting a likely spread of Mediterranean lionfish invasion beyond the predictions of current SDMs. These findings provide novel inputs to forecast the future geographical evolution of the lionfish in the Mediterranean Sea and asses the related risk of invasion.

A comparative analysis of Wolbachia-induced host reproductive phenotypes reveals transition rate heterogeneity.

The endosymbiotic bacterium Wolbachia infects a wide range of arthropods and their relatives. It is an intracellular parasite transmitted through the egg from mother to offspring. Wolbachia can spread and persist through various means of host reproductive manipulation. How these different mechanisms of host manipulation evolved in Wolbachia is unclear. Which host reproductive phenotype is most likely to be ancestral and whether evolutionary transitions between some host phenotypes are more common than others remain unanswered questions. Recent studies have revealed multiple cases where the same Wolbachia strain can induce different reproductive phenotypes in different hosts, raising the question to what degree the induced host phenotype should be regarded as a trait of Wolbachia. In this study, we constructed a phylogenetic tree of Wolbachia and analyzed the patterns of host phenotypes along that tree. We were able to detect a phylogenetic signal of host phenotypes on the Wolbachia tree, indicating that the induced host phenotype can be regarded as a Wolbachia trait. However, we found no clear support for the previously stated hypothesis that cytoplasmic incompatibility is ancestral to Wolbachia in arthropods. Our analysis provides evidence for heterogeneous transition rates between host phenotypes.

Characterization of the Cultivable Gut Microflora in Wild-Caught Mediterranean Fish Species.

BACKGROUND: Microflora of the gastrointestinal tract plays important roles in food digestion, nutrient absorption and in host defense against ingested pathogens. Several studies have focused on the microflora of farmed fishes, but the gut flora of wild fishes remains poorly characterized. The aim of this work was to provide an overview of the bacteria colonizing the gut of wild-caught fishes and to determine whether some bacterial species can be pathogenic. RESULTS: We isolated cultivable bacteria from fifteen wild-caught Mediterranean fish species corresponding to different habitat, diet and origin. Bacterial species identity was determined by 16s rRNA gene sequencing for the 61 isolates. The potential pathogenicity of isolated bacteria was investigated using fruit fly (Drosophila melanogaster) and zebrafish (Danio rerio) as model organisms. Two bacterial strains (Serratia sp. and Aeromonas salmonicida) were lethal when microinjected to Drosophila, while zebrafish did not develop any disease when exposed to any of 34 isolated bacterial strains. However, it was interesting to note that two bacterial strains (Shewanella and Arthrobacter) isolated from marine fishes were able to colonize the guts of freshwater zebrafish. CONCLUSION: The results of this study give an overview of the bacterial species found in the guts of wild fishes living off Beirut seashore. It shows that some parameters believed to be limiting factors to host-gut colonization by bacteria can be overcome by some species. This pilot study could be extended by sampling a larger number of fish species with several specimens per fish species, and by identifying uncultivable bacteria that reside in the fish guts. Our results may have implications for the utilization of certain bacterial species in fish farming or their use as bio-indicators for water and/or food quality.

Wildlife-livestock interactions in a western rangeland setting: quantifying disease-relevant contacts.

Disease transmission between wild ungulates and domestic livestock is an important and challenging animal health issue. The potential for disease transmission between wildlife and livestock is notoriously difficult to estimate. The first step for estimating the potential for between-species disease transmission is to quantify proximity between individuals of different species in space and time. This study estimates second-order statistics of spatio-temporal location data from radio-collared free-ranging deer, elk and cattle in northeast Oregon. Our results indicate, that when observed simultaneously, elk and cattle occur in closer proximity to each other than what would be expected based on general space use of these species. The same is true for deer and elk but not for deer and cattle. Our analysis also demonstrates that average distances between cattle and elk are largely driven by rare events of close co-mingling between the species, which extend over several hours. Behavioral causes for these co-mingling events are currently unknown. Understanding the causes for such events will be important for designing grazing practices that minimize wildlife-livestock contacts.

Emergence and genetic variation of neuraminidase stalk deletions in avian influenza viruses.

When avian influenza viruses (AIVs) are transmitted from their reservoir hosts (wild waterfowl and shorebirds) to domestic bird species, they undergo genetic changes that have been linked to higher virulence and broader host range. Common genetic AIV modifications in viral proteins of poultry isolates are deletions in the stalk region of the neuraminidase (NA) and additions of glycosylation sites on the hemagglutinin (HA). Even though these NA deletion mutations occur in several AIV subtypes, they have not been analyzed comprehensively. In this study, 4,920 NA nucleotide sequences, 5,596 HA nucleotide and 4,702 HA amino acid sequences were analyzed to elucidate the widespread emergence of NA stalk deletions in gallinaceous hosts, the genetic polymorphism of the deletion patterns and association between the stalk deletions in NA and amino acid variants in HA. Forty-seven different NA stalk deletion patterns were identified in six NA subtypes, N1-N3 and N5-N7. An analysis that controlled for phylogenetic dependence due to shared ancestry showed that NA stalk deletions are statistically correlated with gallinaceous hosts and certain amino acid features on the HA protein. Those HA features included five glycosylation sites, one insertion and one deletion. The correlations between NA stalk deletions and HA features are HA-NA-subtype-specific. Our results demonstrate that stalk deletions in the NA proteins of AIV are relatively common. Understanding the NA stalk deletion and related HA features may be important for vaccine and drug development and could be useful in establishing effective early detection and warning systems for the poultry industry.

Fitting parameters of stochastic birth-death models to metapopulation data.

Populations that are structured into small local patches are a common feature of ecological and epidemiological systems. Models describing this structure are often referred to as metapopulation models in ecology or household models in epidemiology. Small local populations are subject to demographic stochasticity. Theoretical studies of household disease models without resistant stages (SIS models) have shown that local stochasticity can be ignored for between patch disease transmission if the number of connected patches is large. In that case the distribution of the number of infected individuals per household reaches a stationary distribution described by a birth-death process with a constant immigration term. Here we show how this result, in conjunction with the balancing condition for birth-death processes, provides a framework to estimate demographic parameters from a frequency distribution of local population sizes. The parameter estimation framework is applicable to estimate parameters of disease transmission models as well as metapopulation models.

Identifying errors in avian influenza virus gene sequences and implications for data usage of public databases.

Public gene sequence databases have become important research tools to understand viruses and other organisms. Evidence suggests that the identifying information for some of the sequences in these databases might not belong to the sequences they are associated with. We developed two tests to conduct a comprehensive analysis of all published sequences of the hemaglutinin and neuramidase genes of avian influenza viruses (AIVs) to identify sequences that may have been misclassified. One test identified sequence pairs with highly similar nucleotide sequences despite a difference of several years between their sampling dates. Another test, which was applied to samples sequenced and deposited more than once, detected sequences with more nucleotide differences to their own than to their closest relatives. All sequences identified as misclassified were further traced to relevant publications to assess the likelihood of contamination and determine if any conclusions were associated with the use of these sequences. Our results suggested that among 4040 published gene sequences examined, approximately 0.8% might be misclassified and that publications using these sequences may include inaccurate statements. Findings from this report suggest that using laboratory-adapted strains and handling multiple samples simultaneously increases the risk of contamination. The tests reported here may be useful for screening new submissions to public sequence databases.

Adaptation and transmission of a duck-origin avian influenza virus in poultry species.

A duck-origin avian influenza virus (AIV) was used to study viral adaptation and transmission patterns in chickens (Gallus gallus domesticus) and Pekin ducks (Anas platyrhynchos domesticus). Inoculated birds were housed with naïve birds of the same species and all birds were monitored for infection. The inoculating duck virus was transmitted effectively by contact in both species. Viruses recovered from infected birds showed mutations as early as 1 or 3 days after inoculation in chickens and ducks, respectively. Amino acid substitutions in hemagglutinin (HA) or deletions in neuraminidase (NA) stalk regions were identified in chicken isolates, but only substitutions in HA were identified in duck isolates. HA substitution-containing viruses replicated more efficiently than those with NA stalk deletions. NA deletion mutants were not recovered from contact chickens, suggesting inefficient transmission. Amino acid substitutions in HA proteins appeared in pairs in chickens, but were independent in ducks, indicating adaptation in chickens. In addition, our findings showed that a duck-origin virus can rapidly adapt to chickens, suggesting that the emergence of new epidemic AIV can be rapid.

Invasions by Eurasian avian influenza virus H6 genes and replacement of the virus' North American clade.

The spread of highly pathogenic avian influenza virus (AIV) (H5N1) underlines the potential for global AIV movement through birds. The phylogenies of AIV genes from avian hosts usually separate into Eurasian and North American clades, reflecting limited bird migration between the hemispheres. However, mounting evidence that some H6 sequences from North America cluster with Eurasian subtype H6 sequences calls the strict hemispheric divide into question. We conducted a comprehensive phylogenetic analysis of the extent and timing of cross-hemisphere movements by the H6 gene. Results suggested that Eurasian H6 subtype has invaded North America several times, with the first invasions occurring 10 years before the first detection of invading isolates. The members of the North American clade decreased from 100% in the 1980s to 20% in the 2000s among H6 isolates from North America. Unraveling the reasons for this large-scale gene movement between hemispheres might identify drivers of global AIV circulation.

Spatial re-establishment dynamics of local populations of vectors of Chagas disease.

BACKGROUND: Prevention of Chagas disease depends mainly on control of the insect vectors that transmit infection. Unfortunately, the vectors have been resurgent in some areas. It is important to understand the dynamics of reinfestation where it occurs. Here we show how continuous- and discrete-time models fitted to patch-level infestation states can elucidate different aspects of re-establishment. Triatoma infestans, the main vector of Chagas disease, reinfested sites in three villages in northwest Argentina after community-wide insecticide spraying in October 1992. METHODOLOGY/PRINCIPAL FINDINGS: Different methods of estimating the probabilities of bug establishment on each site were compared. The results confirmed previous results showing a 6-month time lag between detection of a new infestation and dispersal events. The analysis showed that more new bug populations become established from May to November than from November to May. This seasonal increase in bug establishment coincides with a seasonal increase in dispersal distance. In the fitted models, the probability of new bug establishment increases with increasing time since last detected infestation. CONCLUSIONS/SIGNIFICANCE: These effects of season and previous infestation on bug establishment challenge our current understanding of T. infestans ecology and highlight important gaps in knowledge. Experiments necessary to close these gaps are discussed.

The distribution of eggs per host in a herbivorous insect--intersection of oviposition, dispersal and population dynamics.

1. The dynamics of parasitic organisms depend critically upon the frequency distribution of parasite individuals per host. However, the processes giving rise to this frequency distribution have rarely been modelled and tested for organisms with complex host selection behaviour. 2. In this study Microrhopala vittata, a chrysomelid beetle, was used to investigate how oviposition behaviour, movement and density of host plants interact in shaping the frequency distribution of egg clusters per host in the field. 3. Enclosures were stocked with two different host species and different beetle densities and various stochastic process models were fitted to egg cluster count data obtained from these enclosures. The different models were derived considering different scenarios, in particular whether or not plant density limits oviposition rate, whether or not ovipositing females actively seek out the most attractive plant within their perception radius and whether a female's oviposition rate is determined by plant intrinsic factors, the plant's egg cluster load or the surrounding beetle density. 4. The model parameters fitted to cage data were used to describe the frequency distribution of egg cluster counts obtained in a release experiment in the field. A total of 220 beetle pairs were released at five locations in a field where this beetle was not observed previously. Each release point was at a border between the two host species. 5. One model predicted for the preferred host species the egg cluster count frequencies in the field from parameters estimated in the cages. This model assumed that egg clusters present on a plant increased subsequent oviposition on this plant. All other models could not describe the distribution of egg cluster counts for either of the two host species. 6. The results suggest that females seek out attractive hosts actively and the attractiveness of a plant increases with its egg cluster load. This behaviour creates a frequency distribution of egg clusters per host that depends only on beetle density but not on plant density. This conclusion has important implications for modelling insect-plant interactions.