Microsporidia from the Encephalitozoonidae are obligate intracellular parasites with highly conserved and compacted nuclear genomes: they have few introns, short intergenic regions, and almost identical gene complements and chromosome arrangements. Comparative genomics of Encephalitozoon and microsporidia in general have focused largely on the genomic diversity between different species, and we know very little about the levels of genetic diversity within species. Polymorphism studies with Encephalitozoon are so far restricted to a small number of genes, and a few genetically distinct strains have been identified; most notably, three genotypes (ECI, ECII, and ECIII) of the model species E. cuniculi have been identified based on variable repeats in the rRNA internal transcribed spacer (ITS). To determine if E. cuniculi genotypes are genetically distinct lineages across the entire genome and at the same time to examine the question of intraspecies genetic diversity in microsporidia in general, we sequenced de novo genomes from each of the three genotypes and analyzed patterns of single nucleotide polymorphisms (SNPs) and insertions/deletions across the genomes. Although the strains have almost identical gene contents, they harbor large numbers of SNPs, including numerous nonsynonymous changes, indicating massive intraspecies variation within the Encephalitozoonidae. Based on this diversity, we conclude that the recognized genotypes are genetically distinct and propose new molecular markers for microsporidian genotyping.
Readout-segmented echo planar imaging with 2D navigator-based reacquisition is an uprising technique enabling the sampling of high-resolution diffusion images with reduced susceptibility artifacts. However, low signal from the small voxels and long scan times hamper the clinical applicability. Therefore, we introduce a regularization algorithm based on total variation that is applied directly on the entire diffusion tensor. The spatially varying regularization parameter is determined automatically dependent on spatial variations in signal-to-noise ratio thus, avoiding over- or under-regularization. Information about the noise distribution in the diffusion tensor is extracted from the diffusion weighted images by means of complex independent component analysis. Moreover, the combination of those features enables processing of the diffusion data absolutely user independent. Tractography from in vivo data and from a software phantom demonstrate the advantage of the spatially varying regularization compared to un-regularized data with respect to parameters relevant for fiber-tracking such as Mean Fiber Length, Track Count, Volume and Voxel Count. Specifically, for in vivo data findings suggest that tractography results from the regularized diffusion tensor based on one measurement (16 min) generates results comparable to the un-regularized data with three averages (48 min). This significant reduction in scan time renders high resolution (1×1×2.5 mm3) diffusion tensor imaging of the entire brain applicable in a clinical context.
In this review, we describe our current understanding of translation termination and pharmacological agents that influence the accuracy of this process. A number of drugs have been identified that induce suppression of translation termination at in-frame premature termination codons (PTCs; also known as nonsense mutations) in mammalian cells. We discuss efforts to utilize these drugs to suppress disease-causing PTCs that result in the loss of protein expression and function. In-frame PTCs represent a genotypic subset of mutations that make up ~11% of all known mutations that cause genetic diseases, and millions of patients have diseases attributable to PTCs. Current approaches aimed at reducing the efficiency of translation termination at PTCs (referred to as PTC suppression therapy) have the goal of alleviating the phenotypic consequences of a wide range of genetic diseases. Suppression therapy is currently in clinical trials for treatment of several genetic diseases caused by PTCs, and preliminary results suggest that some patients have shown clinical improvements. While current progress is promising, we discuss various approaches that may further enhance the efficiency of this novel therapeutic approach.
Parasites have adapted to their specialised way of life by a number of means, including the acquisition of genes by horizontal gene transfer. These newly acquired genes seem to come from a variety of sources, but seldom from the host, even in the most intimate associations between obligate intracellular parasite and host . Microsporidian intracellular parasites have acquired a handful of genes, mostly from bacteria, that help them take energy from their hosts or protect them from the environment [2,3]. To date, however, no animal genes have been documented in any microsporidian genome. Here, we have surveyed the genome of the microsporidian Encephalitozoon romaleae, which parasitises arthropods for evidence of animal genes. We found one protein-encoding gene that is absent from publicly available sequence data from other microsporidia. The gene encodes a component of the purine salvage pathway, and has been independently acquired by other parasites through horizontal gene transfer from other donors. In this case, however, the gene shows a very strong phylogenetic signal for arthropod origin.
A major goal of infectious disease epidemiology is to understand and predict the spread of infections within human populations, with the intention of better informing decisions regarding control and intervention. However, the development of fully mechanistic models of transmission requires a quantitative understanding of social interactions and collective properties of social networks. We performed a cross-sectional study of the social contacts on given days for more than 5000 respondents in England, Scotland and Wales, through postal and online survey methods. The survey was designed to elicit detailed and previously unreported measures of the immediate social network of participants relevant to infection spread. Here, we describe individual-level contact patterns, focusing on the range of heterogeneity observed and discuss the correlations between contact patterns and other socio-demographic factors. We find that the distribution of the number of contacts approximates a power-law distribution, but postulate that total contact time (which has a shorter-tailed distribution) is more epidemiologically relevant. We observe that children, public-sector and healthcare workers have the highest number of total contact hours and are therefore most likely to catch and transmit infectious disease. Our study also quantifies the transitive connections made between an individual's contacts (or clustering); this is a key structural characteristic of social networks with important implications for disease transmission and control efficacy. Respondents' networks exhibit high levels of clustering, which varies across social settings and increases with duration, frequency of contact and distance from home. Finally, we discuss the implications of these findings for the transmission and control of pathogens spread through close contact.
social contact; survey; epidemic; infectious disease; network
Although the nation’s local health departments (LHDs) share a common mission, variability in administrative structures is a barrier to identifying common, optimal management strategies. There is a gap in understanding what unifying features LHDs share as organizations that could be leveraged systematically for achieving high performance.
To explore sources of commonality and variability in a range of LHDs by comparing intraorganizational networks.
We used organizational network analysis to document relationships between employees, tasks, knowledge, and resources within LHDs, which may exist regardless of formal administrative structure.
A national sample of 11 LHDs from seven states that differed in size, geographic location, and governance.
Relational network data were collected via an on-line survey of all employees in 11 LHDs. A total of 1 062 out of 1 239 employees responded (84% response rate).
Network measurements were compared using coefficient of variation. Measurements were correlated with scores from the National Public Health Performance Assessment and with LHD demographics. Rankings of tasks, knowledge, and resources were correlated across pairs of LHDs.
We found that 11 LHDs exhibited compound organizational structures in which centralized hierarchies were coupled with distributed networks at the point of service. Local health departments were distinguished from random networks by a pattern of high centralization and clustering. Network measurements were positively associated with performance for 3 of 10 essential services (r > 0.65). Patterns in the measurements suggest how LHDs adapt to the population served.
Shared network patterns across LHDs suggest where common organizational management strategies are feasible. This evidence supports national efforts to promote uniform standards for service delivery to diverse populations.
complex adaptive systems; management; network analysis; organizations; performance; public health
Wide variation in performance of public health (PH) systems, coupled with national interest in improving PH system quality, makes it a priority to identify factors associated with performance. One factor may be congruence between a state’s PH enabling statutes and the obligations outlined in Public Health in America—the collaboratively developed framework that defines the mission and essential services (ESs) of PH.
This research examined the relationship between (1) the degree to which language in a state’s PH enabling statutes reflects PH’s mission and ESs and (2) the performance of local public health systems in delivering ESs, measured by National Public Health Performance Standards scores in 207 local jurisdictions.
Binary logistic regression demonstrated that a high degree of congruence between statutory language and public health’s mission increased the odds of above-average system performance for 5 of 10 ESs.
High levels of congruence between statutory language and the ESs themselves increased odds of above-average system performance for 6 of 10 ESs. Results yielded modest odds ratios (<2.0).
Limitations of the data make it impossible to draw firm conclusions; however, these modest results suggest that statutory language may account for little of the variation in local public health system performance.
essential services; logistic regression; mission; performance; public health law; statute
Introduction. Chronic constipation is common in the elderly, and often no underlying pathology is found. Primary colonic dysmotility has been described in children but is rare in the elderly. Case report. We present an 82-year-old female with long standing constipation presenting acutely with large bowel obstruction. Laparotomy and Hartman's procedure was performed, and a grossly distended sigmoid colon was resected. Histology revealed a primary myopathic process. Conclusion. Primary colonic myopathy should be considered in elderly patients presenting with large bowel obstruction and a long preceding history of constipation, particularly when previous endoscopic examinations were normal.
Proximal thoracic aortic reconstruction performed with or without hypothermic circulatory arrest (HCA) is an effective surgical strategy for aortic pathology. In this study, the clinical outcomes of patients undergoing reoperative proximal thoracic aortic surgery were evaluated. A retrospective review was performed for reoperative proximal aortic surgery from 2004 to date. Patient data were abstracted from the society of thoracic surgeons (STS) institutional database and patient charts. Univariate analysis was conducted on the HCA group in order to determine the impact of variables on in-hospital mortality. Kaplan–Meier survival estimates were calculated for long-term survival analysis. One hundred and twenty-two patients were included in the analysis. Twenty-seven (22.1%) were female, and the mean age was 53.8 years. Seventy-seven (63.1%) patients had an aortic root replacement, and 93 (76.2%) patients underwent aortic arch replacement. Circulatory arrest was performed in 92 (75.4%) patients. Operative mortality occurred in 14 patients (11.5%). Complications included re-exploration for haemorrhage (nine patients, 7.4%), stroke (four, 3.3%), renal failure (13, 10.7%) and major adverse events (18, 14.8%). Univariate and multivariate analyses of HCA patients showed cardiopulmonary bypass (CPB) time, preoperative renal failure and prior coronary revascularization as independent predictors of mortality. Reoperative proximal aortic surgery can be performed with acceptable morbidity and mortality. These data also suggest that HCA represents a safe operative strategy for this patient population.
Aortic surgery; Hypothermic circulatory arrest; Redo surgery
Abnormal tail biting behaviour is a major welfare problem for pigs receiving the behaviour, as well as an indication of decreased welfare in the pigs performing it. However, not all pigs in a pen perform or receive tail biting behaviour and it has recently been shown that these ‘neutral’ pigs not only differ in their behaviour, but also in their gene expression compared to performers and receivers of tail biting in the same pen. To investigate whether this difference was linked to the cause or a consequence of them not being involved in the outbreak of tail biting, behaviour and brain gene expression was compared with ‘control’ pigs housed in pens with no tail biting. It was shown that the pigs housed in control pens performed a wider variety of pig-directed abnormal behaviour (belly nosing 0.95±1.59, tail in mouth 0.31±0.60 and ‘other‘ abnormal 1.53±4.26; mean±S.D) compared to the neutral pigs (belly nosing 0.30±0.62, tail in mouth 0.13±0.50 and “other“ abnormal 0.42±1.06). With Affymetrix gene expression arrays, 107 transcripts were identified as differently expressed (p<0.05) between these two categories of pigs. Several of these transcripts had already been shown to be differently expressed in the neutral pigs when they were compared to performers and receivers of tail biting in the same pen in an earlier study. Hence, the different expression of these genes cannot be a consequence of the neutral pigs not being involved in tail biting behaviour, but rather linked to the cause contributing to why they were not involved in tail biting interactions. These neutral pigs seem to have a genetic and behavioural profile that somehow contributes to them being resistant to performing or receiving pig-directed abnormal behaviour, such as tail biting, even when housed in an environment that elicits that behaviour in other pigs.
Public health systems and services research (PHSSR) examines the organization, financing, and delivery of public health services and the impact of these activities on population health. An accurate description of this PHSSR is needed to empower funding agencies and other stakeholders, to coordinate PHSSR activities, and to foster the development of the field.
To characterize the emerging community of researchers engaged in PHSSR. This study 1) describes dynamics of this growing community; and 2) identifies distinct topics being researched, communities of practice within PHSSR, and collaboration among groups.
Co-authorship network visualization of selected research publications in the Medline bibliographic database.
PHSSR has emerged gradually since 1988, with noticeable growth after 1994 and after 2004. The network of PHSSR research has a core-periphery structure. The core of this network includes highly collaborative researchers focusing on topics pertaining directly to PHSSR, such as the public health workforce, quality improvement and performance, law, and information infrastructure. The periphery consists of groups publishing either more generally on various health services research topics, or on epidemiologic, clinical, or health sciences topics.
While a nucleus group of productive and engaged individuals participate in PHSSR, most authors are also involved in general health services research, issues of population health, or health science topics unrelated to PHSSR. An overview of collaboration in PHSSR is an important step in advancing a coordinated research agenda and attracting sustainable funding streams for this field.
An important missing piece in the puzzle of how plastids spread across the eukaryotic tree of life is a robust evolutionary framework for the host lineages. Four assemblages are known to harbour plastids derived from red algae and, according to the controversial chromalveolate hypothesis, these all share a common ancestry. Phylogenomic analyses have consistently shown that stramenopiles and alveolates are closely related, but haptophytes and cryptophytes remain contentious; they have been proposed to branch together with several heterotrophic groups in the newly erected Hacrobia. Here, we tested this question by producing a large expressed sequence tag dataset for the katablepharid Roombia truncata, one of the last hacrobian lineages for which genome-level data are unavailable, and combined this dataset with the recently completed genome of the cryptophyte Guillardia theta to build an alignment composed of 258 genes. Our analyses strongly support haptophytes as sister to the SAR group, possibly together with telonemids and centrohelids. We also confirmed the common origin of katablepharids and cryptophytes, but these lineages were not related to other hacrobians; instead, they branch with plants. Our study resolves the evolutionary position of haptophytes, an ecologically critical component of the oceans, and proposes a new hypothesis for the origin of cryptophytes.
phylogenomics; plastid; haptophyte; cryptophyte; katablepharid; tree of life
White spruce (Picea glauca) is a dominant conifer of the boreal forests of North America, and providing genomics resources for this commercially valuable tree will help improve forest management and conservation efforts. Sequencing and assembling the large and highly repetitive spruce genome though pushes the boundaries of the current technology. Here, we describe a whole-genome shotgun sequencing strategy using two Illumina sequencing platforms and an assembly approach using the ABySS software. We report a 20.8 giga base pairs draft genome in 4.9 million scaffolds, with a scaffold N50 of 20 356 bp. We demonstrate how recent improvements in the sequencing technology, especially increasing read lengths and paired end reads from longer fragments have a major impact on the assembly contiguity. We also note that scalable bioinformatics tools are instrumental in providing rapid draft assemblies.
Availability: The Picea glauca genome sequencing and assembly data are available through NCBI (Accession#: ALWZ0100000000 PID: PRJNA83435). http://www.ncbi.nlm.nih.gov/bioproject/83435.
Supplementary data are available at Bioinformatics online.
The mountain pine beetle (MPB, Dendroctonus ponderosae) epidemic has affected lodgepole pine (Pinus contorta) across an area of more than 18 million hectares of pine forests in western Canada, and is a threat to the boreal jack pine (Pinus banksiana) forest. Defence of pines against MPB and associated fungal pathogens, as well as other pests, involves oleoresin monoterpenes, which are biosynthesized by families of terpene synthases (TPSs). Volatile monoterpenes also serve as host recognition cues for MPB and as precursors for MPB pheromones. The genes responsible for terpene biosynthesis in jack pine and lodgepole pine were previously unknown.
We report the generation and quality assessment of assembled transcriptome resources for lodgepole pine and jack pine using Sanger, Roche 454, and Illumina sequencing technologies. Assemblies revealed transcripts for approximately 20,000 - 30,000 genes from each species and assembly analyses led to the identification of candidate full-length prenyl transferase, TPS, and P450 genes of oleoresin biosynthesis. We cloned and functionally characterized, via expression of recombinant proteins in E. coli, nine different jack pine and eight different lodgepole pine mono-TPSs. The newly identified lodgepole pine and jack pine mono-TPSs include (+)-α-pinene synthases, (-)-α-pinene synthases, (-)-β-pinene synthases, (+)-3-carene synthases, and (-)-β-phellandrene synthases from each of the two species.
In the absence of genome sequences, transcriptome assemblies are important for defence gene discovery in lodgepole pine and jack pine, as demonstrated here for the terpenoid pathway genes. The product profiles of the functionally annotated mono-TPSs described here can account for the major monoterpene metabolites identified in lodgepole pine and jack pine.
Conifer defence; Pine oleoresin; Terpenoid biosynthesis; Metabolite profile; Prenyl transferase; Cytochrome P450; Conifer genome
eHealth is an application of information and communication technologies across the whole range of functions that affect health. The benefits of eHealth (eg, improvement of health care operational efficiency and quality of patient care) have previously been documented in the literature. Health care providers (eg, medical doctors) are the key driving force in pushing eHealth initiatives. Without their acceptance and actual use, those eHealth benefits would be unlikely to be reaped.
To identify and synthesize influential factors to health care providers’ acceptance of various eHealth systems.
This systematic literature review was conducted in four steps. The first two steps facilitated the location and identification of relevant articles. The third step extracted key information from those articles including the studies’ characteristics and results. In the last step, identified factors were analyzed and grouped in accordance with the Unified Theory of Acceptance and Use of Technology (UTAUT).
This study included 93 papers that have studied health care providers’ acceptance of eHealth. From these papers, 40 factors were identified and grouped into 7 clusters: (1) health care provider characteristics, (2) medical practice characteristics, (3) voluntariness of use, (4) performance expectancy, (5) effort expectancy, (6) social influence, and (7) facilitating or inhibiting conditions.
The grouping results demonstrated that the UTAUT model is useful for organizing the literature but has its limitations. Due to the complex contextual dynamics of health care settings, our work suggested that there would be potential to extend theories on information technology adoption, which is of great benefit to readers interested in learning more on the topic. Practically, these findings may help health care decision makers proactively introduce interventions to encourage acceptance of eHealth and may also assist health policy makers refine relevant policies to promote the eHealth innovation.
technology acceptance; eHealth; health care provider; adoption
In this paper, we simulate outbreaks of foot-and-mouth disease in the Commonwealth of Pennsylvania, USA – after the introduction of a state-wide movement ban – as they might unfold in the presence of mitigation strategies. We have adapted a model previously used to investigate FMD control policies in the UK to examine the potential for disease spread given an infection seeded in each county in Pennsylvania. The results are highly dependent upon the county of introduction and the spatial scale of transmission. Should the transmission kernel be identical to that for the UK, the epidemic impact is limited to fewer than 20 premises, regardless of the county of introduction. However, for wider kernels where infection can spread further, outbreaks seeded in or near the county with highest density of premises and animals result in large epidemics (>150 premises). Ring culling and vaccination reduce epidemic size, with the optimal radius of the rings being dependent upon the county of introduction. Should the kernel width exceed a given county-dependent threshold, ring culling is unable to control the epidemic. We find that a vaccinate-to-live policy is generally preferred to ring culling (in terms of reducing the overall number of premises culled), indicating that well-targeted control can dramatically reduce the risk of large scale outbreaks of foot-and-mouth disease occurring in Pennsylvania.
Foot and mouth disease; Spatial model; USA; Culling; Vaccination
Nonsense suppression therapy is an approach to treat genetic diseases caused by nonsense mutations. This therapeutic strategy pharmacologically suppresses translation termination at Premature Termination Codons (PTCs) in order to restore expression of functional protein. However, the process of Nonsense-Mediated mRNA Decay (NMD), which reduces the abundance of mRNAs containing PTCs, frequently limits this approach. Here, we used a mouse model of the lysosomal storage disease mucopolysaccharidosis I-Hurler (MPS I-H) that carries a PTC in the Idua locus to test whether NMD attenuation can enhance PTC suppression in vivo. Idua encodes alpha-L-iduronidase, an enzyme required for degradation of the glycosaminoglycans (GAGs) heparan sulfate and dermatan sulfate. We found that the NMD attenuator NMDI-1 increased the abundance of the PTC-containing Idua transcript. Furthermore, co-administration of NMDI-1 with the PTC suppression drug gentamicin enhanced alpha-L-iduronidase activity compared to gentamicin alone, leading to a greater reduction of GAG storage in mouse tissues, including the brain. These results demonstrate that NMD attenuation significantly enhances suppression therapy in vivo.
Recently, it was shown that gene conversion between the ends of linear mitochondrial chromosomes can cause telomere expansion and the duplication of subtelomeric loci. However, it is not yet known how widespread this phenomenon is and how significantly it has impacted organelle genome architecture. Using linear mitochondrial DNAs and mitochondrial plasmids from diverse eukaryotes, we argue that telomeric recombination has played a major role in fashioning linear organelle chromosomes. We find that mitochondrial telomeres frequently expand into subtelomeric regions, resulting in gene duplications, homogenizations, and/or fragmentations. We suggest that these features are a product of subtelomeric gene conversion, provide a hypothetical model for this process, and employ genetic diversity data to support the idea that the greater the effective population size the greater the potential for gene conversion between subtelomeric loci.
gene duplication; inverted repeat; mitochondrial DNA; nucleotide diversity; plasmid; telomere
Antiviral treatment offers a fast acting alternative to vaccination; as such it is viewed as a first-line of defence against pandemic influenza in protecting families and households once infection has been detected. In clinical trials, antiviral treatments have been shown to be efficacious in preventing infection, limiting disease and reducing transmission, yet their impact at containing the 2009 influenza A(H1N1)pdm outbreak was limited. To understand this seeming discrepancy, we develop a general and computationally efficient model for studying household-based interventions. This allows us to account for uncertainty in quantities relevant to the 2009 pandemic in a principled way, accounting for the heterogeneity and variability in each epidemiological process modelled. We find that the population-level effects of delayed antiviral treatment and prophylaxis mean that their limited overall impact is quantitatively consistent (at current levels of precision) with their reported clinical efficacy under ideal conditions. Hence, effective control of pandemic influenza with antivirals is critically dependent on early detection and delivery ideally within 24 h.
A(H1N1)pdm; Bayesian; doubling time; Markov chain; R*
The microsporidia are emerging human and veterinary pathogens known to infect every tissue type and organ system. Their infectious spore possesses a number of peculiar organelles, including the diagnostic polar tube. In a proteomics-driven effort to find novel components of this organelle in the human-pathogenic species Encephalitozoon cuniculi, we unexpectedly discovered a protein which localizes to punctate structures consistent with the appearance of relic mitochondria, or mitosomes. However, this novel protein did not colocalize with ferredoxin, a mitochondrial iron-sulfur cluster protein which shows a similar localization pattern by light microscopy. The distribution pattern of this protein thus suggests either a novel vesicular compartment that is similar to mitosomes in size and distribution, the presence of subdomains or branching architecture within mitosomes, or heterogeneity in the protein composition of Encephalitozoon cuniculi mitosomes.
microsporidia; mitosome; mitochondria; proteomics; ferredoxin; polar vesicles
Red algae have the most gene-rich plastid genomes known, but despite their evolutionary importance these genomes remain poorly sampled. Here we characterize three complete and one partial plastid genome from a diverse range of florideophytes. By unifying annotations across all available red algal plastid genomes we show they all share a highly compact and slowly-evolving architecture and uniquely rich gene complements. Both chromosome structure and gene content have changed very little during red algal diversification, and suggest that plastid-to nucleus gene transfers have been rare. Despite their ancient character, however, the red algal plastids also contain several unprecedented features, including a group II intron in a tRNA-Met gene that encodes the first example of red algal plastid intron maturase – a feature uniquely shared among florideophytes. We also identify a rare case of a horizontally-acquired proteobacterial operon, and propose this operon may have been recruited for plastid function and potentially replaced a nucleus-encoded plastid-targeted paralogue. Plastid genome phylogenies yield a fully resolved tree and suggest that plastid DNA is a useful tool for resolving red algal relationships. Lastly, we estimate the evolutionary rates among more than 200 plastid genes, and assess their usefulness for species and subspecies taxonomy by comparison to well-established barcoding markers such as cox1 and rbcL. Overall, these data demonstrates that red algal plastid genomes are easily obtainable using high-throughput sequencing of total genomic DNA, interesting from evolutionary perspectives, and promising in resolving red algal relationships at evolutionarily-deep and species/subspecies levels.
The European spruce bark beetle, Ips typographus, and the North American mountain pine beetle, Dendroctonus ponderosae (Coleoptera: Curculionidae: Scolytinae), are severe pests of coniferous forests. Both bark beetle species utilize aggregation pheromones to coordinate mass-attacks on host trees, while odorants from host and non-host trees modulate the pheromone response. Thus, the bark beetle olfactory sense is of utmost importance for fitness. However, information on the genes underlying olfactory detection has been lacking in bark beetles and is limited in Coleoptera. We assembled antennal transcriptomes from next-generation sequencing of I. typographus and D. ponderosae to identify members of the major chemosensory multi-gene families.
Gene ontology (GO) annotation indicated that the relative abundance of transcripts associated with specific GO terms was highly similar in the two species. Transcripts with terms related to olfactory function were found in both species. Focusing on the chemosensory gene families, we identified 15 putative odorant binding proteins (OBP), 6 chemosensory proteins (CSP), 3 sensory neuron membrane proteins (SNMP), 43 odorant receptors (OR), 6 gustatory receptors (GR), and 7 ionotropic receptors (IR) in I. typographus; and 31 putative OBPs, 11 CSPs, 3 SNMPs, 49 ORs, 2 GRs, and 15 IRs in D. ponderosae. Predicted protein sequences were compared with counterparts in the flour beetle, Tribolium castaneum, the cerambycid beetle, Megacyllene caryae, and the fruit fly, Drosophila melanogaster. The most notable result was found among the ORs, for which large bark beetle-specific expansions were found. However, some clades contained receptors from all four beetle species, indicating a degree of conservation among some coleopteran OR lineages. Putative GRs for carbon dioxide and orthologues for the conserved antennal IRs were included in the identified receptor sets.
The protein families important for chemoreception have now been identified in three coleopteran species (four species for the ORs). Thus, this study allows for improved evolutionary analyses of coleopteran olfaction. Identification of these proteins in two of the most destructive forest pests, sharing many semiochemicals, is especially important as they might represent novel targets for population control.
Ips typographus; Dendroctonus ponderosae; Gene ontology; Transcriptome; Odorant receptor; Ionotropic receptor; Gustatory receptor; Odorant binding protein; Chemosensory Protein; Sensory neuron membrane protein
The parabasalian symbionts of lower termite hindgut communities are well-known for their large size and structural complexity. The most complex forms evolved multiple times independently from smaller and simpler flagellates, but we know little of the diversity of these small flagellates or their phylogenetic relationships to more complex lineages. To understand the true diversity of Parabasalia and how their unique cellular complexity arose, more data from smaller and simpler flagellates are needed. Here, we describe two new genera of small-to-intermediate size and complexity, represented by the type species Cthulhu macrofasciculumque and Cthylla microfasciculumque from Prorhinotermes simplex and Reticulitermes virginicus, respectively (both hosts confirmed by DNA barcoding). Both genera have a single anterior nucleus embeded in a robust protruding axostyle, and an anterior bundle flagella (and likely a single posterior flagellum) that emerge slightly subanteriorly and have a distinctive beat pattern. Cthulhu is relatively large and has a distinctive bundle of over 20 flagella whereas Cthylla is smaller, has only 5 anterior flagella and closely resembles several other parababsalian genera. Molecular phylogenies based on small subunit ribosomal RNA (SSU rRNA) show both genera are related to previously unidentified environmental sequences from other termites (possibly from members of the Tricercomitidae), which all branch as sisters to the Hexamastigitae. Altogether, Cthulhu likely represents another independent origin of relatively high cellular complexity within parabasalia, and points to the need for molecular characterization of other key taxa, such as Tricercomitus.
Microsporidian Nosema bombycis has received much attention because the pébrine disease of domesticated silkworms results in great economic losses in the silkworm industry. So far, no effective treatment could be found for pébrine. Compared to other known Nosema parasites, N. bombycis can unusually parasitize a broad range of hosts. To gain some insights into the underlying genetic mechanism of pathological ability and host range expansion in this parasite, a comparative genomic approach is conducted. The genome of two Nosema parasites, N. bombycis and N. antheraeae (an obligatory parasite to undomesticated silkworms Antheraea pernyi), were sequenced and compared with their distantly related species, N. ceranae (an obligatory parasite to honey bees).
Our comparative genomics analysis show that the N. bombycis genome has greatly expanded due to the following three molecular mechanisms: 1) the proliferation of host-derived transposable elements, 2) the acquisition of many horizontally transferred genes from bacteria, and 3) the production of abundnant gene duplications. To our knowledge, duplicated genes derived not only from small-scale events (e.g., tandem duplications) but also from large-scale events (e.g., segmental duplications) have never been seen so abundant in any reported microsporidia genomes. Our relative dating analysis further indicated that these duplication events have arisen recently over very short evolutionary time. Furthermore, several duplicated genes involving in the cytotoxic metabolic pathway were found to undergo positive selection, suggestive of the role of duplicated genes on the adaptive evolution of pathogenic ability.
Genome expansion is rarely considered as the evolutionary outcome acting on those highly reduced and compact parasitic microsporidian genomes. This study, for the first time, demonstrates that the parasitic genomes can expand, instead of shrink, through several common molecular mechanisms such as gene duplication, horizontal gene transfer, and transposable element expansion. We also showed that the duplicated genes can serve as raw materials for evolutionary innovations possibly contributing to the increase of pathologenic ability. Based on our research, we propose that duplicated genes of N. bombycis should be treated as primary targets for treatment designs against pébrine.
Gene duplication; Horizontal gene transfer; Host-derived transposable element; Host adaptation; Microsporidian; Silkworms