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Seahorses have a specialized morphology that includes a toothless tubular mouth, a body covered with bony plates, a male brood pouch, and the absence of caudal and pelvic fins. Here we report the sequencing and de novo assembly of the genome of the tiger tail seahorse, Hippocampus comes . Comparative genomic analysis identifies higher protein and nucleotide evolutionary rates in H. comes compared with other teleost fish genomes. We identified an astacin metalloprotease gene family that has undergone expansion and is highly expressed in the male brood pouch. We also find that the H. comes genome lacks enamel matrix protein-coding proline/glutamine-rich secretory calcium-binding phosphoprotein genes, which might have led to the loss of mineralized teeth. tbx4 , a regulator of hindlimb development, is also not found in H. comes genome. Knockout of tbx4 in zebrafish showed a ‘pelvic fin-loss’ phenotype similar to that of seahorses. Here, the genome sequence of the tiger tail seahorse is reported and comparative genomic analyses with other ray-finned fishes are used to explore the genetic basis of the unique morphology and reproductive system of the seahorse. Evolution at a gallop Seahorses are prime examples of the exuberance of evolution and are unique among bony fish on several counts, including their equine body shape and male brood pouch. An international collaboration reporting in this issue of Nature has determined the genome sequence of a seahorse ( Hippocampus comes , the tiger tail seahorse). They find it to be the most rapidly evolving fish genome studied so far. H. comes is among the most commonly traded seahorse species—dried for traditional medicines and live for the aquarium trade—and is on the IUCN Red List as a 'vulnerable' species. Analysis of the genomic sequence provides insights into the evolution of its unique morphology. Of note is the absence of a master control gene, tbx4 , which functions in the development of hindlimbs and pelvic fins. Pelvic fins are missing in seahorses, and tbx4 -knockout mutant zebrafish also lack pelvic fins.

Cyclostomes, comprising jawless vertebrates such as lampreys and hagfishes, are the sister group of living jawed vertebrates (gnathostomes) and hence an important group for understanding the origin and diversity of vertebrates. In vertebrates and other metazoans, Hox genes determine cell fate along the anteroposterior axis of embryos and are implicated in driving morphological diversity. Invertebrates contain a single Hox cluster (either intact or fragmented), whereas elephant shark, coelacanth, and tetrapods contain four Hox clusters owing to two rounds of whole-genome duplication (“1R” and “2R”) during early vertebrate evolution. By contrast, most teleost fishes contain up to eight Hox clusters because of an additional “teleost-specific” genome duplication event. By sequencing bacterial artificial chromosome (BAC) clones and the whole genome, here we provide evidence for at least six Hox clusters in the Japanese lamprey (Lethenteron japonicum). This suggests that the lamprey lineage has experienced an additional genome duplication after 1R and 2R. The relative age of lamprey and human paralogs supports this hypothesis. Compared with gnathostome Hox clusters, lamprey Hox clusters are unusually large. Several conserved noncoding elements (CNEs) were predicted in the Hox clusters of lamprey, elephant shark, and human. Transgenic zebrafish assay indicated the potential of CNEs to function as enhancers. Interestingly, CNEs in individual lamprey Hox clusters are frequently conserved in multiple Hox clusters in elephant shark and human, implying a many-to-many orthology relationship between lamprey and gnathostome Hox clusters. Such a relationship suggests that the first two rounds of genome duplication may have occurred independently in the lamprey and gnathostome lineages.

[This corrects the article DOI: 10.1371/journal.pone.0214328.].

The exposure-response association between prenatal and postnatal household air pollution (HAP) and infant growth trajectories is unknown. To evaluate associations between prenatal and postnatal HAP exposure and stove interventions on growth trajectories over the first year of life. The Ghana Randomized Air Pollution and Health Study enrolled pregnant women at gestation from Kintampo, Ghana, and randomized them to liquefied petroleum gas (LPG), improved biomass, or open fire (control) stoves. We quantified HAP exposure by repeated, personal prenatal and postnatal carbon monoxide (CO) and, in a subset, fine particulate matter [PM with an aerodynamic diameter of ( )] assessments. Length, weight, mid-upper arm circumference (MUAC) and head circumference (HC) were measured at birth, 3, 6, 9, and 12 months; weight-for-age, length-for-age (LAZ), and weight-for-length (WLZ)-scores were calculated. For each anthropometric measure, we employed latent class growth analysis to generate growth trajectories over the first year of life and assigned each child to a trajectory group. We then employed ordinal logistic regression to determine associations between HAP exposures and growth trajectory assignments. Associations with stove intervention arm were also considered. Of the 1,306 live births, 1,144 had valid CO data and anthropometric variables measured at least once. Prenatal HAP exposure increased risk for lower length [CO 1.17, 95% CI: 1.01, 1.35 per 1-ppm increase; 1.07, 95% CI: 1.02, 1.13 increase], lower LAZ -score (CO 1.15, 95% CI: 1.01, 1.32 per 1-ppm increase) and stunting (CO 1.25, 95% CI: 1.08, 1.45) trajectories. Postnatal HAP exposure increased risk for smaller HC (CO 1.09, 95% CI: 1.04, 1.13 per 1-ppm increase), smaller MUAC and lower WLZ-score ( 1.07, 95% CI: 1.00, 1.14 and 1.09, 95% CI: 1.01, 1.19 increase, respectively) trajectories. Infants in the LPG arm had decreased odds of having smaller HC and MUAC trajectories as compared with those in the open fire stove arm ( 0.58, 95% CI: 0.37, 0.92 and 0.45, 95% CI: 0.22, 0.90, respectively). Higher early life HAP exposure (during pregnancy and through the first year of life) was associated with poorer infant growth trajectories among children in rural Ghana. A cleaner-burning stove intervention may have improved some growth trajectories. https://doi.org/10.1289/EHP8109.

Background A clinical diagnosis (CDx) of pancreatitis includes evaluation of clinical signs, abdominal ultrasound (AUS), and pancreatic lipase. However, practitioners are using AUS to diagnose pancreatitis and are using AUS severity to guide decisions. The validity of this is unknown. Objectives To determine whether (1) there is a correlation between AUS, specific canine pancreatic lipase (Spec cPL) assay, and CDx; (2) individual AUS abnormalities correlate more closely with CDx than others; (3) AUS severity mirrors clinical severity indices; (4) changes in AUS can be used as a marker for changes in Spec cPL or CDx; and (5) the sensitivity and specificity of AUS for pancreatitis. Animals One hundred fifty‐seven dogs. Methods In this retrospective case study, inclusion criteria were signs of gastrointestinal, pancreatic disease, or both, in addition to having a Spec cPL and AUS performed within 30 hours. Information extracted from the records included bloodwork, Spec cPL, AUS images/clips, and severity of ultrasonographic findings. Results AUS was weakly correlated with Spec cPL (rs = .0178, P = .03) and moderately correlated with CDx (rs = .379, P = <.001). Pancreatic size (rs = .285, P = <.001), echogenicity (rs = .365, P = <.001), and mesenteric echogenicity (rs = .343, P = <.001) were correlated with CDx. Change in AUS was not correlated with Spec cPL or CDx changes. When pancreatic enlargement, echogenicity, or altered mesenteric echogenicity were required for a diagnosis, the sensitivity and specificity were 89% (95% confidence interval [CI] 71.8, 97.7) and 43% (95% CI 34.0, 51.6). When all 3 criteria were required, the sensitivity and specificity were 43% (95% CI 24.5, 62.8) and 92% (95% CI 85.3, 95.7). Conclusions AUS should not be used in isolation to diagnose pancreatitis and is a poor indicator of severity.

The influence of particulate air pollution on respiratory health starts in utero. Fetal lung growth and structural development occurs in stages; thus, effects on postnatal respiratory disorders may differ based on timing of exposure. We implemented an innovative method to identify sensitive windows for effects of prenatal exposure to particulate matter with a diameter less than or equal to 2.5 μm (PM2.5) on children's asthma development in an urban pregnancy cohort. Analyses included 736 full-term (≥37 wk) children. Each mother's daily PM2.5 exposure was estimated over gestation using a validated satellite-based spatiotemporal resolved model. Using distributed lag models, we examined associations between weekly averaged PM2.5 levels over pregnancy and physician-diagnosed asthma in children by age 6 years. Effect modification by sex was also examined. Most mothers were ethnic minorities (54% Hispanic, 30% black), had 12 or fewer years of education (66%), and did not smoke in pregnancy (80%). In the sample as a whole, distributed lag models adjusting for child age, sex, and maternal factors (education, race and ethnicity, smoking, stress, atopy, prepregnancy obesity) showed that increased PM2.5 exposure levels at 16-25 weeks gestation were significantly associated with early childhood asthma development. An interaction between PM2.5 and sex was significant (P = 0.01) with sex-stratified analyses showing that the association exists only for boys. Higher prenatal PM2.5 exposure at midgestation was associated with asthma development by age 6 years in boys. Methods to better characterize vulnerable windows may provide insight into underlying mechanisms.

Dengue fever, a mosquito-borne disease, is caused by dengue virus (DENV) which includes four major serotypes (DENV-1, -2, -3, and -4). Some serotypes cause more severe diseases than the other; severe dengue is associated with secondary infections by a different serotype. Timely serotyping can provide early warning of dengue epidemics to improve management of patients and outbreaks. A mobile insulated isothermal PCR (iiPCR) system is available to allow molecular detection of pathogens near points of need. In this study, side-by-side comparison with the CDC DENV-1-4 Real Time RT-PCR (qRT-PCR) was performed to evaluate the performance of four singleplex DENV-1-4 serotyping reverse transcription-iiPCR (RT-iiPCR) reagents for DENV subtyping on the mobile PCR system. The four RT-iiPCRs did not react with Zika virus and chikungunya virus; tests with serial dilutions of the four DENV serotypes made in human serum showed they had detection endpoints comparable to those of the reference method, indicating great analytical sensitivity and specificity. Clinical performance of the RT-iiPCR reagents was evaluated by testing 40 serum samples each (around 20 target serotype-positive and 20 DENV-negative); all four reagents had high agreement (97.5-100%) with the reference qRT-PCR. Moreover, testing of mosquitoes separately infected experimentally with each serotype showed that the four reagents detected specifically their target DENV serotypes in mosquito. With analytical and clinical performance comparable to the reference qRT-PCR assay, the four index RT-iiPCR reagents on the field-deployable PCR system can serve as a useful tool for DENV detection near points of needs.

Approximately 2.8 billion people are exposed daily to household air pollution from polluting cookstoves. The effects of prenatal household air pollution on lung development are unknown. To prospectively examine associations between prenatal household air pollution and infant lung function and pneumonia in rural Ghana. Prenatal household air pollution exposure was indexed by serial maternal carbon monoxide personal exposure measurements. Using linear regression, we examined associations between average prenatal carbon monoxide and infant lung function at age 30 days, first in the entire cohort (n = 384) and then stratified by sex. Quasi-Poisson generalized additive models explored associations between infant lung function and pneumonia. Multivariable linear regression models showed that average prenatal carbon monoxide exposure was associated with reduced time to peak tidal expiratory flow to expiratory time (β = -0.004; P = 0.01), increased respiratory rate (β = 0.28; P = 0.01), and increased minute ventilation (β = 7.21; P = 0.05), considered separately, per 1 ppm increase in average prenatal carbon monoxide. Sex-stratified analyses suggested that girls were particularly vulnerable (time to peak tidal expiratory flow to expiratory time: β = -0.003, P = 0.05; respiratory rate: β = 0.36, P = 0.01; minute ventilation: β = 11.25, P = 0.01; passive respiratory compliance normalized for body weight: β = 0.005, P = 0.01). Increased respiratory rate at age 30 days was associated with increased risk for physician-assessed pneumonia (relative risk, 1.02; 95% confidence interval, 1.00-1.04) and severe pneumonia (relative risk, 1.04; 95% confidence interval, 1.00-1.08) in the first year of life. Increased prenatal household air pollution exposure is associated with impaired infant lung function. Altered infant lung function may increase risk for pneumonia in the first year of life. These findings have implications for future respiratory health. Clinical trial registered with www.clinicaltrials.gov (NCT 01335490).

How pathogenesis of inflammatory bowel disease (IBD) depends on the complex interplay of host genetics, microbiome and the immune system is not fully understood. Here, we showed that Downstream of Kinase 3 (DOK3), an adapter protein involved in immune signaling, confers protection of mice from dextran sodium sulfate (DSS)-induced colitis. DOK3-deficiency promotes gut microbial dysbiosis and enhanced colitis susceptibility, which can be reversed by the transfer of normal microbiota from wild-type mice. Mechanistically, DOK3 exerts its protective effect by suppressing JAK2/STAT3 signaling in colonic neutrophils to limit their S100a8/9 production, thereby maintaining gut microbial ecology and colon homeostasis. Hence, our findings reveal that the immune system and microbiome function in a feed-forward manner, whereby DOK3 maintains colonic neutrophils in a quiescent state to establish a gut microbiome essential for intestinal homeostasis and protection from IBD.

The emergence of jawed vertebrates (gnathostomes) from jawless vertebrates was accompanied by major morphological and physiological innovations, such as hinged jaws, paired fins and immunoglobulin-based adaptive immunity. Gnathostomes subsequently diverged into two groups, the cartilaginous fishes and the bony vertebrates. Here we report the whole-genome analysis of a cartilaginous fish, the elephant shark ( Callorhinchus milii ). We find that the C. milii genome is the slowest evolving of all known vertebrates, including the ‘living fossil’ coelacanth, and features extensive synteny conservation with tetrapod genomes, making it a good model for comparative analyses of gnathostome genomes. Our functional studies suggest that the lack of genes encoding secreted calcium-binding phosphoproteins in cartilaginous fishes explains the absence of bone in their endoskeleton. Furthermore, the adaptive immune system of cartilaginous fishes is unusual: it lacks the canonical CD4 co-receptor and most transcription factors, cytokines and cytokine receptors related to the CD4 lineage, despite the presence of polymorphic major histocompatibility complex class II molecules. It thus presents a new model for understanding the origin of adaptive immunity. Whole-genome analysis of the elephant shark, a cartilaginous fish, shows that it is the slowest evolving of all known vertebrates, lacks critical bone formation genes and has an unusual adaptive immune system. First genome of a cartilaginous fish The elephant shark ( Callorhinchus milii ) is a cartilaginous fish native to the temperate waters off southern Australia and New Zealand, living at depths of 200 to 500 metres and migrating into shallow waters during spring for breeding. The genome sequence is published in this issue of Nature . Comparison with other vertebrate genomes shows that it is the slowest evolving genome of all known vertebrates — coelacanth included. Genome analysis points to an unusual adaptive immune system lacking the CD4 receptor and some associated cytokines, indicating that cartilaginous fishes possess a primordial gnathostome adaptive immune system. Also absent are genes encoding secreted calcium-binding phosphoproteins, in line with the absence of bone in cartilaginous fish.