Although fundamental to the study of invasion mechanisms, the relationship between mode of reproduction and plant invasion is not well understood. Fallopia japonica (Japanese knotweed), a highly ...aggressive invasive plant in both Europe and North America, serves as a model species for examining this relationship. In Britain, F. japonica var. japonica is a single female clone reproducing solely through vegetative growth or obligate hybridization with other Fallopia spp. In the U.S., however, there is more evidence for sexual reproduction. Here, simple sequence repeat (SSR) markers were developed, and three Massachusetts populations were sampled at regular intervals. The amount of sexual and clonal reproduction in each population was determined based on within-population genetic diversity. Clonal growth was apparent, but the populations together contained 26 genotypes and had evidence of sexual reproduction. One genotype that was present in all populations matched the single aggressive British clone of F. japonica var. japonica. Also, a potentially diagnostic marker for the F. sachalinensis genome provided evidence of inter- and intraspecific sexual reproduction and introgression. These differences observed in U.S. populations compared to European populations have significant implications for management of Fallopia spp. in the U.S. and underscore the importance of regional studies of invasive species.
Hemoglobin A1c (HbA1c) levels diagnose diabetes, predict mortality and are associated with ten single nucleotide polymorphisms (SNPs) in white individuals. Genetic associations in other race groups ...are not known. We tested the hypotheses that there is race-ethnic variation in 1) HbA1c-associated risk allele frequencies (RAFs) for SNPs near SPTA1, HFE, ANK1, HK1, ATP11A, FN3K, TMPRSS6, G6PC2, GCK, MTNR1B; 2) association of SNPs with HbA1c and 3) association of SNPs with mortality.
We studied 3,041 non-diabetic individuals in the NHANES (National Health and Nutrition Examination Survey) III. We stratified the analysis by race/ethnicity (NHW: non-Hispanic white; NHB: non-Hispanic black; MA: Mexican American) to calculate RAF, calculated a genotype score by adding risk SNPs, and tested associations with SNPs and the genotype score using an additive genetic model, with type 1 error = 0.05.
RAFs varied widely and at six loci race-ethnic differences in RAF were significant (p < 0.0002), with NHB usually the most divergent. For instance, at ATP11A, the SNP RAF was 54% in NHB, 18% in MA and 14% in NHW (p < .0001). The mean genotype score differed by race-ethnicity (NHW: 10.4, NHB: 11.0, MA: 10.7, p < .0001), and was associated with increase in HbA1c in NHW (β = 0.012 HbA1c increase per risk allele, p = 0.04) and MA (β = 0.021, p = 0.005) but not NHB (β = 0.007, p = 0.39). The genotype score was not associated with mortality in any group (NHW: OR (per risk allele increase in mortality) = 1.07, p = 0.09; NHB: OR = 1.04, p = 0.39; MA: OR = 1.03, p = 0.71).
At many HbA1c loci in NHANES III there is substantial RAF race-ethnic heterogeneity. The combined impact of common HbA1c-associated variants on HbA1c levels varied by race-ethnicity, but did not influence mortality.
Fallopia japonica (Japanese knotweed, Polygonaceae) is a well-known East Asian perennial that is established throughout the U.S. and Europe. Another congener, F. sachalinensis, and their hybrid, F. ...xbohemica, also persist on both continents. Their invasive success is primarily attributed to their ability to spread via clonal growth. However, mounting evidence suggests invasion history and dynamics differ between continents and that sexual reproduction is more common than previously assumed. We used published morphological traits designed to distinguish the three taxa to characterize their distribution in 24 New England towns. We found continuous variation of all five traits, with 84% of our 81 individuals having at least one trait outside parental limits. Hierarchical cluster analysis, along with two chloroplast and one nuclear species-specific markers, suggests the presence of intercrossing, segregating hybrids, and likely introgression between F1 hybrids and F. japonica. Our markers also show the first evidence of bidirectional hybridization between parental taxa in the U.S., emphasizing the complex structure of populations in our region. This study is a first step toward unraveling the evolutionary forces that have made these taxa such aggressive invaders in the U.S. The data may also affect management strategies originally designed for largely monomorphic, clonal populations.
We isolated and characterized the entire coding sequence of a human gene encoding a protein that interacts with RPGR, a protein that is absent or mutant in many cases of X-linked retinitis ...pigmentosa. The newly identified gene, called
“RPGRIP1” for RPGR-interacting protein (MIM
605446), is located within 14q11, and it encodes a protein predicted to contain 1,259 amino acids. Previously published work showed that both proteins, RPGR and RPGRIP1, are present in the ciliary structure that connects the inner and outer segments of rod and cone photoreceptors. We surveyed 57 unrelated patients who had Leber congenital amaurosis for mutations in
RPGRIP1 and found recessive mutations involving both
RPGRIP1 alleles in 3 (6%) patients. The mutations all create premature termination codons and are likely to be null alleles. Patients with
RPGRIP1 mutations have a degeneration of both rod and cone photoreceptors, and, early in life, they experience a severe loss of central acuity, which leads to nystagmus.
Pathway analysis following association study Ngwa, Julius S; Manning, Alisa K; Grimsby, Jonna L ...
BMC proceedings,
2011-Nov-29, Letnik:
5 Suppl 9, Številka:
S9
Journal Article
Recenzirano
Odprti dostop
Genome-wide association studies often emphasize single-nucleotide polymorphisms with the smallest p-values with less attention given to single-nucleotide polymorphisms not ranked near the top. We ...suggest that gene pathways contain valuable information that can enable identification of additional associations. We used gene set information to identify disease-related pathways using three methods: gene set enrichment analysis (GSEA), empirical enrichment p-values, and Ingenuity pathway analysis (IPA). Association tests were performed for common single-nucleotide polymorphisms and aggregated rare variants with traits Q1 and Q4. These pathway methods were evaluated by type I error, power, and the ranking of the VEGF pathway, the gene set used in the simulation model. GSEA and IPA had high power for detecting the VEGF pathway for trait Q1 (91.2% and 93%, respectively). These two methods were conservative with deflated type I errors (0.0083 and 0.0072, respectively). The VEGF pathway ranked 1 or 2 in 123 of 200 replicates using IPA and ranked among the top 5 in 114 of 200 replicates for GSEA. The empirical enrichment method had lower power and higher type I error. Thus pathway analysis approaches may be useful in identifying biological pathways that influence disease outcomes.
An outbreak of over 1,000 COVID-19 cases in Provincetown, Massachusetts (MA), in July 2021—the first large outbreak mostly in vaccinated individuals in the US—prompted a comprehensive public health ...response, motivating changes to national masking recommendations and raising questions about infection and transmission among vaccinated individuals. To address these questions, we combined viral genomic and epidemiological data from 467 individuals, including 40% of outbreak-associated cases. The Delta variant accounted for 99% of cases in this dataset; it was introduced from at least 40 sources, but 83% of cases derived from a single source, likely through transmission across multiple settings over a short time rather than a single event. Genomic and epidemiological data supported multiple transmissions of Delta from and between fully vaccinated individuals. However, despite its magnitude, the outbreak had limited onward impact in MA and the US overall, likely due to high vaccination rates and a robust public health response.
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•Large Delta outbreak in a highly vaccinated population changed US indoor masking policy•Outbreak included multiple Delta introductions; one introduction led to 83% of cases•Spread from and between vaccinated cases contributed, a picture resolved by genomic data•Outbreak was successfully contained; it did not drive the rise of Delta in MA or the US
Rapid integration of epidemiological and genomic data was used to support the public health response during a large outbreak of the SARS-CoV-2 Delta variant. The outbreak stemmed primarily from a single source spreading the virus at multiple locations, and while numerous likely transmissions from and between vaccinated individuals were observed, the downstream impact of the outbreak was minimized with robust intervention and community engagement.
The SARS-CoV-2 Delta variant rose to dominance in mid-2021, likely propelled by an estimated 40%–80% increased transmissibility over Alpha. To investigate if this ostensible difference in ...transmissibility is uniform across populations, we partner with public health programs from all six states in New England in the United States. We compare logistic growth rates during each variant’s respective emergence period, finding that Delta emerged 1.37–2.63 times faster than Alpha (range across states). We compute variant-specific effective reproductive numbers, estimating that Delta is 63%–167% more transmissible than Alpha (range across states). Finally, we estimate that Delta infections generate on average 6.2 (95% CI 3.1–10.9) times more viral RNA copies per milliliter than Alpha infections during their respective emergence. Overall, our evidence suggests that Delta’s enhanced transmissibility can be attributed to its innate ability to increase infectiousness, but its epidemiological dynamics may vary depending on underlying population attributes and sequencing data availability.
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•SARS-CoV-2 Delta variant emerges 1.37–2.63 times faster than Alpha (state range)•Delta is on average 63%–167% more transmissible than Alpha (state range)•Delta infections average 6.2 times more viral RNA copies per milliliter than Alpha•Variant transmissibility estimates depend on innate, population, and data factors
The SARS-CoV-2 Delta variant displaced the previously dominant Alpha variant by mid-2021, ostensibly because of 40%–80% increased transmissibility. To determine whether this difference is uniform across populations, Earnest et al. estimate variant-specific logistic growth rates and effective reproductive numbers for six states in New England finding substantial heterogeneity.
Fallopia japonica (Japanese knotweed, Polygonaceae) is a well-known East Asian perennial that is established throughout the U.S. and Europe. Another congener, F. sachalinensis, and their hybrid, F. ...×bohemica, also persist on both continents. Their invasive success is primarily attributed to their ability to spread via clonal growth. However, mounting evidence suggests invasion history and dynamics differ between continents and that sexual reproduction is more common than previously assumed. We used published morphological traits designed to distinguish the three taxa to characterize their distribution in 24 New England towns. We found continuous variation of all five traits, with 84% of our 81 individuals having at least one trait outside parental limits. Hierarchical cluster analysis, along with two chloroplast and one nuclear species-specific markers, suggests the presence of intercrossing, segregating hybrids, and likely introgression between F1 hybrids and F. japonica. Our markers also show the first evidence of bidirectional hybridization between parental taxa in the U.S., emphasizing the complex structure of populations in our region. This study is a first step toward unraveling the evolutionary forces that have made these taxa such aggressive invaders in the U.S. The data may also affect management strategies originally designed for largely monomorphic, clonal populations.
Although fundamental to the study of invasion mechanisms, the relationship between mode of reproduction and plant invasion is not well understood. Fallopia japonica (Japanese knotweed), a highly ...aggressive invasive plant in both Europe and North America, serves as a model species for examining this relationship. In Britain, F. japonica var. japonica is a single female clone reproducing solely through vegetative growth or obligate hybridization with other Fallopia spp. In the U.S., however, there is more evidence for sexual reproduction. Here, simple sequence repeat (SSR) markers were developed, and three Massachusetts populations were sampled at regular intervals. The amount of sexual and clonal reproduction in each population was determined based on within-population genetic diversity. Clonal growth was apparent, but the populations together contained 26 genotypes and had evidence of sexual reproduction. One genotype that was present in all populations matched the single aggressive British clone of F. japonica var. japonica. Also, a potentially diagnostic marker for the F. sachalinensis genome provided evidence of inter- and intraspecific sexual reproduction and introgression. These differences observed in U.S. populations compared to European populations have significant implications for management of Fallopia spp. in the U.S. and underscore the importance of regional studies of invasive species. PUBLICATION ABSTRACT
Fallopia japonica (Japanese knotweed, Polygonaceae) is a well-known East Asian perennial that is established throughout the U.S. and Europe. Another congener, F. sachalinensis, and their hybrid, F. ...xbohemica, also persist on both continents. Their invasive success is primarily attributed to their ability to spread via clonal growth. However, mounting evidence suggests invasion history and dynamics differ between continents and that sexual reproduction is more common than previously assumed. We used published morphological traits designed to distinguish the three taxa to characterize their distribution in 24 New England towns. We found continuous variation of all five traits, with 84% of our 81 individuals having at least one trait outside parental limits. Hierarchical cluster analysis, along with two chloroplast and one nuclear species-specific markers, suggests the presence of intercrossing, segregating hybrids, and likely introgression between F1 hybrids and F. japonica. Our markers also show the first evidence of bidirectional hybridization between parental taxa in the U.S., emphasizing the complex structure of populations in our region. This study is a first step toward unraveling the evolutionary forces that have made these taxa such aggressive invaders in the U.S. The data may also affect management strategies originally designed for largely monomorphic, clonal populations. PUBLICATION ABSTRACT
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