Genetic associations with coronary heart disease: Meta-analyses of 12 candidate genetic variants

Aims

The aim of this study was to evaluate the combined contribution of 12 genetic variants to the risk of coronary heart disease (CHD).

Methods

Through a comprehensive literature search for genetic variants involved in the CHD association study, we harvested a total of 10 genes (12 variants) for the current meta-analyses. These genes consisted of GPX1 (rs1050450), PPARD (rs2016520), ALOX15 (rs34210653), SELPLG (rs2228315), FCGR2A (rs1801274), CCL5 (rs2107538), CYP1A1 (rs4646903), TP53 (rs1042522), CX37 (rs1764391), and PECAM1 (rs668, rs12953, and rs1131012).

Results

A total of 45 studies among 23,314 cases and 28,430 controls were retrieved for the meta-analyses of 12 genetic variants. The results showed a significant association between the GPX1 rs1050450 polymorphism and CHD (odd ratio (OR) = 1.61, 95% confidence interval (CI) = 1.25–2.07, P = 0.0002). Other meta-analyses of the rest 11 variants suggested a lack of association with the risk of CHD.

Conclusion

Our results confirmed that GPX1 rs1050450 was associated with susceptibility to CHD in Chinese and Indian populations.     

Complete genome sequencing of sixteen Francisella noatunensis subsp. orientalis isolates: A genomic approach for molecular characterization and spread dynamics of this clonal population

Francisella noatunensis subsp. orientalis (FNO) is an important emerging pathogen associated with disease outbreaks in farm-raised Nile tilapia. FNO genetic diversity using PCR-based typing, no intra-species discrimination was achieved among isolates/strains from different countries, thus demonstrating a clonal behaviour pattern. In this study, we aimed to evaluate the population structure of FNO isolates by comparing whole-genome sequencing data. The analysis of recombination showed that Brazilian isolates group formed a clonal population; whereas other lineages are also supported by this analysis for isolates from foreign countries. The whole-genome multilocus sequence typing (wgMLST) analysis showed varying numbers of dissimilar alleles, suggesting that the Brazilian clonal population are in expansion. Each Brazilian isolate could be identified as a single node by high-resolution gene-by-gene approach, presenting slight genetic differences associated to mutational events. The common ancestry node suggests a single entry into the country before 2012, and the rapid dissemination of this infectious agent may be linked to market sales of infected fingerlings.     

HIV-1 Protease Uses Bi-Specific S2/S2′ Subsites to Optimize Cleavage of Two Classes of Target Sites

Retroviral proteases (PRs) have a unique specificity that allows cleavage of sites with or without a P1′ proline. A P1′ proline is required at the MA/CA cleavage site due to its role in a post-cleavage conformational change in the capsid protein. However, the HIV-1 PR prefers to have large hydrophobic amino acids flanking the scissile bond, suggesting that PR recognizes two different classes of substrate sequences. We analyzed the cleavage rate of over 150 combinations of six different HIV-1 cleavage sites to explore rate determinants of cleavage. We found that cleavage rates are strongly influenced by the two amino acids flanking the amino acids at the scissile bond (P2–P1/P1′–P2′), with two complementary sets of rules. When P1′ is proline, the P2 side chain interacts with a polar region in the S2 subsite of the PR, while the P2′ amino acid interacts with a hydrophobic region of the S2′ subsite. When P1′ is not proline, the orientations of the P2 and P2′ side chains with respect to the scissile bond are reversed; P2 residues interact with a hydrophobic face of the S2 subsite, while the P2′ amino acid usually engages hydrophilic amino acids in the S2′ subsite. These results reveal that the HIV-1 PR has evolved bi-functional S2 and S2′ subsites to accommodate the steric effects imposed by a P1′ proline on the orientation of P2 and P2′ substrate side chains. These results also suggest a new strategy for inhibitor design to engage the multiple specificities in these subsites.     

Insect outbreaks alter nutrient dynamics in a southern African savanna: patchy defoliation of Colophospermum mopane savanna by Imbrasia belina larvae

Invertebrate herbivore outbreaks have important impacts on system biogeochemical cycling, but these effects have been poorly documented in African savanna ecosystems. In semi‐arid African savannas, outbreaks of the lepidopteran Imbrasia belina (mopane worm) affect discrete patches of the dominant Colophospermum mopane trees; larvae may completely defoliate trees for up to six weeks during each of the early and late growing seasons. We studied the impact of mopane worm outbreaks on the availability of nitrogen (N), phosphorus (P), and potassium (K) within mopane savanna by quantifying major nutrient pools in defoliated and non‐defoliated savanna patches, including leaves, leaf litter, worm frass, and the soil beneath trees. Within an outbreak area, approximately 44 percent of trees were infested, supporting ~29,000 worms/ha, leading to ~640 kg/ha dry weight frass deposition at 1.4 g of frass/day‐individual (fourth or fifth instar), compared with an average 1645 kg/ha dry weight of leaf on trees most of which should be deposited by litterfall at the end of the growing season. Frass had twofold higher P, 10 percent higher K, but equivalent N content than litter. Taking frass and litter deposition together, the N, P, and K contents added due to the outbreak event at our study site were 0.88, 5.8, and 2.8 times those measured in non‐outbreak patches, a pattern which was reflected in the nutrient contents of soil surfaces beneath defoliated trees. Invertebrate herbivory appears to be an important driver for mopane savanna but has been largely neglected.     

Litterfall dynamics and nitrogen use efficiency in two evergreen temperate rainforests of southern Chile

Abstract In unpolluted regions, where inorganic nitrogen (N) inputs from the atmosphere are minimal, such as remote locations in southern South America, litterfall dynamics and N use efficiency of tree species should be coupled to the internal N cycle of forest ecosystems. This hypothesis was examined in two evergreen temperate forests in southern Chile (42°30′S), a mixed broad‐leaved forest (MBF) and a conifer forest (CF). Although these forests grow under the same climate and on the same parental material, they differ greatly in floristic structure and canopy dynamics (slower in the CF). In both forests, biomass, N flux, and C/N ratios of fine litterfall were measured monthly from May 1995 to March 1999. There was a continuous litter flux over the annual cycle in both forests, with a peak during autumn in the CF. In the MBF, litterfall decreased during spring. In both forests, the C/N ratios of litterfall varied over the annual cycle with a maximum in autumn. Annual litterfall biomass flux (Mean ± SD = 3.3 ± 0.5 vs 2.0 ± 0.5 Mg ha^?1) and N return (34.8 ± 16 vs 9.1 ± 2.8 kg N ha^?1) were higher in the MBF than in the CF. At the ecosystem level, litterfall C/N was lower in the MBF (mean C/N ratio = 60.1 ± 15, n = 3 years) suggesting decreased N use efficiency compared with CF (mean C/N ratio = 103 ± 19.6, n = 3 years). At the species level, subordinated (subcanopy) tree species in the MBF had significantly lower C/N ratios (<50) of litterfall than the dominant trees in the CF and MBF (>85). The litterfall C/N ratio and percentage N retranslocated were significantly correlated and were lower in the MBF. The higher net N mineralization in soils of the MBF is related to a lower N use efficiency at the ecosystem and species level.     

A multiscale analysis of herbaceous species richness in a Mediterranean ecosystem

Aims Studies of species distribution patterns traditionally have been conducted at a single scale, often overlooking species–environment relationships operating at finer or coarser scales. Testing diversity-related hypotheses at multiple scales requires a robust sampling design that is nested across scales. Our chief motivation in this study was to quantify the contributions of different predictors of herbaceous species richness at a range of local scales.Methods Here, we develop a hierarchically nested sampling design that is balanced across scales, in order to study the role of several environmental factors in determining herbaceous species distribution at various scales simultaneously. We focus on the impact of woody vegetation, a relatively unexplored factor, as well as that of soil and topography. Light detection and ranging (LiDAR) imaging enabled precise characterization of the 3D structure of the woody vegetation, while acoustic spectrophotometry allowed a particularly high-resolution mapping of soil CaCO 3 and organic matter contents.Important findings We found that woody vegetation was the dominant explanatory variable at all three scales (10, 100 and 1000 m 2), accounting for more than 60% of the total explained variance. In addition, we found that the species richness–environment relationship was scale dependent. Many studies that explicitly address the issue of scale do so by comparing local and regional scales. Our results show that efforts to conserve plant communities should take into account scale dependence when analyzing species richness–environment relationships, even at much finer resolutions than local vs. regional. In addition, conserving heterogeneity in woody vegetation structure at multiple scales is a key to conserving diverse herbaceous communities.     

No long-term effect of black bear removal on elk calf recruitment in the southern Appalachians

In 2001 and 2002, 52 elk (Cervus canadensis; 21 males, 31 females), originally obtained from Elk Island National Park, Alberta, Canada, were transported and released into Cataloochee Valley in the northeastern portion of Great Smoky Mountains National Park (GRSM, Park), North Carolina, USA. The annual population growth rate (λ) was negative (0.996, 95% CI = 0.945–1.047) and predation by black bears (Ursus americanus) on elk calves was identified as an important determinant of population growth. From 2006 to 2008, 49 bears from the primary elk calving area (i.e., Cataloochee Valley) were trapped and translocated about 70 km to the southwestern portion of the Park just prior to elk calving. Per capita recruitment (i.e., the number of calves produced per adult female that survive to 1 year of age) increased from 0.306 prior to bear translocation (2001–2005) to 0.544 during years when bears were translocated (2006–2008) and λ increased to 1.118 (95% CI = 1.096–1.140). Our objective was to determine whether per capita calf recruitment rates after bear removal (2009–2019) at Cataloochee were similar to the higher rates estimated during bear removal (i.e., long-term response) or if they returned to rates before bear removal (i.e., short-term response), and how those rates compared with recruitment from portions of our study area where bears were not relocated. We documented 419 potential elk calving events and monitored 129 yearling and adult elk from 2001 to 2019. Known-fate models based on radio-telemetry and observational data supported calf recruitment returning to pre-2006 levels at Cataloochee (short-term response); recruitment of Cataloochee elk before and after bear relocation was lower (0.184) than during bear relocation (0.492). Recruitment rates of elk outside the removal area during the bear relocation period (0.478) were similar to before and after rates (0.420). In the Cataloochee Valley, cause-specific annual calf mortality rates due to predation by bears were 0.319 before, 0.120 during, and 0.306 after bear relocation. In contrast, the cause-specific annual mortality rate of calves in areas where bears were not relocated was 0.033 after the bear relocation period, with no bear predation on calves before or during bear relocation. The mean annual population growth rate for all monitored elk was 1.062 (95% CI = 0.979–1.140) after bear relocation based on the recruitment and survival data. Even though the effects of bear removal were temporary, the relocations were effective in achieving a short-term increase in elk recruitment, which was important for the reintroduction program given that the elk population was small and vulnerable to extirpation.     

佛坪国家级自然保护区植被垂直带谱及其与邻近地区的比较

在首先确定垂直带划分的原则和将佛坪自然保护区植被划分为落叶阔叶林带、中山小叶林带和亚高山针叶林带３个垂直带,各垂直带植被物种组成的区系、生活型组成和物种多样性的差异证实了这种划分的合理性。与邻近地区植被垂直带谱的比较表明,佛坪自然保护区的植被垂直带谱与秦岭北坡有明显差异,表现为典型的暧温带与北亚热带过渡区域的植被景观,虽然基带以上各植被带暖温带特色很明显,但其植被属性应是北亚热带的。     

High abscission rates of damaged expanding leaves: field evidence from seedlings of a Bornean rain forest tree

Herbivore damage is known to cause the premature loss of mature leaves. However, the effects of herbivory on abscission during the early stages of leaf development remain unexplored, even though herbivores frequently prefer unlignified, immature leaves. In a field experiment, we removed 50% of the tissue from leaves at various stages of development on seedlings of Shorea hopeifolia (Dipterocarpaceae), a dominant rain forest tree in Indonesian Borneo. Four weeks following simulated herbivory, >88% of unlignified expanding leaves had been abscised, compared to only 20% of fully expanded, unlignified leaves and 0% of recently lignified, mature leaves. In a separate experiment over 9 wk, simulated herbivory did not increase abscission rates of mature leaves, even when 75% of leaf tissue was removed. Because most (58%) of S. hopeifolia seedlings under natural conditions had lost 1% or less of the tissue from their mature leaves, herbivore damage probably has little effect on the abscission of mature leaves. In contrast, the tendency for damaged expanding leaves to abscise may explain why 49% of S. hopeifolia seedlings had already lost their youngest leaf. If similar patterns occur in other species, herbivore attacks on developing leaves may contribute substantially to both leaf loss and the cumulative impact of herbivory on the growth and survival of whole plants.     

Nutrient resorption patterns of plant functional groups in a tropical savanna: variation and functional significance

Green and senesced leaf nitrogen (N) and phosphorus (P) concentrations of different plant functional groups in savanna communities of Kruger National Park, South Africa were analyzed to determine if nutrient resorption was regulated by plant nutritional status and foliar N:P ratios. The N and P concentrations in green leaves and the N concentrations in senesced leaves differed significantly between the dominant plant functional groups in these savannas: fine-leaved trees, broad-leaved trees and grasses. However, all three functional groups reduced P to comparable and very low levels in senesced leaves, suggesting that P was tightly conserved in this tropical semi-arid savanna ecosystem. Across all functional groups, there was evidence for nutritional control of resorption in this system, with both N and P resorption efficiencies decreasing as green leaf nutrient concentrations increased. However, specific patterns of resorption and the functional relationships between nutrient concentrations in green and senesced leaves varied by nutrient and plant functional group. Functional relationships between N concentrations in green and senesced leaves were indistinguishable between the dominant groups, suggesting that variation in N resorption efficiency was largely the result of inter-life form differences in green leaf N concentrations. In contrast, observed differences in P resorption efficiencies between life forms appear to be the result of both differences in green leaf P concentrations as well as inherent differences between life forms in the fraction of green leaf P resorbed from senescing leaves. Our results indicate that foliar N:P ratios are poor predictors of resorption efficiency in this ecosystem, in contrast to N and P resorption proficiencies, which are more responsive to foliar N:P ratios.