Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic genomes

To study the roles of translational accuracy, translational efficiency, and the Hill-Robertson effect in codon usage bias, we studied the intragenic spatial distribution of synonymous codon usage bias in four prokaryotic (Escherichia coli, Bacillus subtilis, Sulfolobus tokodaii, and Thermotoga maritima) and two eukaryotic (Saccharomyces cerevisiae and Drosophila melanogaster) genomes. We generated supersequences at each codon position across genes in a genome and computed the overall bias at each codon position. By quantitatively evaluating the trend of spatial patterns using isotonic regression, we show that in yeast and prokaryotic genomes, codon usage bias increases along translational direction, which is consistent with purifying selection against nonsense errors. Fruit fly genes show a nearly symmetric M-shaped spatial pattern of codon usage bias, with less bias in the middle and both ends. The low codon usage bias in the middle region is best explained by interference (the Hill-Robertson effect) between selections at different codon positions. In both yeast and fruit fly, spatial patterns of codon usage bias are characteristically different from patterns of GC-content variations. Effect of expression level on the strength of codon usage bias is more conspicuous than its effect on the shape of the spatial distribution.     

Reliance on head versus eyes in the gaze following of great apes and human infants: the cooperative eye hypothesis

As compared with other primates, humans have especially visible eyes (e.g., white sclera). One hypothesis is that this feature of human eyes evolved to make it easier for conspecifics to follow an individual's gaze direction in close-range joint attentional and communicative interactions, which would seem to imply especially cooperative (mututalistic) conspecifics. In the current study, we tested one aspect of this cooperative eye hypothesis by comparing the gaze following behavior of great apes to that of human infants. A human experimenter "looked" to the ceiling either with his eyes only, head only (eyes closed), both head and eyes, or neither. Great apes followed gaze to the ceiling based mainly on the human's head direction (although eye direction played some role as well). In contrast, human infants relied almost exclusively on eye direction in these same situations. These results demonstrate that humans are especially reliant on eyes in gaze following situations, and thus, suggest that eyes evolved a new social function in human evolution, most likely to support cooperative (mututalistic) social interactions.     

Exploring macrophage cell therapy on Diabetic Kidney Disease

Alternatively activated macrophages (M2) have regenerative properties and shown promise as cell therapy in chronic kidney disease. However, M2 plasticity is one of the major hurdles to overcome. Our previous studies showed that genetically modified macrophages stabilized by neutrophil gelatinase‐associated lipocalin (NGAL) were able to preserve their M2 phenotype. Nowadays, little is known about M2 macrophage effects in diabetic kidney disease (DKD). The aim of the study was to investigate the therapeutic effect of both bone marrow‐derived M2 (BM‐фM2) and ф‐NGAL macrophages in the db/db mice. Seventeen‐week‐old mice with established DKD were divided into five treatment groups with their controls: D+BM‐фM2; D+ф‐BM; D+ф‐NGAL; D+ф‐RAW; D+SHAM and non‐diabetic (ND) (db/‐ and C57bl/6J) animals. We infused 1 × 10⁶ macrophages twice, at baseline and 2 weeks thereafter. BM‐фM2 did not show any therapeutic effect whereas ф‐NGAL significantly reduced albuminuria and renal fibrosis. The ф‐NGAL therapy increased the anti‐inflammatory IL‐10 and reduced some pro‐inflammatory cytokines, reduced the proportion of M1 glomerular macrophages and podocyte loss and was associated with a significant decrease of renal TGF‐β1. Overall, our study provides evidence that ф‐NGAL macrophage cell therapy has a therapeutic effect on DKD probably by modulation of the renal inflammatory response caused by the diabetic milieu.     

Carrier subunit of plasma membrane transporter is required for oxidative folding of its helper subunit

We study the amino acid transport system b(0,+) as a model for folding, assembly, and early traffic of membrane protein complexes. System b(0,+) is made of two disulfide-linked membrane subunits: the carrier, b(0,+) amino acid transporter (b(0,+)AT), a polytopic protein, and the helper, related to b(0,+) amino acid transporter (rBAT), a type II glycoprotein. rBAT ectodomain mutants display folding/trafficking defects that lead to type I cystinuria. Here we show that, in the presence of b(0,+)AT, three disulfides were formed in the rBAT ectodomain. Disulfides Cys-242-Cys-273 and Cys-571-Cys-666 were essential for biogenesis. Cys-673-Cys-685 was dispensable, but the single mutants C673S, and C685S showed compromised stability and trafficking. Cys-242-Cys-273 likely was the first disulfide to form, and unpaired Cys-242 or Cys-273 disrupted oxidative folding. Strikingly, unassembled rBAT was found as an ensemble of different redox species, mainly monomeric. The ensemble did not change upon inhibition of rBAT degradation. Overall, these results indicated a b(0,+)AT-dependent oxidative folding of the rBAT ectodomain, with the initial and probably cotranslational formation of Cys-242-Cys-273, followed by the oxidation of Cys-571-Cys-666 and Cys-673-Cys-685, that was completed posttranslationally.     

Microbial carbon limitation: The need for integrating microorganisms into our understanding of ecosystem carbon cycling

Numerous studies have demonstrated that fertilization with nutrients such as nitrogen, phosphorus, and potassium increases plant productivity in both natural and managed ecosystems, demonstrating that primary productivity is nutrient limited in most terrestrial ecosystems. In contrast, it has been demonstrated that heterotrophic microbial communities in soil are primarily limited by organic carbon or energy. While this concept of contrasting limitations, that is, microbial carbon and plant nutrient limitation, is based on strong evidence that we review in this paper, it is often ignored in discussions of ecosystem response to global environment changes. The plant‐centric perspective has equated plant nutrient limitations with those of whole ecosystems, thereby ignoring the important role of the heterotrophs responsible for soil decomposition in driving ecosystem carbon storage. To truly integrate carbon and nutrient cycles in ecosystem science, we must account for the fact that while plant productivity may be nutrient limited, the secondary productivity by heterotrophic communities is inherently carbon limited. Ecosystem carbon cycling integrates the independent physiological responses of its individual components, as well as tightly coupled exchanges between autotrophs and heterotrophs. To the extent that the interacting autotrophic and heterotrophic processes are controlled by organisms that are limited by nutrient versus carbon accessibility, respectively, we propose that ecosystems by definition cannot be ‘limited’ by nutrients or carbon alone. Here, we outline how models aimed at predicting non‐steady state ecosystem responses over time can benefit from dissecting ecosystems into the organismal components and their inherent limitations to better represent plant–microbe interactions in coupled carbon and nutrient models.     

Leaf traits from stomata to morphology are associated with climatic and edaphic variables for dominant tropical forest evergreen oaks

热带森林优势种青冈叶片气孔、解剖和形态性状与气候、土壤因子的关联 了解优势树种叶片多水平的功能性状沿海拔梯度的变化及其内在关联,有助于预测优势种应对气候变化的响应与适应。本文研究了青冈属树种叶片气孔、解剖和形态性状沿海拔梯度的变化及其与环境调控因子的关联,探究了其生态策略是否随海拔发生改变。在海南尖峰岭热带森林,沿海拔梯度(400–1400 m)采集了6种常绿青冈：竹叶青冈(Cyclobalanopsis bambusaefolia)、雷公青冈(C. hui)、托盘青冈 (C. patelliformis)、饭甄青冈(C. fleuryi)、吊罗山青冈(C. tiaoloshanica)和亮叶青冈(C. phanera)叶片,用于气孔、解剖和形态性状的测定。研究结果表明,随海拔升高,青冈树种叶片气孔密度、气孔孔隙度指数和叶面积显著增加,但海绵组织厚度比和干物质含量则显着降低。叶片气孔、解剖和形态性状沿海拔梯 度的变化主要受年均温、年降水量和土壤pH 值调控。在低海拔和高海拔处,青冈属采取“耐受”和“竞 争”策略,而在中海拔处,则是“竞争”策略。土壤磷含量和土壤pH 值随海拔的变化可能是驱动其生态 策略转变的主要原因。该结果揭示,热带森林优势树种青冈可通过从气孔细胞-组织解剖结构-叶片水平功能性状的改变来响应环境变化。     

Relationships between Methylobacteria and Glyphosate with Native and Invasive Plant Species: Implications for Restoration

After removing invasive plants, whether by herbicides or other means, typical restoration design focuses on rebuilding native plant communities while disregarding soil microbial communities. However, microbial–plant interactions are known to influence the relative success of native versus invasive plants. Therefore, the abundance and composition of soil microorganisms may affect restoration efforts. We assessed the effect of herbicide treatment on phytosymbiotic pink‐pigmented facultative methylotrophic (PPFM) bacteria and the potential consequences of native and invasive species establishment post‐herbicide treatment in the lab and in a coastal sage scrub (CSS)/grassland restoration site. Lab tests showed that 4% glyphosate reduced PPFM abundance. PPFM addition to seeds increased seedling length of a native plant (Artemisia californica) but not an invasive plant (Hirschfeldia incana). At the restoration site, methanol addition (a PPFM substrate) improved native bunchgrass (Nassella pulchra) germination and size by 35% over controls. In a separate multispecies field experiment, PPFM addition stimulated the germination of N. pulchra, but not that of three invasive species. Neither PPFM nor methanol addition strongly affected the growth of any plant species. Overall, these results are consistent with the hypothesis that PPFMs have a greater benefit to native than invasive species. Together, these experiments suggest that methanol or PPFM addition could be useful in improving CSS/grassland restorations. Future work should test PPFM effects on additional species and determine how these results vary under different environmental conditions.