Reduced Root Cortical Tissue with an Increased Root Xylem Investment Is Associated with High Wheat Yields in Central China

Trait-based approaches are increasingly used to understand crop yield improvement, although they have not been widely applied to anatomical traits. Little is known about the relationships between root and leaf anatomy and yield in wheat. We selected 20 genotypes that have been widely planted in Luoyang, in the major wheat-producing area of China, to explore these relationships. A field study was performed to measure the yields and yield components of the genotypes. Root and leaf samples were collected at anthesis to measure the anatomical traits relevant to carbon allocation and water transport. Yield was negatively correlated with cross-sectional root cortex area, indicating that reduced root cortical tissue and therefore reduced carbon investment have contributed to yield improvement in this region. Yield was positively correlated with root xylem area, suggesting that a higher water transport capacity has also contributed to increased yields in this study. The area of the leaf veins did not significantly correlate with yield, showing that the high-yield genotypes did not have larger veins, but they may have had a conservative water use strategy, with tight regulation of water loss from the leaves. This study demonstrates that breeding for higher yields in this region has changed wheat's anatomical traits, reducing the roots' cortical tissue and increasing the roots' xylem investment.

Agroecological genetics of biomass allocation in wheat uncovers genotype interactions with canopy shade and plant size

How plants distribute biomass among organs influences resource acquisition, reproduction and plant-plant interactions, and is essential in understanding plant ecology, evolution, and yield production in agriculture. However, the genetic mechanisms regulating allocation responses to the environment are largely unknown. We studied recombinant lines of wheat (Triticum spp.) grown as single plants under sunlight and simulated canopy shade to investigate genotype-by-environment interactions in biomass allocation to the leaves, stems, spikes, and grains. Size-corrected mass fractions and allometric slopes were employed to dissect allocation responses to light limitation and plant size. Size adjustments revealed light-responsive alleles associated with adaptation to the crop environment. Combined with an allometric approach, we demonstrated that polymorphism in the DELLA protein is associated with the response to shade and size. While a gibberellin-sensitive allelic effect on stem allocation was amplified when plants were shaded, size-dependent effects of this allele drive allocation to reproduction, suggesting that the ontogenetic trajectory of the plant affects the consequences of shade responses for allocation. Our approach provides a basis for exploring the genetic determinants underlying investment strategies in the face of different resource constraints and will be useful in predicting social behaviours of individuals in a crop community.

miRNAs from Inflamed Gingiva Link Gene Signaling to Increased MET Expression

Several array-based microRNA (miRNA) expression studies independently showed increased expression of miRNAs hsa-miR-130a-3p, -142-3p, -144-3p, -144-5p, -223-3p, -17-5p, and -30e-5p in gingiva affected by periodontal inflammation. We aimed to determine direct target genes and signaling pathways regulated by these miRNAs to identify processes relevant to gingival inflammatory responses and tissue homeostasis. We transfected miRNA mimics (mirVana) for each of the 7 miRNAs separately into human primary gingival fibroblasts cultured from 3 different donors. Following RNA sequencing, differential gene expression and second-generation gene set enrichment analyses were performed. miRNA inhibition and upregulation was validated at the transcript and protein levels using quantitative reverse transcriptase polymerase chain reaction, Western blotting, and reporter gene assays. All 7 miRNAs significantly increased expression of the gene MET proto-oncogene, receptor tyrosine kinase (MET). Expression of known periodontitis risk genes CPEB1, ABCA1, and ATP6V1C1 was significantly repressed by hsa-miR-130a-3p, -144-3p, and -144-5p, respectively. The genes WASL, ENPP5, ARL6IP1, and IDH1 showed the most significant and strongest downregulation after hsa-miR-142-3p, -17-5p, -223-3p, and -30e-5p transfection, respectively. The most significantly regulated gene set of each miRNA related to cell cycle (hsa-miRNA-144-3p and -5p [Padj = 4 × 10-40 and Padj = 4 × 10-6], -miR-17-5p [Padj = 9.5 × 10-23], -miR-30e-5p [Padj = 8.2 × 10-18], -miR-130a-3p [Padj = 5 × 10-15]), integrin cell surface interaction (-miR-223-3p [Padj = 2.4 × 10-7]), and interferon signaling (-miR-142-3p [Padj = 5 × 10-11]). At the end of acute inflammation, gingival miRNAs bring together complex regulatory networks that lead to increased expression of the gene MET. This underscores the importance of mesenchymal cell migration and invasion during gingival tissue remodeling and proliferation in restoring periodontal tissue homeostasis after active inflammation. MET, a receptor of the mitogenic hepatocyte growth factor fibroblast secreted, is a core gene of this process.

The heme-responsive PrrH sRNA regulates Pseudomonas aeruginosa pyochelin gene expression

Pseudomonas aeruginosa is an opportunistic pathogen that requires iron for growth and virulence, yet this nutrient is sequestered by the innate immune system during infection. When iron is limiting, P. aeruginosa expresses the PrrF1 and PrrF2 small RNAs (sRNAs), which post-transcriptionally repress expression of nonessential iron-containing proteins, thus sparing this nutrient for more critical processes. The genes for the PrrF1 and PrrF2 sRNAs are arranged in tandem on the chromosome, allowing for the transcription of a longer heme-responsive sRNA, termed PrrH. While the functions of PrrF1 and PrrF2 have been extensively studied, the role of PrrH in P. aeruginosa physiology and virulence is not well understood. In this study, we performed transcriptomic and proteomic studies to identify the PrrH regulon. In shaking cultures, the pyochelin synthesis proteins were increased in two distinct prrH mutants compared to the wild type, while the mRNAs for these proteins were not affected by the prrH mutation. We identified complementarity between the PrrH sRNA and the sequence upstream of the pchE mRNA, suggesting the potential for PrrH to directly regulate the expression of genes for pyochelin synthesis. We further showed that pchE mRNA levels were increased in the prrH mutants when grown in static but not shaking conditions. Moreover, we discovered that controlling for the presence of light was critical for examining the impact of PrrH on pchE expression. As such, our study reports on the first likely target of the PrrH sRNA and highlights key environmental variables that will allow for future characterization of PrrH function. IMPORTANCE In the human host, iron is predominantly in the form of heme, which Pseudomonas aeruginosa can acquire as an iron source during infection. We previously showed that the iron-responsive PrrF small RNAs (sRNAs) are critical for mediating iron homeostasis during P. aeruginosa infection; however, the function of the heme-responsive PrrH sRNA remains unclear. In this study, we identified genes for pyochelin siderophore biosynthesis, which mediates uptake of inorganic iron, as a novel target of PrrH regulation. This study therefore highlights a novel relationship between heme availability and siderophore biosynthesis in P. aeruginosa.

Do plant communities show constant final yield?

Total biomass production of plant monocultures growing over a range of densities and harvested after a period of growth increases monotonically with density and then levels out at higher densities. This pattern is called constant final yield (CFY) and is considered one of the most general phenomena in plant ecology. If CFY applies to plant communities, it would be a key to understanding and predicting many community-level phenomena. We tested two primary hypotheses experimentally: (1) Mixtures of several species show CFY. (2) If so, the proportion of biomass production by the component species in a mixture does not change at densities above the density that reaches CFY. We performed a series of glasshouse experiments over 3 years using a "community density series," in which the overall density of five species was varied while their proportions remained unchanged. In the first experiment, we grew a mixture of annual and perennial herbaceous species in mesocosms, and all species were also grown in monocultures at the corresponding densities. A similar experiment was performed in the second and third years, but only with annuals. A third experiment with mixtures only was performed in pots over 2 years. In all cases, aboveground biomass was harvested, separated by species, dried, and weighed. Perennials with underground storage organs produced maximum aboveground biomass at low or intermediate densities. In the second experiment, two of the species produced maximum biomass at the second-highest density in monoculture, while mixtures of all five species showed classical CFY behavior, and the contribution of the species to the mixture changed very little above the lowest density producing CFY. The results of the third experiment were also consistent with the hypotheses. In conclusion, CFY in aboveground biomass production was observed in communities of annual species, and the contribution of the individual species was relatively insensitive to an increase in density above that reaching CFY, i.e., competitive performance of the species changed with density until CFY was reached. Evidence for CFY was stronger in mixture than in monoculture. Coexistence theory must include density as well as frequency dependence if densities are below CFY.

Biomass Allocation Responses to Root Interactions in Wheat Cultivars Support Predictions of Crop Evolutionary Ecology Theory

The goal of agriculture is to optimize the population yield, but natural selection has produced active competition among plants, which decreases population performance. Therefore, cultivar breeding should be based on group selection, increasing yield by weakening individual competitive responses. We hypothesize that this has occurred inadvertently to some degree, so modern cultivars have weakened competitive traits and responses, such as reduced root proliferation in response to neighboring roots. We conducted a field experiment with eight cultivars of spring wheat that have been released over the last hundred years, which we grew at two densities. Two contrasting wheat cultivars, a landrace and a modern cultivar, were used in a second field experiment on competition within and between the two cultivars to quantify their competitiveness. Finally, a greenhouse experiment was conducted with these two cultivars gown (a) in mixture and monoculture, (b) at four densities, (c) two watering levels, and (d) with permeable vs. non-permeable soil dividers, to study root proliferation responses to competition. Results of field experiment 1 showed that the population aboveground biomass (AGB) had increased, while belowground biomass had decreased over the course of breeding, so that the root to shoot ratio (R/S) was negatively correlated with the release year of the cultivar. The landrace had stronger competitiveness than the modern cultivar in the field experiment 2. There was clear evidence of root proliferation and a resultant reduction in AGB in response to neighboring roots in the greenhouse experiment, and the modern variety showed less root proliferation in response to neighbors. We conclude that the newer cultivar was a weaker competitor but higher-yielding in two ways: (1) it had higher reproductive effort and therefore less allocation to structures that increase competitive ability, and (2) it had reduced root proliferation in response to the roots of neighboring plants. Our results show that wheat plants change their biomass allocation in response to resource levels and the presence of neighboring roots. The presence of root proliferation in the modern cultivar, albeit less than in the landrace, suggests that further increases in yield via group selection are possible.

BACH1 Binding Links the Genetic Risk for Severe Periodontitis with ST8SIA1

Genome-wide association studies identified various loci associated with periodontal diseases, but assigning causal alleles remains difficult. Likewise, the generation of biological meaning underlying a statistical association has been challenging. Here, we characterized the genetic association at the gene ST8SIA1 that increases the risk for severe periodontitis in smokers. We used CRISPR/dCas9 activation and RNA-sequencing to identify genetic interaction partners of ST8SIA1 and to determine its function in the cell. We used reporter gene assays to identify regulatory elements at the associated single-nucleotide polymorphisms (SNPs) and to determine effect directions and allele-specific changes of enhancer activity. Antibody electrophoretic mobility shift assays proved allele-specific transcription factor binding at the putative causal SNPs. We found the reported periodontitis risk gene ABCA1 as the top upregulated gene following ST8SIA1 activation. Gene set enrichment analysis showed highest effects on integrin cell surface interactions (area under the curve [AUC] = 0.85; q = 4.9 × 10-6) and cell cycle regulation (AUC = 0.89; q = 1.6 × 10-5). We identified 2 associated repressor elements in the introns of ST8SIA1 that bind the transcriptional repressor BACH1. The putative causative variant rs2012722 decreased BACH1 binding by 40%. We also pinpointed ST8SIA1 as the target gene of the association. ST8SIA1 inhibits cell adhesion with extracellular matrix proteins, integrins, and cell cycle, as well as enhances apoptosis. Likewise, tobacco smoke reportedly results in an inhibition of cell adhesion and a decrease in integrin-positive cells and cell growth. We conclude that impaired ST8SIA1 repression, independently caused by reduced BACH1 binding at the effect T allele, as well as by tobacco smoke, contributes to higher ST8SIA1 levels, and in smokers who carry the effect T allele, both factors would be additive with damaging effects on the gingival barrier integrity. The activity of ST8SIA1 is also linked with the periodontitis risk gene ABCA1.

Human total fertility rate affected by ambient temperatures in both the present and previous generations

Elevated temperatures negatively affect human reproduction through several processes that regulate nutrient uptake and resource allocation in pregnant women. These can interfere with foetal development, resulting in low birth weight neonates with altered development trajectories. Temperatures that affect the current generation could, therefore, also have an impact on the following generation. We asked whether heat stress affected offspring fertility by asking if current and past ambient temperatures influenced total fertility rates (TFR) in human populations distributed across the world. We analysed time series data in 65 countries using simple regression analyses based on maximum temperatures and temperature amplitudes over 55 years. Supplemental longer time series (up to 100 years) provided information on response patterns in Northern Europe and Greenland's colder climates. There were clear and strong effects of temperatures on the TFR in the concurrent and the previous generation. Our temperature-based models account for 71-95% of the variation in TRF in European countries and Greenland, and 56-99% of the variation in 65 countries worldwide. Our findings are consistent with studies of seasonal variation in fertility and suggest that increased temperatures will negatively influence populations subjected to monthly maximum temperatures above 15-20 °C, while fertility in colder climates benefits from elevated temperatures. Our results provide strong evidence that ambient temperatures have important effects on human fertility, and that these effects persist into the following generation.

Allometry and Yield Stability of Cereals

Crop plants grow, and then, they allocate resources to different structures, including seeds and fruits, which represent yield in most crops. We define the yield stability of a genotype as its ability to reduce the effects of temporal variation in resources and conditions on yield production, and we argue that yield stability can be understood in terms of two processes: (1) crop survival and growth (biomass production): the ability of the crop plants to survive and produce biomass under the range of conditions to which it is exposed and (2) the pattern of allocation of this biomass to yield across this range of conditions. Plant breeders and crop physiologists have focused on (1), but much less attention has been paid to (2). We hypothesize that (2) is primarily the result of reproductive allometry: the quantitative relationship between vegetative and reproductive biomass. Ecological theory and the allometric models we present predict a tradeoff between (a) the ability of a genotype to produce yield over a wide variety of conditions and (b) its ability to produce very high yields under optimal or near-optimal conditions. We reanalyze the data from two recent studies, and the results are consistent with this hypothesis. Yield stability in crops corresponds to bet-hedging in evolutionary ecological theory. It is the most appropriate strategy for smallholder farmers in developing countries, a group that comprises most of the farmers in the world. Researchers and crop breeders need to rethink their objectives if they want to develop optimal varieties for these farmers.

Entamoeba gingivalis Exerts Severe Pathogenic Effects on the Oral Mucosa

The protozoan Entamoeba gingivalis colonizes the healthy oral mucosa with a prevalence of 15%. Colonization can be asymptomatic, and it is considered not pathogenic. However, it is able to invade lacerated oral mucosa, where it ingests fragments of live cells, suggesting pathogenous potential. Here, we characterized the transcriptomes of gingival cells after infection with E. gingivalis using RNA sequencing and observed pathogen interaction with the epithelial monolayer barrier by scanning electron microscopy. In epithelial and fibroblast cells, strongest differential expression showed gene set “chemokines and inflammatory molecules in myeloid cells” (area under the curve [AUC] = 0.9, effect size 5.15, adjusted P = 3.1 × 10⁻¹⁹) and “cell cycle and growth arrest” (AUC = 0.91, effect size = 4.56, adjusted P = 4.8 × 10⁻⁹), respectively. The most upregulated genes were TNF (fold change 430) and IL8 (fold change 359) in epithelial cells and ZN331 (fold change 18) in fibroblasts. We showed that E. gingivalis killed live epithelial cells by trogocytosis, demonstrating strong pathogenic potential.

Effects of Intra- and Interspecific Plant Density on Rhizosphere Bacterial Communities

There have been very few studies on the effects of plant competition on the rhizosphere bacterial community. To investigate the impacts of intra- and interspecific plant competition, we analyzed the responses of rhizosphere bacterial communities to plant density as determined by 16S rRNA gene targeted sequencing. We included five weedy plant species growing in field soil in monocultures and mixed cultures at three densities in a greenhouse experiment. The rhizosphere bacterial community of each species changed more with density in a mixture of all five plant species than in monocultures, so intra- and interspecific plant competition had different effects on the bacterial community. For the dominant plant competitor, Centaurea cyanus, neither intra- nor interspecific competition had major effects on the composition of its rhizosphere bacterial communities. In contrast, the bacterial communities of the weakest competitor, Trifolium repens, were affected differently by intra- and interspecific competition. During increasing intraspecific competition T. repens maintained a highly specialized bacterial community dominated by Rhizobium; while during interspecific competition, the relative abundance of Rhizobium declined while other nitrogen fixing and potentially plant growth promoting taxa became more abundant. Contrary to previous observations made for soil microbial communities, the bacterial rhizosphere community of the weakest competitor did not become more similar to that of the dominant species. Thus, the process of competition, as well as the plant species themselves, determined the rhizosphere bacterial community. Our results emphasize the role of plant-plant interactions for rhizosphere bacterial communities. These effects may feedback to affect plant-plant interactions, and this is an important hypothesis for future research.

Looking in the Wrong Direction for Higher-Yielding Crop Genotypes

A misunderstanding of evolution via natural selection has led many plant physiologists and genetic engineers to look in the wrong direction for higher-yielding crop genotypes. Large investments in attempts to make 'better' plants by improving basic physiological processes are not likely to succeed because natural selection has been optimizing these for millions of years. Increases in yield from plant breeding have usually resulted from decreases, not increases, in plant fitness. Examples include reduced plant height and more vertical root growth in cereals. Plant scientists and breeders should generate hypotheses based on what evolutionary biologists call 'group selection', looking for attributes that increase yield in ways that decrease fitness, rather than attempting to improve upon the achievements of natural selection.

Evolutionary agroecology: Trends in root architecture during wheat breeding

Root system characteristics determine soil space exploration and resource acquisition, and these characteristics include competitive traits that increase individual fitness but reduce population performance. We hypothesize that crop breeding for increased yield is often a form of "group selection" that reduces such "selfish" traits to increase population yield. To study trends in root architecture resulting from plant breeding and test the hypothesis that increased yields result in part from group selection on root traits, we investigated root growth and branching behavior in a historical sequence of wheat (Triticum aestivum) cultivars that have been widely grown in northwestern China. Plants were grown in gel-filled chambers to examine growth angles, numbers, and lengths of seminal roots, and in soil-filled chambers under eight soil resource levels for fractal analysis of root system architecture. Yield in field was evaluated at standard and low planting densities. Newer cultivars produced higher yields than older ones only at the higher sowing density, showing that increased yield results from changes in competitive behavior. Seminal root number and growth angles were negatively correlated with yield, while primary seminal root length was positively correlated with yield. Roots of higher-yielding modern varieties were simpler and less branched, grew deeper but spread less laterally than modern varieties. The fractal dimension of root branching was negatively correlated with the yield of cultivars at all resource levels. Root:shoot ratio was negatively correlated with yield under high soil resource levels. The results are consistent with the hypothesis that the success of wheat breeding for higher yields over past 100 years in northwestern China has been in part due to unconscious group selection on root traits, resulting in smaller, less branched, and deeper roots, suggesting a direction for further increases in crop yield in the future.

Latitudinal pattern of flowering synchrony in an invasive wind-pollinated plant

Flowering synchrony can play an important role in plants' reproductive success, which is essential for the successful establishment and spread of invasive plants. Although flowering synchrony has been found to be closely related to climatic factors, the effects of variation in such factors along latitudinal gradient on flowering synchrony and the role of flowering synchrony in the reproductive success of invading populations remain largely unexplored. In a 2-year field study, we examined the latitudinal variation of flowering phenology, especially flowering synchrony, in an invasive plant, Spartina alterniflora, along coastal China, and its relationship with population seed set across three climatic zones. We found that first flowering date was delayed, and flowering synchrony increased with increasing latitude. Flowering synchrony was negatively related to temperature during flowering season but not to soil properties or precipitation, suggesting that climate has shaped the latitudinal pattern of flowering synchrony. Moreover, a positive correlation between flowering synchrony and seed set across latitudes indicates the possible role of flowering synchrony in the latitudinal pattern of sexual reproduction in S. alterniflora These results suggest that, in addition to the effects of climate on the growth of invasive species, climatic factors can play an important role in the invasion success of alien plants by regulating the flowering synchrony and thus the reproductive success of invasive plants.

Increasing plant diversity with border crops reduces insecticide use and increases crop yield in urban agriculture

Urban agriculture is making an increasing contribution to food security in large cities around the world. The potential contribution of biodiversity to ecological intensification in urban agricultural systems has not been investigated. We present monitoring data collected from rice fields in 34 community farms in mega-urban Shanghai, China, from 2001 to 2015, and show that the presence of a border crop of soybeans and neighboring crops (maize, eggplant and Chinese cabbage), both without weed control, increased invertebrate predator abundance, decreased the abundance of pests and dependence on insecticides, and increased grain yield and economic profits. Two 2 year randomized experiments with the low and high diversity practices in the same locations confirmed these results. Our study shows that diversifying farming practices can make an important contribution to ecological intensification and the sustainable use of associated ecosystem services in an urban ecosystem.

Fine root responses to temporal nutrient heterogeneity and competition in seedlings of two tree species with different rooting strategies

There is little direct evidence for effects of soil heterogeneity and root plasticity on the competitive interactions among plants. In this study, we experimentally examined the impacts of temporal nutrient heterogeneity on root growth and interactions between two plant species with very different rooting strategies: Liquidambar styraciflua (sweet gum), which shows high root plasticity in response to soil nutrient heterogeneity, and Pinus taeda (loblolly pine), a species with less plastic roots. Seedlings of the two species were grown in sandboxes in inter‐ and intraspecific combinations. Nutrients were applied in a patch either in a stable (slow‐release) or in a variable (pulse) manner. Plant aboveground biomass, fine root mass, root allocation between nutrient patch and outside the patch, and root vertical distribution were measured. L. styraciflua grew more aboveground (40% and 27% in stable and variable nutrient treatment, respectively) and fine roots (41% and 8% in stable and variable nutrient treatment, respectively) when competing with P. taeda than when competing with a conspecific individual, but the growth of P. taeda was not changed by competition from L. styraciflua. Temporal variation in patch nutrient level had little effect on the species’ competitive interactions. The more flexible L. styraciflua changed its vertical distribution of fine roots in response to competition from P. taeda, growing more roots in deeper soil layers compared to its roots in conspecific competition, leading to niche differentiation between the species, while the fine root distribution of P. taeda remained unchanged across all treatments. Synthesis. L. styraciflua showed greater flexibility in root growth by changing its root vertical distribution and occupying space of not occupied by P. taeda. This flexibility gave L. styraciflua an advantage in interspecific competition.

Human immunology studies using organ donors: Impact of clinical variations on immune parameters in tissues and circulation

Organ donors are sources of physiologically healthy organs and tissues for life-saving transplantation, and have been recently used for human immunology studies which are typically confined to the sampling of peripheral blood. Donors comprise a diverse population with different causes of death and clinical outcomes during hospitalization, and the effects of such variations on immune parameters in blood and tissues are not known. We present here a coordinate analysis of innate and adaptive immune components in blood, lymphoid (bone marrow, spleen, lymph nodes), and mucosal (lungs, intestines) sites from a population of brain-dead organ donors (2 months-93 years; n = 291) across eight clinical parameters. Overall, the blood of donors exhibited similar monocyte and lymphocyte content and low serum levels of pro-inflammatory cytokines as healthy controls; however, donor blood had increased neutrophils and serum levels of IL-8, IL-6, and MCP-1 which varied with cause of death. In tissues, the frequency and composition of monocytes, neutrophils, B lymphocytes and T cell subsets in lymphoid or mucosal sites did not vary with clinical state, and was similar in donors independent of the extent of clinical complications. Our results reveal that organ donors maintain tissue homeostasis, and are a valuable resource for fundamental studies in human immunology.

Reducing shade avoidance responses in a cereal crop

Several researchers have hypothesized that shade avoidance behaviour is favoured by natural selection because it increases the fitness of individuals. Shade avoidance can be disadvantageous for crops, however, because it reduces allocation of resources to reproductive yield, increases the risk of lodging and reduces weed suppression. One approach to develop varieties with reduced shade avoidance and enhanced agronomic performance is by inducing mutations followed by phenotypic screening. We treated spring wheat seeds with ethyl methanesulfonate and screened the seedlings repeatedly under green filters for plants showing reduced elongation of the first leaf sheath and second leaf lamina. The shade avoidance responses of five promising mutant lines were further compared to non-mutated plants in a climate chamber experiment with added far-red light. Two of the selected lines displayed significantly reduced elongation under all light treatments while two lines showed reduced elongation only in added far-red light. The most promising mutant line did not differ in height from the non-mutated cultivar in neutral light, but elongated 20.6% less in strong far-red light. This traditional forward approach of screening mutagenized spring wheat produced plants with reduced shade avoidance responses. These mutants may generate new molecular handles to modify the reaction of plants to changes in light spectral distribution in traditional and novel cultivation systems.

Evolutionary agroecology: individual fitness and population yield in wheat (Triticum aestivum)

Although the importance of group selection in nature is highly controversial, several researchers have argued that plant breeding for agriculture should be based on group selection, because the goal in agriculture is to optimize population production, not individual fitness. A core hypothesis behind this claim is that crop genotypes with the highest individual fitness in a mixture of genotypes will not produce the highest population yield, because fitness is often increased by "selfish" behaviors, which reduce population performance. We tested this hypothesis by growing 35 cultivars of spring wheat (Triticum aestivum L.) in mixtures and monocultures, and analyzing the relationship between population yield in monoculture and individual yield in mixture. The relationship was unimodal, as predicted. The highest-yielding populations were from cultivars that had intermediate fitness, and these produced, on average, 35% higher yields than cultivars with the highest fitness. It is unlikely that plant breeding or genetic engineering can improve traits that natural selection has been optimizing for millions of years, but there is unutilized potential in traits that increase crop yield by decreasing individual fitness.

Effects of nitrogen and water addition on trace element stoichiometry in five grassland species

A 9-year manipulative experiment with nitrogen (N) and water addition, simulating increasing N deposition and changing precipitation regime, was conducted to investigate the bioavailability of trace elements, iron (Fe), manganese (Mn), copper (Cu), and zinc (Zn) in soil, and their uptake by plants under the two environmental change factors in a semi-arid grassland of Inner Mongolia. We measured concentrations of trace elements in soil and in foliage of five common herbaceous species including 3 forbs and 2 grasses. In addition, bioaccumulation factors (BAF, the ratio of the chemical concentration in the organism and the chemical concentration in the growth substrate) and foliar Fe:Mn ratio in each plant was calculated. Our results showed that soil available Fe, Mn and Cu concentrations increased under N addition and were negatively correlated with both soil pH and cation exchange capacity. Water addition partly counteracted the positive effects of N addition on available trace element concentrations in the soil. Foliar Mn, Cu and Zn concentrations increased but Fe concentration decreased with N addition, resulting in foliar elemental imbalances among Fe and other selected trace elements. Water addition alleviated the effect of N addition. Forbs are more likely to suffer from Mn toxicity and Fe deficiency than grass species, indicating more sensitivity to changing elemental bioavailability in soil. Our results suggested that soil acidification due to N deposition may accelerate trace element cycling and lead to elemental imbalance in soil-plant systems of semi-arid grasslands and these impacts of N deposition on semi-arid grasslands were affected by water addition. These findings indicate an important role for soil trace elements in maintaining ecosystem functions associated with atmospheric N deposition and changing precipitation regimes in the future.

Nitrogen:phosphorous supply ratio and allometry in five alpine plant species

In terrestrial ecosystems, atmospheric nitrogen (N) deposition has greatly increased N availability relative to other elements, particularly phosphorus (P). Alterations in the availability of N relative to P can affect plant growth rate and functional traits, as well as resource allocation to above- versus belowground biomass (MA and MB). Biomass allocation among individual plants is broadly size-dependent, and this can often be described as an allometric relationship between MA and MB, as represented by the equation MA=αMBβ, or log MA = logα + βlog MB. Here, we investigated whether the scaling exponent or regression slope may be affected by the N:P supply ratio. We hypothesized that the regression slope between MA and MB should be steeper under a high N:P supply ratio due to P limitation, and shallower under a low N:P supply ratio due to N limitation. To test these hypotheses, we experimentally altered the levels of N, P, and the N:P supply ratio (from 1.7:1 to 135:1) provided to five alpine species representing two functional groups (grasses and composite forbs) under greenhouse conditions; we then measured the effects of these treatments on plant morphology and tissue content (SLA, leaf area, and leaf and root N/P concentrations) and on the scaling relationship between MA and MB. Unbalanced N:P supply ratios generally negatively affected plant biomass, leaf area, and tissue nutrient concentration in both grasses and composite forbs. High N:P ratios increased tissue N:P ratios in both functional groups, but more in the two composite forbs than in the grasses. The positive regression slopes between log MA and log MB exhibited by plants raised under a N:P supply ratio of 135:1 were significantly steeper than those observed under the N:P ratio of 1.7:1 and 15:1.

SYNTHESIS

Plant biomass allocation is highly plastic in response to variation in the N:P supply ratio. Studies of resource allocation of individual plants should focus on the effects of nutrient ratios as well as the availability of individual elements. The two forb species were more sensitive than grasses to unbalanced N:P supplies. To evaluate the adaptive significance of this plasticity, the effects of unbalanced N:P supply ratio on individual lifetime fitness must be measured.

Does climate directly influence NPP globally?

The need for rigorous analyses of climate impacts has never been more crucial. Current textbooks state that climate directly influences ecosystem annual net primary productivity (NPP), emphasizing the urgent need to monitor the impacts of climate change. A recent paper challenged this consensus, arguing, based on an analysis of NPP for 1247 woody plant communities across global climate gradients, that temperature and precipitation have negligible direct effects on NPP and only perhaps have indirect effects by constraining total stand biomass (Mtot ) and stand age (a). The authors of that study concluded that the length of the growing season (lgs ) might have a minor influence on NPP, an effect they considered not to be directly related to climate. In this article, we describe flaws that affected that study's conclusions and present novel analyses to disentangle the effects of stand variables and climate in determining NPP. We re-analyzed the same database to partition the direct and indirect effects of climate on NPP, using three approaches: maximum-likelihood model selection, independent-effects analysis, and structural equation modeling. These new analyses showed that about half of the global variation in NPP could be explained by Mtot combined with climate variables and supported strong and direct influences of climate independently of Mtot , both for NPP and for net biomass change averaged across the known lifetime of the stands (ABC = average biomass change). We show that lgs is an important climate variable, intrinsically correlated with, and contributing to mean annual temperature and precipitation (Tann and Pann ), all important climatic drivers of NPP. Our analyses provide guidance for statistical and mechanistic analyses of climate drivers of ecosystem processes for predictive modeling and provide novel evidence supporting the strong, direct role of climate in determining vegetation productivity at the global scale.

Differential transcriptomic and metabolic profiles of M. africanum- and M. tuberculosis-infected patients after, but not before, drug treatment

The epidemiology of Mycobacterium tuberculosis (Mtb) and M. africanum (Maf) suggest differences in their virulence, but the host immune profile to better understand the pathogenesis of tuberculosis (TB) have not been studied. We compared the transcriptomic and metabolic profiles between Mtb and Maf-infected TB cases to identify host biomarkers associated with lineages-specific pathogenesis and response to anti-TB chemotherapy. Venous blood samples from Mtb- and Maf-infected patients obtained before and after anti-TB treatment were analysed for cell composition, gene expression and metabolic profiles. Prior to treatment, similar transcriptomic profiles were seen in Maf- and Mtb-infected patients. In contrast, post-treatment, over 1600 genes related to immune responses and metabolic diseases were differentially expressed between the groups. Notably, the upstream regulator hepatocyte nuclear factor 4-alpha (HNF4α), which regulated 15% of these genes, was markedly enriched. Serum metabolic profiles were similar in both group pre-treatment, but the decline in pro-inflammatory metabolites post-treatment were most pronounced in Mtb-infected patients. Together, the differences in both peripheral blood transcriptomic and serum metabolic profiles between Maf- and Mtb-infected patients observed over the treatment period, might be indicative of intrinsic host factors related to susceptibility to TB and/or differential efficacy of the standard anti-TB treatment on the two lineages.

Photosensitisation studies of silicone polymer doped with methylene blue and nanogold for antimicrobial applications

2 nm gold nanoparticle (AuNP) and methylene blue (MB) incorporated into medical-grade silicone polymer for antimicrobial applications.

Contrasts between whole-plant and local nutrient levels determine root growth and death in Ailanthus altissima (Simaroubaceae)

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PREMISE OF THE STUDY

There is an ongoing debate about the importance of whole-plant control vs. local modular mechanisms for root growth. We conducted a split-root experiment with different patch/background levels of nitrogen to examine whether local root growth and death are controlled by local resource levels or at the whole-plant level.•

METHODS

Three microrhizotrons with 0, 10, and 100 µg N/g growth medium levels (74 g growth medium each) were attached to pots of high or low soil N in which one Ailanthus altissima individual was growing. One fine root was guided into each of the microrhizotrons and photographed every 4 d. Plants were harvested after 28 d; root growth and mortality in the microrhizotrons were recorded. Changes in root length, number of laterals, and interlateral length were determined from the photos and analyzed.•

KEY RESULTS

While overall plant growth was influenced by background N level, both patch and background N levels influenced root growth and mortality in patches. Local roots proliferated most when the patch N level was high and background level low, and they proliferated least and showed highest mortality when patch N was low and the background level high.•

CONCLUSIONS

The fate of roots growing in a patch is influenced by the resource environment of the plant's other roots as well as the resource levels in the patch itself. Thus, the growth and death of roots in patches is determined by both modular and whole-plant mechanisms.

Recent advances towards tuberculosis control: vaccines and biomarkers

Of all infectious diseases, tuberculosis (TB) remains one of the most important causes of morbidity and mortality. Recent advances in understanding the biology of Mycobacterium tuberculosis (Mtb) infection and the immune response of the infected host have led to the development of several new vaccines, a number of which are already undergoing clinical trials. These include pre-exposure prime vaccines, which could replace bacille Calmette-Guérin (BCG), and pre-exposure booster vaccines given in addition to BCG. Infants are the target population of these two types of vaccines. In addition, several postexposure vaccines given during adolescence or adult life, in addition to BCG as a priming vaccine during infancy, are undergoing clinical testing. Therapeutic vaccines are currently being assessed for their potential to cure active TB as an adjunct to chemotherapy. BCG replacement vaccines are viable recombinant BCG or double-deletion mutants of Mtb. All booster vaccines are composed of one or several antigens, either expressed by viral vectors or formulated with adjuvants. Therapeutic vaccines are killed mycobacterial preparations. Finally, multivariate biomarkers and biosignatures are being generated from high-throughput data with the aim of providing better diagnostic tools to specifically determine TB progression. Here, we provide a technical overview of these recent developments as well of the relevant computational approaches and highlight the obstacles that still need to be overcome.

Plant interactions alter the predictions of metabolic scaling theory

Metabolic scaling theory (MST) is an attempt to link physiological processes of individual organisms with macroecology. It predicts a power law relationship with an exponent of −4/3 between mean individual biomass and density during density-dependent mortality (self-thinning). Empirical tests have produced variable results, and the validity of MST is intensely debated. MST focuses on organisms’ internal physiological mechanisms but we hypothesize that ecological interactions can be more important in determining plant mass-density relationships induced by density. We employ an individual-based model of plant stand development that includes three elements: a model of individual plant growth based on MST, different modes of local competition (size-symmetric vs. -asymmetric), and different resource levels. Our model is consistent with the observed variation in the slopes of self-thinning trajectories. Slopes were significantly shallower than −4/3 if competition was size-symmetric. We conclude that when the size of survivors is influenced by strong ecological interactions, these can override predictions of MST, whereas when surviving plants are less affected by interactions, individual-level metabolic processes can scale up to the population level. MST, like thermodynamics or biomechanics, sets limits within which organisms can live and function, but there may be stronger limits determined by ecological interactions. In such cases MST will not be predictive.

Asymmetric competition in plant populations

Recently there has been much interest in the hypothesis that competition between individual plants is asymmetric or onesided: larger individuals obtain a disproportionate share of the resources (for their relative size) and suppress the growth of smaller individuals. This has important implications for population structure, for the analysis of competition between plants at the individual, population and community levels, and for our understanding of competition as a selective force in the evolution of plant populations.