Tryptophan metabolism and bacterial commensals prevent fungal dysbiosis in Arabidopsis roots

In nature, roots of healthy plants are colonized by multikingdom microbial communities that include bacteria, fungi, and oomycetes. A key question is how plants control the assembly of these diverse microbes in roots to maintain host–microbe homeostasis and health. Using microbiota reconstitution experiments with a set of immunocompromised Arabidopsis thaliana mutants and a multikingdom synthetic microbial community (SynCom) representative of the natural A. thaliana root microbiota, we observed that microbiota-mediated plant growth promotion was abolished in most of the tested immunocompromised mutants. Notably, more than 40% of between-genotype variation in these microbiota-induced growth differences was explained by fungal but not bacterial or oomycete load in roots. Extensive fungal overgrowth in roots and altered plant growth was evident at both vegetative and reproductive stages for a mutant impaired in the production of tryptophan-derived, specialized metabolites (cyp79b2/b3). Microbiota manipulation experiments with single- and multikingdom microbial SynComs further demonstrated that 1) the presence of fungi in the multikingdom SynCom was the direct cause of the dysbiotic phenotype in the cyp79b2/b3 mutant and 2) bacterial commensals and host tryptophan metabolism are both necessary to control fungal load, thereby promoting A. thaliana growth and survival. Our results indicate that protective activities of bacterial root commensals are as critical as the host tryptophan metabolic pathway in preventing fungal dysbiosis in the A. thaliana root endosphere.

Allele and genotype variation of follicle stimulating hormone receptor gene of Indonesian Friesian Holstein in Boyolali District, Central Java

Follicle Stimulating Hormone Receptor (FSHR) is a gene that has function to regulate reproductive performance by controlling oogenesis in females and also spermatogenesis in male. Since dairy cattle operation lies on the reproductive trait efficiency, therefore it’s became a logical reason to use FSHR genes as part of selection criteria. This study aimed to determine allele and genotype variation of FSHR gene in local Indonesian Friesian Holstein (IFH) dairy cattle in Boyolali District, Central Java. In total 20 IFH cattle we sampled for DNA source. Allele and genotype variation was determined by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) using AluI restriction enzyme. The methods started with DNA extraction, PCR, and DNA digestion, followed by allele and genotype frequencies calculation. Two alleles were observed in this study, C and G with respective frequencies 0.75 and 0.25. According to that, we found three genotype combinations that are CC, CG, and GG, the frequencies were 0.56, 0.38, and 0.06, respectively. To use that result as a part of selection criteria in dairy cattle, especially in females, further association study with reproductive trait needs to be done.

Emersion-Associated Responses of an Intertidal Coral and Its Suitability for Transplantation to Ecologically Engineer Seawalls

There is a growing interest in transplanting corals onto the intertidal section of artificial coastal defences (e.g., seawalls) as an ecological engineering strategy to enhance biodiversity on urban shores. However, this inevitably results in exposure to the harsh environmental conditions associated with emersion (aerial exposure). Although the effects of a multitude of environmental stressors on corals have been examined, their photophysiological and gene expression responses to emersion stress remain understudied, as does the among-genotype variation in these responses. In this study, we conducted an in situ experiment to test the effects of increased daily emersion duration on a locally common intertidal coral, Dipsastraea cf. lizardensis. Coral fragments (n = 3) from five genotypically distinct colonies were subjected to two treatments: (1) increased daily emersion duration (~4.5 h d−1) and, (2) control (~3 h d−1) for three consecutive days during spring low tide. We examined the post-experimental photophysiological responses and expression level of a stress-associated gene, Hsp16. Relative to the controls, coral fragments that were exposed to longer daily emersion duration displayed significantly reduced effective quantum yield, while endosymbiont density varied significantly among genotypes across the experimental conditions. We found no significant differences in chlorophyll a concentration and Hsp16 gene expression level, suggesting that changes in these processes may be gradual and the duration of treatment that the corals were subjected to is likely within their tolerance limits. Taken together, it appears that D. cf. lizardensis displays substantial capacity to cope with sup-optimal conditions associated with emersion which makes it a promising candidate for transplantation onto intertidal seawalls. However, within-species variation in their stress response indicates that not all genotypes respond similarly to emersion, and this should be taken into account when selecting donor colonies for transplantation.

Seedling Emergence Comparison of Several Romanian Tomato and Pepper Varieties

Nowadays people are turning to sustainable/ecological agriculture. Romanian local varieties with valuable traits can be used to develop novel organic varieties. Nine Romanian tomato (Solanum lycopersicum L.) and seven pepper (Capsicum annuum L.) varieties were compared during seedling emergence in growth chamber and greenhouse conditions. The aim of this study was to observe the variation of several emergence indicators among the varieties of the same species under the same growing conditions, differences that can be correlated with genotype variation in further genotyping research, with the final goal of using these results as a basis for genotype-assisted breeding programs. The present survey demonstrated significant differences in the emergence indicators among the varieties studied, both in the growth chamber and in the greenhouse growing conditions. Ștefănești 24 tomato variety stood out with the longest mean emergence time, mean emergence rate, synchrony and highest uncertainty of emergence, whereas Vladimir pepper variety had the lowest values for percentage of emergence, homogeneity and uncertainty of emergence.

Cross-species evolutionary rewiring in the enteric bacterium Campylobacter

The lateral transfer of genes among bacterial strains and species has opposing effects, conferring potentially beneficial adaptations whilst introducing disharmony in coadapted genomes. The prevailing outcome will depend upon the fitness cost of disrupting established epistatic interactions between genes. It is challenging to understand this in nature because it requires population-scale analysis of recombination and genomic coadaptation, and laboratory confirmation of the functional significance of genotype variation. By assigning the ancestry of DNA in the genomes of two species of the world's most common enteric bacterial pathogen, we show that up to 28% of the Campylobacter coli genome has been recently introgressed from Campylobacter jejuni. Then, by quantifying covariation across the genome we show that >83% of putative epistatic links are between introgressed C. jejuni genes in divergent genomic positions (>20kb apart), consistent with independent acquisition. Much of this covariation is between 16 genes, with just 5 genes accounting for 99% of epistatic SNP pairs. Laboratory mutagenesis and complementation cloning assays demonstrated functional links between these genes, specifically related to formate dehydrogenase (FDH) activity. These findings suggest that the genetic confederations that define genomic species may be transient. Even for complex traits such as central metabolism in the bacterial cell, conditions can arise where epistatic genes can be decoupled, transferred and reinstated in a new genetic background.

Maternal 17q21 genotype influences prenatal vitamin D effects on offspring asthma/recurrent wheeze

BackgroundPrenatal vitamin D3 supplementation has been linked to reduced risk of early life asthma/recurrent wheeze. This protective effect appears to be influenced by variations in the 17q21 functional SNP rs12936231 of the child, which regulates the expression of ORMDL3, and for which the high-risk CC-genotype is associated with early-onset asthma. However, this does not fully explain the differential effects of supplementation. We investigated the influence of maternal rs12936231 genotype variation on the protective effect of prenatal vitamin D3 supplementation against offspring asthma/recurrent wheeze.MethodsWe determined the rs12936231 genotype of mother-child pairs from two randomised-controlled trials: the Vitamin D Antenatal Asthma Reduction Trial (VDAART, n=613) and the Copenhagen Prospective Studies on Asthma in Childhood 2010 (COPSAC2010, n=563) to examine the effect of maternal genotype variation on offspring asthma/recurrent wheeze at age 0–3 years between groups who received high-dose prenatal vitamin D3 supplementation versus placebo.ResultsOffspring of mothers with low-risk GG-genotype or GC-genotype who received high-dose vitamin D3 supplementation had a significantly reduced risk of asthma/recurrent wheeze when compared to the placebo group (hazard ratio [HR], 0.54; 95% confidence interval [CI], 0.37–0.77; p<0.001 for VDAART and HR, 0.56; 95% CI, 0.35–0.92; p=0.021 for COPSAC2010), whereas no difference was observed among the offspring of mothers with high-risk CC-genotype (HR, 1.05; 95% CI, 0.61–1.84; p=0.853 for VDAART and HR, 1.11; 95% CI, 0.54–2.28; p=0.785 for COPSAC2010).ConclusionMaternal 17q21 genotype has an important influence on the protective effects of prenatal vitamin D3 supplementation against offspring asthma/recurrent wheeze.

Low immunogenicity of common cancer hot spot mutations resulting in false immunogenic selection signals

Cancer is driven by somatic mutations that result in a cellular fitness advantage. This selective advantage is expected to be counterbalanced by the immune system when these driver mutations simultaneously lead to the generation of neoantigens, novel peptides that are presented at the cancer cell membrane via HLA molecules from the MHC complex. The presentability of these peptides is determined by a patient’s MHC genotype and it has been suggested that this results in MHC genotype-specific restrictions of the oncogenic mutational landscape. Here, we generated a set of virtual patients, each with an identical and prototypical MHC genotype, and show that the earlier reported HLA affinity differences between observed and unobserved mutations are unrelated to MHC genotype variation. We demonstrate how these differences are secondary to high frequencies of 13 hot spot driver mutations in 6 different genes. Several oncogenic mechanisms were identified that lower the peptides’ HLA affinity, including phospho-mimicking substitutions in BRAF, destabilizing tyrosine mutations in TP53 and glycine-rich mutational contexts in the GTP-binding KRAS domain. In line with our earlier findings, our results emphasize that HLA affinity predictions are easily misinterpreted when studying immunogenic selection processes.