jaw-1D: a gain-of-function mutation responsive to paramutation-like induction of epigenetic silencing

The Arabidopsis thaliana gain-of-function T-DNA insertion mutant jaw-1D produces miR319A, a microRNA that represses genes encoding CIN-like TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTORs (TCPs), a family of transcription factors that play key roles in leaf morphogenesis. In this study, we show that jaw-1D is responsive to paramutation-like epigenetic silencing. A genetic cross of jaw-1D with the polycomb gene mutant curly leaf-29 (clf-29) leads to attenuation of the jaw-1D mutant plant phenotype. This induced mutation, jaw-1D*, was associated with down-regulation of miR319A, was heritable independently from clf-29, and displayed paramutation-like non-Mendelian inheritance. Down-regulation of miR319A in jaw-1D* was linked to elevated levels of histone H3 lysine 9 dimethylation and DNA methylation at the CaMV35S enhancer located within the activation-tagging T-DNA of the jaw-1D locus. Examination of 21 independent T-DNA insertion mutant lines revealed that 11 could attenuate the jaw-1D mutant phenotype in a similar way to the paramutation induced by clf-29. These paramutagenic mutant lines shared the common feature that their T-DNA insertion was present as multi-copy tandem repeats and contained high levels of CG and CHG methylation. Our results provide important insights into paramutation-like epigenetic silencing, and caution against the use of jaw-1D in genetic interaction studies

Low-Protein Diet Supplemented with Keto Acids Is Associated with Suppression of Small-Solute Peritoneal Transport Rate in Peritoneal Dialysis Patients

Objective. We investigate whether low-protein diet would show benefits in suppressing peritoneal transport rate in peritoneal dialysis (PD) patients. Methods. This is a supplemented analysis of our previously published trial, which randomized 60 PD patients to receive low- (LP: dietary protein intake of 0.6–0.8 g/kg/d), keto-acid-supplemented low- (sLP: 0.6–0.8 g/kg/d with 0.12 g/kg/d of keto acids), or high- (HP: 1.0–1.2 g/kg/d) protein diet and lasted for one year. In this study, the variations of peritoneal transport rate were assessed. Results. While baseline D/Pcr (dialysate-to-plasma concentration ratio for creatinine at 4 hour) and D/D0glu (dialysate glucose at 4 hour to baseline dialysate glucose concentration ratio) were similar, D/Pcr in group sLP was lower, and D/D0glu was higher than those in the other two groups (P < 0.05) at 12th month. D/D0glu increased (P < 0.05), and D/Pcr tended to decrease, (P = 0.071) in group sLP. Conclusions. Low-protein diet with keto acids may benefit PD patients by maintaining peritoneum at a lower transport rate

Linking PHYTOCHROME-INTERACTING FACTOR to Histone Modification in Plant Shade Avoidance

Shade avoidance syndrome (SAS) allows a plant grown in a densely populated environment to maximize opportunities to access to sunlight. Although it is well established that SAS is accompanied by gene expression changes, the underlying molecular mechanism needs to be elucidated. Here, we identify the H3K4me3/H3K36me3-binding proteins, Morf Related Gene (MRG) group proteins MRG1 and MRG2, as positive regulators of shade-induced hypocotyl elongation in Arabidopsis (Arabidopsis thaliana). MRG2 binds PHYTOCHROME-INTERACTING FACTOR7 (PIF7) and regulates the expression of several common downstream target genes, including YUCCA8 and IAA19 involved in the auxin biosynthesis or response pathway and PRE1 involved in brassinosteroid regulation of cell elongation. In response to shade, PIF7 and MRG2 are enriched at the promoter and gene-body regions and are necessary for increase of histone H4 and H3 acetylation to promote target gene expression. Our study uncovers a mechanism in which the shade-responsive factor PIF7 recruits MRG1/MRG2 that binds H3K4me3/H3K36me3 and brings histone-acetylases to induce histone acetylations to promote expression of shade responsive genes, providing thus a molecular mechanistic link coupling the environmental light to epigenetic modification in regulation of hypocotyl elongation in plant SAS

Nest-site selection and breeding ecology of Streaked Wren-Babbler (Napothera brevicaudata) in a tropical limestone forest of southern China

Abstract Background The breeding information of most birds in Asian tropical areas, especially in limestone forests, is still poorly known. The Streaked Wren-Babbler (Napothera brevicaudata) is an uncommon tropical limestone bird with a small range. We studied its nest-site selection and breeding ecology, in order to understand the adaptations of birds to the conditions of tropical limestone forest in southern China. Methods We used methods of systematical searching and parent-following to locate the nests of the Streaked Wren-Babbler. We measured characteristics of nest sites and rock cavities. Data loggers and video cameras were used to monitor the breeding behavior. Results All the observed nests of the Streaked Wren-Babbler were placed in natural shallow cavities or deep holes in large boulders or limestone cliffs. The great majority (96.6%) of Streaked Wren-Babbler nests had three eggs with an average fresh weight of 3.46 ± 0.43 g (n = 36, range 2.52‒4.20 g). Most (80.4%) females laid their first eggs between March and April (n = 46). The average incubation and nestling period of the Streaked Wren-Babbler was 10.2 ± 0.4 days (n = 5, range 10‒11 days) and 10.5 ± 0.8 days (n = 6, range 9‒11 days), respectively. Most (87.9%) nests had at least one nestling fledge between 2011 and 2013 (n = 33). Conclusions Our study suggests that several features of the breeding ecology of the Streaked Wren-Babbler, including building nests in rocky cavities, commencing breeding earlier than most species, and reducing foraging times during the incubation period, are well-adapted to the unique habitat of tropical limestone forest

Nest predation on birds that nest in rock cavities in a tropical limestone forest of southern China

High nest predation is often found in tropical birds, though data from tropical limestone regions are lacking. In a limestone karst rainforest of south China, two species of babblers breed in rock cavities in different seasonal periods: the endangered Nonggang Babbler (Stachyris nonggangensis) breeds in May, like most birds, and the common Streaked Wren Babbler (Napothera brevicaudata) breeds in March. We tested the hypothesis that nest predation varied by nesting period using an artificial nest experiment. We used natural rock cavities that varied in their distance to the forest edge, checked nests at different intervals and measured characteristics of cavity location. We found nest predation to be much higher in May (65 of 99 nests) than March (14 of 83); predation tended to be higher when nests were visited only once, but no other factor significantly influenced the result. The higher predation rate during warmer weather, and the fact that eggs disappeared mostly at once, yet predators were not detected on infrared nest cameras, suggests that snakes could be important predators; further research is needed to confirm this hypothesis. We conclude that the aberrant nesting period of the Streaked Wren Babbler may be a strategy to escape nest predation

Ecology of two Pittas (Pitta soror and Pitta nympha) in limestone forests of South China

The ecology and life history of bird species inhabiting limestone forests, which are under major conservation threats, is currently poorly known. To cover this gap of knowledge, in this study we report for the first time on several aspects of the breeding ecology of the Blue-rumped Pitta (Pitta soror) and the Fairy Pitta (P. nympha) inhabiting two typical limestone forests of south China. The mean density of Fairy Pittas in our study locations was 3.13 ± 2.82 and 1.05 ± 2.09 individuals/km2. The Blue-rumped Pitta was common in Nonggang and showed a mean density of 4.67 ± 2.44 individuals/km2, yet was absent in the other. We found nine nests between February 2009 and June 2015, including five of the Blue-rumped Pitta and four of the Fairy Pitta. Blue-rumped Pittas laid 4.8 ± 0.4 eggs with a mean fresh mass of 8.10 ± 0.40 g. Fairy Pittas had a clutch size of 5.2 ± 0.45 eggs with a mean fresh mass of 6.03 ± 0.22 g. Blue-rumped and Fairy Pitta parents fed their nestlings 4.0 ± 1.2 times and 3.9 ± 1.5 times per hour, respectively. Earthworms were the most common food item delivered to nestlings by Blue-rumped (93.6%) and Fairy Pitta (91.2%) parents. Blue-rumped Pittas bred successfully in 40% of nests (two of five), whilst in the case of Fairy Pittas nest success reached 75% (three of four). The two Pittas had larger clutch sizes than in southern populations of the same species and also than most other bird species inhabiting limestone forests. This would imply that Pittas show differences in life history traits within limestone ecosystems

A network meta-analysis on comparison of invasive and non-invasive sampling methods to characterize intestinal microbiota of birds

Birds maintain complex and intimate associations with a diverse community of microbes in their intestine. Multiple invasive and non-invasive sampling methods are used to characterize these communities to answer a multitude of eco-evolutionary questions related to host-gut microbiome symbioses. However, the comparability of these invasive and non-invasive sampling methods is sparse with contradicting findings. Through performing a network meta-analysis for 13 published bird gut microbiome studies, here we attempt to investigate the comparability of these invasive and non-invasive sampling methods. The two most used non-invasive sampling methods (cloacal swabs and fecal samples) showed significantly different results in alpha diversity and taxonomic relative abundances compared to invasive samples. Overall, non-invasive samples showed decreased alpha diversity compared to intestinal samples, but the alpha diversities of fecal samples were more comparable to the intestinal samples. On the contrary, the cloacal swabs characterized significantly lower alpha diversities than in intestinal samples, but the taxonomic relative abundances acquired from cloacal swabs were similar to the intestinal samples. Phylogenetic status, diet, and domestication degree of host birds also influenced the differences in microbiota characterization between invasive and non-invasive samples. Our results indicate a general pattern in microbiota differences among intestinal mucosal and non-invasive samples across multiple bird taxa, while highlighting the importance of evaluating the appropriateness of the microbiome sampling methods used to answer specific research questions. The overall results also suggest the potential importance of using both fecal and cloacal swab sampling together to properly characterize bird microbiomes

Significant recent ornithological records from the limestone area of south-west Guangxi, south China, 2004-2012

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