Recurrent allopolyploidizations diversify ecophysiological traits in marsh orchids (Dactylorhiza majalis s.l.).

Whole-genome duplication has shaped the evolution of angiosperms and other organisms, and is important for many crops. Structural reorganization of chromosomes and repatterning of gene expression are frequently observed in allopolyploids, with physiological and ecological consequences. Recurrent origins from different parental populations are widespread among polyploids, resulting in an array of lineages that provide excellent models to uncover mechanisms of adaptation to divergent environments in early phases of polyploid evolution. We integrate here transcriptomic and ecophysiological comparative studies to show that sibling allopolyploid marsh orchid species (Dactylorhiza, Orchidaceae) occur in different habitats (low nutrient fens vs. meadows with mesic soils) and are characterized by a complex suite of intertwined, pronounced ecophysiological differences between them. We uncover distinct features in leaf elemental chemistry, light-harvesting, photoprotection, nutrient transport and stomata activity of the two sibling allopolyploids, which appear to match their specific ecologies, in particular soil chemistry differences at their native sites. We argue that the phenotypic divergence between the sibling allopolyploids has a clear genetic basis, generating ecological barriers that maintain distinct, independent lineages, despite pervasive interspecific gene flow. This suggests that recurrent origins of polyploids bring about a long-term potential to trigger and maintain functional and ecological diversity in marsh orchids and other groups.

Non-ubiquitous expression of core spliceosomal protein SmB/B' in chick and mouse embryos.

BACKGROUND: Although splicing is an integral part of the expression of many genes in our body, genetic syndromes with spliceosomal defects affect only specific tissues. To help understand the mechanism, we investigated the expression pattern of a core protein of the major spliceosome, SmB/B' (Small Nuclear Ribonucleoprotein Polypeptides B/B'), which is encoded by SNRPB. Loss-of-function mutations of SNRPB in humans cause cerebro-costo-mandibular syndrome (CCMS) characterized by rib gaps, micrognathia, cleft palate, and scoliosis. Our expression analysis focused on the affected structures as well as non-affected tissues, using chick and mouse embryos as model animals. RESULTS: Embryos at young stages (gastrula) showed ubiquitous expression of SmB/B'. However, the level and pattern of expression became tissue-specific as differentiation proceeded. The regions relating to CCMS phenotypes such as cartilages of ribs and vertebrae and palatal mesenchyme express SmB/B' in the nucleus sporadically. However, cartilages that are not affected in CCMS also showed similar expressions. Another spliceosomal gene, SNRNP200, which mutations cause retinitis pigmentosa, was also prominently expressed in cartilages in addition to the retina. CONCLUSION: The expression of SmB/B' is spatiotemporally regulated during embryogenesis despite the ubiquitous requirement of the spliceosome, however, the expression pattern is not strictly correlated with the phenotype presentation.

Applying Promiscuous RiPP Enzymes to Peptide Backbone N-Methylation Chemistry.

The methylation of peptide backbone amides is a hallmark of bioactive natural products, and it also greatly modifies the pharmacology of synthetic peptides. Usually, bioactive N-methylated peptides are cyclic. However, there is very limited knowledge about how post-translational enzymes can be applied to the synthesis of designed N-methylated peptides or peptide libraries. Here, driven by the established ability of some RiPP enzymes to process diverse substrates, we sought to define catalysts for the in vivo and in vitro macrocyclization of backbone-methylated peptides. We developed efficient methods in which short, synthetic N-methylated peptides could be modified using side chain and mainchain macrocyclases, PsnB and PCY1 from plesiocin and orbitide biosynthetic pathways, respectively. Most significantly, a strategy for PsnB cyclase was designed enabling simple in vitro methods compatible with solid-phase peptide synthesis. We show that cyanobactin N-terminal protease PatA is a broadly useful catalyst that is also compatible with N-methylation chemistry, but that cyanobactin macrocyclase PatG is strongly biased against N-methylated substrates. Finally, we sought to marry these macrocyclase tools with an enzyme that N-methylates its core peptide: OphMA from the omphalotin pathway. However, instead, we reveal some limitations of OphMA and demonstrate that it unexpectedly and extensively modified the enzyme itself in vivo. Together, these results demonstrate proof-of-concept for enzymatic synthesis of N-methylated peptide macrocycles.

Plant science. Biosynthesis, regulation, and domestication of bitterness in cucumber.

Cucurbitacins are triterpenoids that confer a bitter taste in cucurbits such as cucumber, melon, watermelon, squash, and pumpkin. These compounds discourage most pests on the plant and have also been shown to have antitumor properties. With genomics and biochemistry, we identified nine cucumber genes in the pathway for biosynthesis of cucurbitacin C and elucidated four catalytic steps. We discovered transcription factors Bl (Bitter leaf) and Bt (Bitter fruit) that regulate this pathway in leaves and fruits, respectively. Traces in genomic signatures indicated that selection imposed on Bt during domestication led to derivation of nonbitter cucurbits from their bitter ancestors.

Independent associations of body-size adjusted fat mass and fat-free mass with the metabolic syndrome in Chinese.

BACKGROUND: Excess fat leads to adverse health outcomes. Most previous studies investigating body fatness using BMI or fat percentage, which contain both fat mass and fat-free mass, were not able to differentiate the exposure. AIM: The present study assessed the independent association of fat and fat-free mass with metabolic syndrome (MetS) in Chinese. SUBJECTS AND METHODS: A population-based study of 1144 subjects aged 50-70 from urban and rural areas of Shanghai in 2005-2006 was employed. Body composition was measured with DEXA. Fat mass index (FMI) and fat-free mass index (FFMI) were calculated. MetS was defined using the National Cholesterol Education Program Adult Treatment Panel III (NCEP ATP III) criteria without waist circumference for its high correlation with body composition. RESULTS: Both FMI and FFMI were significantly related with higher odds of MetS (OR 3.97, 95% CI 2.58-6.09 for FMI; OR 2.67, 95% CI 1.70-4.18 for FFMI, the highest quartile vs the lowest group) after adjusting for age, residence, sex, smoking, drinking, physical activity, medication, family history of chronic diseases, and fat-free mass (for FMI) or fat mass (for FFMI). CONCLUSION: Both FMI and FFMI are independently associated with increased MetS risks. Proper expression of body composition is essential in assessing body composition and disease risk association.

Differences in bone mineral status between urban and rural Chinese men and women.

BACKGROUND: Few studies have investigated differences in bone health and associated lifestyle factors between urban and rural populations in countries, such as China, undergoing rapid nutrition transition. Such a study may help to identify risk factors of osteoporosis and provide evidence for future preventive strategies. OBJECTIVE: To determine primarily whether differences in bone mineral content (BMC) and bone mineral density (BMD) exist between urban and rural Chinese men and women and secondly whether any urban-rural differences could be explained by body size or lifestyle factors. METHODS: In total, 490 men and 689 women aged 50-70 were included in the study. 535 of them were from urban Shanghai and 644 from surrounding rural areas. Anthropometric measurements were conducted and spine lumber 1-4 BMC measurements were determined by dual-energy X-ray absorptiometry (DEXA). Information on socioeconomic status, medical history, smoking and drinking habits and physical activity were collected. RESULTS: Urban men and women had significantly higher spine BMC, BMD and bone area than their rural counterparts (P<0.01). After controlling body size, the differences between urban-rural spine BMC and BMD remained in women (P<0.001), but were no longer significant in men. The urban and rural differences of BMC and BMD in women could not be explained by including the lifestyle factors such as income, intake of milk, vitamin D and calcium, total physical activity level, walking and social activity. CONCLUSION: This study found the significant differences in both spine BMC and BMD between urban and rural men and women in Shanghai, China. This difference could be explained by the body size in men; however, it remained unexplained in women after adjusting for body size and certain lifestyle risk factors.