Phylogenomics and the rise of the angiosperms

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins5-7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes8. This 15-fold increase in genus-level sampling relative to comparable nuclear studies9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.

The origin and speciation of orchids

Orchids constitute one of the most spectacular radiations of flowering plants. However, their origin, spread across the globe, and hotspots of speciation remain uncertain due to the lack of an up-to-date phylogeographic analysis. We present a new Orchidaceae phylogeny based on combined high-throughput and Sanger sequencing data, covering all five subfamilies, 17/22 tribes, 40/49 subtribes, 285/736 genera, and c. 7% (1921) of the 29 524 accepted species, and use it to infer geographic range evolution, diversity, and speciation patterns by adding curated geographical distributions from the World Checklist of Vascular Plants. The orchids' most recent common ancestor is inferred to have lived in Late Cretaceous Laurasia. The modern range of Apostasioideae, which comprises two genera with 16 species from India to northern Australia, is interpreted as relictual, similar to that of numerous other groups that went extinct at higher latitudes following the global climate cooling during the Oligocene. Despite their ancient origin, modern orchid species diversity mainly originated over the last 5 Ma, with the highest speciation rates in Panama and Costa Rica. These results alter our understanding of the geographic origin of orchids, previously proposed as Australian, and pinpoint Central America as a region of recent, explosive speciation.

Revised Species Delimitation in the Giant Water Lily Genus Victoria (Nymphaeaceae) Confirms a New Species and Has Implications for Its Conservation

Reliably documenting plant diversity is necessary to protect and sustainably benefit from it. At the heart of this documentation lie species concepts and the practical methods used to delimit taxa. Here, we apply a total-evidence, iterative methodology to delimit and document species in the South American genus Victoria (Nymphaeaceae). The systematics of Victoria has thus far been poorly characterized due to difficulty in attributing species identities to biological collections. This research gap stems from an absence of type material and biological collections, also the confused diagnosis of V. cruziana. With the goal of improving systematic knowledge of the genus, we compiled information from historical records, horticulture and geography and assembled a morphological dataset using citizen science and specimens from herbaria and living collections. Finally, we generated genomic data from a subset of these specimens. Morphological and geographical observations suggest four putative species, three of which are supported by nuclear population genomic and plastid phylogenomic inferences. We propose these three confirmed entities as robust species, where two correspond to the currently recognized V. amazonica and V. cruziana, the third being new to science, which we describe, diagnose and name here as V. boliviana Magdalena and L. T. Sm. Importantly, we identify new morphological and molecular characters which serve to distinguish the species and underpin their delimitations. Our study demonstrates how combining different types of character data into a heuristic, total-evidence approach can enhance the reliability with which biological diversity of morphologically challenging groups can be identified, documented and further studied.

Adherence to a Mediterranean Dietary Pattern and Functional Parameters: A Cross-Sectional Study in an Older Population

OBJECTIVES

In older adults, diet and physical activity are among the most important behaviours that influence health. The Mediterranean Dietary Pattern has been related to longevity and can benefit physical function in older adults. The present study aims to quantify the association of adherence to a Mediterranean Dietary Pattern with physical functioning through by handgrip strength, as well as, with sedentary behaviour based on sitting time, in a sample of older adults.

METHODS

A cross-sectional study was conducted in 1,491 older adults ≥ 65 years old. The adherence or non-adherence to a Mediterranean Dietary Pattern was assessed using the previously validated and translated 14 item questionnaire, the PREDIMED (Prevención com Dieta Mediterránea). Handgrip strength was measured with a Jamar Dynamometer. Sitting time per day was used as an indicator of sedentary behaviour. Multinomial logistic regressions were performed to quantify the association of adherence to a Mediterranean Dietary Pattern with handgrip strength and sitting time.

RESULTS

Compared to participants who adhered to a Mediterranean Dietary Pattern, those who did not adhere to this diet have a significantly higher adjusted odds ratio for low handgrip strength [adjusted odds ratio: 1.50; 95% confidence interval: 1.09-2.05], as well as for longer sitting time [adjusted odds ratio: 1.43; 95% confidence interval: 1.04-1.96].

CONCLUSION

In older adults, the non-adherence to a Mediterranean Dietary Pattern was associated with both lower values of handgrip strength and longer sitting time.

Vitamin D status and functional parameters: A cross-sectional study in an older population

The present study aims to clarify the association of vitamin D status with functionality, measured through gait speed and hand grip strength, in a sample of older adults, considering sex-specific characteristics and the potential confounding effect of lifestyle factors, disease, skin phenotype, season of blood collection and vitamin D supplementation. The Nutrition UP 65 cross-sectional study was conducted in a population-based sample of 1,425 older adults ≥ 65 years old. Serum levels of 25-hydroxyvitamin D were quantified through electrochemiluminescence immunoassay. Multinomial logistic regressions were carried out using quartiles of gait speed and of hand grip strength as dependent variables. Participants at risk of vitamin D inadequacy (30.0-49.9 nmol/L) and deficiency (< 30.0 nmol/L) presented higher adjusted odds ratio of the lowest values of gait speed and hand grip strength than those with adequate vitamin D levels (≥ 50.0 nmol/L). These associations were strongest among men at risk of vitamin D deficiency [adjusted odds ratio for the lowest quartile of gait speed = 3.24; 95% CI: 1.56–6.73 and for the lowest quartile of hand grip strength = 3.28; 95% CI: 1.47-7.31] than in women at risk of vitamin D deficiency [adjusted odds ratio for the lowest quartile of gait speed = 2.72; 95% CI: 1.37-5.41 and for the lowest quartile of hand grip strength = 1.56; 95% CI: 0.81–3.00]. In conclusion, in older adults, particularly in men, the risk of vitamin D deficiency was directly associated with the lowest values of gait speed and of hand grip strength. However, randomized controlled trials are needed to overcome the possibility of reverse causation and residual confounding. Present results emphasise the need for strategies to promote the reduction of the high prevalence of low vitamin D status among the Portuguese older adult population.

Co-circulation in a single biome of the Juquitiba and Araraquara hantavirus detected in human sera in a sub-tropical region of Brazil

Hantaviruses is an emerging infectious disease. Although HCPS has been reported in several regions of Brazil, more cases of HCPS have recently been reported in Minas Gerais than in any other state. In 2009, we analyzed 27 samples presenting antibodies against hantaviruses. These samples originated from 688 symptomatic patients, as determined based on the Hemorrhagic Fever Protocol. A subsequent SYBR Green-based real-time RT-PCR demonstrated the presence of the virus in 22 of the samples. Among the RT-PCR-positive samples, 17 were analyzed using DNA sequencing; these sequences were compared with others deposited in GenBank and showed similarity with the Araraquara and Juquitiba virus clusters. This work describe the detection of Juquitiba virus, including three fatal cases, in Minas Gerais state, furthermore, showed that it is feasible to characterize the circulating strains using a small fragment of S segment. Finally, the results suggest the co-circulation of Araraquara and Juquitiba virus in a single biome in Minas Gerais state.

Long-term high-fat consumption leads to downregulation of Akt phosphorylation of eNOS at Ser1177 and upregulation of Sirtuin-1 expression in rat cavernous tissue

Long-term consumption of high-fat diets negatively interferes with metabolic status and promotes endothelial dysfunction and inflammation. In the cavernous tissue, these outcomes become conspicuous in the elderly and strongly affect penile erection, a vascular process highly dependent on local nitric oxide bioavailability. Although epidemiological data links erectile dysfunction to nutritional patterns, the underlying molecular mechanisms remain unclear. Therefore, we investigated the effects of long-term high-fat diet on endothelial nitric oxide synthase (eNOS)-Sirtuin-1 axis and Akt/eNOS phosphorylation in the cavernous tissue of Sprague-Dawley rats, and compared with energy-restricted animals. We demonstrated that high-fat diet intake led to a noteworthy decrease in eNOS phosphorylation at Ser1177 residue through the Akt pathway, which seems to be compensated by upregulation of phosphorylation at Ser615, but without an increment in nitric oxide production. These results are accompanied by an increase of systemic inflammatory markers and upregulation of the inducible NOS and of the deacetylase Sirtuin-1 in the cavernous tissue to levels apparently detrimental to cells and to metabolic homeostasis. Conversely, in long-term energy-restricted animals, the rate of phosphorylation of eNOS at Ser1177 diminished, but the activation of the enzyme increased through phosphorylation of eNOS at Ser615, resulting in an enhancement in nitric oxide bioavailability. Taken together, our results demonstrate that long-term nutritional conditions override the influence of age on the eNOS expression and activation in rat cavernous tissue.

Increased circulating platelet microparticles as a potential biomarker in asthma

BACKGROUND

Endothelial (EMPs) and platelet microparticles (PMPs) have been studied as biomarkers in several inflammatory diseases and as central players in intercellular communication.

METHODS

In this cross-sectional study, we aimed to assess microparticle levels in asthma. Circulating microparticles and inflammatory and angiogenic markers were assessed by clinical and laboratorial evaluation, flow cytometry, and immunoassays, in a group of 20 asthmatic and 15 nonasthmatic subjects.

RESULTS

Circulating levels of PMPs (either CD31+/42b+ or CD31+/42b+/AnV+) were significantly increased in asthmatics (P = 0.021) even after adjustment for confounders. Apoptotic EMPs (CD31+/42b--/AnV+) were significantly increased before (P = 0.005) but not after adjustments (P = 0.117).

CONCLUSIONS

We propose that PMPs may be putative asthma biomarkers, playing a role in asthma pathophysiology.

Fusion of Sendai virus with model membranes as affected by dehydrating agents and pH: correlation between viral envelope hydrophobicity and fusion activity

We have studied the importance of hydrophobic interactions in the fusion activity of Sendai virus. Viral fusion activity towards model lipid membranes was monitored using a fluorescence dequenching assay. Fusion was dependent on the composition of the target membrane and was more rapid and extensive at low pH. Dehydrating agents such as dimethylsulfoxide and dimethylsulfone greatly enhanced the initial rate and extent of the fusion process, the effect of dimethylsulfone doubling that of dimethylsulfoxide. However, dehydrating agents had a less pronounced stimulatory effect at low pH. Using the fluorescent probe ANS (1-aminonaphthalene-8-sulfonate) we have shown that low pH by itself involves a marked increase in the viral envelope hydrophobicity, probably resulting in the observed lower stimulation of viral fusion activity by dehydrating agents. Therefore, there seems to be a strong correlation between viral envelope hydrophobicity and viral fusion activity.

Role of hydrophobic interactions in the fusion activity of influenza and Sendai viruses towards model membranes

We have studied the role of hydrophobic interactions in the fusion activity of two lipid enveloped viruses, influenza and Sendai. Using the fluorescent probe ANS (1-aminonaphtalene-8-sulfonate) we have shown that low-pH-dependent influenza virus activation involves a marked increase in the viral envelope hydrophobicity. The effect of dehydrating agents on the fusion activity of both viruses towards model lipid membranes was studied using a fluorescence dequenching assay. Dehydrating agents such as dimethylsulfoxide and dimethylsulfone greatly enhanced the initial rate of the fusion process, the effect of dimethylsulfone doubling that of dimethylsulfoxide. The effect of poly(ethylene glycol) on the fusion process was found to be dependent on the polymer concentration and molecular weight. In general, similar observations were made for both viruses. These results stress the importance of dehydration and hydrophobic interactions in the fusion activity of influenza and Sendai viruses, and show that these factors may be generally involved in membrane fusion events mediated by many other lipid enveloped viruses.