A detailed study of leaf micromorphology and anatomy of New World Vitis L. subgenus Vitis within a phylogenetic and ecological framework reveals evolutionary convergence

We investigated leaf anatomy and micromorphology in the New World Vitis using light and scanning electron microscopy to understand the correlation of these traits to molecular phylogenetic relationships and environmental affinity. We observed traits known to differ among species of Vitis with importance in traditional taxonomy of Vitis: trichome type, stomata morphology, mesophyll organization, and midrib vascularization. We found that traits associated with water conductance and photosynthesis comprised the highest loadings of axis one of a principal components analysis (PCA) while traits related to gas exchange (i.e., the stomatal apparatus) had high loadings on axis two. Using the PCA, we identified seven clusters of species, which showed little correlation to recently reported molecular phylogenetic relationships. Moreover, analyses using Bayes Traits and Bayesian Binary Method revealed little to no phylogenetic signal in trait evolution. PCA axes one and two separated species occurring in dry southwestern North American habitats from those in mesic places. For example, a cluster of V. monticola and V. arizonica occurred adjacent to a cluster of V. californica and V. girdiana in ordination space, and the latter three species share key leaf anatomical traits. Nevertheless, among these, only V. arizonica and V. girdiana are closely related according to molecular phylogeny. Thus, the leaf micromorphological/anatomical traits of Vitis observed in this study are highly correlated with environment, but not phylogenetic relationships. We expect that trait similarities among distantly related species may result from evolutionary convergences, especially within xeric habitats of western North America.     

How to build an inducible cartilage-specific transgenic mouse

Transgenic mice are used to study the roles of specific proteins in an intact living system. Use of transgenic mice to study processes in cartilage, however, poses some challenges. First of all, many factors involved in cartilage homeostasis and disease are also crucial factors in embryogenesis. Therefore, meddling with these factors often leads to death before birth, and mice who do survive cannot be considered normal. The build-up of cartilage in these mice is altered, making it nearly impossible to truly interpret the role of a protein in adult cartilage function. An elegant way to overcome these limitations is to make transgenic mice time- and tissue-specific, thereby omitting side-effects in tissues other than cartilage and during embryology. This review discusses the potential building blocks for making an inducible cartilage-specific transgenic mouse. We review which promoters can be used to gain chondrocyte-specificity - all chondrocytes or a specific subset thereof - as well as different systems that can be used to enable inducibility of a transgene.     

Inflammatory changes in the airways of mice caused by cigarette smoke exposure are only partially reversed after smoking cessation

Background

The inhalation of allergens by allergic asthmatics results in the early asthmatic response (EAR), which is characterized by acute airway obstruction beginning within a few minutes. The EAR is the earliest indicator of the pathological progression of allergic asthma. Because the molecular mechanism underlying the EAR is not fully defined, this study will contribute to a better understanding of asthma.

Methods

In order to gain insight into the molecular basis of the EAR, we examined changes in protein expression patterns in the lung tissue of asthmatic rats during the EAR using 2-DE/MS-based proteomic techniques. Bioinformatic analysis of the proteomic data was then performed using PPI Spider and KEGG Spider to investigate the underlying molecular mechanism.

Results

In total, 44 differentially expressed protein spots were detected in the 2-DE gels. Of these 44 protein spots, 42 corresponded to 36 unique proteins successfully identified using mass spectrometry. During subsequent bioinformatic analysis, the gene ontology classification, the protein-protein interaction networking and the biological pathway exploration demonstrated that the identified proteins were mainly involved in glycolysis, calcium binding and mitochondrial activity. Using western blot and semi-quantitative RT-PCR, we confirmed the changes in expression of five selected proteins, which further supports our proteomic and bioinformatic analyses.

Conclusions

Our results reveal that the allergen-induced EAR in asthmatic rats is associated with glycolysis, calcium binding and mitochondrial activity, which could establish a functional network in which calcium binding may play a central role in promoting the progression of asthma.     

Population genetic structure and evolutionary history of Psammochloa villosa (Trin.) Bor (Poaceae) revealed by AFLP marker

Psammochloa villosa is an ecologically important desert grass that occurs in the Inner Mongolian Plateau where it is frequently the dominant species and is involved in sand stabilization and wind breaking. We sought to generate a preliminary demographic framework for P. villosa to support the future studies of this species, its conservation, and sustainable utilization. To accomplish this, we characterized the genetic diversity and structure of 210 individuals from 43 natural populations of P. villosa using amplified fragment length polymorphism (AFLP) markers. We obtained 1,728 well‐defined amplified bands from eight pairs of primers, of which 1,654 bands (95.7%) were polymorphic. Results obtained from the AFLPs suggested effective alleles among populations of 1.32, a Nei''s standard genetic distance value of 0.206, a Shannon index of 0.332, a coefficient of gene differentiation (G _ST) of 0.469, and a gene flow parameter (Nm) of 0.576. All these values indicate that there is abundant genetic diversity in P. villosa, but limited gene flow. An analysis of molecular variance (AMOVA) showed that genetic variation mainly exists within populations (64.2%), and we found that the most genetically similar populations were often not geographically adjacent. Thus, this suggests that the mechanisms of gene flow are surprisingly complex in this species and may occur over long distances. In addition, we predicted the distribution dynamics of P. villosa based on the spatial distribution modeling and found that its range has contracted continuously since the last interglacial period. We speculate that dry, cold climates have been critical in determining the geographic distribution of P. villosa during the Quaternary period. Our study provides new insights into the population genetics and evolutionary history of P. villosa in the Inner Mongolian Plateau and provides a resource that can be used to design in situ conservation actions and prioritize sustainable utilization.     

Mitochondrial control-region sequences in two shorebird species, the turnstone and the dunlin, and their utility in population genetic studies

We determined the mitochondrial control-region sequences of five turnstones (Arenaria interpres) and three dunlins (Calidris alpina). Comparisons revealed that the central part (part II) is conserved relative to much more variable parts at the beginning (part I) and the end (part III). This pattern of sequence conservation is also found in the control regions of other vertebrates. The average sequence divergence between turnstone and dunlin was 21.8% for part I, 7.5% for part II, and 29.5% for part III. Within-species sequence divergence over the entire control region was much lower, at 0.9% for turnstones and 2.0% for dunlins. In both shorebird species, part III contains a repetitive sequence composed only of A and C nucleotides, which has not been found in the control regions of other birds. A survey of the part I sequences of 25 turnstones and 25 dunlins sampled around the world revealed that these species have very different population genetic structures. Dunlins are not only much more differentiated in their sequences but also have a strongly subdivided population genetic structure. Pleistocene vicariant events combined with strong natal philopatry and high mutation rates of the sequences are likely responsible for this population genetic subdivision. Conversely, part I sequences of turnstones are weakly differentiated and are geographically unstructured. We argue that this is not the result of global gene flow but that, instead turnstones have recently expanded from a refugial population that was bottlenecked.      

Assessing the maternal origin in the polyploid complex of <Emphasis Type="Italic">Camellia reticulata</Emphasis> based on the chloroplast <Emphasis Type="Italic">rpl</Emphasis>16 intron sequences: implications for camellia cross breeding

Camellia reticulata is a well-known woody ornamental species endemic to Southwest China. It represents a polyploid complex with diploids, allotetraploids, and allohexaploids. The parentage of the allotetraploids and allohexaploids has been reported by genomic in situ hybridization, but the maternal parents still remain unknown. In this study, sequences of the chloroplast rpl16 intron of 105 cultivars of C. reticulata and 7 congeneric species were used to infer the maternal origin of the allopolyploids. The results showed that (1) the allotetraploids were derived from C. pitardii as the maternal parental species and the diploid C. reticulata as the paternal parental species; (2) the allohexaploid C. reticulata was derived from the allotetraploid C. reticulata as the maternal parent and C. saluenensis as the paternal parent; and (3) the C. reticulata cultivars were derived from hexaploid C. reticulata as the maternal parents. These results indicated that C. pitardii, the allotetraploid and allohexaploid C. reticulata may serve as good potential maternal parents for the cross breeding of Camellia.     

A population genetics perspective on the evolutionary histories of three clonal,endemic, and dominant grass species of the Qinghai–Tibet Plateau: Orinus (Poaceae)

We performed analyses of amplified fragment length polymorphism (AFLP) in order to characterize the evolutionary history of Orinus according to its population genetic structure, as well as to investigate putative hybrid origins of O. intermedius and to provide additional insights into relationships among species. The genus Orinus comprises three clonal grasses that are dominant species within xeric alpine grasslands of the Qinghai–Tibet Plateau (QTP). Here, we used eight selectively obtained primer pairs of EcoRI/MseI to perform amplifications in 231 individuals of Orinus representing 48 populations and all three species. We compared our resulting data to genetic models of hybridization using a Bayesian algorithm within NewHybrids software. We determined that genetic variation in Orinus was 56.65% within populations while the among‐species component was 30.04% using standard population genetics statistics. Nevertheless, we detected that species of Orinus were clustered into three highly distinct genetic groups corresponding to classic species identities. Our results suggest that there is some introgression among species. Thus, we tested explicit models of hybridization using a Bayesian approach within NewHybrids software. However, O. intermedius likely derives from a common ancestor with O. kokonoricus and is probably not the result of hybrid speciation between O. kokonoricus and O. thoroldii. We suspect that recent isolation of species of Orinus in allopatry via vicariance may explain the patterns in diversity that we observed, and this is corroborated by a Mantel test that showed significant positive correlation between geographic and genetic distance (r = 0.05, p < 0.05). Recent isolation may explain why Orinus differs from many other clonal species by exhibiting the highest diversity within populations rather than among them.