Intraspecific trait variation influences physiological performance and fitness in the South Africa shrub genus Protea (Proteaceae)

Background and AimsGlobal plant trait datasets commonly identify trait relationships that are interpreted to reflect fundamental trade-offs associated with plant strategies, but often these trait relationships are not identified when evaluating them at smaller taxonomic and spatial scales. In this study we evaluate trait relationships measured on individual plants for five widespread Protea species in South Africa to determine whether broad-scale patterns of structural trait (e.g. leaf area) and physiological trait (e.g. photosynthetic rates) relationships can be detected within natural populations, and if these traits are themselves related to plant fitness.MethodsWe evaluated the variance structure (i.e. the proportional intraspecific trait variation relative to among-species variation) for nine structural traits and six physiological traits measured in wild populations. We used a multivariate path model to evaluate the relationships between structural traits and physiological traits, and the relationship between these traits and plant size and reproductive effort.Key ResultsWhile intraspecific trait variation is relatively low for structural traits, it accounts for between 50 and 100 % of the variation in physiological traits. Furthermore, we identified few trait associations between any one structural trait and physiological trait, but multivariate regressions revealed clear associations between combinations of structural traits and physiological performance (R² = 0.37–0.64), and almost all traits had detectable associations with plant fitness.ConclusionsIntraspecific variation in structural traits leads to predictable differences in individual-level physiological performance in a multivariate framework, even though the relationship of any particular structural trait to physiological performance may be weak or undetectable. Furthermore, intraspecific variation in both structural and physiological traits leads to differences in plant size and fitness. These results demonstrate the importance of considering measurements of multivariate phenotypes on individual plants when evaluating trait relationships and how trait variation influences predictions of ecological and evolutionary outcomes.     

In silico identification of novel lncRNAs with a potential role in diagnosis of gastric cancer

Abstract

Gastric cancer (GC) is the second leading cause of cancer-related deaths in the world. Due to the shortage of adequate symptoms in the early stages, it is diagnosed when the tumor has spread to distant organs. Early recognition of GC enhances the chance of successful treatment. Molecular mechanisms of GC are still poorly understood. LncRNAs are emerging as new players in cancer in both oncogene and tumor suppressor roles. High-throughput technologies such as RNA-Seq, have revealed thousands of lncRNAs which are dysregulated in GC. In this study, we retrieved lncRNAs obtained by High-throughput technologies from OncoLnc database. Consequently, retrieved lncRNAs were compared in literature-based databases including PubMed. As a result, two lists, including experimentally validated lncRNAs and predicted lncRNAs were provided. We found 43 predicted lncRNAs that had not been experimentally validated in GC, so far. Further Bioinformatics analyses were performed to obtain the expression profile of predicted lncRNAs in tumor and normal tissues. Also, the roles and targets of predicted lncRNAs in GC were identified by related databases. Finally, using the GEPIA database was reviewed the significant relationship of predicted lncRNAs with the survival of GC patients. By recognizing the lncRNAs involved in initiation and progression of GC, they may be considered as potential biomarkers in the GC early diagnosis or targeted treatment and lead to novel therapeutic strategies.

Communicated by Ramaswamy H. Sarma     

Wetland ecosystem comparison using a suite of plant assessment measures

In light of extensive human impact on wetlands it is necessary that we develop an effective way to monitor the effects of impact in order to prevent further destruction. One method is plant community assessment, specifically Floristic Quality Assessment (FQA), which is common, but can be subjective. In this case study, we implement FQA, as well as specific morphological and chemical assessment measures over a two-year period in order to compare two wetlands in the Lake George watershed in the Adirondack mountains and their response to human impact. While the wetlands studied demonstrated very different water chemistry profiles makeups, FQA did not reveal substantial differences between plant communities. However, more specific analyses of plant morphology and tissue chemistry did reveal significant differences that reflected the level of impact at these two sites. Namely, the simple plant Lemna minor had consistently shorter roots and Nuphar lutea contained higher amounts of nitrogen in above ground tissues when growing in an anthropogenically impacted wetland. We suggest that FQA and specific plant morphology and tissue chemistry measurements be performed concurrently to provide indication of both long- and short-term effects of human impact in wetland ecosystems.     

Toward a better understanding of the "Transverse Range break": lineage diversification in southern California

The Transverse Ranges in southern California have been identified as having a prominent phylogeographic role. Numerous studies have identified distinct north-south and/or east-west lineage breaks involving the Transverse Ranges. However, in evaluating their findings, most authors have regarded this complex system somewhat simplistically. In this study we more deeply investigate these breaks using two approaches: first we examine the phylogeographic history of Sepedophilus castaneus (Coleoptera: Staphylinidae) and then implement a comparative phylogeography approach applying Brooks parsimony analysis to the topologies of nine additional taxa. Phylogenetic analysis, nested clade analysis, and AMOVAs for S. castaneus agree that there is a major lineage break between the eastern and western Transverse Ranges, localized between the Sierra Pelona and the San Gabriel Mountains. The comparative phylogeographic analysis supports a generally strong concordance of area relationships with geographic proximity. It is notable, however, that the Transverse Ranges as a group do not show phylogenetic cohesion, but rather they are split into three main regions: an eastern region (San Gabriel, San Bernardino, and San Jacinto Mountains), a central region (central Transverse Ranges and Sierra Pelona) that is often grouped with the Tehachapi and Sierra Nevada populations, and a western region (northwestern Transverse Ranges and Santa Ynez Mountains) that is consistently grouped with coast range areas to the north. The lineage break between east and west Transverse Ranges is attributable to the presence of a marine embayment in what is now the Santa Clara River valley 5-2.5 million years ago.     

Automated system for gene annotation and metabolic pathway reconstruction using general sequence databases

Despite the growing number of genomes published or currently being sequenced, there is a relative paucity of software for functional classification of newly discovered genes and their assignment to metabolic pathways. Available software for such analyses has a very steep learning curve and requires the installation, configuration, and maintenance of large amounts of complex infrastructure, including complementary software and databases. Many such tools are restricted to one or a few data sources and classification schemes. In this work, we report an automated system for gene annotation and metabolic pathway reconstruction (ASGARD), which was designed to be powerful and generalizable, yet simple for the biologist to install and run on centralized, commonly available computers. It avoids the requirement for complex resources such as relational databases and web servers, as well as the need for administrator access to the operating system. Our methodology contributes to a more rapid investigation of the potential biochemical capabilities of genes and genomes by the biological researcher, and is useful in biochemical as well as comparative and evolutionary studies of pathways and networks.     

Endemic flora biodiversity in the south of the Iberian Peninsula: altitudinal distribution,life forms and dispersal modes

The south of the Iberian Peninsula, with an altitudinal range varying from sea level to 3482m and annual average rainfall ranging from 206 to 2223mm, has 516 vascular endemic species or subspecies, that is, an endemicity rate of 13%. This survey deals with parameters such as species richness, originality, life forms and dispersal modes of these plants, in relation to altitudinal and rainfall gradients. Although most of the endemic plants occur between 600 and 1400m a.s.l. and in the range of 600–1000mm annual average rainfall, floristic originality (rate of endemic taxa per area unit) increases exponentially with altitude. The biological spectrum of this endemic flora does not follow the usual patterns observed either in local floras in the south of the Iberian Peninsula or in other regions of the Mediterranean Basin. Chamaephytes (46.08%) and hemicryptophytes (31.37%) are very abundant, whereas therophytes (11.96%) and phanerophytes (0.98%) are comparatively rare. There is a statistically significant correlation between life form and both altitudinal and rainfall gradients. Chamaephytes reach their highest density rates within 1400–2000m a.s.l., but these records tend to decrease as rainfall rates increase. Abundance of hemicryptophytes is directly dependent on rainfall rates and inversely dependent on temperature. The altitudinal distribution pattern of therophytes is opposite to that of hemicryptophytes, but there is no clear correlation as far as rainfall gradient is concerned. Considering both the endemic plants as a whole and each of the life form groups, the relationships between the dispersal modes used and the altitudinal and rainfall gradients are analysed. Up to 44.51% of the endemic plants do not present evident adaptations to promote the dispersion of their diaspores. However, only in the group of therophytes, whose occurrence is positively related to areas of minor altitude, does this difficulty of dispersion play a significant role in the maintenance of stenochory.     

NMRShiftDB -- compound identification and structure elucidation support through a free community-built web database

Compound identification and support for computer-assisted structure elucidation via a free community-built web database for organic structures and their NMR data is described. The new database NMRShiftDB is available on . As the first NMR database, NMRShiftDB allows not only open access to the database but also open and peer reviewed submission of datasets, enabling the natural products community to build its first free repository of assigned 1H and 13C NMR spectra. In addition to the open access, the underlying database software is built solely from free software and is available under an open source license. This allows collaborating laboratories to fully replicate the database and to create a highly available network of NMRShiftDB mirrors. The database contains about 10,000 structures and assigned spectra, with new datasets constantly added. Its functionality includes (sub-) spectra and (sub-) structure searches as well as shift prediction of 13C spectra based on the current database material.