MicroRNAs (miRNAs) play an essential role in gene regulators in many biological and molecular phenomena. Unraveling the involvement of miRNA as a key cellular factor during in vitro canine parvovirus (CPV) infection may facilitate the discovery of potential intervention candidates. However, the examination of miRNA expression profiles in CPV in tissue culture systems has not been fully elucidated.

Plant flavonoid metabolism has served as a platform for understanding a range of fundamental biological phenomena, including providing some of the early insights into the subcellular organization of metabolism. Evidence assembled over the past three decades points to the organization of the component enzymes as a membrane-associated complex centered on the entry-point enzyme, chalcone synthase (CHS), with flux into branch pathways controlled by competitive protein interactions. Flavonoid enzymes have also been found in the nucleus in a variety of plant species, raising the possibility of alternative, or moonlighting functions for these proteins in this compartment. Here, we present evidence that CHS interacts with MOS9, a nuclear-localized protein that has been linked to epigenetic control of R genes that mediate effector-triggered immunity. Overexpression of MOS9 results in a reduction of CHS transcript levels and a metabolite profile that substantially intersects with the effects of a null mutation in CHS. These results suggest that the MOS9-CHS interaction may point to a previously-unknown mechanism for controlling the expression of the highly dynamic flavonoid pathway.

Patients with dilated cardiomyopathy, increased ventricular volume, pressure overload or dysynergistic ventricular contraction and relaxation are susceptible to develop serious ventricular arrhythmias (VA). These phenomena are primarily based on a theory of mechanoelectric feedback, which reflects mechanical changes that produce alterations in electrical activity. However, very few systematic studies have provided evidence of the preventive effects of artemisinin (ART) on VA in response to left ventricle (LV) afterload increases. MicroRNAs (miRNAs) are endogenous small non-coding RNAs that regulate expression of multiple genes by suppressing mRNAs post-transcriptionally.

Osteoporosis is a major public health problem that is associated with high morbidity and mortality, and its prevalence is increasing as the world's population ages. Therefore, understanding the molecular basis of the disease is becoming a high priority. In this regard, studies have shown that an imbalance in adipogenic and osteogenic differentiation of bone marrow mesenchymal stem cells (MSCs) is associated with osteoporosis. In this study, we conducted a Weighted Gene Co-Expression Network Analysis to identify gene modules associated with the differentiation of bone marrow MSCs. Gene Ontology and Kyoto Encyclopedia of Genes and Genome enrichment analysis showed that the most significant module, the brown module, was enriched with genes involved in cell cycle regulation, which is in line with the initial results published using these data. In addition, the Cytoscape platform was used to identify important hub genes and lncRNAs correlated with the gene modules. Furthermore, differential gene expression analysis identified 157 and 40 genes that were upregulated and downregulated, respectively, after 3 h of MSCs differentiation. Interestingly, regulatory network analysis, and comparison of the differentially expressed genes with those in the brown module identified potential novel biomarker genes, including two transcription factors (ZNF740, FOS) and two hub genes (FOXQ1, SGK1), which were further validated for differential expression in another data set of differentiation of MSCs. Finally, Gene Set Enrichment Analysis suggested that the two most important candidate hub genes are involved in regulatory pathways, such as the JAK-STAT and RAS signaling pathways. In summary, we have revealed new molecular mechanisms of MSCs differentiation and identified novel genes that could be used as potential therapeutic targets for the treatment of osteoporosis.

Cassiopea xamachana jellyfish are an attractive model system to study metamorphosis and/or cnidarian-dinoflagellate symbiosis due to the ease of cultivation of their planula larvae and scyphistomae through their asexual cycle, in which the latter can bud new larvae and continue the cycle without differentiation into ephyrae. Then, a subsequent induction of metamorphosis and full differentiation into ephyrae is believed to occur when the symbionts are acquired by the scyphistomae. Although strobilation induction and differentiation into ephyrae can be accomplished in various ways, a controlled, reproducible metamorphosis induction has not been reported. Such controlled metamorphosis induction is necessary for an ensured synchronicity and reproducibility of biological, biochemical, and molecular analyses. For this purpose, we tested if differentiation could be pharmacologically stimulated as in Aurelia aurita, by the metamorphic inducers thyroxine, KI, NaI, Lugol's iodine, H2O2, indomethacin, or retinol. We found reproducibly induced strobilation by 50 μM indomethacin after six days of exposure, and 10-25 μM after 7 days. Strobilation under optimal conditions reached 80-100% with subsequent ephyrae release after exposure. Thyroxine yielded inconsistent results as it caused strobilation occasionally, while all other chemicals had no effect. Thus, indomethacin can be used as a convenient tool for assessment of biological phenomena through a controlled metamorphic process in C. xamachana scyphistomae.

Saproxylic beetles play a crucial role in key processes occurring in forest ecosystems, and together with fungi contribute to the decomposition and mineralization of wood. Among this group are mycetophilic beetles which associate with wood-decaying fungi and use the fruiting body for nourishment and development. Therefore, their feeding strategy (especially in the case of fungivorous species) requires special digestive capabilities to take advantage of the nutritional value of fungal tissue. Although polypore-beetle associations have been investigated in numerous studies, detailed studies focusing on the microbiome associated with species feeding on fruiting bodies of polypores remain limited. Here we investigated the bacterial communities associated with larvae and adults of Bolitophagus reticulatus collected from Fomes fomentarius growing on two different host tree: beech (Fagus sp.) and birch (Betula sp.), respectively. Among 24 identified bacterial phyla, three were the most relatively abundant (Proteobacteria, Actinobacteria and Bacteroidetes). Moreover, we tried to find unique patterns of bacteria abundances which could be correlated with the long-term field observation showing that the fruiting bodies of F. fomentarius, growing on birch are more inhabited by beetles than fruiting bodies of the same fungus species growing on beech. Biochemical analyses showed that the level of protease inhibitors and secondary metabolites in F. fomentarius is higher in healthy fruiting bodies than in the inhabited ones. However, tested microbiome samples primarily clustered by developmental stage of B. reticulatus and host tree did not appear to impact the taxonomic distribution of the communities. This observation was supported by statistical analyses.

In the present study we used the high-throughput sequencing technology Illumina MiSeq to develop 26 polymorphic microsatellite loci for the marine snail Gibbula divaricata. Four to 32 alleles were detected per locus across 30 samples analyzed. Observed and expected heterozygosities ranged from 0.130 to 0.933 and from 0.294 to 0.956, respectively. No significant linkage disequilibrium existed. Seven loci deviated from Hardy-Weinberg equilibrium that could not totally be explained by the presence of null alleles. Sympatric distribution with other species of the genus Gibbula, as G. rarilineata and G. varia, lead us to test the cross utility of the developed markers in these two species, which could be useful to test common biogeographic patterns or potential hybridization phenomena, since morphological intermediate specimens were found.

Experimental evolution of microbes can be used to empirically address a wide range of questions about evolution and is increasingly employed to study complex phenomena ranging from genetic evolution to evolutionary rescue. Regardless of experimental aims, fitness assays are a central component of this type of research, and low-throughput often limits the scope and complexity of experimental evolution studies. We created an experimental evolution system in Saccharomyces cerevisiae that utilizes genetic barcoding to overcome this challenge.

Motivation. Alternative splicing events (ASEs) are prevalent in the transcriptome of eukaryotic species and are known to influence many biological phenomena. The identification and quantification of these events are crucial for a better understanding of biological processes. Next-generation DNA sequencing technologies have allowed deep characterization of transcriptomes and made it possible to address these issues. ASEs analysis, however, represents a challenging task especially when many different samples need to be compared. Some popular tools for the analysis of ASEs are known to report thousands of events without annotations and/or graphical representations. A new tool for the identification and visualization of ASEs is here described, which can be used by biologists without a solid bioinformatics background. Results. A software suite named Splicing Express was created to perform ASEs analysis from transcriptome sequencing data derived from next-generation DNA sequencing platforms. Its major goal is to serve the needs of biomedical researchers who do not have bioinformatics skills. Splicing Express performs automatic annotation of transcriptome data (GTF files) using gene coordinates available from the UCSC genome browser and allows the analysis of data from all available species. The identification of ASEs is done by a known algorithm previously implemented in another tool named Splooce. As a final result, Splicing Express creates a set of HTML files composed of graphics and tables designed to describe the expression profile of ASEs among all analyzed samples. By using RNA-Seq data from the Illumina Human Body Map and the Rat Body Map, we show that Splicing Express is able to perform all tasks in a straightforward way, identifying well-known specific events. Availability and Implementation. Splicing Express is written in Perl and is suitable to run only in UNIX-like systems. More details can be found at: http://www.bioinformatics-brazil.org/splicingexpress.

Characterizing transcriptomes in non-model organisms has resulted in a massive increase in our understanding of biological phenomena. This boon, largely made possible via high-throughput sequencing, means that studies of functional, evolutionary, and population genomics are now being done by hundreds or even thousands of labs around the world. For many, these studies begin with a de novo transcriptome assembly, which is a technically complicated process involving several discrete steps. The Oyster River Protocol (ORP), described here, implements a standardized and benchmarked set of bioinformatic processes, resulting in an assembly with enhanced qualities over other standard assembly methods. Specifically, ORP produced assemblies have higher Detonate and TransRate scores and mapping rates, which is largely a product of the fact that it leverages a multi-assembler and kmer assembly process, thereby bypassing the shortcomings of any one approach. These improvements are important, as previously unassembled transcripts are included in ORP assemblies, resulting in a significant enhancement of the power of downstream analysis. Further, as part of this study, I show that assembly quality is unrelated with the number of reads generated, above 30 million reads. Code Availability: The version controlled open-source code is available at https://github.com/macmanes-lab/Oyster_River_Protocol. Instructions for software installation and use, and other details are available at http://oyster-river-protocol.rtfd.org/.

Ensign wasps (Hymenoptera: Evaniidae) develop as predators of cockroach eggs (Blattodea), have a wide distribution and exhibit numerous interesting biological phenomena. The taxonomy of this lineage has been the subject of several recent, intensive efforts, but the lineage lacked a robust phylogeny. In this paper we present a new phylogeny, based on increased taxonomic sampling and data from six molecular markers (mitochondrial 16S and COI, and nuclear markers 28S, RPS23, CAD, and AM2), the latter used for the first time in phylogenetic reconstruction. Our intent is to provide a robust phylogeny that will stabilize and facilitate revision of the higher-level classification. We also show the continued utility of molecular motifs, especially the presence of an intron in the RPS23 fragments of certain taxa, to diagnose evaniid clades and assist with taxonomic classification. Furthermore, we estimate divergence times among evaniid lineages for the first time, using multiple fossil calibrations. Evaniidae radiated primarily in the Early Cretaceous (134.1-141.1 Mya), with and most extant genera diverging near the K-T boundary. The estimated phylogeny reveals a more robust topology than previous efforts, with the recovery of more monophyletic taxa and better higher-level resolution. The results facilitate a change in ensign wasp taxonomy, with Parevania, and Papatuka, syn. nov. becoming junior synonyms of Zeuxevania, and Acanthinevania, syn. nov. being designated as junior synonym of Szepligetella. We transfer 30 species to Zeuxevania, either reestablishing past combinations or as new combinations. We also transfer 20 species from Acanthinevania to Szepligetella as new combinations.

One of the main challenges of the post-genomic era is the understanding of how gene expression is controlled. Changes in gene expression lay behind diverse biological phenomena such as development, disease and the adaptation to different environmental conditions. Despite the availability of well-established methods to identify these changes, tools to discern how gene regulation is orchestrated are still required. The regulation of gene expression is usually depicted as a Gene Regulatory Network (GRN) where changes in the network structure (i.e., network topology) represent adjustments of gene regulation. Like other networks, GRNs are composed of basic building blocks; small induced subgraphs called graphlets. Here we present LoTo, a novel method that using Graphlet Based Metrics (GBMs) identifies topological variations between different states of a GRN. Under our approach, different states of a GRN are analyzed to determine the types of graphlet formed by all triplets of nodes in the network. Subsequently, graphlets occurring in a state of the network are compared to those formed by the same three nodes in another version of the network. Once the comparisons are performed, LoTo applies metrics from binary classification problems calculated on the existence and absence of graphlets to assess the topological similarity between both network states. Experiments performed on randomized networks demonstrate that GBMs are more sensitive to topological variation than the same metrics calculated on single edges. Additional comparisons with other common metrics demonstrate that our GBMs are capable to identify nodes whose local topology changes between different states of the network. Notably, due to the explicit use of graphlets, LoTo captures topological variations that are disregarded by other approaches. LoTo is freely available as an online web server at http://dlab.cl/loto.

Habitat fragmentation is one of the greatest threats to biodiversity conservation and ecosystem productivity mediated by direct human impact. Its consequences include genetic depauperation, comprising phenomena such as inbreeding depression or reduction in genetic diversity. While the capacity of wild and domestic herbivores to sustain long-distance seed dispersal has been proven, the impact of herbivore corridors in plant population genetics remains to be observed. We conducted this study in the Conquense Drove Road in Spain, where sustained use by livestock over centuries has involved transhumant herds passing twice a year en route to winter and summer pastures. We compared genetic diversity and inbreeding coefficients of Plantago lagopus populations along the drove road with populations in the surrounding agricultural matrix, at varying distances from human settlements. We observed significant differences in coefficients of inbreeding between the drove road and the agricultural matrix, as well as significant trends indicative of higher genetic diversity and population nestedness around human settlements. Trends for higher genetic diversity along drove roads may be present, although they were only marginally significant due to the available sample size. Our results illustrate a functional landscape with human settlements as dispersal hotspots, while the findings along the drove road confirm its role as a pollinator reservoir observed in other studies. Drove roads may possibly also function as linear structures that facilitate long-distance dispersal across the agricultural matrix, while local P. lagopus populations depend rather on short-distance seed dispersal. These results highlight the role of herbivore corridors for conserving the migration capacity of plants, and contribute towards understanding the role of seed dispersal and the spread of invasive species related to human activities.