Identification of novel soybean microRNAs involved in abiotic and biotic stresses

<p>Abstract</p> <p>Background</p> <p>Small RNAs (19-24 nt) are key regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in eukaryotes. Current studies have demonstrated that microRNAs (miRNAs) act in several plant pathways associated with tissue proliferation, differentiation, and development and in response to abiotic and biotic stresses. In order to identify new miRNAs in soybean and to verify those that are possibly water deficit and rust-stress regulated, eight libraries of small RNAs were constructed and submitted to Solexa sequencing.</p> <p>Results</p> <p>The libraries were developed from drought-sensitive and tolerant seedlings and rust-susceptible and resistant soybeans with or without stressors. Sequencing the library and subsequent analyses detected 256 miRNAs. From this total, we identified 24 families of novel miRNAs that had not been reported before, six families of conserved miRNAs that exist in other plants species, and 22 families previously reported in soybean. We also observed the presence of several isomiRNAs during our analyses. To validate novel miRNAs, we performed RT-qPCR across the eight different libraries. Among the 11 miRNAs analyzed, all showed different expression profiles during biotic and abiotic stresses to soybean. The majority of miRNAs were up-regulated during water deficit stress in the sensitive plants. However, for the tolerant genotype, most of the miRNAs were down regulated. The pattern of miRNAs expression was also different for the distinct genotypes submitted to the pathogen stress. Most miRNAs were down regulated during the fungus infection in the susceptible genotype; however, in the resistant genotype, most miRNAs did not vary during rust attack. A prediction of the putative targets was carried out for conserved and novel miRNAs families.</p> <p>Conclusions</p> <p>Validation of our results with quantitative RT-qPCR revealed that Solexa sequencing is a powerful tool for miRNA discovery. The identification of differentially expressed plant miRNAs provides molecular evidence for the possible involvement of miRNAs in the process of water deficit- and rust-stress responses.</p

On the nature of the prototype LBV AG Carinae I. Fundamental parameters during visual minimum phases and changes in the bolometric luminosity during the S-Dor cycle

We present a detailed spectroscopic analysis of the luminous blue variable AG Carinae during the last two visual minimum phases of its S-Dor cycle (1985-1990 and 2000-2003). The analysis reveals an overabundance of He, N, and Na, and a depletion of H, C, and O, on the surface of AG Car, indicating the presence of CNO-processed material. Furthermore, the ratio N/O is higher on the stellar surface than in the nebula. We found that the minimum phases of AG Car are not equal to each other, since we derived a noticeable difference between the maximum effective temperature achieved during 1985-1990 (22,800 K) and 2000-2001 (17,000 K). While the wind terminal velocity was 300 km/s in 1985-1990, it was as low as 105 km/s in 2001. The mass-loss rate, however, was lower from 1985-1990 (1.5 x 10^(-5) Msun/yr) than from 2000-2001 (3.7 x 10^(-5) Msun/yr). We found that the wind of AG Car is significantly clumped (f=0.10 - 0.25) and that clumps must be formed deep in the wind. We derived a bolometric luminosity of 1.5 x 10^6 Lsun during both minimum phases which, contrary to the common assumption, decreases to 1.0 x 10^6 Lsun as the star moves towards maximum flux in the V band. Assuming that the decrease in the bolometric luminosity of AG Car is due to the energy used to expand the outer layers of the star (Lamers 1995), we found that the expanding layers contain roughly 0.6 - 2 Msun. Such an amount of mass is an order of magnitude lower than the nebular mass around AG Car, but is comparable to the nebular mass found around lower-luminosity LBVs and to that of the Little Homunculus of Eta Car. If such a large amount of mass is indeed involved in the S Dor-type variability, we speculate that such instability could be a failed Giant Eruption, with several solar masses never becoming unbound from the star.(abridged)Comment: 22 pages, 13 figures, ApJ in press. A high-resolution PDF version is also available at http://www.mpifr-bonn.mpg.de/staff/jgroh/agcar.htm

Transcriptional and genomic parallels between the monoxenous parasite Herpetomonas muscarum and Leishmania

Trypanosomatid parasites are causative agents of important human and animal diseases such as sleeping sickness and leishmaniasis. Most trypanosomatids are transmitted to their mammalian hosts by insects, often belonging to Diptera (or true flies). These are called dixenous trypanosomatids since they infect two different hosts, in contrast to those that infect just insects (monoxenous). However, it is still unclear whether dixenous and monoxenous trypanosomatids interact similarly with their insect host, as fly-monoxenous trypanosomatid interaction systems are rarely reported and under-studied–despite being common in nature. Here we present the genome of monoxenous trypanosomatid Herpetomonas muscarum and discuss its transcriptome during in vitro culture and during infection of its natural insect host Drosophila melanogaster. The H. muscarum genome is broadly syntenic with that of human parasite Leishmania major. We also found strong similarities between the H. muscarum transcriptome during fruit fly infection, and those of Leishmania during sand fly infections. Overall this suggests Drosophila-Herpetomonas is a suitable model for less accessible insect-trypanosomatid host-parasite systems such as sand fly-Leishmania

Genome of the Avirulent Human-Infective Trypanosome—Trypanosoma rangeli

Background: Trypanosoma rangeli is a hemoflagellate protozoan parasite infecting humans and other wild and domestic mammals across Central and South America. It does not cause human disease, but it can be mistaken for the etiologic agent of Chagas disease, Trypanosoma cruzi. We have sequenced the T. rangeli genome to provide new tools for elucidating the distinct and intriguing biology of this species and the key pathways related to interaction with its arthropod and mammalian hosts.  Methodology/Principal Findings: The T. rangeli haploid genome is ,24 Mb in length, and is the smallest and least repetitive trypanosomatid genome sequenced thus far. This parasite genome has shorter subtelomeric sequences compared to those of T. cruzi and T. brucei; displays intraspecific karyotype variability and lacks minichromosomes. Of the predicted 7,613 protein coding sequences, functional annotations could be determined for 2,415, while 5,043 are hypothetical proteins, some with evidence of protein expression. 7,101 genes (93%) are shared with other trypanosomatids that infect humans. An ortholog of the dcl2 gene involved in the T. brucei RNAi pathway was found in T. rangeli, but the RNAi machinery is non-functional since the other genes in this pathway are pseudogenized. T. rangeli is highly susceptible to oxidative stress, a phenotype that may be explained by a smaller number of anti-oxidant defense enzymes and heatshock proteins.  Conclusions/Significance: Phylogenetic comparison of nuclear and mitochondrial genes indicates that T. rangeli and T. cruzi are equidistant from T. brucei. In addition to revealing new aspects of trypanosome co-evolution within the vertebrate and invertebrate hosts, comparative genomic analysis with pathogenic trypanosomatids provides valuable new information that can be further explored with the aim of developing better diagnostic tools and/or therapeutic targets

CUBES: a UV spectrograph for the future

In spite of the advent of extremely large telescopes in the UV/optical/NIR range, the current generation of 8-10m facilities is likely to remain competitive at ground-UV wavelengths for the foreseeable future. The Cassegrain U-Band Efficient Spectrograph (CUBES) has been designed to provide high-efficiency (>40%) observations in the near UV (305-400 nm requirement, 300-420 nm goal) at a spectral resolving power of R>20,000, although a lower-resolution, sky-limited mode of R ~ 7,000 is also planned. CUBES will offer new possibilities in many fields of astrophysics, providing access to key lines of stellar spectra: a tremendous diversity of iron-peak and heavy elements, lighter elements (in particular Beryllium) and light-element molecules (CO, CN, OH), as well as Balmer lines and the Balmer jump (particularly important for young stellar objects). The UV range is also critical in extragalactic studies: the circumgalactic medium of distant galaxies, the contribution of different types of sources to the cosmic UV background, the measurement of H2 and primordial Deuterium in a regime of relatively transparent intergalactic medium, and follow-up of explosive transients. The CUBES project completed a Phase A conceptual design in June 2021 and has now entered the Phase B dedicated to detailed design and construction. First science operations are planned for 2028. In this paper, we briefly describe the CUBES project development and goals, the main science cases, the instrument design and the project organization and management