The small-subunit ribosomal RNA gene sequences from the hypotrichous ciliates Oxytricha nova and Stylonychia pustulata

We have determined the complete nucleotide sequence of the small- subunit ribosomal RNA genes for the ciliate protozoans Stylonychia pustulata and Oxytricha nova. The sequences are homologous and sufficiently similar that these organisms must be closely related. In a phylogeny inferred from comparisons of several eukaryotic small-subunit ribosomal RNAs, the divergence of the ciliates from the eukaryotic line of descent is seen to coincide with the radiation of the plants, the animals, and the fungi. This radiation is preceded by the divergence of the slime mold, Dictyostelium discoideum.      

Assessment of two CRISPR-Cas9 genome editing protocols for rapid generation of Trypanosoma cruzi gene knockout mutants

CRISPR/Cas9 technology has been used to edit genomes in a variety of organisms. Using the GP72 gene as a target sequence, we tested two distinct approaches to generate Trypanosoma cruzi knockout mutants using the Cas9 nuclease and in vitro transcribed single guide RNA. Highly efficient rates of disruption of GP72 were achieved either by transfecting parasites stably expressing Streptococcus pyogenes Cas9 with single guide RNA or by transfecting wild type parasites with recombinant Staphylococcus aureus Cas9 previously associated with single guide RNA. In both protocols, we used single-stranded oligonucleotides as a repair template for homologous recombination and insertion of stop codons in the target gene.     

Seasonal flooding,topography, and organic debris interact to influence the emergence and distribution of seedlings in a tropical grassland

In seasonally flooded wetlands, inundation and associated organic debris deposition followed by a drawdown period can promote plant community diversity across space and time. Post‐flood regeneration might be influenced by the direct effect of flooding on seed dispersal and seedling emergence, as well as the indirect effect of organic debris on seed trapping and germination. Our objective was to examine the influence of seasonal flooding, topography, and organic debris cover on seedling distribution in a seasonally flooded grassland. We measured species richness, seedling abundance, and organic debris cover for 3 yr in a seasonally flooded grassland in the Pantanal, Brazil, at three topographic levels at the end of the flood season and during the dry season when there was no debris deposition. A total of 43 species were recorded, with no difference in species richness detected between seasons. However, the abundance of some species was higher post‐flood than during the dry period. The greatest seedling abundance and richness were found post‐flood at intermediate elevations, followed by high and the lowest elevations. Seed germination and seedling establishment were likely suppressed at low topographic positions due to shading from organic debris and poor drainage. Therefore, areas with predictable annual floods promote diversity by creating spatial and temporal variations in environmental conditions.     

Effects of Host Interspecific Interaction in the <Emphasis Type="Italic">Maculinea</Emphasis>–<Emphasis Type="Italic">Myrmica</Emphasis> Parasite–Host System

A model of interspecific host competition in a system with one parasite (butterfly—Maculinea) and multiple potential hosts (ants—Myrmica) is presented. Results indicate that host interspecific competition increases the occurrence of multiple host behaviour in Maculinea natural populations but decreases the ability of the parasite populations to adapt to the most abundant host species. These qualitative predictions were compared with data on host specificity, with good agreement. Analysis of the data also indicates that Maculinea teleius and Maculinea arion respond differently to changes in relative host abundances. Maculinea teleius shows a larger fraction of sites where it displays multiple host behaviour and a larger fraction of sites where the niches of the hosts overlap. In some instances, Maculinea teleius is adapted to Myrmica hosts that are present in lower frequencies. Maculinea arion is locally more host-specific and occurs at sites where host interspecific competition is unlikely and is more frequently adapted to the most abundant host species.     

Sugarcane Bagasse Hydrothermal Pretreatment Liquors as Suitable Carbon Sources for Hemicellulase Production by <Emphasis Type="Italic">Aspergillus niger</Emphasis>

The aim of this study was to valorize the hemicellulose-rich liquid fraction (liquor) arising from hydrothermal pretreatment of sugarcane bagasse (SCB) through its utilization as an unconventional, soluble carbon source for the production of hemicellulases, namely xylanases and α-L-arabinofuranosidases (ABFases), by Aspergillus niger DCFS11. Through the use of factorial design, pretreatment conditions producing liquors optimized for either early- or late-phase enzyme production were identified. Subsequent deep characterization of liquor components using liquid chromatography and mass spectrometry was performed to identify compounds likely responsible for hemicellulase induction. SCB liquors arising from various pretreatment configurations induced up to 2- and 8.6-fold higher xylanase and ABFase production, respectively, by A. niger DCFS11 than raw SCB substrate owing to the strong inducing potential of arabinosylated xylooligosaccharides and free arabinose solubilized during pretreatment. Notably, unlike the severe pretreatment conditions required for maximum cellulose saccharification and ethanol yields during biomass conversion, low severity and low biomass loading are required if enzyme production from liquor is desired at early-phase growth with no additional detoxification steps. This suggests that for effective application in biorefineries, separate or multi-step processes would be required to optimize both hemicellulase production by A. niger DCFS11 and cellulose digestion. This work demonstrates the potential of hydrothermal pretreatment of lignocellulosic substrates as a tool to increase the production of enzymes by filamentous fungi.     

Relationships among msx gene structure and function in zebrafish and other vertebrates

The zebrafish genome contains at least five msx homeobox genes, msxA, msxB, msxC, msxD, and the newly isolated msxE. Although these genes share structural features common to all Msx genes, phylogenetic analyses of protein sequences indicate that the msx genes from zebrafish are not orthologous to the Msx1 and Msx2 genes of mammals, birds, and amphibians. The zebrafish msxB and msxC are more closely related to each other and to the mouse Msx3. Similarly, although the combinatorial expression of the zebrafish msx genes in the embryonic dorsal neuroectoderm, visceral arches, fins, and sensory organs suggests functional similarities with the Msx genes of other vertebrates, differences in the expression patterns preclude precise assignment of orthological relationships. Distinct duplication events may have given rise to the msx genes of modern fish and other vertebrate lineages whereas many aspects of msx gene functions during embryonic development have been preserved.      

Morphological and dietary responses of chipmunks to a century of climate change

Predicting how individual taxa will respond to climatic change is challenging, in part because the impacts of environmental conditions can vary markedly, even among closely related species. Studies of chipmunks (Tamias spp.) in Yosemite National Park provide an important opportunity to explore the reasons for this variation in response. While the alpine chipmunk (T. alpinus) has undergone a significant elevational range contraction over the past century, the congeneric and partially sympatric lodgepole chipmunk (T. speciosus) has not experienced an elevational range shift during this period. As a first step toward identifying the factors underlying this difference in response, we examined evidence for dietary changes and changes in cranial morphology in these species over the past century. Stable isotope analyses of fur samples from modern and historical museum specimens of these species collected at the same localities indicated that signatures of dietary change were more pronounced in T. alpinus, although diet breadth did not differ consistently between the study species. Morphometric analyses of crania from these specimens revealed significant changes in cranial shape for T. alpinus, with less pronounced changes in shape for T. speciosus; evidence of selection on skull morphology was detected for T. alpinus, but not for T. speciosus. These results are consistent with growing evidence that T. alpinus is generally more responsive to environmental change than T. speciosus, but emphasize the complex and often geographically variable nature of such responses. Accordingly, future studies that make use of the taxonomically and spatially integrative approach employed here may prove particularly informative regarding relationships between environmental conditions, range changes, and patterns of phenotypic variation.     

Land use change emission scenarios: anticipating a forest transition process in the Brazilian Amazon

Following an intense occupation process that was initiated in the 1960s, deforestation rates in the Brazilian Amazon have decreased significantly since 2004, stabilizing around 6000 km² yr^?1 in the last 5 years. A convergence of conditions contributed to this, including the creation of protected areas, the use of effective monitoring systems, and credit restriction mechanisms. Nevertheless, other threats remain, including the rapidly expanding global markets for agricultural commodities, large‐scale transportation and energy infrastructure projects, and weak institutions. We propose three updated qualitative and quantitative land‐use scenarios for the Brazilian Amazon, including a normative ‘Sustainability’ scenario in which we envision major socio‐economic, institutional, and environmental achievements in the region. We developed an innovative spatially explicit modelling approach capable of representing alternative pathways of the clear‐cut deforestation, secondary vegetation dynamics, and the old‐growth forest degradation. We use the computational models to estimate net deforestation‐driven carbon emissions for the different scenarios. The region would become a sink of carbon after 2020 in a scenario of residual deforestation (~1000 km² yr^?1) and a change in the current dynamics of the secondary vegetation – in a forest transition scenario. However, our results also show that the continuation of the current situation of relatively low deforestation rates and short life cycle of the secondary vegetation would maintain the region as a source of CO₂ – even if a large portion of the deforested area is covered by secondary vegetation. In relation to the old‐growth forest degradation process, we estimated average gross emission corresponding to 47% of the clear‐cut deforestation from 2007 to 2013 (using the DEGRAD system data), although the aggregate effects of the postdisturbance regeneration can partially offset these emissions. Both processes (secondary vegetation and forest degradation) need to be better understood as they potentially will play a decisive role in the future regional carbon balance.