From RNA-seq reads to differential expression results

Many methods and tools are available for preprocessing high-throughput RNA sequencing data and detecting differential expression.     

Restricted feeding improves postischemic recovery of Langendorff-perfused rat hearts

The goal of the present study was to assess the effects of a restricted feeding schedule (RFS) on postischemic contractile recovery in relation to triacylglycerol (TAG), glycogen, and ATP content. Glucose-6-phosphate dehydrogenase (G6PDH) activity, reduced/oxidized glutathione ratio (GSH/GSSG), and thiobarbituric acid reactive substances (TBARS) levels were also determined. Isolated rat hearts entrained to daily RFS (2 h food access starting at 1200) or fed ad libitum (FED) for 3 weeks were Langendorff-perfused (25 min ischemia, 30 min reperfusion) with Krebs-Ringer bicarbonate solution (10?mmol/L glucose). RFS improved the recovery of contractility and reduced creatine kinase (CK) release upon reperfusion. Further, at the end of reperfusion, RFS hearts exhibited increased G6PDH activity and repletion of tissue glycogen, TAG, and ATP that was not observed in the FED hearts. GSH/GSSG at the end of reperfusion fell to the same value in both nutritional states, and TBARS levels were higher in the RFS hearts. In conclusion, RFS improved postischemic functional recovery, which was accompanied by a reduction in CK release and a striking energy recovery. Although enhanced G6PDH activity was displayed, RFS was unable to reduce lipid peroxidation, supporting a clear dissociation between protection against mechanical dysfunction and CK release on the one hand and oxidative damage on the other.     

Direct and plant trait‐mediated effects of the local environmental context on butterfly oviposition patterns

Variation in the intensity of plant–animal interactions over different spatial scales is widespread and might strongly influence fitness and trait selection in plants. Differences in traits among plant individuals have been shown to influence variation in interaction intensities within populations, while differences in environmental factors and community composition are shown to be important for variation over larger scales. However, little is still known about the relative importance of the local environmental context vs. plant traits for the outcome of interactions within plant populations. We investigated how oviposition by the seed‐predator butterfly Phengaris alcon on its host plant Gentiana pneumonanthe was related to host plant traits and to local environmental variation, as well as how oviposition patterns translated into effects on host plant fruit set. We considered the local environmental context in terms of height of the surrounding vegetation and abundance of the butterfly's second host, Myrmica ants. The probability of oviposition was higher in plants that were surrounded by lower vegetation, and both the probability of oviposition and the number of eggs increased in early‐flowering and tall plants with many flowers in the three study populations. Flowering phenology, shoot height and flower production were, in turn, related to higher surrounding vegetation. Myrmica abundance was correlated with vegetation height, but had no effect on oviposition patterns. Oviposition and subsequent seed predation by the caterpillars strongly reduced host plant fruit set. Our results show that plant–animal interactions are context‐dependent not only because the context influences the abundance or the behavior of the animal interactor, but also because it influences the expression of plant traits that affect the outcome of the interaction. The results also demonstrate that heterogeneity in environmental conditions at a very local scale can be important for the outcomes of interactions.     

Native woody vegetation in central Argentina: Classification of Chaco and Espinal forests

Question

What are the composition and spatial patterns of native woody plant communities in the southern Great Chaco and Espinal?

Location

Córdoba Province, central Argentina, an area of ca. 161,000 km².

Methods

We collected 351 geo‐referenced relevés representative of the geographic, topographic and ecological variation of the Chaco and Espinal woody vegetation in central Argentina. The relevés were classified into vegetation types using the hierarchical ISOPAM method. Forest and shrubland types were described on the basis of diagnostic species occurrences and their distribution in relation to environmental factors. A map of the actual vegetation derived from remote‐sensed images (Landsat) and field data was used to describe the current distribution and abundance of the different vegetation types.

Results

The classification of the 351 plots × 837 species matrix revealed two major clusters comprising seven woody vegetation types corresponding to Chaco lowland and mountain forests and shrublands, Espinal forests and edaphic vegetation. The most important gradients in woody vegetation types are related to elevation, temperature and rainfall variables.

Conclusions

Subtropical seasonally dry woody plant communities from the southern extreme of the Great Chaco and Espinal forests were described for the first time based on complete floristic data. Our results show that lowland Chaco native forests, as well as replacement communities, are still present in its southern distribution range and are well distinguishable from other vegetation types such as the Espinal and mountain forests. Overall, extensive Espinal forests have almost disappeared while Chaco vegetation is highly fragmented and degraded.

     

Protein complexes associated with β-catenin differentially influence the differentiation profile of neonatal and adult CD8+ T cells

The canonical Wnt signaling pathway is a master cell regulator involved in CD8⁺ T cell proliferation and differentiation. In human CD8⁺ T cells, this pathway induces differentiation into memory cells or a “stem cell memory like” population, which is preferentially present in cord blood. To better understand the role of canonical Wnt signals in neonatal or adult blood, we compared the proteins associated with β-catenin, in nonstimulated and Wnt3a-stimulated human neonatal and adult naive CD8⁺ T cells. Differentially recruited proteins established different complexes in adult and neonatal cells. In the former, β-catenin-associated proteins were linked to cell signaling and immunological functions, whereas those of neonates were linked to proliferation and metabolism. Wnt3a stimulation led to the recruitment and overexpression of Wnt11 in adult cells and Wnt5a in neonatal cells, suggesting a differential connexion with planar polarity and Wnt/Ca²⁺ noncanonical pathways, respectively. The chromatin immunoprecipitation polymerase chain reaction β-catenin was recruited to a higher level on the promoters of cell renewal genes in neonatal cells and of differentiation genes in those of adults. We found a preferential association of β-catenin with CBP in neonatal cells and with p300 in the adult samples, which could be involved in a higher self-renewal capacity of the neonatal cells and memory commitment in those of adults. Altogether, our results show that different proteins associated with β-catenin during Wnt3a activation mediate a differential response of neonatal and adult human CD8⁺ T cells.     

The Influence of Chemical Stimuli from Predators on Precopulatory Pairing by the Amphipod,Gammarus pseudolimnaeus

Many amphipod crustaceans exhibit precopulatory mate guarding. Field samples of the amphipod Gammarus pseudolimnaeus indicated that pairs were positively size assortative. Receptive individuals readily formed pairs in the laboratory and the latency to formation of precopulatory pairs was decreased under threat of predation. In addition, females and, under conditions of extreme danger, males that formed pairs were significantly smaller when under the threat of predation. Amphipods distinguished between chemical stimuli (aquarium water) from predatory and nonpredatory fishes and between chemical cues from fish predators (trout) that had recently eaten conspecific amphipods vs. those fed a control diet of pelleted commercial fish food. These data indicate that chemical stimuli associated with predators can influence reproductive behavior of amphipods. The results also suggest the hypotheses that: 1. search time may be costly in terms of probability of predation; and 2. small pairs may be safer from predation than larger pairs.     

Macrophage-specific responses to human- and animal-adapted tubercle bacilli reveal pathogen and host factors driving multinucleated cell formation

The Mycobacterium tuberculosis complex (MTBC) is a group of related pathogens that cause tuberculosis (TB) in mammals. MTBC species are distinguished by their ability to sustain in distinct host populations. While Mycobacterium bovis (Mbv) sustains transmission cycles in cattle and wild animals and causes zoonotic TB, M. tuberculosis (Mtb) affects human populations and seldom causes disease in cattle. The host and pathogen determinants underlying host tropism between MTBC species are still unknown. Macrophages are the main host cell that encounters mycobacteria upon initial infection, and we hypothesised that early interactions between the macrophage and mycobacteria influence species-specific disease outcome. To identify factors that contribute to host tropism, we analysed blood-derived primary human and bovine macrophages (hMϕ or bMϕ, respectively) infected with Mbv and Mtb. We show that Mbv and Mtb reside in different cellular compartments and differentially replicate in hMϕ whereas both Mbv and Mtb efficiently replicate in bMϕ. Specifically, we show that out of the four infection combinations, only the infection of bMϕ with Mbv promoted the formation of multinucleated giant cells (MNGCs), a hallmark of tuberculous granulomas. Mechanistically, we demonstrate that both MPB70 from Mbv and extracellular vesicles released by Mbv-infected bMϕ promote macrophage multinucleation. Importantly, we extended our in vitro studies to show that granulomas from Mbv-infected but not Mtb-infected cattle contained higher numbers of MNGCs. Our findings implicate MNGC formation in the contrasting pathology between Mtb and Mbv for the bovine host and identify MPB70 from Mbv and extracellular vesicles from bMϕ as mediators of this process.     

Two new species of <Emphasis Type="Italic">Parspina</Emphasis> Pearse, 1920 (Digenea: Cryptogonimidae) from freshwater fishes (Gymnotiformes) of the Paraná River basin in Argentina

Two new species of the cryptogonimid genus Parspina Pearse, 1920 are described from gymnotiform fishes of the Paraná River basin, P. carapo n. sp. from the banded knifefish Gymnotus carapo Linnaeus and P. virescens n. sp. from the glass knifefish Eigenmannia virescens (Valenciennes). Parspina carapo differs from P. virescens in the number of oral spines (32–39 vs 30–33) and their length (28–47 vs 16–28 μm), the distribution of tegumental spines and their anchorage, the types of sensory papillae on the body surface (three vs two types), the extent of body length posterior to the caeca (5 vs 13% of the total body length), the dimensions of the pars prostatica (52 × 34 vs 24 × 10 μm), and in the absence of a gonotyl (vs presence). Both P. carapo and P. virescens differ from P. bagre Pearse, 1920 and P. argentinensis (Szidat, 1954) in the number of oral spines (20–21 and 21–28 in the latter pair) and their length (28–32 and 35–60 μm), and in total body length. Additionally, the two new species differ from P. argentinensis in the arrangement of the vitelline follicles (one continuous band vs two groups on each side of the body) and in having a smaller pars prostatica (149 × 49 μm in the latter). Parspina carapo is the fifth intestinal helminth found in G. carapo, and P. virescens is the first found in E. virescens.