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.     

The population of Odonata (dragonflies) in small tropical rivers with reference to asynchronous growth patterns

The odonate larval communities in three small rivers in Penang Island were studied. More species of dragonflies were found in the Botanical Garden and Titi Teras rivers (13 and 11 respectively) of relatively similar environmental parameters. Fewer (nine) dragonfly species were collected from the Youth Park River which has a lower dissolved oxygen (DO) and a higher biological oxygen demand (BOD), conductivity and turbidity. A mixture of sand, gravel and pebble substrate of Botanical Garden River with dense growth of submerged Hydrilla, grasses and Cladias (Araceae) provided suitable habitats for the dragonflies. The sandy substrate and relatively fast flowing water of Titi Teras River was highly preferred by gomphids. In the Youth Park River, the small community of dragonfly larvae was dominated by tolerant Pseudagrion rubriceps, P. microcephalum, Orthetrum chrysis and Crocothemis servilia. Based on the larval instar distribution of Ictinogomphus decoratus and O. chrysis, very asynchronous populations of these dragonflies occurred in each river. Young larvae were continuously introduced into the populations resulting in undulating growth rate curves. The growth rates of these two species were higher in the Titi Teras River when compared to those in other rivers. Density-dependent mortality, asynchronous cannibalism and fish predation could play important roles in regulating the larval dragonfly population in these rivers.     

Donor–Acceptor–Acceptor's Molecules for Vacuum‐Deposited Organic Photovoltaics with Efficiency Exceeding 9%

Three vacuum‐deposited donor–acceptor–acceptor (d–a–a') small molecule donors are studied with different side chains attached to an asymmetric heterotetracene donor block for use in high efficiency organic photovoltaics (OPVs). The donor with an isobutyl side chain yields the highest crystal packing density compared to molecules with 2‐ethylhexyl or n‐butyl chains, leading to the largest absorption coefficient and short circuit current in an OPV. It also exhibits a higher fill factor, consistent with its preferred out‐of‐plane molecular π–π stacking arrangement that facilitates charge transport in the direction perpendicular to the substrate. A power conversion efficiency of 9.3 ± 0.5% is achieved under 1 sun intensity, AM 1.5 G simulated solar illumination, which is significantly higher than 7.5 ± 0.4% of the other two molecules. These results indicate that side chain modification of d–a–a' small molecules offers an effective approach to control the crystal packing configuration, thereby improving the device performance.     

Involvement of ethylene signaling in Azospirillum sp. B510-induced disease resistance in rice

A bacterial endophyte Azospirillum sp. B510 induces systemic disease resistance in the host without accompanying defense-related gene expression. To elucidate molecular mechanism of this induced systemic resistance (ISR), involvement of ethylene (ET) was examined using OsEIN2-knockdown mutant rice. Rice blast inoculation assay and gene expression analysis indicated that ET signaling is required for endophyte-mediated ISR in rice.

Abbreviations: ACC: 1-aminocyclopropane-1-carboxylic acid; EIN2: ethylene-insensitive protein 2; ET: ethylene; ISR: induced systemic resistance; JA: jasmonic acid; RNAi: RNA interference; SA: salicylic acid; SAR: systemic acquired resistance     

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.

     

Baseline sensitivity and control efficacy of fluazinam against Sclerotinia sclerotiorum in Henan Province,China

Sclerotinia stem rot, caused by Sclerotinia sclerotiorum, is a devastating disease in Henan Province, of the main rapeseed production areas in China. Fluazinam belongs to the broad‐spectrum phenylpyridinamine fungicides, which have high activity in inhibiting the mycelial growth of S. sclerotiorum. In this study, 191 field isolates were obtained from different oilseed rape fields in Henan Province, before being exposed to fluazinam in 2015. The baseline sensitivity of S. sclerotiorum to fluazinam was established. The effective concentration for 50% inhibition of mycelial growth (EC₅₀) ranged from 0.0019 to 0.0337 μg/ml, and the mean EC₅₀ value was 0.0084 ± 0.0055 μg/ml. The range of the frequency distribution was narrow. The results of a cross‐resistance assay revealed no cross‐resistance between fluazinam and carbendazim, dimethachlone, boscalid or fludioxonil. Field efficacy tests showed that the control efficacies of fluazinam (50% WG) applied at 150, 225 and 300 g ai ha^?1 were 67%, 73% and 88%, respectively. In contrast, the control efficacies of boscalid (50% WG) and carbendazim (50% WP) applied at 225 and 1,500 g ai ha^?1 were 71% and 52%, respectively.