Blotched snakehead virus is a new aquatic birnavirus that is slightly more related to avibirnavirus than to aquabirnavirus

By different approaches, we characterized the birnavirus blotched snakehead virus (BSNV). The sequence of genomic segment A revealed the presence of two open reading frames (ORFs): a large ORF with a 3,207-bp-long nucleotide sequence and a 417-nucleotide-long small ORF located within the N-terminal half of the large ORF, but in a different reading frame. The large ORF was found to encode a polyprotein cotranslationally processed by the viral protease VP4 to generate pVP2 (the VP2 precursor), a 71-amino-acid-long peptide ([X]), VP4, and VP3. The two cleavage sites at the [X]-VP4 and VP4-VP3 junctions were identified by N-terminal sequencing. We showed that the processing of pVP2 generated VP2 and several small peptides (amino acids [aa] 418 to 460, 461 to 467, 468 to 474, and 475 to 486). Two of these peptides (aa 418 to 460 and 475 to 486) were positively identified in the viral particles with 10 additional peptides derived from further processing of the peptide aa 418 to 460. The results suggest that VP4 cleaves multiple Pro-X-Ala downward arrow Ala motifs, with the notable exception of the VP4-VP3 junction. Replacement of the members of the predicted VP4 catalytic dyad (Ser-692 and Lys-729) confirmed their indispensability in the polyprotein processing. The genomic segment B sequence revealed a single large ORF encoding a putative polymerase, VP1. Our results demonstrate that BSNV should be considered a new aquatic birnavirus species, slightly more related to IBDV than to IPNV.     

Decadally cycling soil carbon is more sensitive to warming than faster‐cycling soil carbon

The response of soil organic carbon (SOC) pools to globally rising surface temperature crucially determines the feedback between climate change and the global carbon cycle. However, there is a lack of studies investigating the temperature sensitivity of decomposition for decadally cycling SOC which is the main component of total soil carbon stock and the most relevant to global change. We tackled this issue using two decadally ¹³C‐labeled soils and a much improved measuring system in a long‐term incubation experiment. Results indicated that the temperature sensitivity of decomposition for decadally cycling SOC (>23 years in one soil and >55 years in the other soil) was significantly greater than that for faster‐cycling SOC (<23 or 55 years) or for the entire SOC stock. Moreover, decadally cycling SOC contributed substantially (35–59%) to the total CO₂ loss during the 360‐day incubation. Overall, these results indicate that the decomposition of decadally cycling SOC is highly sensitive to temperature change, which will likely make this large SOC stock vulnerable to loss by global warming in the 21st century and beyond.     

Grass competition is more important than fire for suppressing encroachment of Acacia sieberiana seedlings

Plant Ecology - Understanding the factors controlling tree seedling recruitment is an integral research priority for savanna ecosystems, particularly for the management of woody plant encroachment....     

There is more than one way to skin a G matrix

Because of its importance in directing evolutionary trajectories, there has been considerable interest in comparing variation among genetic variance-covariance (G) matrices. Numerous statistical approaches have been suggested but no general analysis of the relationship among these methods has previously been published. In this study, we used data from a half-sib experiment and simulations to explore the results of applying eight tests (T method, modified Mantel test, Bartlett's test, Flury hierarchy, jackknife-manova, jackknife-eigenvalue test, random skewers, selection skewers). Whereas a randomization approach produced acceptable estimates, those from a bootstrap were typically unacceptable and we recommend randomization as the preferred method. All methods except the jackknife-eigenvalue test gave similar results although a fine-scale analysis suggested that the former group can be subdivided into two or possibly three groups, hierarchical tests, skewers and the rest (jackknife-manova, modified Mantel, T method, probably Bartlett's). An advantage of the jackknife methods is that they permit tests of association with other factors, such as in this case, temperature and sex. We recommend applying all the tests described in this article, with the exception of the T method, and provide R functions for this purpose.     

Turbot resistance to Philasterides dicentrarchi is more dependent on humoral than on cellular immune responses

Philasterides dicentrarchi is a ciliate that causes high mortalities in cultured turbot, Psetta maxima (L.). This pathogen displays high phagocytic activity and after entering the body it multiplies and feeds on host cells and tissue components. In previous studies, we found that complement, activated through the classical pathway, is a potent killer of P. dicentrarchi. Here, we compared the killing activity of turbot leucocytes and humoral factors against two virulent isolates of P. dicentrarchi, in order to determine the importance of leucocytes in the defence against this pathogen. Components of P. dicentrarchi (ciliary and membrane) stimulated turbot leucocytes, and increased the respiratory burst, degranulation and the expression of pro-inflammatory cytokines. We tested the susceptibility of ciliates to reactive oxygen and nitrogen species, by incubating them with different oxidative systems (H₂O₂, Fe/ascorbate, which induces lipid peroxidation, an O₂^? donor (XOD/HX), an NO donor (SNAP) and an ONOO^? donor (SIN-1)), for 24 h. Both isolates were susceptible to high concentrations of H₂O_2, Fe/ascorbate, XOD/HX, and SIN-1 but were resistant to incubation with SNAP. Leucocytes became strongly activated when they were in contact with or were phagocytosed by the ciliate. Incubation of P. dicentrarchi with a combination of fresh serum and specific antibodies killed most of the ciliates, but the addition of leucocytes to ciliate cultures did not increase the toxicity to the ciliates. On the contrary, the number of ciliates increased when leucocytes were added to the culture because the ciliates fed on them. Despite being activated, leucocytes did not produce sufficiently high concentrations of toxic substances to kill the parasite. The most virulent isolate was that which induced greatest activation of leucocytes but was least susceptible to complement. We concluded that humoral factors such as complement (activated through the classical pathway) are critical for fish defence against P. dicentrarchi and that cellular responses appear to play a minor role, if any, in defence against this ciliate.     

Blood flow response to muscle contractions is more closely related to metabolic rate than contractile work.

The magnitude of the blood flow response to exercise has been linked to both the contractile work performed and the metabolic cost of the activity. Under certain conditions, contractile work and metabolic cost may be dissociated. This study examined the blood flow response to trains of contractions when contraction duration was manipulated under conditions of similar tension-time indexes (isometric analog of work). Previous investigations have shown that trains of short-duration contractions have a greater ATP utilization, which may result from an augmented ion transport required for muscle activation and relaxation. On the basis of these findings, we hypothesized that the blood flow response would be greater to a train of short-duration contractions than a train of long-duration contractions. Canine gastrocnemius-plantaris muscle (n = 8) was isolated, and blood flow assessed with an ultrasound flow probe placed around the popliteal artery. The sciatic nerve was stimulated to produce two contraction protocols that resulted in similar contraction-to-rest ratios: short duration: 0.25 s/0.75 s vs. long duration: 1 s /3 s. In accord with the design of the experiment, the tension-time indexes were identical for the two contraction protocols (short: 18.6 +/- 1.0 vs. long: 18.6 +/- 1.0 kN.s). Steady-state oxygen consumption was greater in the short-duration contractions (17.2 +/- 0.9 ml.100 g(-1).min(-1)) than in the long-duration contractions (11.7 +/- 0.7 ml.100 g(-1).min(-1)). Similarly, the steady-state blood flow was greater in contractions of short duration (125 +/- 7 ml/min) compared with long-duration contractions (92 +/- 7 ml/min). Contractions of short duration resulted in significantly higher oxygen consumptions and blood flows compared with contractions of long duration despite the same total contractile work. The blood flow response to muscle contraction appears to be more closely associated with muscle metabolism than contractile work performed.     

TcpA from the Clostridium perfringens plasmid pCW3 is more closely related to the DNA translocase FtsK than to coupling proteins

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The mitochondrial genome of the thermal dimorphic fungus Penicillium marneffei is more closely related to those of molds than yeasts

We report the complete sequence of the mitochondrial genome of Penicillium marneffei, the first complete mitochondrial DNA sequence of a thermal dimorphic fungus. This 35 kb mitochondrial genome contains the genes encoding ATP synthase subunits 6, 8, and 9 (atp6, atp8, and atp9), cytochrome oxidase subunits I, II, and III (cox1, cox2, and cox3), apocytochrome b (cob), reduced nicotinamide adenine dinucleotide ubiquinone oxireductase subunits (nad1, nad2, nad3, nad4, nad4L, nad5, and nad6), ribosomal protein of the small ribosomal subunit (rps), 28 tRNAs, and small and large ribosomal RNAs. Analysis of gene contents, gene orders, and gene sequences revealed that the mitochondrial genome of P. marneffei is more closely related to those of molds than yeasts.     

Exogenous phenol increase resistance of Ulmus minor to Dutch elm disease through formation of suberin-like compounds on xylem tissues

The survival of some elms to Dutch elm disease (DED) epidemics could be related with the application of disinfectant products based on simple phenols. To test this hypothesis, the protective effect of different phenolic treatments in Ulmus minor trees was evaluated through inoculations with Ophiostoma novo-ulmi, the current DED pathogen. During spring 2004 and spring 2005, 4-year-old elms were: (i) watered with a 0.02% solution of the phenolic fraction of phenolic oil, (ii) watered with a 0.02 and 0.2% solution of a phenol–cresol mixture, and (iii) trunk injected with a 0.2% solution of phenol–cresol mixture. In May, trees were artificially inoculated with O. novo-ulmi. At the end of the 2004 and 2005 vegetative periods, phenol-treated trees showed significantly lower wilting values than control trees. One week of bud break delay was observed in trees watered with the 0.2% solution of phenol–cresol mixture. Fourier transform-infrared spectroscopy and electrospray ionisation mass spectrometry evidenced enhanced levels of suberin-like compounds in phenol-treated trees with respect to non-treated trees. The deposition of suberin in xylem tissues, as a response to phenol treatments, might be considered as one of the mechanisms of resistance of elms to O. novo-ulmi.     

Is there more than one way to skin a newt? Convergent toxin resistance in snakes is not due to a common genetic mechanism

Convergent evolution of tetrodotoxin (TTX) resistance, at both the phenotypic and genetic levels, characterizes coevolutionary arms races between amphibians and their snake predators around the world, and reveals remarkable predictability in the process of adaptation. Here we examine the repeatability of the evolution of TTX resistance in an undescribed predator–prey relationship between TTX-bearing Eastern Newts (Notophthalmus viridescens) and Eastern Hog-nosed Snakes (Heterodon platirhinos). We found that that local newts contain levels of TTX dangerous enough to dissuade most predators, and that Eastern Hog-nosed Snakes within newt range are highly resistant to TTX. In fact, these populations of Eastern Hog-nosed Snakes are so resistant to TTX that the potential for current reciprocal selection might be limited. Unlike all other cases of TTX resistance in vertebrates, H. platirhinos lacks the adaptive amino acid substitutions in the skeletal muscle sodium channel that reduce TTX binding, suggesting that physiological resistance in Eastern Hog-nosed Snakes is conferred by an alternate genetic mechanism. Thus, phenotypic convergence in this case is not due to parallel molecular evolution, indicating that there may be more than one way for this adaptation to arise, even among closely related species.     

There is more to autophagy than induction: regulating the roller coaster

Considerable attention has been paid to the topic of autophagy induction. In part, this is because of the potential for modulating this process for therapeutic purposes. Of course we know that induced autophagy can also be problematic—for example, when trying to eliminate an established tumor that might be relying on autophagy for its own cytoprotective uses. Accordingly, inhibitory mechanisms have been considered; however, the corresponding studies have tended to focus on the pathways that block autophagy under noninducing conditions, such as when nutrients are available. In contrast, relatively little is known about the mechanisms for inhibiting autophagy under inducing conditions. Yet, this type of regulation must be occurring on a routine basis. We know that dysregulation of autophagy, e.g., due to improper activation of Beclin 1 leading to excessive autophagy activity, can cause cell death.¹ Accordingly, we assume that during starvation or other inducing conditions there must be a mechanism to modulate autophagy. That is, once you turn it on, you do not want to let it continue unchecked. But how is autophagy downregulated when the inducing conditions still exist?Key words: Atg1, autophagosome, flux, lysosome, macroautophagy, phagophore, regulation, stress, TOR, Ulk1, vacuoleOne possibility for downregulating macroautophagy is suggested by Tom Neufeld’s lab, which showed that p70S6 kinase is a positive regulatory factor for autophagy in the Drosophila fat body.² Accordingly, inhibition of TOR activity ultimately results in decreased p70S6K function, which in turn downregulates autophagy. An alternate suggestion from Fred Meijer and Patrice Codogno is that p70S6K acts in part by negatively regulating the class I PtdIns 3-kinase.³ In this scenario, when TOR is inhibited the decrease in p70S6K activity results in the eventual reactivation of the class I PtdIns3K, which then stimulates TOR and downregulates autophagy.Further insight into this question is provided by a relatively recent study from Adi Kimchi’s lab. The conserved protein DAP1 is an mTOR substrate that inhibits macroautophagy. In nutrient-rich conditions, active mTORC1 inhibits DAP1 so that the latter has no effect on autophagy. The inhibition of mTORC1 during nutrient starvation results in the dephosphorylation and activation of DAP1, and the subsequent inhibition of macroautophagy, which limits the magnitude of autophagy-dependent degradation.^4,5Another mechanism of regulation is indicated in studies by Li Yu and colleagues who showed that autophagy is downregulated through mTOR reactivation in an autophagy-dependent manner that requires protein degradation in autolysosomes.⁶ This negative feedback mechanism provides another simple means of self-regulation whereby the nutrient levels within the cell dictate whether autophagy needs to be maintained or shut down. A study described in this issue of the journal provides further support for this mechanism, demonstrating that autophagy can be downregulated during starvation in yeast.⁷ Shin and Huh found that TOR activity is recovered during prolonged starvation, and that this again depends on autophagy (see Fig. 1 in the Autophagic Flux section, p. 803). These studies suggest that autophagy may cycle on and off repeatedly during starvation as nutrient supplies are consumed and then resupplied, ensuring that autophagy is maintained at optimal, and not excessive, levels. The latter mechanism, however, cannot explain how autophagy is regulated during other types of stress, suggesting that multiple control systems are involved.In closing, we introduce a new category of papers and a new section to the journal that we are calling Resource and Autophagic Flux, respectively. Resource papers will provide information that may be useful to the autophagy community, but that may not have specific mechanistic information, such as may occur with large-scale screens. For example, in this issue, see the paper from Marja Jäättelä’s lab that describes the use of a human kinome siRNA library to identify new kinases that regulate macroautophagy. Finally, we have chosen the name Autophagic Flux for the new section because it encompasses the full spectrum of the autophagic process. The schematic summary in Figure 1 of that section highlights the paper by Shin and Huh that we mention here. Our intention is to provide schematic highlights of most of the research papers in the Autophagic Flux section, providing readers with a quick overview and summary of the key point(s) of the study. We hope you find this useful; we welcome feedback.     

Signaling to the ribosome in cancer--It is more than just mTORC1

It is becoming increasingly clear that dysregulation of protein synthesis contributes to a range of diseases characterized by tissue overgrowth. These include arterial stenosis, cardiac hypertrophy, hamartomas, and cancer. The central hub for the regulation of protein synthesis is the ribosome, where the key signaling pathways downstream of RAS, MYC, and phosphatidylinositol-3-kinase (PI3K) converge to confer exquisite, coordinated control of ribosome synthesis and function. Such cooperation ensures strict regulation of protein synthesis rates and cell growth. This review will focus on the role the PI3K/AKT/mammalian target of rapamycin complex 1 (mTORC1) pathway plays in regulating ribosome function during both health and disease, its interaction with the other key growth regulatory pathways activated by RAS and MYC, and the therapeutic potential for targeting this network.     

There is more to life than death: a moonlighting function of a Bcl-2 member

Members of the Bcl-2 family proteins are best known for their roles in apoptosis regulation. In this issue of Developmental Cell, Popgeorgiev et al. (2011) have uncovered a new, nonapoptotic role for a Bcl-2 homolog during early embryogenesis in zebrafish.     

Dissolved carbon leaching from soil is a crucial component of the net ecosystem carbon balance

Estimates of carbon leaching losses from different land use systems are few and their contribution to the net ecosystem carbon balance is uncertain. We investigated leaching of dissolved organic carbon (DOC), dissolved inorganic carbon (DIC), and dissolved methane (CH₄), at forests, grasslands, and croplands across Europe. Biogenic contributions to DIC were estimated by means of its δ¹³C signature. Leaching of biogenic DIC was 8.3±4.9 g m^?2 yr^?1 for forests, 24.1±7.2 g m^?2 yr^?1 for grasslands, and 14.6±4.8 g m^?2 yr^?1 for croplands. DOC leaching equalled 3.5±1.3 g m^?2 yr^?1 for forests, 5.3±2.0 g m^?2 yr^?1 for grasslands, and 4.1±1.3 g m^?2 yr^?1 for croplands. The average flux of total biogenic carbon across land use systems was 19.4±4.0 g C m^?2 yr^?1. Production of DOC in topsoils was positively related to their C/N ratio and DOC retention in subsoils was inversely related to the ratio of organic carbon to iron plus aluminium (hydr)oxides. Partial pressures of CO₂ in soil air and soil pH determined DIC concentrations and fluxes, but soil solutions were often supersaturated with DIC relative to soil air CO₂. Leaching losses of biogenic carbon (DOC plus biogenic DIC) from grasslands equalled 5–98% (median: 22%) of net ecosystem exchange (NEE) plus carbon inputs with fertilization minus carbon removal with harvest. Carbon leaching increased the net losses from cropland soils by 24–105% (median: 25%). For the majority of forest sites, leaching hardly affected actual net ecosystem carbon balances because of the small solubility of CO₂ in acidic forest soil solutions and large NEE. Leaching of CH₄ proved to be insignificant compared with other fluxes of carbon. Overall, our results show that leaching losses are particularly important for the carbon balance of agricultural systems.     

Warmer winters increase the rhizosphere carbon flow to mycorrhizal fungi more than to other microorganisms in a temperate grassland

A decisive set of steps in the terrestrial carbon (C) cycle is the fixation of atmospheric C by plants and the subsequent C‐transfer to rhizosphere microorganisms. With climate change winters are expected to become milder in temperate ecosystems. Although the rate and pathways of rhizosphere C input to soil could be impacted by milder winters, the responses remain unknown. To address this knowledge‐gap, a winter‐warming experiment was established in a seminatural temperate grassland to follow the C flow from atmosphere, via the plants, to different groups of soil microorganisms. In situ ¹³CO₂ pulse labelling was used to track C into signature fatty acids of microorganisms. The winter warming did not result in any changes in biomass of any of the groups of microorganisms. However, the C flow from plants to arbuscular mycorrhizal (AM) fungi, increased substantially by winter warming. Saprotrophic fungi also received large amounts of plant‐derived C—indicating a higher importance for the turnover of rhizosphere C than biomass estimates would suggest—still, this C flow was unaffected by winter warming. AM fungi was the only microbial group positively affected by winter warming—the group with the closest connection to plants. Winter warming resulted in higher plant productivity earlier in the season, and this aboveground change likely induced plant nutrient limitation in warmed plots, thus stimulating the plant dependence on, and C allocation to, belowground nutrient acquisition. The preferential C allocation to AM fungi was at the expense of C flow to other microbial groups, which were unaffected by warming. Our findings imply that warmer winters may shift rhizosphere C‐fluxes to become more AM fungal‐dominated. Surprisingly, the stimulated rhizosphere C flow was matched by increased microbial turnover, leading to no accumulation of soil microbial biomass.     

Rat d-aspartate oxidase is more similar to the human enzyme than the mouse enzyme

d-Aspartate oxidase (DDO) is a degradative enzyme that is stereospecific for the acidic amino acid d-aspartate, an endogenous agonist of the N-methyl-d-aspartate (NMDA) receptor. Dysregulation of NMDA receptor-mediated neurotransmission has been implicated in the onset of various neuropsychiatric disorders including schizophrenia, as well as chronic pain. Thus, appropriate regulation of d-aspartate is believed to be important for maintaining proper neural activity in the nervous system. Accordingly, much attention has been paid to the role(s) of DDO in the metabolism of d-aspartate in vivo, and the physiological functions of DDO have been actively investigated using experimental rats and mice. However, detailed characterisation of rat DDO has not yet been performed, and little is known about species-specific differences in the properties of mammalian DDOs. In this study, the structural and enzymatic properties of purified recombinant rat, mouse and human DDOs were examined and compared. The results showed that rat DDO is more similar to human DDO than to mouse DDO. This work provides useful insight into the use of rats as an experimental model for investigating the biological significance of human DDO and/or d-aspartate.This article is part of a Special Issue entitled: d-Amino acids: biology in the mirror, edited by Dr. Loredano Pollegioni, Dr. Jean-Pierre Mothet and Dr. Molla Gianluca.