Pelagic fish and zooplankton species assemblages in relation to water mass characteristics in the northern Bering and southeast Chukchi seas

This research explores the distributions and community composition of pelagic species in the sub-Arctic and Arctic waters of the northern Bering and central and southern Chukchi seas during September 2007 by linking pelagic zooplankton and fish assemblages to water masses. Juvenile saffron cod (Eleginus gracilis), polar cod (Boreogadus saida), and shorthorn sculpin (Myoxocephalus scorpius) were most abundant in warm, low salinity Alaska Coastal Water (ACW) of the central Chukchi Sea, characterized by low chlorophyll, low nutrients, and small zooplankton taxa. Adult Pacific herring (Clupea pallasii) were more abundant in the less stratified Bering Strait waters and in the colder, saltier Bering Shelf Water of the northern Bering and southern Chukchi seas, characterized by high chlorophyll, high nutrients, and larger zooplankton taxa. Juvenile pink (Oncorhynchus gorbuscha) and chum (O. keta) salmon were most abundant in the less stratified ACW in the central Chukchi Sea and Bering Strait. Abundances of large zooplankton were dominated by copepods (Eucalanus bungii, Calanus glacialis/marshallae, Metridia pacifica) followed by euphausiids (juvenile Thysanoessa raschii and unidentified taxa), whereas small zooplankton were dominated by bivalve larvae and copepods (Centropages abdominalis, Oithona similis, Pseudocalanus sp.). Pelagic community composition was related to environmental factors, with highest correlations between bottom salinity and large zooplankton taxa, and latitude and fish species. These data were collected in a year with strong northward retreat of summer sea ice and therefore provide a baseline for assessing the effects of future climate warming on pelagic ecosystems in sub-Arctic and Arctic regions.     

Response of soil microbial activity to grazing, nitrogen deposition, and exotic cover in a serpentine grassland

Background and aims

Exotic species, nitrogen (N) deposition, and grazing are major drivers of change in grasslands. However little is known about the interactive effects of these factors on below-ground microbial communities.

Methods

We simulated realistic N deposition increases with low-level fertilization and manipulated grazing with fencing in a split-plot experiment in California’s largest serpentine grassland. We also monitored grazing intensity using camera traps and measured total available N to assess grazing and nutrient enrichment effects on microbial extracellular enzyme activity (EEA), microbial N mineralization, and respiration rates in soil.

Results

Continuous measures of grazing intensity and N availability showed that increased grazing and N were correlated with increased microbial activity and were stronger predictors than the categorical grazing and fertilization measures. Exotic cover was also generally correlated with increased microbial activity resulting from exotic-driven nutrient cycling alterations. Seasonal effects, on abiotic factors and plant phenology, were also an important factor in EEA with lower activity occurring at peak plant biomass.

Conclusions

In combination with previous studies from this serpentine grassland, our results suggest that grazing intensity and soil N availability may affect the soil microbial community indirectly via effects on exotic cover and associated changes in nutrient cycling while grazing directly impacts soil community function.     

Summer rain pulses may stimulate a CO2 release rather than absorption in desert halophyte communities

Background and aims

The response of plants and soil to rain pulses determines seasonal variations in the exchange of materials and energy at the ecosystem scale in arid and semi-arid regions. We assessed how the ecosystem carbon exchange (NEE) of desert halophyte communities of different plant functional-types responds to summer precipitation pulses in Tamarix and Haloxylon communities.

Methods

Plant water status, photosynthetic gas exchange, soil respiration and net ecosystem carbon exchange were measured to test the hypothesis that high physiological sensitivity may induce a greater changes in NEE resulting from the summer precipitation pulses in Haloxylon community.

Results

Plant water status and photosynthetic assimilation did not differ before and after summer precipitation pulses in either community. In contrast, soil respiration and NEE responded strongly to summer precipitation events in both communities. At the ecosystem level, precipitation pulses induced a pulse of CO₂ release, rather than absorption. The NEE response to summer precipitation was less in the deep-rooted Tamarix community, compared to the shallow-rooted Haloxylon community, which was even converted into a carbon source after summer precipitation inputs. As a result, the effect of summer precipitation inputs on soil respiration was more important than the plant (carbon assimilation) response in determining the ecosystem response to episodic precipitation pulses.     

Strong interactions between stoichiometric constraints and algal defenses: evidence from population dynamics of Daphnia and algae in phosphorus-limited microcosms

The dynamic interactions among nutrients, algae and grazers were tested in a 2 × 3 factorial microcosm experiment that manipulated grazers (Daphnia present or absent) and algal composition (single species cultures and mixtures of an undefended and a digestion-resistant green alga). The experiment was run for 25 days in 10-L carboys under mesotrophic conditions that quickly led to strong phosphorus limitation of algal growth (TP ? 0.5 μM, N:P 40:1). Four-day Daphnia juvenile growth assays tested for Daphnia P-limitation and nutrient-dependent or grazer-induced algal defenses. The maximal algal growth rate of undefended Ankistrodesmus (mean ± SE for three replicate microcosms; 0.92 ± 0.02 day^?1) was higher than for defended Oocystis (0.62 ± 0.03 day^?1), but by day 6, algal growth was strongly P-limited in all six treatments (molar C:P ratio >900). The P-deficient algae were poor quality resources in all three algal treatments. However, Daphnia population growth, reproduction, and survival were much lower in the digestion-resistant treatment even though growth assays provided evidence for Daphnia P-limitation in only the undefended and mixed treatments. Growth assays provided little or no support for simple threshold element ratio (TER) models that fail to consider algae defenses that result in viable gut passage. Our results show that strong P-limitation of algal growth enhances the defenses of a digestion-resistant alga, favoring high abundance of well-defended algae and energy limitation of zooplankton growth.     

Pan-Mammalian Target of Rapamycin (mTOR) Inhibitor AZD8055 Primes Rhabdomyosarcoma Cells for ABT-737-induced Apoptosis by Down-regulating Mcl-1 Protein

The PI3K/mammalian Target of Rapamycin (mTOR) pathway is often aberrantly activated in rhabdomyosarcoma (RMS) and represents a promising therapeutic target. Recent evaluation of AZD8055, an ATP-competitive mTOR inhibitor, by the Preclinical Pediatric Testing Program showed in vivo antitumor activity against childhood solid tumors, including RMS. Therefore, in the present study, we searched for AZD8055-based combination therapies. Here, we identify a new synergistic lethality of AZD8055 together with ABT-737, a BH3 mimetic that antagonizes Bcl-2, Bcl-x_L, and Bcl-w but not Mcl-1. AZD8055 and ABT-737 cooperate to induce apoptosis in alveolar and embryonal RMS cells in a highly synergistic fashion (combination index < 0.2). Synergistic induction of apoptosis by AZD8055 and ABT-737 is confirmed on the molecular level, as AZD8055 and ABT-737 cooperate to trigger loss of mitochondrial membrane potential, activation of caspases, and caspase-dependent apoptosis that is blocked by the pan-caspase inhibitor Z-VAD-fmk. Similar to AZD8055, the PI3K/mTOR inhibitor NVP-BEZ235, the PI3K inhibitor NVP-BKM120 and Akt inhibitor synergize with ABT-737 to trigger apoptosis, whereas no cooperativity is found for the mTOR complex 1 inhibitor RAD001. Interestingly, molecular studies reveal a correlation between the ability of different PI3K/mTOR inhibitors to potentiate ABT-737-induced apoptosis and to suppress Mcl-1 protein levels. Importantly, knockdown of Mcl-1 increases ABT-737-induced apoptosis similar to AZD8055/ABT-737 cotreatment. This indicates that AZD8055-mediated suppression of Mcl-1 protein plays an important role in the synergistic drug interaction. By identifying a novel synergistic interaction of AZD8055 and ABT-737, our findings have important implications for the development of molecular targeted therapies for RMS.     

The Common Ancestor Process Revisited

We consider the Moran model in continuous time with two types, mutation, and selection. We concentrate on the ancestral line and its stationary type distribution. Building on work by Fearnhead (J. Appl. Probab. 39 (2002), 38–54) and Taylor (Electron. J. Probab. 12 (2007), 808–847), we characterise this distribution via the fixation probability of the offspring of all individuals of favourable type (regardless of the offspring’s types). We concentrate on a finite population and stay with the resulting discrete setting all the way through. This way, we extend previous results and gain new insight into the underlying particle picture.     

Imidazo[4,5-b]pyridine inhibitors of B-Raf kinase

This Letter details the synthesis and evaluation of imidazo[4,5-b]pyridines as inhibitors of B-Raf kinase. These compounds bind in a DFG-in, αC-helix out conformation of B-Raf, which is a binding mode associated with significant kinase selectivity. Structure–activity relationship studies involved optimization of the ATP-cleft binding region of these molecules, and led to compound 23, an inhibitor with excellent enzyme/cell potency, and kinase selectivity.     

Using pooled data to estimate variance components and breeding values for traits affected by social interactions

Background

Through social interactions, individuals affect one another’s phenotype. In such cases, an individual’s phenotype is affected by the direct (genetic) effect of the individual itself and the indirect (genetic) effects of the group mates. Using data on individual phenotypes, direct and indirect genetic (co)variances can be estimated. Together, they compose the total genetic variance that determines a population’s potential to respond to selection. However, it can be difficult or expensive to obtain individual phenotypes. Phenotypes on traits such as egg production and feed intake are, therefore, often collected on group level. In this study, we investigated whether direct, indirect and total genetic variances, and breeding values can be estimated from pooled data (pooled by group). In addition, we determined the optimal group composition, i.e. the optimal number of families represented in a group to minimise the standard error of the estimates.

Methods

This study was performed in three steps. First, all research questions were answered by theoretical derivations. Second, a simulation study was conducted to investigate the estimation of variance components and optimal group composition. Third, individual and pooled survival records on 12 944 purebred laying hens were analysed to investigate the estimation of breeding values and response to selection.

Results

Through theoretical derivations and simulations, we showed that the total genetic variance can be estimated from pooled data, but the underlying direct and indirect genetic (co)variances cannot. Moreover, we showed that the most accurate estimates are obtained when group members belong to the same family. Additional theoretical derivations and data analyses on survival records showed that the total genetic variance and breeding values can be estimated from pooled data. Moreover, the correlation between the estimated total breeding values obtained from individual and pooled data was surprisingly close to one. This indicates that, for survival in purebred laying hens, loss in response to selection will be small when using pooled instead of individual data.

Conclusions

Using pooled data, the total genetic variance and breeding values can be estimated, but the underlying genetic components cannot. The most accurate estimates are obtained when group members belong to the same family.     

Structure of a translocation signal domain mediating conjugative transfer by type IV secretion systems

Relaxases are proteins responsible for the transfer of plasmid and chromosomal DNA from one bacterium to another during conjugation. They covalently react with a specific phosphodiester bond within DNA origin of transfer sequences, forming a nucleo‐protein complex which is subsequently recruited for transport by a plasmid‐encoded type IV secretion system. In previous work we identified the targeting translocation signals presented by the conjugative relaxase TraI of plasmid R1. Here we report the structure of TraI translocation signal TSA. In contrast to known translocation signals we show that TSA is an independent folding unit and thus forms a bona fide structural domain. This domain can be further divided into three subdomains with striking structural homology with helicase subdomains of the SF1B family. We also show that TSA is part of a larger vestigial helicase domain which has lost its helicase activity but not its single‐stranded DNA binding capability. Finally, we further delineate the binding site responsible for translocation activity of TSA by targeting single residues for mutations. Overall, this study provides the first evidence that translocation signals can be part of larger structural scaffolds, overlapping with translocation‐independent activities.