Climate change affects soil labile organic carbon fractions in a Tibetan alpine meadow

Purpose

Changes in bioactive soil C pools and their temperature sensitivities will dominate the fate of soil organic C in a warmer future, which is not well understood in highland ecosystems. This study was conducted in order to evaluate climate change, especially cooling effects, on soil labile organic C (LOC) pools in a Tibetan alpine meadow.

Materials and methods

A short-term reciprocal translocation experiment was implemented to stimulate climate warming (downward translocation) and cooling (upward translocation) using an elevation gradient on the Tibetan Plateau. Variations in soil microbial biomass C (MBC), dissolved organic C (DOC) and LOC were analyzed.

Results and discussion

Over the range of soil temperature from 0.02 to 5.5 °C, warming averagely increased soil MBC, DOC and LOC by 15.3, 17.0 and 3.7 % while cooling decreased them by 11.0, 11.9 and 3.2 %, respectively. Moreover, warming generally increased the proportion of DOC in LOC but cooling had an opposite effect, while the response of the MBC proportion to DOC and LOC varied depending on vegetation type. Soil MBC, DOC and LOC pools were positively related to soil temperature and showed a hump-shaped relationship with soil moisture with a threshold of about 30–35 %. Although soil DOC was more sensitive to warming (5.1 % °C^?1) than to cooling (3.0 % °C^?1), soil LOC showed a symmetrical response due to regulation by soil moisture.

Conclusions

Our results indicated that climate change would not only change the size of soil LOC pools but also their quality. Therefore, cooling effects and regulation of soil moisture should be considered to evaluate the fate of soil organic C in Tibetan alpine meadows in a warmer future.

     

Treatment additives reduced arsenic and cadmium bioavailability and increased 1,2-dichloroethane biodegradation and microbial enzyme activities in co-contaminated soil

Purpose

Bioremediation of co-contaminated environments is difficult because of the mixed nature of the contaminants and the fact that the two components often must be treated differently. This study investigated the use of inorganic treatment additives, namely calcium carbonate (CaCO₃), gypsum (CaSO₄·2H₂O), and disodium phosphate (Na₂HPO₄) to improve remediation of soil co-contaminated with 1,2-dichloroethane (1,2-DCA) and arsenic or cadmium.

Materials and methods

The soil samples were collected from a specific site in the Westville area in Durban, KwaZulu-Natal, South Africa. Microcosms were set up by artificially co-contaminating the soil sample (100 g mixed with 75 ml of synthetic groundwater in sterile screw-capped 250-ml serum bottles) with 1,2-DCA + risk elements; As³⁺ (150 mg/kg); or Cd²⁺ (170 mg/kg). Thereafter, each microcosm was amended with either 5 g CaCO₃, 2 g CaSO₄·2H₂O, or 1.12 g Na₂HPO₄ + 0.046 g NaCl, separately. The samples were analyzed for the degradation of 1,2-DCA using GC–MS, while total 1,2-DCA degrading bacterial populations were determined at different sampling times using a standard spread plate technique. Soil dehydrogenase and urease activities were also monitored during the experimental period using standard enzyme assays.

Results and discussion

Addition of CaCO₃ resulted in an approximately 2-fold increase in 1,2-DCA degradation in both the As³⁺ and the Cd²⁺ co-contaminated soil as compared to the co-contaminated soil without CaCO₃. All the treatment additives were more effective in the As³⁺ co-contaminated soil resulting in 11.19, 9.25, and 5.63% increase in 1,2-DCA degradation in the presence of CaCO₃, Na₂HPO₄ + NaCl, and CaSO₄·2H₂O, respectively, compared to the Cd²⁺ co-contaminated soil. The total 1,2-DCA degrading bacterial population increased in treated soils over time. Overall, soil dehydrogenase and urease activities were lower in the heavy metal co-contaminated samples compared to the treated soil. The inhibitory effect of heavy metal was less in As³⁺ co-contaminated soil for both CaCO₃- and Na₂HPO₄ + NaCl-treated soil, with up to 7.92% increase in dehydrogenase activity obtained compared to soil co-contaminated with Cd²⁺.

Conclusions

Results from this study indicate that treatment additives can be used to reduce bioavailable fractions of risk elements in the soil matrices, thereby limiting the toxicity of these risk elements to 1,2-DCA degrading microorganisms. Thus, this approach can be applied to enhance organic compound degradation in co-contaminated soil environments.

     

Identification and characterization of EST-SSRs in finger millet (<Emphasis Type="Italic">Eleusine coracana</Emphasis> (L.) Gaertn.)

In recent years, microsatellites have become the most used markers for studying population genetic diversity. The increased availability of the DNA sequences has given the possibility to develop EST-derived SSR markers. A total of 1,927 ESTs of Eleusine coracana available in the NCBI database were mined for SSRs. Di-nucleotides are the most occurring motifs accounting for more than 50% of the repeats, of which GA was the most abundant motif and tetra-nucleotides are the least occurring motifs. Of the 132 markers identified, 30 primer pairs based were synthesized. SSR markers were used for variety discrimination and genetic assessment in 15 finger millet accessions; 20 primers showed polymorphism and 13 primers were identified as having a PIC value above 0.5. On the basis of the distribution of these polymorphic alleles, the 15 accessions were classified into two groups. This study has demonstrated the potential of EST-derived SSR primer pairs in finger millet. These primers will serve as valuable source for further breeding programs.     

Phenotypic segregation and relationships of agronomic traits in Monastrell × Syrah wine grape progeny

The aim of this work was to study the phenotypic segregation of different agronomic and fruit quality traits, and their relationships, in Monastrell × Syrah wine grape progeny. Twenty-two agronomic traits were evaluated and compared for three consecutive years in this progeny. The results show the phenotypic diversity existing in a cross between two different wine grape cultivars. Most of the phenological, productive, morphological, and enological parameters evaluated displayed continuous variation within the progeny, suggesting a polygenic inheritance. Some correlations between traits were detected by the Spearman correlation test, although high coefficients were not found for most of them. Cluster analysis of the progeny grouped the hybrids based on criteria with significance for wine grape breeding. Also, we investigated the relationship between the skin color and total content of anthocyanins with the VvmybA genotype, using the CAPS (Cleaved Amplified Polymorphic Sequence) marker 20D18CB9. The results show that hybrids with two copies of the functional color allele tend to have increased anthocyanins content. Based on this study, 14 genotypes were pre-selected from the breeding population for additional quality studies.     

Transformation of <Emphasis Type="Italic">Campanula</Emphasis> by wild type <Emphasis Type="Italic">Agrobacterium rhizogenes</Emphasis>

Compact growth is an important quality criterion in horticulture. Many Campanula species and cultivars exhibit elongated growth which is suppressed by chemical retardation and cultural practice during production to accommodate to the consumer’s desire. The production of compact plants via transformation with wild type Agrobacterium rhizogenes is an approach with great potential to produce plants that are non-GMO. Efficient transformation and regeneration procedures vary widely among both plant genera and species. Here we present a transformation protocol for Campanula. Hairy roots were produced on 26–90% of the petioles that were used for transformation of C. portenschlagiana (Cp), a C. takesimana × C. punctata hybrid (Chybr) and C. glomerata (Cg). Isolated hairy roots grew autonomously and vigorously without added hormones. The Cg hairy roots produced chlorophyll and generated plantlets in response to treatments with cytokinin (42 µM 2iP) and auxin (0.67 µM NAA). In contrast, regeneration attempts of transformed Cp and Chybr roots lead neither to the production of chlorophyll nor to the regeneration of shoots. Agropine A. rhizogenes strains integrate split T-DNA in T_L- and T_R-DNA fragments into the plant genome. In this study, regenerated plants of Cg did not contain T_R-DNA, indicating that a selective pressure against this T-DNA fragment may exist in Campanula.     

Using an individual-based model to examine the roles of habitat fragmentation and behavior on predator–prey relationships in seagrass landscapes

Seagrasses, which form critical subtidal habitats for marine organisms worldwide, are fragmented via natural processes but are increasingly being fragmented and degraded by boating, fishing, and coastal development. We constructed an individual-based model to test how habitat fragmentation and loss influenced predator–prey interactions and cohort size for a group of settling juvenile blue crabs (Callinectes sapidus Rathbun) in seagrass landscapes. Using results from field studies suggesting that strong top-down processes influence the relationship between cannibalistic blue crab populations and seagrass landscape structure, we constructed a model in which prey (juvenile blue crabs) are eaten by mesopredators (larger blue crabs) which in turn are eaten by top-level predators (e.g., large fishes). In our model, we varied the following parameters within four increasingly fragmented seagrass landscapes to test for their relative effects on cohort size: juvenile blue crab (prey) predator avoidance response, hunting ability of mesopredators and predators, the presence of a top-level predator, and prey settlement routines. Generally, prey cohort size was maximized in the presence of top-level predators and when mesopredators and predators exhibited random searching behavior vs. directed hunting. Cohort size for stationary (tethered) prey was maximized in fragmented landscapes, which corresponds to results from field experiments, whereas mobile prey able to detect and avoid predators had higher survival in continuous landscapes. Prey settlement patterns had relatively small influences on cohort size. We conclude that the effects of seagrass fragmentation and loss on organisms such as blue crabs will depend heavily on behaviors of prey and predatory organisms and how these behaviors change with landscape structure.     

Stable cell-surface expression of Japanese flounder growth hormone in yeast <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis> and growth-promoting effect on juvenile fish by oral administration

A cost-effective method for producing and using recombinant growth hormone (GH) has been developed. A cell-surface protein display system was constructed to produce recombinant Japanese flounder growth hormone (r-JfGH) in yeast Saccharomyces cerevisiae and the biological activity of expressed r-JfGH was evaluated by oral delivery to juvenile Japanese flounder. The expression vector pYD-E2, containing the JfGH gene, S. cerevisiae GAL1 promoter, and the S.cerevisiae URA3 gene downstream and upstream sequences, was designed and constructed to integrate the GH gene into the yeast genome and secrete r-JfGH stably on the surface of the yeast cell. Expression of r-JfGH was confirmed by flow cytometry until the 50th continuous generation of transgenic yeast strain y-E2, and over 0.98 μg r-JfGH per 1 mg total protein of y-E2 was estimated by an ELISA–RA assay. Growth of Japanese flounder was promoted significantly by the direct supplementation of freeze-dried transgenic yeast into the Japanese flounder juvenile feed at levels of 0.5 and 1%. The weight-specific growth rate and feed conversion ratio of the treated groups were 23.07 and 21.57% (0.5% feeding level) and 28.85 and 41.18% (1% feeding level), respectively, higher than that of the control group in a 7-week bioactivity study.     

Carbonic anhydrase and Na/K-ATPase activities at different molting stages of the giant freshwater prawn <Emphasis Type="Italic">Macrobrachium rosenbergii</Emphasis>

ABSTRACT:   In the present study, the role of carbonic anhydrase (CA) and Na/K-ATPase in the gill and epidermal tissues in the giant freshwater prawn Macrobrachium rosenbergii was examined as a function of molting stage. CA activity levels in the front and back gills were low at the intermolt stage C₀, but increased significantly at premolt stage D₃, and then decreased after molting. In the epidermal tissue, activity levels decreased gradually towards premolt to a minimum level at stage D₃, but became elevated at postmolt stages A and B. Na/K-ATPase levels in the front and back gills did not change significantly during the molt cycle. CA in the gill is possibly involved in supplying counter-ions for ion uptake, while CA in the epidermal tissue may play a role in mineralizing the exoskeleton after ecdysis. Na/K-ATPase in the gills may function in ion uptake from the ambient medium; however, since its activity was not influenced by the molt cycle, it probably does not have a major role in osmoregulation in the freshwater environment.     

Improving Application Performance of <Emphasis Type="Italic">in situ</Emphasis> Polymerization and Crosslinking System of Maleic Acid/Itaconic Acid for Cotton Fabric

Maleic acid (MA) and itaconic acid (IA) used as crosslinking agents for cotton fabrics are more cost-effective than the most efficient nonformaldehyde crosslinker 1,2,3,4-butanetetracarboxylic acid (BTCA), but poor stability of finishing bath and fabric yellowing are the main disadvantage of MA/IA in situ polymerization and crosslinking system. In this research, the application performance improvement of MA/IA crosslinking system for cotton fabrics was studied. Replacement of the widely used sodium hypophosphite (SHP) with potassium hypophosphite (PHP) as catalyst allowed for obtaining a stable finishing bath under ambient temperature and led to improved final durable press (DP) performance of the treated fabrics. The influences of PHP concentration, curing temperature, and curing time on the performance of finished fabrics were investigated. Cotton fabrics treated by MA/IA/PHP crosslinking system exhibited comparable DP performance and laundering durability to that finished with BTCA. To address the fabric yellowing problem, the residual MA and IA attached on the treated fabrics by single-ended ester linkage was determined by HPLC. The data indicated that the degree of fabric yellowing was linearly related to the unpolymerized carboxylic acid MA and IA concentration on the treated fabrics. Several approaches were explored to improve the whiteness of MA/IA/PHP crosslinked fabrics. It was found that steam drying with 30-50 % humidity could effectively improve fabric whiteness. The findings of this study have significant implications for better application of unsaturated polycarboxylic acids in crosslinking of cellulose.     

Supporting cognition in systems biology analysis: findings on users' processes and design implications

Background

Current usability studies of bioinformatics tools suggest that tools for exploratory analysis support some tasks related to finding relationships of interest but not the deep causal insights necessary for formulating plausible and credible hypotheses. To better understand design requirements for gaining these causal insights in systems biology analyses a longitudinal field study of 15 biomedical researchers was conducted. Researchers interacted with the same protein-protein interaction tools to discover possible disease mechanisms for further experimentation.

Results

Findings reveal patterns in scientists' exploratory and explanatory analysis and reveal that tools positively supported a number of well-structured query and analysis tasks. But for several of scientists' more complex, higher order ways of knowing and reasoning the tools did not offer adequate support. Results show that for a better fit with scientists' cognition for exploratory analysis systems biology tools need to better match scientists' processes for validating, for making a transition from classification to model-based reasoning, and for engaging in causal mental modelling.

Conclusion

As the next great frontier in bioinformatics usability, tool designs for exploratory systems biology analysis need to move beyond the successes already achieved in supporting formulaic query and analysis tasks and now reduce current mismatches with several of scientists' higher order analytical practices. The implications of results for tool designs are discussed.