Identification of drought responsive proteins using gene ontology hierarchy

The availability of the complete genome sequences has facilitated access to essential information to identify proteins. The determination of Arabidopsis genome sequence has had a great impact to annotate data. The genome sequencing of Sorghum bicolor has been only recently completed and hither to the global response to abiotic stresses in this important crop remains largely unexplored. We used 2-D gel electrophoresis based proteomic approach refined with MALDI-TOF to analyze drought-stress response proteins in sorghum. Major changes in protein complement of sorghum were observed in hydroponic cultures at 96 hours under drought stress. Six most highly expressed proteins were excised for functional identification. Here, we developed a method to obtain functional distances between GO terms and analyzed distance values to allocate shortest path (SP) in GO hierarchy. The shortest paths for expressed proteins were noted for most informative common ancestor (MICA) terms, viz. binding, catalytic activity and primary metabolic process. We observed the expressed proteins belonged to the functional group of signal transduction mechanisms, carbohydrate transport and metabolism. These identified functions of proteins suggest a different mechanism of drought-stress tolerant in sorghum. The novel approach applied in this study may have great importance in further identifying proteins involved in abiotic and biotic stress conditions in crops.     

Comparing Platforms for C. elegans Mutant Identification Using High-Throughput Whole-Genome Sequencing

Background

Whole-genome sequencing represents a promising approach to pinpoint chemically induced mutations in genetic model organisms, thereby short-cutting time-consuming genetic mapping efforts.

Principal Findings

We compare here the ability of two leading high-throughput platforms for paired-end deep sequencing, SOLiD (ABI) and Genome Analyzer (Illumina; “Solexa”), to achieve the goal of mutant detection. As a test case we used a mutant C. elegans strain that harbors a mutation in the lsy-12 locus which we compare to the reference wild-type genome sequence. We analyzed the accuracy, sensitivity, and depth-coverage characteristics of the two platforms. Both platforms were able to identify the mutation that causes the phenotype of the mutant C. elegans strain, lsy-12. Based on a 4 MB genomic region in which individual variants were validated by Sanger sequencing, we observe tradeoffs between rates of false positives and false negatives when using both platforms under similar coverage and mapping criteria.

Significance

In conclusion, whole-genome sequencing conducted by either platform is a viable approach for the identification of single-nucleotide variations in the C. elegans genome.     

Significance of riverine carbon transport: A case study of a large tropical river, Godavari (India)

Although riverine carbon fluxes are a minor component of the global carbon cycle, thetransfer of organic carbon from land to ocean represents a flux of potential carbon storage, irre-versible over 10~3 to 10~4 a. Future carbon transfers through river basins are expected to accelerate,with respect to both sources and sinks, because of the large-scale human driven land-use and land-cover changes. Thus, the increased amounts of carbon transported to and sequestered inmarine sediments (through fertilization by river-borne inorganic nutrients) may be an important netsink for anthropogenic CO_2. Particularly, the humid tropics of South Asia are regions very sensitiveto this lateral C transport because of high precipitation and high rates of land use and cover change. In this paper we report on the role of upland tributaries in the transport processes influ-encing the lateral carbon and nitrogen fluxes of the Godavari, a large tropical river of India. By far,dissolved inorganic carbon (DIC) is the dominant form of carbon transport in the river basin. It con-stitutes as much as 75% to the total carbon load. Particulate and dissolved organic carbon (POC and DOC) fluxes account for 21% and 4%, respectively. In the upper basin, DOC fluxes exceedthat of POC due to large-scale anthropogenic activities. In contrast, tributaries in the central basinare characterized by comparable fluxes of POC and DOC. However, downriver POC export is 35%less than the import from upriver and tributaries due to the entrainment of sediments in river channels and dam sites. We argue that for highly disturbed watersheds in tropical regions, down-stream transport of sediments and carbon requires long-term sampling programmes.     

Interleukin-2-induced decrease in the buoyant density of cytotoxic cells and its relationship with proliferation

Interleukin 2 (IL-2) is known to induce an augmentation of natural killer activity. In the present study we have used discontinuous Percoll density gradients to investigate the changes in the buoyant density of killer effector cells generated in response to IL-2. In all systems examined (mouse and rat spleen cells and human peripheral blood mononuclear cells), the cytolytic effectors generated in response to IL-2 have markedly lower buoyant densities compared to fresh natural killer cells. Our results also suggest that if a single layer of 44.2% (v/v) Percoll is used, almost all IL-2-induced cytolytic activity can be enriched in the cells which float on this layer whereas the heavier cells from the pellet are devoid of cytotoxic activity. The contribution of proliferative activity to (a) the generation of cytotoxicity and (b) the decrease in the buoyant density of the IL-2-induced killer cells was also studied in the mouse system. Natural killer levels in mouse spleen cells treated with mitomycin C could be significantly augmented by IL-2. Moreover, the effector cells generated in control as well as mitomycin-C-treated spleen cells in response to IL-2 had the same low buoyant densities. These results indicate that proliferation is not a prerequisite for the activation of killer activity and a reduction in buoyant density in response to IL-2.     

Effects of Soil Salinity and Growth Regulators on Germination and Seedling Metabolism of Wheat

Germination studies were carried out with the wheat varieties NP823, Karchia, Sonora 63, Sonora 64, Mayo 64 and Lerma Rojo in artificially salinized soil maintained at EC_e 2, 8, 12 and 16 mmhos/cm at 25°C. Early seedling growth and metabolism of variety NP 823 was studied in salt solutions alone and with addition of the growth regulators GA₃ and Cycocel (2-chloroethyl trimethylammonium chloride). Soil salinity both depressed and delayed the germination. Among the varieties tested NP 823 and Karchia were relatively less susceptible to salt injury while Lerma Rojo exhibited a maximum susceptibility. Salt supply also brought about a reduction in the early seedling growth, the release of reducing sugar and the amylase activity. The adverse effect on amylase activity was not mediated through the synthesis of enzyme protein but by an inhibition of the enzyme activity. Exogenous supply of GA₃ counteracted the adverse effect of salt on amylase activity and the release of reducing sugar but not on the early seedling growth.     

Significance of riverine carbon transport: A case study of a large tropical river, Godavari (India)

Although riverine carbon fluxes are a minor component of the global carbon cycle, the transfer of organic carbon from land to ocean represents a flux of potential carbon storage, irreversible over 103 to 104 a. Future carbon transfers through river basins are expected to accelerate, with respect to both sources and sinks, because of the large-scale human driven land-use and land-cover changes. Thus, the increased amounts of carbon transported to and sequestered in marine sediments (through fertilization by river-borne inorganic nutrients) may be an important net sink for anthropogenic CO2. Particularly, the humid tropics of South Asia are regions very sensitive to this lateral C transport because of high precipitation and high rates of land use and cover change. In this paper we report on the role of upland tributaries in the transport processes influencing the lateral carbon and nitrogen fluxes of the Godavari, a large tropical river of India. By far, dissolved inorganic carbon (DIC) is the dominant form of carbontransport in the river basin. It constitutes as much as 75% to the total carbonload. Particulate and dissolved organic carbon (POC and DOC) fluxes account for21% and 4%, respectively. In the upper basin, DOC fluxes exceed that of POC dueto large-scale anthropogenic activities. In contrast, tributaries in the central basin are characterized by comparable fluxes of POC and DOC. However, downriver POC export is 35% less than the import from upriver and tributaries due to theentrainment of sediments in river channels and dam sites. We argue that for highly disturbed watersheds in tropical regions, downstream transport of sediments and carbon requires long-term sampling programmes.