Linkage and association analysis of candidate genes for TB and TNFα cytokine expression: evidence for association with IFNGR1, IL-10, and TNF receptor 1 genes

Tuberculosis (TB) is a growing public health threat globally and several studies suggest a role of host genetic susceptibility in increased TB risk. As part of a household contact study in Kampala, Uganda, we have taken a unique approach to the study of genetic susceptibility to TB by developing an intermediate phenotype model for TB susceptibility, analyzing levels of tumor necrosis factor-α (TNFα) in response to culture filtrate as the phenotype. In the present study, we analyzed candidate genes related to TNFα regulation and found that interleukin (IL)-10, interferon-gamma receptor 1 (IFNGR1), and TNFα receptor 1 (TNFR1) genes were linked and associated to both TB and TNFα. We also show that these associations are with progression to active disease and not susceptibility to latent infection. This is the first report of an association between TB and TNFR1 in a human population and our findings for IL-10 and IFNGR1 replicate previous findings. By observing pleiotropic effects on both phenotypes, we show construct validity of our intermediate phenotype model, which enables the characterization of the role of these genetic polymorphisms on TB pathogenesis. This study further illustrates the utility of such a model for disentangling complex traits. C. C. Whalen and S. K. Iyengar contributed equally as senior authors of this work.     

Decolorization and partial degradation of monoazo dyes in sequential fixed-film anaerobic batch reactor (SFABR)

Decolorization of two monoazo dyes, acid orange 6 (AO6) and acid orange 7 (AO7), were studied in sequential fixed-film anaerobic batch reactor (SFABR) with varying dye concentrations and 500 mg/L glucose as the co-substrate. More than 90% dye decolorization could be achieved, even at 300 mg/L, with both AO6 and AO7 and dye decolorization rates were 168 mg/L/d and 176 mg/L/d, respectively. COD removals with these two monoazo dyes were significantly different, as 75% and 35% decrease were observed with AO6 and AO7, respectively. UV-visible spectral as well as HPLC analysis of SFABR treated effluent showed the accumulation of 4-aminobenzenesulfonate (4-ABS) from AO6 and AO7. Aminoresorcinol (AR) formed from AO6 decolorization could not be detected at the end of SFABR cycle. This along with high COD removal indicated its further degradation. Formation of pink coloration on exposure to air indicated the presence of 1-amino-2-naphthol (AN) in AO7 fed reactor effluent. Thus both 4-ABS and AN were resistant to further degradation under anaerobic conditions. Presence of nitrate did not decrease the observed decolorization at the end of 24h SFABR cycle, although initial rate was decreased. This indicates the suitability of SFABR configuration for the treatment of azo-dye containing wastewaters in the presence of nitrate.     

Silencing synaptic communication between random interneurons during Drosophila larval locomotion

Genetic manipulation of individual neurons provides a powerful approach toward understanding their contribution to stereotypic behaviors. We describe and evaluate a method for identifying candidate interneurons and associated neuropile compartments that mediate Drosophila larval locomotion. We created Drosophila larvae that express green fluorescent protein (GFP) and a shibire(ts1) (shi(ts1)) transgene (a temperature-sensitive neuronal silencer) in small numbers of randomly selected cholinergic neurons. These larvae were screened for aberrant behavior at an elevated temperature (31-32°C). Among larvae with abnormal locomotion or sensory-motor responses, some had very small numbers of GFP-labeled temperature-sensitive interneurons. Labeled ascending interneurons projecting from the abdominal ganglia to specific brain neuropile compartments emerged as candidates for mediation of larval locomotion. Random targeting of small sets of neurons for functional evaluation, together with anatomical mapping of their processes, provides a tool for identifying the regions of the central nervous system that are required for normal locomotion. We discuss the limitations and advantages of this approach to discovery of interneurons that regulate motor behavior.     

Phenotype and function of human natural killer cells purified by using a clinical-scale immunomagnetic method

Infection, disease relapse, graft failure, and graft-versus-host disease (GVHD) are significant adverse events associated with allogeneic bone marrow transplantation. Donor natural killer (NK) cells may be an ideal cell type for prevention or treatment of all these adverse events. Therefore, we investigated the phenotype and function of human NK cells purified by using a clinical-scale immunomagnetic method. We found that the NK cell purification procedures did not adversely affect the expression of killer cell immunoglobulin-like receptors, adhesion molecules, intracellular cytokines, perforin, and granzyme B. Purified NK cells had extensive proliferative capacity and potent antitumor activity when assessed using an immunodeficient mouse model. While all mice transplanted with unpurified mononuclear cells developed GVHD, none of the mice transplanted with purified NK cells did. NK cells were highly susceptible to lysis by antithymocyte globulin (ATG), whereas G-CSF had a minimal effect on their natural cytotoxicity. These results support future clinical investigation of the use of purified NK cells for adoptive immunotherapy in the absence of ATG.     

Determinants of antileukemia effects of allogeneic NK cells

In HLA-nonidentical bone marrow transplantation, we studied the characteristics of donor NK cells, recipient leukemia cells, and the cytokine environment that predict the antileukemia effects of allogeneic NK cells. We found that the risk of relapse in pediatric patients with hematologic malignancies was best predicted by a model taking into consideration the presence of inhibitory killer cell Ig-like receptors (KIRs) on the donor's NK cells and the absence of corresponding KIR ligand in the recipient's HLA repertoire (a receptor-ligand model). The risk of relapse was prognosticated less precisely by the Perugia donor-recipient KIR ligand-ligand mismatch model or by a natural cytotoxicity model. In contrast to the ligand-ligand model, we found that the new receptor-ligand model was accurate when analysis was applied to patients with lymphoid malignancy. These findings corroborate our observations that the recipient's KIR repertoire, which was derived from highly purified, HLA-disparate CD34+ cells, resumed a donor-specific pattern within 3 mo of transplantation, but did not correlate evidently with the donor or recipient ligand repertoire. In an in vitro assay and an in vivo mouse model, human NK cell cytotoxicity toward human leukemia cells with 11q23 chromosomal rearrangement increased with the number of receptor-ligand mismatch pairs or prestimulation with IL-12 and IL-18. These findings provide new insights into the determinants of antileukemia effects of allogeneic NK cells and therapeutic strategies.     

Ecoinformatics using wireless sensor networks: An overview

Wireless sensor networks have the potential to become significant subsystems of ecological experiment. Sensor networks consist of large number of tiny sensor nodes, all of which have sensing capabilities. These networks allow coordinated signal detection, monitoring, and tracking to enable sensor nodes to simultaneously capture geographically distinct measurements. Sensor nodes do not require predetermined positioning making such networks especially useful for applications in remote, inhospitable environments. In this paper we have tried to see the various ecological experimental scenarios, and how wireless sensor networks can be used in that field. One of the most challenging bottlenecks in the usage of wireless sensor networks in large scale experiments is the energy constraint. Various routing protocols which have tried to optimize the energy usage are also studied in the paper.     

Mineralization of 4-aminobenzenesulfonate (4-ABS) by Agrobacterium sp. strain PNS-1

A bacterial strain, PNS-1, isolated from activated sludge, could utilize sulphanilic acid (4-ABS) as the sole organic carbon and energy source under aerobic conditions. Determination and comparison of 16S r DNA sequences showed that the strain PNS-1 is closely related to the species of Agrobacterium genus. Growth on 4-ABS was accompanied with ammonia and sulfate release. TOC results showed complete mineralization of sulphanilic acid. This strain was highly specific for 4-ABS as none of the sulphonated aromatics used in the present study including other ABS isomers were utilized. Strain PNS-1 could, however, utilize all the tested monocyclic aromatic compounds devoid of a sulfonate group. No intermediates could be detected either in the growth phase or with dense cell suspensions. Presence of chloramphenicol completely inhibited 4-ABS degradation by cells pregrown on succinate, indicating that degradation enzymes are inducible. No plasmid could be detected in the Agrobacterium sp. Strain PNS-1 suggesting that 4-ABS degradative genes may be chromosomal encoded.     

A microsatellite-based consensus linkage map for species of Eucalyptus and a novel set of 230 microsatellite markers for the genus

Background  

Eucalypts are the most widely planted hardwood trees in the world occupying globally more than 18 million hectares as an important source of carbon neutral renewable energy and raw material for pulp, paper and solid wood. Quantitative Trait Loci (QTLs) in Eucalyptus have been localized on pedigree-specific RAPD or AFLP maps seriously limiting the value of such QTL mapping efforts for molecular breeding. The availability of a genus-wide genetic map with transferable microsatellite markers has become a must for the effective advancement of genomic undertakings. This report describes the development of a novel set of 230 EMBRA microsatellites, the construction of the first comprehensive microsatellite-based consensus linkage map for Eucalyptus and the consolidation of existing linkage information for other microsatellites and candidate genes mapped in other species of the genus.     

From components to regulatory motifs in signalling networks.

The developments in biochemistry and molecular biology over the past 30 years have produced an impressive parts list of cellular components. It has become increasingly clear that we need to understand how components come together to form systems. One area where this approach has been growing is cell signalling research. Here, instead of focusing on individual or small groups of signalling proteins, researchers are now using a more holistic perspective. This approach attempts to view how many components are working together in concert to process information and to orchestrate cellular phenotypic changes. Additionally, the advancements in experimental techniques to measure and visualize many cellular components at once gradually grow in diversity and accuracy. The multivariate data, produced by experiments, introduce new and exciting challenges for computational biologists, who develop models of cellular systems made up of interacting cellular components. The integration of high-throughput experimental results and information from legacy literature is expected to produce computational models that would rapidly enhance our understanding of the detail workings of mammalian cells.