Emergent Properties of Balinese Water Temple Networks: Coadaptation on a Rugged Fitness Landscape

For over a thousand years, generations of Balinese farmers have gradually transformed the landscape of their island, clearing forests, digging irrigation canals, and terracing hillsides to enable themselves and their descendants to grow irrigated rice. Paralleling the physical system of terraces and irrigation works, the Balinese have also constructed intricate networks of shrines and temples dedicated to agricultural deities. Ecological modeling shows that water temple networks can have macroscopic effects on the topography of the adaptive landscape, and may be representative of a class of complex adaptive systems that have evolved to manage agroecosystems.     

Quantifying electricity generation and waste transformations in a low-cost, plug-flow anaerobic digestion system

Methane production, electricity production, and wastewater transformations were quantified for a digestion system that combines biogas from a swine digester and dairy digester in Costa Rica. The low-cost, plug-flow digesters were not heated and were operated in the lower portion of the mesophilic range (25–27 °C).The dairy digester produced 27.5 m³/day of biogas with 62.6% methane and reduced organic matter (COD) by 86%. The swine digester produced 6.0 m³/day of biogas with 76.4% methane and reduced COD by 92%. Combining biogas from a swine and dairy digester, increased electricity production due to the higher biogas production rate of the dairy farm and the higher quality biogas obtained from the swine farm. The farm’s 2-h peak electricity demand (12.9 kW/day) was 81.8% met. The electricity was produced using manure equivalent to the quantity excreted by 5 dairy cows and 40 pigs remaining in corrals 100% of the time.The $21,000 capital cost of the digester project will be recovered in 10.1 years through electricity savings and reductions in wastewater fines. If the generator were more appropriately sized for the farm, the capital recovery time would have been 7.6 years.     

Plankton composition,biomass, phylogeny and toxin genes in Lake Big Momela,Tanzania

Lake Big Momela, one of the East African soda lakes in Northern Tanzania characterised by highly saline-alkaline conditions, making them inhospitable to a range of organisms, although supporting massive growths of some adapted planktonic microorganisms that serve as food for birds, such as Lesser Flamingo. The temporal dynamics of plankton, with an emphasis on cyanobacteria, were examined in 2007 using morphological traits and ribosomal genetic markers (16S and 18S rRNA). Cyanobacterial genes encoding for hepatotoxins (mcyE and ndaF) were also screened. Rotifers and copepods dominated the zooplankton, whereas cyanobacteria, such as Anabaenopsis elenkinii and Arthrospira fusiformis dominated the phytoplankton community, and these being related to representatives in other East African soda lakes. The cyanobacteria community also showed distinct seasonal patterns influenced by environmental parameters, mainly salinity, pH and nitrate. Significant positive correlations were found between phytoplankton abundance and nitrate concentrations (r = 0.617, p = 0.033). No signals of the hepatotoxin synthetase genes mcyE and ndaF were retrieved from cyanobacteria during the whole year. In general, our data illustrate the presence of rich planktonic communities, including some unique and potentially endemic cyanobacteria.     

A simple method for predicting serum protein binding of compounds from IC(50) shift analysis for in vitro assays

The shift in apparent IC(50) that attends addition of serum proteins to in vitro cellular, enzymatic, and receptor binding assays can be used to determine the dissociation constant for compound-serum protein complexes. We show here that a simple linear relationship exists between the apparent IC(50) in the presence of serum protein and the inverse of the apparent K(d) for the compound-serum protein complex. Using a series of cell-active kinase inhibitors we demonstrate that the K(d) value derived in this way can be used to predict the extent of protein binding in serum for various compounds. This method should provide a simple means of assessing the relative serum protein binding propensity of compounds early in the compound optimization phase of drug discovery campaigns.     

Identification of genes encoding exported Mycobacterium tuberculosis proteins using a Tn552'phoA in vitro transposition system

Secreted and cell envelope-associated proteins are important to both Mycobacterium tuberculosis pathogenesis and the generation of protective immunity to M. tuberculosis. We used an in vitro Tn552'phoA transposition system to identify exported proteins of M. tuberculosis. The system is simple and efficient, and the transposon inserts randomly into target DNA. M. tuberculosis genomic libraries were targeted with Tn552'phoA transposons, and these libraries were screened in M. smegmatis for active PhoA translational fusions. Thirty-two different M. tuberculosis open reading frames were identified; eight contain standard signal peptides, six contain lipoprotein signal peptides, and seventeen contain one or more transmembrane domains. Four of these proteins had not yet been assigned as exported proteins in the M. tuberculosis databases. This collection of exported proteins includes factors that are known to participate in the immune response of M. tuberculosis and proteins with homologies, suggesting a role in pathogenesis. Nine of the proteins appear to be unique to mycobacteria and represent promising candidates for factors that participate in protective immunity and virulence. This technology of creating comprehensive fusion libraries should be applicable to other organisms.     

Recent Advances in Plant Organelle Dynamics

<正>Organelles are eukaryotic subcellular structures each possessing a specific set of functions.The morphology,abundance,and content of the organelles also undergo constant changes for optimal function     

Value of a newly sequenced bacterial genome

Next-generation sequencing(NGS) technologies have made high-throughput sequencing available to medium- and small-size laboratories, culminating in a tidal wave of genomic information. The quantity of sequenced bacterial genomes has not only brought excitement to the field of genomics but also heightened expectations that NGS would boost antibacterial discovery and vaccine development. Although many possible drug and vaccine targets have been discovered, the success rate of genome-based analysis has remained below expectations. Furthermore, NGS has had consequences for genome quality, resulting in an exponential increase in draft(partial data) genome deposits in public databases. If no further interests are expressed for a particular bacterial genome, it is more likely that the sequencing of its genome will be limited to a draft stage, and the painstaking tasks of completing the sequencing of its genome and annotation will not be undertaken. It is important to know what is lost when we settle for a draft genome and to determine the "scientific value" of a newly sequenced genome. This review addresses the expected impact of newly sequenced genomes on antibacterial discovery and vaccinology. Also, it discusses the factors that could be leading to the increase in the number of draft deposits and the consequent loss of relevant biological information.