Metagenomic analysis of the human distal gut microbiome

The human intestinal microbiota is composed of 10(13) to 10(14) microorganisms whose collective genome ("microbiome") contains at least 100 times as many genes as our own genome. We analyzed approximately 78 million base pairs of unique DNA sequence and 2062 polymerase chain reaction-amplified 16S ribosomal DNA sequences obtained from the fecal DNAs of two healthy adults. Using metabolic function analyses of identified genes, we compared our human genome with the average content of previously sequenced microbial genomes. Our microbiome has significantly enriched metabolism of glycans, amino acids, and xenobiotics; methanogenesis; and 2-methyl-d-erythritol 4-phosphate pathway-mediated biosynthesis of vitamins and isoprenoids. Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes.     

Modelling of ring yarn unevenness by soft computing approach

This paper demonstrates the application of two soft computing approaches namely artificial neural network (ANN) and neural-fuzzy system to forecast the unevenness of ring spun yarns. The cotton fiber properties measured by advanced fiber information system (AFIS) and yarn count have been used as inputs. The prediction accuracy of the ANN and neural-fuzzy models was compared with that of linear regression model. It was found that the prediction performance was very good for all the three models although ANN and neural-fuzzy models seem to have some edge over the linear regression model. The linguistic rules developed by the neural-fuzzy system unearth the role of input variables on the yarn unevenness.     

Biodegradation and Detoxification Efficiency of Azo-Dye Reactive Orange 16 by <Emphasis Type="Italic">Pichia kudriavzevii</Emphasis> CR-Y103

In consideration of the hazards associated with the presence of the textile azo-dye and their biotransformation products in the environment, the goal of this work was to study bioremediation process by the yeast strain Pichia kudriavzevii CR-Y103 related to the ability to degrade and detoxify the sulfonated Reactive Orange 16 azo-dye. In experimental conditions, the optimal inoculum/dye concentration ratio required for complete decolorization (100%) of culture medium and biomass within 24 h has been 1 g L^?1 yeast cell (dry weight)/50 mg L^?1 Reactive Orange 16. In the presence of 400 mg L^?1 of Reactive Orange 16 (RO16), 95% of the dye was removed after 72 h of incubation. Also, the yeast strain could decolorize other eight textile dyes (56.48–99.98% decolorization within 24 h). NADH-DCIP reductase and azo reductase activities were significantly increased (ca. 5.4 times and ca. 37 times, respectively) during the decolorization process. UV-VIS spectra, high-performance liquid chromatography (HPLC), and Fourier transform infrared spectroscopy (FTIR) analysis confirmed the presence of new biotransformation products in extracted metabolites, highlighting the partial biodegradation of the dye by the new yeast isolate. The phytotoxicity evaluation strongly supported the decreased toxicity of biodegraded products as minor inhibition on germination (%), root and shoots elongation of T. pratense L. and T. aestivum L. seedlings. Increasing of mitotic index value and decreasing the frequency of chromosomal aberrations in tested plant meristem cells treated with biodegraded products, compared with RO16 treatment (500 ppm), confirmed their slightly toxic nature. A cell viability assay also confirmed the reduced toxicity of biodegraded products on healthy monkey kidney cells (Vero cells).     

The dog genome: survey sequencing and comparative analysis

A survey of the dog genome sequence (6.22 million sequence reads; 1.5x coverage) demonstrates the power of sample sequencing for comparative analysis of mammalian genomes and the generation of species-specific resources. More than 650 million base pairs (>25%) of dog sequence align uniquely to the human genome, including fragments of putative orthologs for 18,473 of 24,567 annotated human genes. Mutation rates, conserved synteny, repeat content, and phylogeny can be compared among human, mouse, and dog. A variety of polymorphic elements are identified that will be valuable for mapping the genetic basis of diseases and traits in the dog.     

LTSER platforms as a place-based transdisciplinary research infrastructure: learning landscape approach through evaluation

Landscape Ecology - Place-based transdisciplinary research involves multiple academic disciplines and non-academic actors. Long-Term Socio-Ecological Research (LTSER) platform is one concept with ~...     

Geographic information system (GIS) application for windthrow mapping and management in Iezer Mountains, Southern Carpathians

Windthrow problem is a difficult task for the forest managers in the Romanian Carpathians and especially in Iezer Mountains. The last windthrow, in July 2005, affected about 370 ha within the study area and left unprotected large slopes with important declivities (20-30°). In our study, we try to propose a tool for forest management, in order to control and minimize the negative effect of wind upon the mountain forest ecosystem. The digital data input derived from forestry data (forest stand typology, age, canopy coverage index, forest productivity class) and from the forest biotope features (soil and topography parameters). The main goal was to find a more objective way for digital layer reclassification in order to obtain the windthrow areas susceptibility map for the Iezer Mountains. Each digital layer has its own weight within the analysis and one of them was difficult to be modeled (the wind features). A statistical approach was developed on the basis of local phenomena and the windthrow features in the Romanian Carpathians. This allowed us to obtain the reclassification conditions for each digital layer. Forest canopy typology and soil features (mainly its volume) were considered as the key factors for the windthrow occurrence analysis. The final windthrow susceptibility map was validated with the help of the statistic occurrence of windthrow areas within each susceptibility class and after a field check of the sites. The result was encouraging, because 92.5% of the windthrow areas fall into the highest windthrow susceptibility class.     

Sex-specific connectivity modelling for brown bear conservation in the Carpathian Mountains

Landscape Ecology - Romania is currently one of the best-connected landscapes, with high-quality habitats and a high density of brown bears. However, regional development measures are needed for...     

Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis

Comparison of the whole-genome sequence of Bacillus anthracis isolated from a victim of a recent bioterrorist anthrax attack with a reference reveals 60 new markers that include single nucleotide polymorphisms (SNPs), inserted or deleted sequences, and tandem repeats. Genome comparison detected four high-quality SNPs between the two sequenced B. anthracis chromosomes and seven differences among different preparations of the reference genome. These markers have been tested on a collection of anthrax isolates and were found to divide these samples into distinct families. These results demonstrate that genome-based analysis of microbial pathogens will provide a powerful new tool for investigation of infectious disease outbreaks.     

Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold

The manipulation of protein backbone structure to control interaction and function is a challenge for protein engineering. We integrated computational design with experimental selection for grafting the backbone and side chains of a two-segment HIV gp120 epitope, targeted by the cross-neutralizing antibody b12, onto an unrelated scaffold protein. The final scaffolds bound b12 with high specificity and with affinity similar to that of gp120, and crystallographic analysis of a scaffold bound to b12 revealed high structural mimicry of the gp120-b12 complex structure. The method can be generalized to design other functional proteins through backbone grafting.