Functional responses of methanogenic archaea to syntrophic growth.

Methanococcus maripaludis grown syntrophically with Desulfovibrio vulgaris was compared with M. maripaludis monocultures grown under hydrogen limitation using transcriptional, proteomic and metabolite analyses. These measurements indicate a decrease in transcript abundance for energy-consuming biosynthetic functions in syntrophically grown M. maripaludis, with an increase in transcript abundance for genes involved in the energy-generating central pathway for methanogenesis. Compared with growth in monoculture under hydrogen limitation, the response of paralogous genes, such as those coding for hydrogenases, often diverged, with transcripts of one variant increasing in relative abundance, whereas the other was little changed or significantly decreased in abundance. A common theme was an apparent increase in transcripts for functions using H(2) directly as reductant, versus those using the reduced deazaflavin (coenzyme F(420)). The greater importance of direct reduction by H(2) was supported by improved syntrophic growth of a deletion mutant in an F(420)-dependent dehydrogenase of M. maripaludis. These data suggest that paralogous genes enable the methanogen to adapt to changing substrate availability, sustaining it under environmental conditions that are often near the thermodynamic threshold for growth. Additionally, the discovery of interspecies alanine transfer adds another metabolic dimension to this environmentally relevant mutualism

Enhancing student access and retention

The goals of developmental education include promoting educational opportunity through efforts that enhance both access and retention. Although the measures taken and the issues related to access and retention may overlap, they are not synonymous and must be addressed separately. Defining access is more complicated than it might appear. Traditionally, access has been viewed as opening the door to postsecondary education. With the proliferation of public community colleges and technical institutions in many states, some educators and legislators alike have assumed that the problem of access has been addressed because relatively low-cost programs are available to anyone with a high school diploma or its equivalent. However, numerous other issues related to access are overlooked

Use of an Integrated Pest Management Assessment Administered Through TurningPoint as an Educational, Needs Assessment, and Evaluation Tool

University of Minnesota educators use an integrated pest management (IPM) survey conducted during private pesticide applicator training as an educational, needs assessment, and evaluation tool. By incorporating the IPM Assessment, as the survey is called, into a widely attended program and using TurningPoint audience response devices, Extension educators can gather information from a significant number of farmers in a timely and efficient manner. Interspersing TurningPoint questions throughout presentations also increases audience engagement and overall quality of the training. For example, weed management programming efforts around herbicide-resistance management have been significantly influenced and enhanced by results of the IPM Assessment

Further Evidence for Chemical Fractionation from Ultraviolet Observations of Carbon Monoxide

Ultraviolet absorption from interstellar 12CO and 13CO was detected toward rho Oph A and chi Oph. The measurements were obtained at medium resolution with the Goddard High Resolution Spectrograph on the Hubble Space Telescope. Column density ratios, N(12CO)/N(13CO), of 125 \pm 23 and 117 \pm 35 were derived for the sight lines toward rho Oph A and chi Oph, respectively. A value of 1100 \pm 600 for the ratio N(12C16O)/N(12C18O) toward rho Oph A was also obtained. Absorption from vibrationally excited H_2 (v" = 3) was clearly seen toward this star as well. The ratios are larger than the isotopic ratios for carbon and oxygen appropriate for ambient interstellar material. Since for both carbon and oxygen the more abundant isotopomer is enhanced, selective isotopic photodissociation plays the key role in the fractionation process for these directions. The enhancement arises because the more abundant isotopomer has lines that are more optically thick, resulting in more self shielding from dissociating radiation. A simple argument involving the amount of self shielding [from N(12CO)] and the strength of the ultraviolet radiation field premeating the gas (from the amount of vibrationally excited H_2) shows that selective isotopic photodissociation controls the fractionation seen in these two sight lines, as well as the sight line to zeta Oph.Comment: 40 pages, 8 figures, to appear in 10 July 2003 issue of Ap

Technology Development to Explore the Relationship Between Oral Health and the Oral Microbial Community

The human oral cavity contains a complex microbial community that, until recently, has not been well characterized. Studies using molecular tools have begun to enumerate and quantify the species residing in various niches of the oral cavity; yet, virtually every study has revealed additional new species, and little is known about the structural dynamics of the oral microbial community or how it changes with disease. Current estimates of bacterial diversity in the oral cavity range up to 700 species, although in any single individual this number is much lower. Oral microbes are responsible for common chronic diseases and are suggested to be sentinels of systemic human diseases. Microarrays are now being used to study oral microbiota in a systematic and robust manner. Although this technology is still relatively young, improvements have been made in all aspects of the technology, including advances that provide better discrimination between perfect-match hybridizations from non-specific (and closely-related) hybridizations. This review addresses a core technology using gel-based microarrays and the initial integration of this technology into a single device needed for system-wide studies of complex microbial community structure and for the development of oral diagnostic devices

Isolation of Salmonella spp. and bacteriophage active against Salmonella spp. from commercial swine

Bacteriophage are viruses that prey on bacteria and may be a potential strategy to reduce foodborne pathogemc bactena in the gastromtestlnal tract of food animals Phages are fairly common in the gastrointestinal microbial ecosystem of mammals, but the incidence is unknown. If phage are to be an intervention strategy, we must understand their role in the microbial ecology of the gut. From a regulatory perspective, knowing incidence of phage is crucial. Therefore the current study was designed to determine the incidence of phage active against Salmonella spp in the feces of commercial finishing swine in the United States. Fecal samples (n=60) were collected from each of six commercial swine finishing operations. Samples were collected from 10 randomly selected pens throughout each operation. Total number of fecal samples collected in this study was n=360 Salmonella spp were found in 66% of the fecal samples Salmonella spp. were isolated from only 2 farms and the serotypes represented were Schwarzengrund, Anatum, Ohio and Heidelberg Bacteriophages were isolated from fecal sample through 2 parallel methods, 1) initlal enrichment in Salmonella Typhimunum, or 2) initial ennchment in E. colt B (a strain very sensitive to phages), followed by direct spot-testing against Salmonella Typhimurium Bacteriophages active against Salmonella Typhimunum were isolated from 1.1% 4/360) of the individual fecal samples when initially enriched in Salmonella Typhimurium, but E coli S-killing phages were 1solated from 43.8% (158/360) of the fecal samples but only 2 of these Isolates were capable of k1ll1ng Salmonella Typhimunum. Our results mdicate that bactenophage capable of killing Salmonella Typh1murium are fairly w1despread across commercial swine production facilities but may be present at relatively low populat1ons These results md1cate that phage (predator) populations may vary along w1th Salmonella (prey) populations and that phage could potentially be used as a food safety pathogen reduction strategy

Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity.

BackgroundThe newly defined superphylum Patescibacteria such as Parcubacteria (OD1) and Microgenomates (OP11) has been found to be prevalent in groundwater, sediment, lake, and other aquifer environments. Recently increasing attention has been paid to this diverse superphylum including > 20 candidate phyla (a large part of the candidate phylum radiation, CPR) because it refreshed our view of the tree of life. However, adaptive traits contributing to its prevalence are still not well known.ResultsHere, we investigated the genomic features and metabolic pathways of Patescibacteria in groundwater through genome-resolved metagenomics analysis of > 600 Gbp sequence data. We observed that, while the members of Patescibacteria have reduced genomes (~ 1 Mbp) exclusively, functions essential to growth and reproduction such as genetic information processing were retained. Surprisingly, they have sharply reduced redundant and nonessential functions, including specific metabolic activities and stress response systems. The Patescibacteria have ultra-small cells and simplified membrane structures, including flagellar assembly, transporters, and two-component systems. Despite the lack of CRISPR viral defense, the bacteria may evade predation through deletion of common membrane phage receptors and other alternative strategies, which may explain the low representation of prophage proteins in their genomes and lack of CRISPR. By establishing the linkages between bacterial features and the groundwater environmental conditions, our results provide important insights into the functions and evolution of this CPR group.ConclusionsWe found that Patescibacteria has streamlined many functions while acquiring advantages such as avoiding phage invasion, to adapt to the groundwater environment. The unique features of small genome size, ultra-small cell size, and lacking CRISPR of this large lineage are bringing new understandings on life of Bacteria. Our results provide important insights into the mechanisms for adaptation of the superphylum in the groundwater environments, and demonstrate a case where less is more, and small is mighty

Arrestin recruitment to dopamine D2 receptor mediates locomotion but not incentive motivation

The dopamine (DA) D2 receptor (D2R) is an important target for the treatment of neuropsychiatric disorders such as schizophrenia and Parkinson's disease. However, the development of improved therapeutic strategies has been hampered by our incomplete understanding of this receptor's downstream signaling processes in vivo and how these relate to the desired and undesired effects of drugs. D2R is a G protein-coupled receptor (GPCR) that activates G protein-dependent as well as non-canonical arrestin-dependent signaling pathways. Whether these effector pathways act alone or in concert to facilitate specific D2R-dependent behaviors is unclear. Here, we report on the development of a D2R mutant that recruits arrestin but is devoid of G protein activity. When expressed virally in "indirect pathway" medium spiny neurons (iMSNs) in the ventral striatum of D2R knockout mice, this mutant restored basal locomotor activity and cocaine-induced locomotor activity in a manner indistinguishable from wild-type D2R, indicating that arrestin recruitment can drive locomotion in the absence of D2R-mediated G protein signaling. In contrast, incentive motivation was enhanced only by wild-type D2R, signifying a dissociation in the mechanisms that underlie distinct D2R-dependent behaviors, and opening the door to more targeted therapeutics

Synthesis and structural characterization of a mimetic membrane-anchored prion protein

During pathogenesis of transmissible spongiform encephalopathies (TSEs) an abnormal form (PrPSc) of the host encoded prion protein (PrPC) accumulates in insoluble fibrils and plaques. The two forms of PrP appear to have identical covalent structures, but differ in secondary and tertiary structure. Both PrPC and PrPSc have glycosylphospatidylinositol (GPI) anchors through which the protein is tethered to cell membranes. Membrane attachment has been suggested to play a role in the conversion of PrPC to PrPSc, but the majority of in vitro studies of the function, structure, folding and stability of PrP use recombinant protein lacking the GPI anchor. In order to study the effects of membranes on the structure of PrP, we synthesized a GPI anchor mimetic (GPIm), which we have covalently coupled to a genetically engineered cysteine residue at the C-terminus of recombinant PrP. The lipid anchor places the protein at the same distance from the membrane as does the naturally occurring GPI anchor. We demonstrate that PrP coupled to GPIm (PrP-GPIm) inserts into model lipid membranes and that structural information can be obtained from this membrane-anchored PrP. We show that the structure of PrP-GPIm reconstituted in phosphatidylcholine and raft membranes resembles that of PrP, without a GPI anchor, in solution. The results provide experimental evidence in support of previous suggestions that NMR structures of soluble, anchor-free forms of PrP represent the structure of cellular, membrane-anchored PrP. The availability of a lipid-anchored construct of PrP provides a unique model to investigate the effects of different lipid environments on the structure and conversion mechanisms of PrP

Characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer.

The processing of sediment to accurately characterize the spatially-resolved depth profiles of geophysical and geochemical properties along with signatures of microbial density and activity remains a challenge especially in complex contaminated areas. This study processed cores from two sediment boreholes from background and contaminated core sediments and surrounding groundwater. Fresh core sediments were compared by depth to capture the changes in sediment structure, sediment minerals, biomass, and pore water geochemistry in terms of major and trace elements including pollutants, cations, anions, and organic acids. Soil porewater samples were matched to groundwater level, flow rate, and preferential flows and compared to homogenized groundwater-only samples from neighboring monitoring wells. Groundwater analysis of nearby wells only revealed high sulfate and nitrate concentrations while the same analysis using sediment pore water samples with depth was able to suggest areas high in sulfate- and nitrate-reducing bacteria based on their decreased concentration and production of reduced by-products that could not be seen in the groundwater samples. Positive correlations among porewater content, total organic carbon, trace metals and clay minerals revealed a more complicated relationship among contaminant, sediment texture, groundwater table, and biomass. The fluctuating capillary interface had high concentrations of Fe and Mn-oxides combined with trace elements including U, Th, Sr, Ba, Cu, and Co. This suggests the mobility of potentially hazardous elements, sediment structure, and biogeochemical factors are all linked together to impact microbial communities, emphasizing that solid interfaces play an important role in determining the abundance of bacteria in the sediments