Seasonal dynamics of shallow-hyporheic-zone microbial community structure along a heavy-metal contamination gradient

Heavy metals contaminate numerous freshwater streams and rivers worldwide. Previous work by this group demonstrated a relationship between the structure of hyporheic microbial communities and the fluvial deposition of heavy metals along a contamination gradient during the fall season. Seasonal variation has been documented in microbial communities in numerous terrestrial and aquatic environments, including the hyporheic zone. The current study was designed to assess whether relationships between hyporheic microbial community structure and heavy-metal contamination vary seasonally by monitoring community structure along a heavy-metal contamination gradient for more than a year. No relationship between total bacterial abundance and heavy metals was observed (R(2) = 0.02, P = 0.83). However, denaturing gradient gel electrophoresis pattern analysis indicated a strong and consistent linear relationship between the difference in microbial community composition (populations present) and the difference in the heavy metal content of hyporheic sediments throughout the year (R(2) = 0.58, P < 0.001). Correlations between heavy-metal contamination and the abundance of four specific phylogenetic groups (most closely related to the alpha, beta, and gamma-proteobacteria and cyanobacteria) were apparent only during the fall and early winter, when the majority of organic matter is deposited into regional streams. These seasonal data suggest that the abundance of susceptible populations responds to heavy metals primarily during seasons when the potential for growth is highest.     

Cadherin-mediated cell-cell adhesion and tissue segregation in relation to malignancy

We review evidence concerning the basis for tissue segregation during embryonic development. This compartmentalization is shown to be an immiscibility phenomenon caused by changes in the strengths of adhesions between mobile cells which accompany their differentiation and generate interfacial tensions at cell population boundaries. The mobile cells exchange neighbors in response to these adhesion-generated forces which impel the system toward the configuration of maximal binding. Cadherins dominate these intercellular adhesions, but integrin-fibronectin-based adhesions also contribute to them as well as to cell-matrix adhesions. At the interface between two segregating cell populations are three kinds of cell-cell interfaces: a-a, b-b and a-b. Tissue immiscibility (segregation) results when the cross-adhesion is weaker than the mean value of the two kinds of self-adhesions, does not require (although it permits) qualitative changes in cell adhesion molecules and is easily generated even by moderate changes in the quantities of adhesion molecules on the cell surfaces. All type I and II cadherins tested cross-adhere, in most cases with strengths close to those of their self-adhesions. Is malignant invasion a process of cell segregation in reverse, in which the cross-adhesion between cancer cells and host tissue components is strong relative to their self-adhesions? We review evidence for cadherin involvement in breast, prostate and brain cancers. Despite evidence that N-cadherin enhances the invasiveness of certain cancer cells, we have found that increasing the expression not only of functional E-cadherin but also of P- or N-cadherin restrains the spreading of other malignant cell lines over (and through) a reconstituted extracellular matrix.     

Modeling Sustainability of Arctic Communities: An Interdisciplinary Collaboration of Researchers and Local Knowledge Holders

How will climate change affect the sustainability of Arctic villages over the next 40 years? This question motivated a collaboration of 23 researchers and four Arctic communities (Old Crow, Yukon Territory, Canada; Aklavik, Northwest Territories, Canada; Fort McPherson, Northwest Territories, Canada; and Arctic Village, Alaska, USA) in or near the range of the Porcupine Caribou Herd. We drew on existing research and local knowledge to examine potential effects of climate change, petroleum development, tourism, and government spending cutbacks on the sustainability of four Arctic villages. We used data across eight disciplines to develop an Arctic Community Synthesis Model and a Web-based, interactive Possible Futures Model. Results suggested that climate warming will increase vegetation biomass within the herd’s summer range. However, despite forage increasing, the herd was projected as likely to decline with a warming climate because of increased insect harassment in the summer and potentially greater winter snow depths. There was a strong negative correlation between hypothetical, development-induced displacement of cows and calves from utilized calving grounds and calf survival during June. The results suggested that climate warming coupled with petroleum development would cause a decline in caribou harvest by local communities. Because the Synthesis Model inherits uncertainties associated with each component model, sensitivity analysis is required. Scientists and stakeholders agreed that (1) although simulation models are incomplete abstractions of the real world, they helped bring scientific and community knowledge together, and (2) relationships established across disciplines and between scientists and communities were a valuable outcome of the study. Additional project materials, including the Web-based Possible Futures Model, are available at http://www.taiga.net/sustain.     

POSaM: a fast,flexible, open-source,inkjet oligonucleotide synthesizer and microarrayer

DNA arrays are valuable tools in molecular biology laboratories. Their rapid acceptance was aided by the release of plans for a pin-spotting microarrayer by researchers at Stanford. Inkjet microarraying is a flexible, complementary technique that allows the synthesis of arrays of any oligonucleotide sequences de novo. We describe here an open-source inkjet arrayer capable of rapidly producing sets of unique 9,800-feature arrays.     

Evaluating metabolic syndrome in a medical physiology laboratory

The metabolic syndrome, a cluster of factors linked to obesity that contribute to risk for atherosclerosis and Type 2 diabetes, may affect 20-25% of the adults in the United States. We designed a medical physiology laboratory to evaluate and discuss the physiological and nutritional principles involved in the metabolic syndrome. The five criteria used to diagnose this syndrome (fasting blood triglycerides, high-density lipoprotein cholesterol, and glucose, blood pressure, central obesity) were measured by students on each other either previously or during this exercise. In addition, to illustrate nutritional factors involved in causation and treatment of the metabolic syndrome, a meal was provided during the laboratory. Class members were randomized to groups allowed ad libitum meal composition, or constrained to the National Cholesterol Education Program Step I or Step II diets. The composition of the diet (including saturated fat, cholesterol, dietary fiber, and carbohydrate content) was discussed in the context of blood cholesterol, triglyceride, and glucose levels. This laboratory allows a comprehensive analysis of the physiological and nutritional factors involved in the development of the metabolic syndrome.     

Expression, purification, and characterization of authentic monoferric and apo-human serum transferrins

Transferrin is a bilobal protein with the ability to bind iron in two binding sites situated at the bottom of a cleft in each lobe. We have previously described the production of recombinant non-glycosylated human serum transferrins (hTF-NG), containing a factor Xa cleavage site and a hexa-His tag at the amino-terminus. Constructs in this background that contain strategic mutations to completely prevent iron binding in each lobe or in both lobes have now been produced. These monoferric hTFs will allow dissection of the contribution of each lobe to transferrin function. In addition, the construct completely lacking in the ability to bind iron in either lobe provides an opportunity to assess whether hTF has any other functions in addition to iron transport. Following insertion of the His-tagged hTF molecules into the pNUT vector, transfection into baby hamster kidney cells and selection with methotrexate, the secreted recombinant proteins were isolated from the tissue culture medium and characterized with regard to their iron binding properties. Significant improvements over our previous protocol include: (1) addition of butyric acid at a level of 1mM which leads to a substantial increase in protein production (as much as a 65% increase compared to control cells); and (2) elimination of an anion exchange column prior to isolation on a Qiagen Ni-NTA column which makes purification of the His-tagged constructs faster and therefore more efficient. These improvements should be applicable to expression of other recombinant proteins in mammalian cells.     

Differential effects of chronic escapable versus inescapable stress on male syrian hamster (Mesocricetus auratus) reproductive behavior

Stress decreases sexual activity, but it is uncertain which aspects of stress are detrimental to reproduction. This study used an escapable/inescapable stress paradigm to attempt to dissociate physical from psychological components of stress, and assess each component's impact on reproductive behavior in the male Syrian hamster (Mesocricetus auratus). Two experiments were completed using this protocol where two animals receive the same physical stressor (an electric footshock) but differ in the psychological aspect of control. One group (executive) could terminate the shock for themselves as well as a second group (yoked) by pressing a bar. Experiment 1 demonstrated a significant increase in plasma glucocorticoids at the end of a single 90-min stress session with no difference in glucocorticoid levels between the executive and yoked groups at any time point. Experiment 2 quantified male reproductive behavior prior to and immediately following 12 days of escapable or inescapable stress in executive, yoked, and no-stress control hamsters (n = 12/group). Repeated-measures analysis of variance revealed a number of significant changes in reproductive behavior before and after stress in the three treatment groups. The most striking difference was a decrease in hit rate observed only in the animals that could not control their stress (yoked group). Hit rate in the executive males that received the exact same physical stressor but could terminate the shock by pressing a bar was nearly identical to control animals that never received any foot shock. Therefore, we conclude that coping or control can ameliorate the negative effects of stress on male reproductive behavior.     

Telomeric P elements associated with cytotype regulation of the P transposon family in Drosophila melanogaster

P elements inserted at the left end of the Drosophila X chromosome were isolated genetically from wild-type P strains. Stocks carrying these elements were tested for repression of P-strain-induced gonadal dysgenesis in females and for repression of transposase-catalyzed P-element excision in males and females. Both traits were repressed by stocks carrying either complete or incomplete P elements inserted near the telomere of the X chromosome in cytological region 1A, but not by stocks carrying only nontelomeric X-linked P elements. All three of the telomeric P elements that were analyzed at the molecular level were inserted in one of the 1.8-kb telomere-associated sequence (TAS) repeats near the end of the X chromosome. Stocks with these telomeric P elements strongly repressed P-element excision induced in the male germline by a P strain or by the transposase-producing transgenes H(hsp/CP)2, H(hsp/CP)3, a combination of these two transgenes, and P(ry(+), delta2-3)99B. For H(hsp/CP)2 and P(ry(+), delta2-3)99B, the repression was also effective when the flies were subjected to heat-shock treatments. However, these stocks did not repress the somatic transposase activity of P(ry(+), delta2-3)99B. Repression of transposase activity in the germline required maternal transmission of the telomeric P elements themselves. Paternal transmission of these elements, or maternal transmission of the cytoplasm from carriers, both were insufficient to repress transposase activity. Collectively, these findings indicate that the regulatory abilities of telomeric P elements are similar to those of the P cytotype.     

Approaches to interval mapping of QTL in a multigeneration pedigree: the example of porcine chromosome 4

Quantitative trait loci (QTLs) have been mapped in many studies of F2 populations derived from crosses between diverse lines. One approach to confirming these effects and improving the mapping resolution is genetic chromosome dissection through a backcrossing programme. Analysis by interval mapping of the data generated is likely to provide additional power and resolution compared with treating data marker by marker. However, interval mapping approaches for such a programme are not well developed, especially where the founder lines were outbred. We explore alternative approaches to analysis using, as an example, data from chromosome 4 in an intercross between wild boar and Large White pigs where QTLs have been previously identified. A least squares interval mapping procedure was used to study growth rate and carcass traits in a subsequent second backcross generation (BC2). This procedure requires the probability of inheriting a wild boar allele for each BC2 animal for locations throughout the chromosome. Two methods for obtaining these probabilities were compared: stochastic or deterministic. The two methods gave similar probabilities for inheriting wild boar alleles and, hence, gave very similar results from the QTL analysis. The deterministic approach has the advantage of being much faster to run but requires specialized software. A QTL for fatness and for growth were confirmed and, in addition, a QTL for piglet growth from weaning at 5 weeks up to 7 weeks of age and another for carcass length were detected.