Using geographic information systems as a common ground for dialogue about watershed stewardship

To help prepare professionals for leadership positions in watershed stewardship, the Center for Watershed Stewardship (CWS) at Penn State University has adapted GIS for use in its curriculum. The GIS is used as a common ground for communication between graduate students representing several departments or programs in an interdisciplinary, yearlong Keystone Project. The Keystone Project group works with a community organization to produce a watershed stewardship plan. Currently, Environmental Systems Research Institute (ESRI) ArcView 3.2a and 8.1 and several extensions are used routinely. Arc/Info 8.1 is also available for more complicated analyses and data management. This software is available in a dedicated computer laboratory with a 100-megabit network connecting 8 desktop and 2 laptop computers, with a dedicated geo-database and print server. CWS has committed funding for a teaching assistantship to support the computer operations and provide technical support. Students in the program come with varied GIS experience. Students have the option to take several GIS courses around the university and via CWS-sponsored short courses offered to professionals in business, government, and the nonprofit sectors. The students help each other to learn how to work with the data to develop a story of the watershed of interest, reinforcing a collaborative learning environment

Sperm Factor Initiates Capacitance and Conductance Changes in Mouse Eggs That Are More Similar to Fertilization Than IP3- or Ca2+-induced Changes

AbstractWe used patch clamp electrophysiology and concurrent imaging with the Ca2+-sensitive dye, fura-2, to study the temporal relationship between membrane capacitance and conductance and intracellular free Ca2+ concentration ([Ca2+]i) during mouse egg fertilization. We found an ∼2 pF step increase in egg membrane capacitance and a minor increase in conductance with no change in [Ca2+]i at sperm fusion. This was followed ∼1 min later by a rise in [Ca2+]i that led to larger changes in capacitance and conductance. The most common pattern for these later capacitance changes was an initial capacitance decrease, followed by a larger increase and eventual return to the approximate starting value. There was some variation in this pattern, and sub-μM peak [Ca2+]i favored capacitance decrease, while higher [Ca2+]i favored capacitance increase. The magnitude of accompanying conductance increases was variable and did not correlate well with peak [Ca2+]i. The intracellular introduction of porcine sperm factor reproduced the postfusion capacitance and conductance changes with a similar [Ca2+]i dependence. Raising [Ca2+]i by the intracellular introduction of IP3 initiated fertilization-like capacitance changes, but the conductance changes were slower to activate. Capacitance decrease could be induced when [Ca2+]i was increased modestly by activation of an endogenous Ca2+ current, with little effect on resting conductance. These results suggest that net turnover of the mouse egg surface membrane is sensitive to [Ca2+]i and that sperm and the active component of sperm factor may be doing more than initiating the IP3-mediated release of intracellular Ca2+

The analysis on the single particle model of CDW

Gruner put forward a single particle model of charge-density wave, which is a typical nonlinear differential equation, and also a mathematical model of pendulum. This Letter analyzes the solution of equation by the rotated vector fields theory, providing the relation between the applied field E and the periodic solution, and the conclusion that the critical value of E for the periodic solution is fixed in the over-damped situation. With these conclusions, it derives the formulae of nonlinear conductivity, narrow-band noise, which are consistent with the empirical ones given by Fleming.Comment: This is a version with a physics focus, the part with a mathematical focus is submitted at arXiv:0807.328

Is there evidence of selection in the dopamine receptor D4 gene in Australian invasive starling populations?

 Although population genetic theory is largely based on the premise that loci under study are selectively neutral, it has been acknowledged that the study of DNA sequence data under the influence of selection can be useful. In some circumstances, these loci show increased population differentiation and gene diversity. Highly polymorphic loci may be especially useful when studying populations having low levels of diversity overall, such as is often the case with threatened or newly established invasive populations. Using common starlings Sturnus vulgaris sampled from invasive Australian populations, we investigated sequence data of the dopamine receptor D4 gene (DRD4), a locus suspected to be under selection for novelty-seeking behaviour in a range of taxa including humans and passerine birds. We hypothesised that such behaviour may be advantageous when species encounter novel environments, such as during invasion. In addition to analyses to detect the presence of selection, we also estimated population differentiation and gene diversity using DRD4 data and compared these estimates to those from microsatellite and mitochondrial DNA sequence data, using the same individuals. We found little evidence for selection on DRD4 in starlings. However, we did find elevated levels of within-population gene diversity when compared to microsatellites and mitochondrial DNA sequence, as well as a greater degree of population differentiation. We suggest that sequence data from putatively nonneutral loci are a useful addition to studies of invasive populations, where low genetic variability is expected

Expected Shannon entropy and Shannon differentiation between subpopulations for neutral genes under the finite island model

<div><p>Shannon entropy <i>H</i> and related measures are increasingly used in molecular ecology and population genetics because (1) unlike measures based on heterozygosity or allele number, these measures weigh alleles in proportion to their population fraction, thus capturing a previously-ignored aspect of allele frequency distributions that may be important in many applications; (2) these measures connect directly to the rich predictive mathematics of information theory; (3) Shannon entropy is completely additive and has an explicitly hierarchical nature; and (4) Shannon entropy-based differentiation measures obey strong monotonicity properties that heterozygosity-based measures lack. We derive simple new expressions for the expected values of the Shannon entropy of the equilibrium allele distribution at a neutral locus in a single isolated population under two models of mutation: the infinite allele model and the stepwise mutation model. Surprisingly, this complex stochastic system for each model has an entropy expressable as a simple combination of well-known mathematical functions. Moreover, entropy- and heterozygosity-based measures for each model are linked by simple relationships that are shown by simulations to be approximately valid even far from equilibrium. We also identify a bridge between the two models of mutation. We apply our approach to subdivided populations which follow the finite island model, obtaining the Shannon entropy of the equilibrium allele distributions of the subpopulations and of the total population. We also derive the expected mutual information and normalized mutual information (“Shannon differentiation”) between subpopulations at equilibrium, and identify the model parameters that determine them. We apply our measures to data from the common starling (<i>Sturnus vulgaris</i>) in Australia. Our measures provide a test for neutrality that is robust to violations of equilibrium assumptions, as verified on real world data from starlings.</p></div

Identification of new, emerging HIV-1 unique recombinant forms and drug resistant viruses circulating in Cameroon

<p>Abstract</p> <p>Background</p> <p>The HIV epidemic in Cameroon is characterized by a high degree of viral genetic diversity with circulating recombinant forms (CRFs) being predominant. The goal of our study was to determine recent trends in virus evolution and emergence of drug resistance in blood donors and HIV positive patients.</p> <p>Methodology</p> <p>Blood specimens of 73 individuals were collected from three cities and a few villages in Cameroon and viruses were isolated by co-cultivation with PBMCs. Nested PCR was performed for gag p17 (670 bp) pol (840 bp) and Env gp41 (461 bp) genes. Sequences were phylogenetically analyzed using a reference set of sequences from the Los Alamos database.</p> <p>Results</p> <p>Phylogenetic analysis based on partial sequences revealed that 65% (n = 48) of strains were CRF02_AG, 4% (n = 3) subtype F2, 1% each belonged to CRF06 (n = 1), CRF11 (n = 1), subtype G (n = 1), subtype D (n = 1), CRF22_01A1 (n = 1), and 26% (n = 18) were Unique Recombinant Forms (URFs). Most URFs contained CRF02_AG in one or two HIV gene fragments analyzed. Furthermore, pol sequences of 61 viruses revealed drug resistance in 55.5% of patients on therapy and 44% of drug naïve individuals in the RT and protease regions. Overall URFs that had a primary HIV subtype designation in the pol region showed higher HIV-1 p24 levels than other recombinant forms in cell culture based replication kinetics studies.</p> <p>Conclusions</p> <p>Our results indicate that although CRF02_AG continues to be the predominant strain in Cameroon, phylogenetically the HIV epidemic is continuing to evolve as multiple recombinants of CRF02_AG and URFs were identified in the individuals studied. CRF02_AG recombinants that contained the pol region of a primary subtype showed higher replicative advantage than other variants. Identification of drug resistant strains in drug-naïve patients suggests that these viruses are being transmitted in the population studied. Our findings support the need for continued molecular surveillance in this region of West Central Africa and investigating impact of variants on diagnostics, viral load and drug resistance assays on an ongoing basis.</p

Immunolocalisation of phosphorylated STAT3, interleukin 11 and leukaemia inhibitory factor in endometrium of women with unexplained infertility during the implantation window.

BACKGROUND: Uterine receptivity and embryo implantation are critical in the establishment of pregnancy. The diagnosis of endometrial fertility requires more precise measurements of endometrial receptivity. Interleukin (IL-11) and leukemia inhibitory factor (LIF) are essential for murine implantation and signal via intracellular phosphorylation (p) of STAT3 in the endometrium. Both cytokines are present in the endometrium of women duiring the receptive window. Endometrial IL-11, IL-11 receptor alpha (IL-11Ralpha), LIF and pSTAT3 in women with primary unexplained infertility was compared to normal fertile women during the implantation window. METHODS: LH timed endometrial biopsies (LH+6 to LH+10) were collected from women with unexplained infertility and normal fertility. pSTAT3, IL-11, IL-11Ralpha and LIF production was determined by immunohistochemistry. Staining intensity was determoned by two independent observers blind to the fertility status of the patient from whom the biopsy was taken. Staining intensity and heterogeneity in each of the endometrial compartments (epithelium; stroma, including decidualized stromal cells; and vasculature) was assessed. The Mann-Whitney U test was used to analyze IL-11, pSTAT3, IL-11Ralpha and LIF immunostaining intensities in the samples. RESULTS: IL-11, IL-11Ralpha and LIF were present predominantly in glandular epithelium, whilst luminal epithelium showed patchy staining. pSTAT3 was present in both glandular epithelium and stroma. IL-11 and pSTAT3 immunostaining was significantly lower in glandular epithelium in infertile women compared to controls (P < 0.05) whilst IL-11Ralpha and LIF staining did not differ. CONCLUSION: This is the first demonstration of reduced endometrial pSTAT3 and IL-11 in some women with unexplained infertility. This suggests IL-11 and pSTAT3 may be involved in the secretory transformation of glandular epithelium during receptivity. Reduced IL-11 production and STAT3 phosphorylation may contribute to unexplained infertility in some women.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are