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At an organic farm in California, managed biodiversity was manipulated by establishing a mustard cover crop (MCC) and fallow during winter, and after incorporation, tomato mixtures of one, three, and five cultivars were planted in the spring (1-cv, 3-cv, and 5-cv, respectively). It was hypothesized that cultivar mixtures may increase yields over a monoculture if disease pressure or nitrogen (N) availability is affected by the previous cover crop. The monoculture (1-cv) of the grower’s preferred cultivar was compared with mixtures of it and other high-yielding cultivars in the region. Soil nitrogen, soil microbial biomass carbon (MBC), soil emissions of carbon dioxide (CO2) and nitrous oxide (N2O), crop nutrient uptake, biomass, fruit quality, intercepted photosynthetically active radiation (PAR), and disease symptoms were measured. The MCC reduced soil N leaching potential during winter and immobilized soil N early in the tomato season as suggested by higher soil MBC and CO2 emissions. Tomatoes had higher PAR, aboveground biomass, fruit yields, and harvest index in the winter fallow than in the winter MCC, likely due to higher N availability in the fallow plots after transplanting. All cultivar mixtures had fairly similar yield and shoot biomass within fallow and MCC, probably explained by the low genetic diversity among California modern tomato cultivars. However, at mid-season (75 days after planting (DAP)), the 3-cv mixture had higher shoot and fruit biomass, by 46% and 63%, than the monoculture in the MCC, indicating some plasticity under lower N availability. In the fallow treatment, soil CO2 emissions were lower in the 3-cv mixture than the monoculture at 77 and 100 DAP. Tomatoes in the 3-cv mixture were redder than the monoculture. The 3-cv mixture thus had some minor advantages compared with the monoculture, but overall, there was little evidence of higher ecosystem functions from mixtures vs. monoculture. Further research on mixtures of processing tomatoes may only be warranted for conditions of higher environmental stress than occur in California organic farms or if specific genotypic traits become available such as for disease resistance or improved nutrient uptake.

The vernal pool fairy shrimp (Branchinecta lynchi) (Eng et al. in J Crustac Biol 10:247–277, 1990) is broadly distributed throughout California’s Central Valley with disjunct populations in southern California and southern Oregon. A survey of genetic variation at the mitochondrial cytochrome c oxidase subunit I (COI) gene was conducted from individuals collected throughout the range of the species. Phylogenetic analysis of unique haplotypes could not resolve any significant genetic partitions below the species level. A detailed analysis of samples from two pools indicates that sample sizes underestimate overall variation, but that the general phylogeographic pattern still holds. Evidence was found for a putative long-distance dispersal event between Central Valley sites and the Oregon site. These results indicate that geographically limiting stochastic colonization followed by local diversification may be important in governing current genetic structure for this species. Future and current conservation/restoration efforts should recognize the geographic limitations to population structure for this species and focus on local endemic genetic variation.

We tested the hypothesis that stabilizing α-helix of Epstein–Barr virus gH-derived peptide 11438 used for binding human cells will increase its biological activity. Non-stable α-helix of peptide 11438 was unfolded in an entropy-driven process, despite the opposing effect of the enthalpy factor. Adding and/or changing amino acids in peptide 11438 allowed the designing of peptides 33207, 33208 and 33210; peptides 33208 and 33210 displayed higher helical content due to a decreased unfolding entropy change as was determined by AGADIR, molecular dynamics and circular dichroism analysis. Peptides 33207, 33208 and 33210 inhibited EBV invasion of peripheral blood mononuclear cells and displayed epitopes more similar to native protein than peptide 11438; these peptides could be useful for detecting antibodies induced by native gH protein since they displayed high reactivity with anti-EBV antibodies. Anti-peptide 33207 antibodies showed higher reactivity with EBV than anti-peptide 11438 antibodies being useful for inducing antibodies against EBV. Anti-peptide 33210 antibodies inhibit EBV invasion of epithelial cells better than anti-peptide 11438 antibodies. Peptide 33210 bound to normal T lymphocytes and Raji cells stronger than peptide 11438 and also induced apoptosis of monocytes and Raji cells but not of normal T cells in a similar way to EBV-gH. Peptide 33210 inhibited the monocytes’ development toward dendritic cells better than EBV and peptide 11438. In conclusion, stabilizing the α-helix in peptides 33208 and 33210 designed from peptide 11438 increased the antigenicity and the ability of the antibodies induced by peptides of inhibiting EBV invasion of host cells.

The identity-by-descent (IBD) based variance component analysis is an important method for mapping quantitative trait loci (QTL) in outbred populations. The interval-mapping approach and various modified versions of it may have limited use in evaluating the genetic variances of the entire genome because they require evaluation of multiple models and model selection. In this study, we developed a multiple variance component model for genome-wide evaluation using both the maximum likelihood (ML) method and the MCMC implemented Bayesian method. We placed one QTL in every few cM on the entire genome and estimated the QTL variances and positions simultaneously in a single model. Genomic regions that have no QTL usually showed no evidence of QTL while regions with large QTL always showed strong evidence of QTL. While the Bayesian method produced the optimal result, the ML method is computationally more efficient than the Bayesian method. Simulation experiments were conducted to demonstrate the efficacy of the new methods.

The Wnt/beta-catenin/TCF4 pathway plays critical roles in the maintenance of small intestinal epithelium; however, downstream targets of the beta-catenin/TCF4 complex are not extensively characterized. We identified miR-30e as an immediate target activated by the beta-catenin/TCF4 complex. miR-30e was detected in the peri-nuclear region of the intestinal crypt IEC-6 cells. Bioinformatics analysis revealed clustered beta-catenin/TCF4 binding sites within the miR-30e promoter region. This promoter region was cloned into pGL3-control luciferase reporter vector, with the enhancer region removed. Transfection of pCMV-SPORT6-beta-catenin expression vector dose-dependently increased luciferase activity, and co-transfection of pCMV-SPORT6-TCF4 expression vector further enhanced the promoter activity. Dexamethasone-induced IEC-6 cells differentiation caused a 2.5-fold increase in miR-30e expression, and upon beta-catenin siRNA transfection, miR-30e increased 1.3-fold. Electrophoretic mobility shift assay and chromatin immunoprecipitation assay confirmed the binding between beta-catenin/TCF4 complexes from IEC-6 nuclear extracts and the putative sequences in the miR-30e promoter. These results demonstrate that beta-catenin/TCF4 transactivates miR-30e during intestinal cell differentiation.

Siphons in a chemical reaction system are subsets of the species that have the potential of being absent in a steady state. We present a characterization of minimal siphons in terms of primary decomposition of binomial ideals, we explore the underlying geometry, and we demonstrate the effective computation of siphons using computer algebra software. This leads to a new method for determining whether given initial concentrations allow for various boundary steady states.

Conservation managers of oak woodlands have been reintroducing fire both as an ecological process per se and to assist in restoring native plant communities. To increase our understanding of the impacts of reintroduced fire on ground-dwelling invertebrates we examined the response of ants and spiders to a late season (autumn) prescribed fire conducted in a blue oak (Quercus douglasii) woodland ecosystem in northern California. Twelve 100 m × 100 m plots were established, six plots received a burn treatment and the remaining six plots were unburned controls. Ants and spiders were sampled using pitfall traps left open continuously and collected approximately every 32 days. Sampling was conducted over a year, consisting of four pre-burn and nine post-burn collections. Abundance was analyzed using a repeated measures ANOVA, which showed seed-harvester ants decreased significantly in the two months following the fire. Total spider abundance also showed a significant decrease in two months, although this did not occur immediately after the burn. One spider hunting guild, the ‘diurnal ambush’ group (Thomisidae) remained suppressed for up to nine months. Correspondence analysis measures of ant species abundance with environmental and vegetation variables (percent rock, bare ground, plant species richness and height of herbaceous vegetation) were higher than expected by chance, which assists in explaining some of the responses. Findings from this study revealed that the reintroduction of autumn burns has modest and short-term effect on the invertebrates sampled, suggesting that late season fires are compatible with other conservation goals for oak woodland ecosystems.

The mitotic spindle uses dynamic microtubules and mitotic motors to generate the pico-Newton scale forces that are needed to drive the mitotic movements that underlie chromosome capture, alignment and segregation. Here, we consider the biophysical and molecular basis of force-generation for chromosome movements in the spindle, and, with reference to the Drosophila embryo mitotic spindle, we briefly discuss how mathematical modeling can complement experimental analysis to illuminate the mechanisms of chromosome-to-pole motility during anaphase A and spindle elongation during anaphase B.

Many populations live and disperse in advective media. A fundamental question, known as the “drift paradox” in stream ecology, is how a closed population can survive when it is constantly being transported downstream by the flow. Recent population-level models have focused on the role of diffusive movement in balancing the effects of advection, predicting critical conditions for persistence. Here, we formulate an individual-based stochastic analog of the model described in (Lutscher et al., SIAM Rev. 47(4):749–772, 2005) to quantify the effects of demographic stochasticity on persistence. Population dynamics are modeled as a logistic growth process and dispersal as a position-jump process on a finite domain divided into patches. When there is no correlation in the interpatch movement of residents, stochasticity simply smooths the persistence-extinction boundary. However, when individuals disperse in “packets” from one patch to another and the flow field is memoryless on the timescale of packet transport, the probability of persistence is greatly enhanced. The latter transport mechanism may be characteristic of larval dispersal in the coastal ocean or wind-dispersed seed pods.

We used radiocarbon measurements of dissolved organic carbon (DOC) to resolve sources of riverine carbon within agriculturally dominated landscapes in California. During 2003 and 2004, average Δ14C for DOC was −254‰ in agricultural drains in the Sacramento–San Joaquin Delta, −218‰ in the San Joaquin River, −175‰ in the California State Water Project and −152‰ in the Sacramento River. The age of bulk DOC transiting the rivers of California’s Central Valley is the oldest reported for large rivers and suggests wide-spread loss of soil organic matter caused by agriculture and urbanization. Using DAX 8 adsorbent, we isolated and measured 14C concentrations in hydrophobic acid fractions (HPOA); river samples showed evidence of bomb-pulse carbon with average Δ14C of 91 and 76‰ for the San Joaquin and Sacramento Rivers, respectively, with older HPOA, −204‰, observed in agricultural drains. An operationally defined non-HPOA fraction of DOC was observed in the San Joaquin River with seasonally computed Δ14C values of between −275 and −687‰; the source of this aged material was hypothesized to be physically protected organic-matter in high clay-content soils and agrochemicals (i.e., radiocarbon-dead material) applied to farmlands. Mixing models suggest that the Sacramento River contributes about 50% of the DOC load in the California State Water Project, and agricultural drains contribute approximately one-third of the load. In contrast to studies showing stabilization of soil carbon pools within one or two decades following land conversion, sustained loss of soil organic matter, occurring many decades after the initial agricultural-land conversion, was observed in California’s Central Valley.

Human activities have profoundly altered the global nitrogen (N) cycle. Increases in anthropogenic N have had multiple effects on the atmosphere, on terrestrial, freshwater and marine ecosystems, and even on human health. Unfortunately, methodological limitations challenge our ability to directly measure natural N inputs via biological N fixation (BNF)—the largest natural source of new N to ecosystems. This confounds efforts to quantify the extent of anthropogenic perturbation to the N cycle. To address this gap, we used a pair of indirect methods—analytical modeling and N balance—to generate independent estimates of BNF in a presumed hotspot of N fixation, a tropical rain forest site in central Rondônia in the Brazilian Amazon Basin. Our objectives were to attempt to constrain symbiotic N fixation rates in this site using indirect methods, and to assess strengths and weaknesses of this approach by looking for areas of convergence and disagreement between the estimates. This approach yielded two remarkably similar estimates of N fixation. However, when compared to a previously published bottom-up estimate, our analysis indicated much lower N inputs via symbiotic BNF in the Rondônia site than has been suggested for the tropics as a whole. This discrepancy may reflect errors associated with extrapolating bottom-up fluxes from plot-scale measures, those resulting from the indirect analyses, and/or the relatively low abundance of legumes at the Rondônia site. While indirect methods have some limitations, we suggest that until the technological challenges of directly measuring N fixation are overcome, integrated approaches that employ a combination of model-generated and empirically-derived data offer a promising way of constraining N inputs via BNF in natural ecosystems.

Centrioles are cylinders made of nine microtubule (MT) triplets present in many eukaryotes. Early studies, where centrosomes were seen at the poles of the mitotic spindle led to their coining as “the organ for cell division”. However, a variety of subsequent observational and functional studies showed that centrosomes might not always be essential for mitosis. Here we review the arguments in this debate. We describe the centriole structure and its distribution in the eukaryotic tree of life and clarify its role in the organization of the centrosome and cilia, with an historical perspective. An important aspect of the debate addressed in this review is how centrioles are inherited and the role of the spindle in this process. In particular, germline inheritance of centrosomes, such as their de novo formation in parthenogenetic species, poses many interesting questions. We finish by discussing the most likely functions of centrioles and laying out new research avenues.

One hundred ninety-four germplasm accessions of fig representing the four fig types, Common, Smyrna, San Pedro, and Caprifig were analyzed for genetic diversity, structure, and differentiation using genetic polymorphism at 15 microsatellite loci. The collection showed considerable polymorphism with observed number of alleles per locus ranging from four for five different loci, MFC4, LMFC14, LMFC22, LMFC31 and LMFC35 to nine for LMFC30 with an average of 4.9 alleles per locus. Seven of the 15 loci included in the genetic structure analyses exhibited significant deviation from panmixia, of which two showed excess and five showed deficiency of heterozygote. The cluster analysis (CA) revealed ten groups with 32 instances of synonymy among cultivars and groups differed significantly for frequency and composition of alleles for different loci. The principal components analysis (PCA) confirmed the results of CA with some groups more differentiated than the others. Further, the model based Bayesian approach clustering suggested a subtle population structure with mixed ancestry for most figs. The gene diversity analysis indicated that much of the total variation is found within groups (H G /H T = 0.853; 85.3%) and the among groups within total component (G GT = 0.147) accounted for the remaining 14.7%, of which ~64% accounted for among groups within clusters (G GC = 0.094) and ~36% among clusters (G CT = 0.053). The analysis of molecular variance (AMOVA) showed approximately similar results with nearly 87% of variation within groups and ~10% among groups within clusters, and ~3% among clusters. Overall, the gene pool of cultivated fig analyzed possesses substantial genetic polymorphism but exhibits narrow differentiation. It is evident that fig accessions from Turkmenistan are somewhat genetically different from the rest of the Mediterranean and the Caucasus figs. The long history of domestication and cultivation with widespread dispersal of cultivars with many synonyms has resulted in a great deal of confusion in the identification and classification of cultivars in fig.

Precise information about endangered species, in particular identifying their resources requirements, is needed to identify areas that might support populations. Little is known about the endangered Mount Hermon June Beetle (Polyphylla barbata) found only within Zayante soils region of Santa Cruz County, California. We investigated the beetle’s host plant selection, habitat association and mating behavior between June 2004 and September 2005. We identified angiosperm and Pteridophyta phyla, and fungi within the frass pellets of Mount Hermon June Beetle larvae demonstrating that they are not specialist feeders but are microhabitat specialists. Larval species was confirmed by DNA analysis. Significant differences were found in vegetation assemblages between regions where the Mount Hermon June Beetle did and did not occur for Chorizanthe pungens var. hartwegiana, and bare ground.

Swimming microorganisms such as bacteria or spermatozoa are typically found in dense suspensions, and exhibit collective modes of locomotion qualitatively different from that displayed by isolated cells. In the dilute limit where fluid-mediated interactions can be treated rigorously, the long-time hydrodynamics of a collection of cells result from interactions with many other cells, and as such typically eludes an analytical approach. Here, we consider the only case where such problem can be treated rigorously analytically, namely when the cells have spatially confined trajectories, such as the spermatozoa of some marine invertebrates. We consider two spherical cells swimming, when isolated, with arbitrary circular trajectories, and derive the long-time kinematics of their relative locomotion. We show that in the dilute limit where the cells are much further away than their size, and the size of their circular motion, a separation of time scale occurs between a fast (intrinsic) swimming time, and a slow time where hydrodynamic interactions lead to change in the relative position and orientation of the swimmers. We perform a multiple-scale analysis and derive the effective dynamical system—of dimension two—describing the long-time behavior of the pair of cells. We show that the system displays one type of equilibrium, and two types of rotational equilibrium, all of which are found to be unstable. A detailed mathematical analysis of the dynamical systems further allows us to show that only two cell-cell behaviors are possible in the limit of t→∞, either the cells are attracted to each other (possibly monotonically), or they are repelled (possibly monotonically as well), which we confirm with numerical computations. Our analysis shows therefore that, even in the dilute limit, hydrodynamic interactions lead to new modes of cell-cell locomotion.

This study examines whether in nature endangered quino checkerspot (Euphydryas editha quino) larvae will return to diapause and if so where they choose to hide. Multiple years of diapause probably help larvae survive drought years and sites chosen have high survival value to the species. Ninety square meters of habitat were created by removing non native plants and replacing them with natives found at checkerspot occupied sites. During the 2005–2006 winter 1,000 post-diapause larvae were released. From these larvae 31 adults (20 males and 11 females) developed over a 2.5 month period (March 20–June 6) from 41 pupae. One chrysalis was parasitized by a parasitic wasp Pteromalus puparum (L.) in the family Pteromalidae, one was partially eaten by an animal, while the remaining eight pupae died of unknown causes. Thirty quadrats (1 square meter each) were cleared of vegetation, leaf and branch litter, rocks, and checkerspot larvae from July 5 to August 1, 2006. Forty-nine larvae were found that returned to diapause. Most larvae (31) chose to make shelters on California buckwheat, which is not a checkerspot food plant, two to five cm above the ground. One shelter had 22, another had seven, and two others had single larvae. Five of 10 larvae found in leaf litter below California buckwheat were crawling and not associated with shelters suggesting they had been dislodged from shelters. California buckwheat may be important in habitat restoration for the checkerspot, particularly at sites below 900 meters elevation where summer conditions are hot and dry. No additional larvae were found the following spring, when they should have exited diapause. Therefore 910 (91%) larvae were lost to some undocumented form of mortality.

It is well known that microbial-mediated soil respiration, the major source of CO2 from terrestrial ecosystems, is sensitive to temperature. Here, we hypothesize that some mechanisms, such as acclimation of microbial respiration to temperature and/or regulation by plant fresh C inputs of the temperature sensitivity of decomposition of soil organic matter (SOM), should be taken into account to predict soil respiration correctly. Specifically, two hypotheses were tested: (1) under warm conditions, temperature sensitivity (Q10) and basal rates of microbial-mediated soil respiration (Bs20, respiration at a given temperature) would be primarily subjected to presence/absence of plant fresh C inputs; and (2) under cold conditions, where labile C depletion occurred more slowly, microbial-mediated soil respiration could adjust its optimal temperatures to colder temperatures (acclimation), resulting in a net increase of respiration rates for a given temperature (Bs20). For this purpose, intact soil cores from an oak savanna ecosystem were incubated with sufficient water supply at two contrasting temperatures (10 and 30°C) during 140 days. To study temperature sensitivity of soil respiration, short-term temperature cycles (from 5 to 40°C at 8 h steps) were applied periodically to the soils. Our results confirmed both hypotheses. Under warm conditions ANCOVA and likelihood ratio tests confirmed that both Q10 and Bs20 decreased significantly during the incubation. Further addition of glucose at the end of the incubation period increased Bs20 and Q10 to initial values. The observed decrease in temperature sensitivity (Q10) in absence of labile C disagrees with the broadly accepted fact that temperature sensitivity of the process increases as quality of the substrate decreases. Our experiment also shows that after 2 months of incubation cold-incubated soils doubled the rates of respiration at cold temperatures causing a strong increase in basal respiration rates (Bs20). This suggest that microbial community may have up-regulated their metabolism at cold conditions (cold-acclimation), which also disagrees with most observations to date. The manuscript discusses those two apparent contradictions: the decrease in temperature sensitivity in absence of labile C and the increase in microbial-mediated soil respiration rates at cold temperatures. While this is only a case study, the trends observed could open the controversy over the validity of current soil respiration models.

Understanding and predicting the responses of plant communities to multiple overlapping disturbances remains a challenging task. Hurricane Wilma represents a large, yet infrequent type of disturbance that was superimposed on an existing disturbance gradient of time since fire. We examined disturbance and recovery patterns in response to these overlapping disturbances by measuring how canopy structure, fine roots, mycorrhizae, and soil nitrogen dynamics, varied along a fire chronosequence in the 2 years after Hurricane Wilma. Hurricane damage increased canopy openness in all seral stages. In the early-seral stage, canopy openness returned to pre-hurricane conditions within 2 years, whereas canopy openness in the late-seral stage remained significantly higher throughout the study. We observed no significant change in root length density in the early- and mid-seral stages. However, in the late-seral stage, root length density was significantly reduced immediately after the hurricane and remained so 2 years after the hurricane. In the late-seral stage, we also observed a significant reduction in percent soil nitrogen and a significant increase in soil nitrogen isotopic composition (δ15N) values, indicating a loss of soil nitrogen. In contrast, in the early- and mid-seral stages, there were no significant changes in percent nitrogen or soil δ15N values. Results from this study suggest that forest fire disturbance history influences responses to hurricane damage. Moreover, feedbacks between aboveground and belowground processes have the potential to influence forest recovery.

We examined seasonal and spatial linkages between N cycling and organic matter for a suburban stream in Maryland and addressed the question: How do longitudinal NH4 + uptake patterns vary seasonally and what is the effect of organic matter, stream size, transient storage and debris dams? We applied a longitudinal (stream channel corridor) approach in a forested stream section and conducted short-term nutrient addition experiments (adapted to account for the effect of nutrient saturation) covering 14–16 reaches, and compared two distinct seasons (late fall 2003 and late summer 2004). Longitudinal NH4 + uptake rate patterns had a distinct seasonal reversal; fall had the highest uptake rates in the upper reaches, while summer had the highest uptake rates in the lower reaches. This seasonal reversal was attributed to organic matter and evidenced by DON patterns. Transient storage did not have an expected effect on uptake rates in fall because it was confounded by leaf litter; litter produced higher uptakes, but also may have reduced transient storage. In summer however, uptake rates had a positive correlation with transient storage. Debris dams had no distinct effect on uptake in fall because of their recent formation. In summer however, the debris dam effect was significant; although the debris dams were hydraulically inactive then, the upstream reaches had 2–5 fold higher uptake rates. The seasonal and longitudinal differences in NH4 + uptake reflect interactions between flow conditions and the role of organic matter. Urbanization can alter both of these characteristics, hence affect stream N processing.

We examined the effect of concentration on nitrogen uptake patterns for a suburban stream in Maryland and addressed the question: How does NO3 − uptake change as a function of concentration and how do uptake patterns compare with those found for NH4 +? We applied a longitudinal (stream channel corridor) approach in a forested stream section and conducted short-term nutrient addition experiments in late summer 2004. In the downstream direction, NO3 − concentrations decreased because of residential development in headwaters and downstream dilution; NH4 + concentrations slightly increased. The uptake patterns for NO3 − were very different from NH4 +. While NH4 + had a typical negative relationship between first-order uptake rate constant (K c ) and stream size, NO3 − had a reverse pattern. We found differences for other metrics, including uptake velocity (V f ) and areal uptake rate (U). We attributed these differences to a stream size effect, a concentration effect and a biological uptake capacity effect. For NO3 − these combined effects produced a downstream increase in K c , V f and U; for NH4 + they produced a downstream decrease in K c and V f , and a not well defined pattern for U. We attributed a downstream increase in NO3 − uptake capacity to an increase in hyporheic exchange and a likely increase in carbon availability. We also found that K c and V f were indirectly related with concentration. Similar evidence of ‘nutrient saturation’ has been reported in other recent studies. Our results suggest that higher-order uptake models might be warranted when scaling NO3 − uptake across watersheds that are subject to increased nitrogen loading.

Experiments were conducted in laboratory bioreactors and in field plots to test effects of certain cultivated members of the grass family (Poaceae = Gramineae), including wheat (Triticum aestivum cv. Yolo), barley (Hordeum vulgare cv. UC337), oats (Avena sativa cv. Montezuma), triticale (X Triticosecale), and a sorghum-sudangrass hybrid (Sorghum bicolor x S. sudanense = “sudex”, cv. Green Grazer V) for soil disinfestation potential. Soilborne pest organisms tested for effects on survival and activity included the phytopathogens Sclerotium rolfsii, Pythium ultimum and Meloidogyne incognita, and a variety of weed taxa. Following soil amendment, bioreactors were incubated for 7 days at ambient (23°C) or elevated, but sublethal (38°C day/27°C night), soil heating regimens. Addition of each of the poaceous amendments to soil at 23°C resulted in inconsistently reduced tomato root galling (49–97%) by M. incognita, or reduced recovery of S. rolfsii and P. ultimum (0–100%) fungi in soil, after 7 days’ incubation (P ≤ 0.05). When the organisms were exposed to the poaceous soil amendments at the 38o/27o temperature regimen, nematode galling and recovery of active fungi were consistently and significantly reduced by 98–100%. These results demonstrated feasibility of soil disinfestation (“biofumigation”) by activity of poaceous amendments, further aided by combining plant residues with soil heating (e.g. solarization). Results from three field experiments with sudex cover crops, conducted throughout the growing season, demonstrated biocidal activity on a range of weedy plants, including Amaranthus retroflexus, Calandrinia ciliata, Cerastium arvense, Digitaria sanguinalis, Echinochloa crus-galli and Poa annua. Both shoots and roots of sudex provided allelopathic weed biomass reductions of 35–100%, and for at least 106 days after shredding. Deleterious activity of shredded residues incorporated in soil was less persistent. These properties in poaceous crops can be useful for soil disinfestation; however, harmful phytotoxicity to subsequent crops may also result. In order to take full advantage of these low-input measures for controlling soilborne diseases and pests, further understanding of their properties must be gained, and user guidelines developed.

Platelets interact with bacterial pathogens through a wide array of cellular and molecular mechanisms. The consequences of this interaction may significantly influence the balance between infection and immunity. On the one hand, recent data indicate that certain bacteria may be capable of exploiting these interactions to gain a virulence advantage. Indeed, certain bacterial pathogens appear to have evolved specific ways in which to subvert activated platelets. Hence, it is conceivable that some bacterial pathogens exploit platelet responses. On the other hand, platelets are now known to possess unambiguous structures and functions of host defense effector cells. Recent discoveries emphasize critical features enabling such functions, including expression of toll-like receptors that detect hallmark signals of bacterial infection, an array of microbicidal peptides, as well as other host defense molecules and functions. These concepts are consistent with increased risk and severity of bacterial infection as correlates of clinical abnormalities in platelet quantity and quality. In these respects, the molecular and cellular roles of platelets in host defense against bacterial pathogens are explored with attention on advances in platelet immunobiology.

Habitat mitigation frequently leads to planting of new habitat, assuming that it can replace lost natural habitat. Yet this practice has rarely been examined in detail. In the USA habitat mitigation is frequently allowed under the US Endangered Species Act, providing monitoring reports which represent a potentially valuable data source for imperiled species. We used publicly available reports for the US threatened Valley elderberry longhorn beetle (Desmocerus californicus dimorphus) to assess record keeping practices used by US Fish and Wildlife Service (FWS), and the utility of such analyses for improving conservation. A large portion of mitigation reports known to exist were missing from FWS files, indicating problems with data management, and a loss of important information. Transplanted brought mature beetle host plants and beetles to sites, promoting beetle colonization. Conversely, few sites with seedlings were colonized. Results indicate a need for improved data management by FWS and longer term monitoring.

Carcinogenesis and cancer progression are often modeled using population dynamics equations for a diverse somatic cell population undergoing mutations or other alterations that alter the fitness of a cell and its progeny. Usually it is then assumed, paralleling standard mathematical approaches to evolution, that such alterations are slow compared to selection, i.e., compared to subpopulation frequency changes induced by unequal subpopulation proliferation rates. However, the alterations can be rapid in some cases. For example, results in our lab on in vitro analogues of transformation and progression in carcinogenesis suggest there could be periods where rapid alterations triggered by horizontal intercellular transfer of genetic material occur and quickly result in marked changes of cell population structure.We here initiate a mathematical study of situations where alterations are rapid compared to selection. A classic selection-mutation formalism is generalized to obtain a “proliferation-alteration” system of ordinary differential equations, which we analyze using a rapid-alteration approximation. A system-theoretical estimate of the total-population net growth rate emerges. This rate characterizes the diverse, interacting cell population acting as a single system; it is a weighted average of subpopulation rates, the weights being components of the Perron–Frobenius eigenvector for an ergodic Markov-process matrix that describes alterations by themselves. We give a detailed numerical example to illustrate the rapid-alteration approximation, suggest a possible interpretation of the fact that average aneuploidy during cancer progression often appears to be comparatively stable in time, and briefly discuss possible generalizations as well as weaknesses of our approach.

DNA mismatch repair proteins play an essential role in maintaining genomic integrity during replication and genetic recombination. We successfully isolated a full length MSH2 and partial MSH7 cDNAs from tomato, based on sequence similarity between MutS and plant MSH homologues. Semi-quantitative RT-PCR reveals higher levels of mRNA expression of both genes in young leaves and floral buds. Genetic mapping placed MSH2 and MSH7 on chromosomes 6 and 7, respectively, and indicates that these genes exist as single copies in the tomato genome. Analysis of protein sequences and phylogeny of the plant MSH gene family show that these proteins are evolutionarily conserved, and follow the classical model of asymmetric protein evolution. Genetic manipulation of the expression of these MSH genes in tomato will provide a potentially useful tool for modifying genetic recombination and hybrid fertility between wide crosses.

Biophysicists use single particle tracking (SPT) methods to probe the dynamic behavior of individual proteins and lipids in cell membranes. The mean squared displacement (MSD) has proven to be a powerful tool for analyzing the data and drawing conclusions about membrane organization, including features like lipid rafts, protein islands, and confinement zones defined by cytoskeletal barriers. Here, we implement time series analysis as a new analytic tool to analyze further the motion of membrane proteins. The experimental data track the motion of 40 nm gold particles bound to Class I major histocompatibility complex (MHCI) molecules on the membranes of mouse hepatoma cells.Our first novel result is that the tracks are significantly autocorrelated. Because of this, we developed linear autoregressive models to elucidate the autocorrelations. Estimates of the signal to noise ratio for the models show that the autocorrelated part of the motion is significant. Next, we fit the probability distributions of jump sizes with four different models. The first model is a general Weibull distribution that shows that the motion is characterized by an excess of short jumps as compared to a normal random walk. We also fit the data with a chi distribution which provides a natural estimate of the dimension d of the space in which a random walk is occurring. For the biological data, the estimates satisfy 1

When Charles Darwin published The Origin of Species 150 years ago he consciously avoided discussing the origin of life. However, analysis of some other texts written by Darwin, and of the correspondence he exchanged with friends and colleagues demonstrates that he took for granted the possibility of a natural emergence of the first life forms. As shown by notes from the pages he excised from his private notebooks, as early as 1837 Darwin was convinced that “the intimate relation of Life with laws of chemical combination, & the universality of latter render spontaneous generation not improbable”. Like many of his contemporaries, Darwin rejected the idea that putrefaction of preexisting organic compounds could lead to the appearance of organisms. Although he favored the possibility that life could appear by natural processes from simple inorganic compounds, his reluctance to discuss the issue resulted from his recognition that at the time it was possible to undertake the experimental study of the emergence of life.

Associative learning is key to how bees recognize and return to rewarding floral resources. It thus plays a major role in pollinator floral constancy and plant gene flow. Honeybees are the primary model for pollinator associative learning, but bumblebees play an important ecological role in a wider range of habitats, and their associative learning abilities are less well understood. We assayed learning with the proboscis extension reflex (PER), using a novel method for restraining bees (capsules) designed to improve bumblebee learning. We present the first results demonstrating that bumblebees exhibit the memory spacing effect. They improve their associative learning of odor and nectar reward by exhibiting increased memory acquisition, a component of long-term memory formation, when the time interval between rewarding trials is increased. Bombus impatiens forager memory acquisition (average discrimination index values) improved by 129% and 65% at inter-trial intervals (ITI) of 5 and 3 min, respectively, as compared to an ITI of 1 min. Memory acquisition rate also increased with increasing ITI. Encapsulation significantly increases olfactory memory acquisition. Ten times more foragers exhibited at least one PER response during training in capsules as compared to traditional PER harnesses. Thus, a novel conditioning assay, encapsulation, enabled us to improve bumblebee-learning acquisition and demonstrate that spaced learning results in better memory consolidation. Such spaced learning likely plays a role in forming long-term memories of rewarding floral resources.

The soil emission rates (fluxes) of nitrous oxide (N2O) and nitrogen oxides (NO + NO2 = NO x ) through a seasonal snowpack were determined by a flux gradient method from near-continuous 2-year measurements using an automated system for sampling interstitial air at various heights within the snowpack from a subalpine site at Niwot Ridge, Colorado. The winter seasonal-averaged N2O fluxes of 0.047–0.069 nmol m−2 s−1 were ~15 times higher than observed NO x fluxes of 0.0030–0.0067 nmol m−2 s−1. During spring N2O emissions first peaked and then dropped sharply as the soil water content increased from the release of snowpack meltwater, while other gases, including NO x and CO2 did not show this behavior. To compare and contrast the winter fluxes with snow-free conditions, N2O fluxes were also measured at the same site in the summers of 2006 and 2007 using a closed soil chamber method. Summer N2O fluxes followed a decreasing trend during the dry-out period after snowmelt, interrupted by higher values related to precipitation events. These peaks were up to 2–3 times higher than the background summer levels. The integrated N2O-N loss over the summer period was calculated to be 1.1–2.4 kg N ha−1, compared to ~0.24–0.34 kg N ha−1 for the winter season. These wintertime N2O fluxes from subniveal soil are generally higher than the few previously published data. These results are of the same order of magnitude as data from more productive ecosystems such as fertilized grasslands and high-N-cycling forests, most likely because of a combination of the relatively well-developed soils and the fact that subnivean biogeochemical processes are promoted by the deep, insulating snowpack. Hence, microbially mediated oxidized nitrogen emissions occurring during the winter can be a significant part of the N-cycle in seasonally snow-covered subalpine ecosystems.

Fluxes of CO2 during the snow-covered season contribute to annual carbon budgets, but our understanding of the mechanisms controlling the seasonal pattern and magnitude of carbon emissions in seasonally snow-covered areas is still developing. In a subalpine meadow on Niwot Ridge, Colorado, soil CO2 fluxes were quantified with the gradient method through the snowpack in winter 2006 and 2007 and with chamber measurements during summer 2007. The CO2 fluxes of 0.71 μmol m−2 s−1 in 2006 and 0.86 μmol m−2 s−1 in 2007 are among the highest reported for snow-covered ecosystems in the literature. These fluxes resulted in 156 and 189 g C m−2 emitted over the winter, ~30% of the annual soil CO2 efflux at this site. In general, the CO2 flux increased during the winter as soil moisture increased. A conceptual model was developed with distinct snow cover zones to describe this as well as the three other reported temporal patterns in CO2 flux from seasonally snow-covered soils. As snow depth and duration increase, the factor controlling the CO2 flux shifts from freeze–thaw cycles (zone I) to soil temperature (zone II) to soil moisture (zone III) to carbon availability (zone IV). The temporal pattern in CO2 flux in each zone changes from periodic pulses of CO2 during thaw events (zone I), to CO2 fluxes reaching a minimum when soil temperatures are lowest in mid-winter (zone II), to CO2 fluxes increasing gradually as soil moisture increases (zone III), to CO2 fluxes decreasing as available carbon is consumed. This model predicts that interannual variability in snow cover or directional shifts in climate may result in dramatically different seasonal patterns of CO2 flux from seasonally snow-covered soils.

The coding of olfactory stimuli across a wide range of organisms may rely on fundamentally similar mechanisms in which a complement of specific odorant receptors on olfactory sensory neurons respond differentially to airborne chemicals to initiate the process by which specific odors are perceived. The question that we address in this review is the role of specific neurons in mediating this sensory system—an identity code—relative to the role that temporally specific responses across many neurons play in producing an olfactory perception—a temporal code. While information coded in specific neurons may be converted into a temporal code, it is also possible that temporal codes exist in the absence of response specificity for any particular neuron or subset of neurons. We review the data supporting these ideas, and we discuss the research perspectives that could help to reveal the mechanisms by which odorants become perceptions.

Carbon dioxide is taken up by agricultural crops and released soon after during the consumption of agricultural commodities. The global net impact of this process on carbon flux to the atmosphere is negligible, but impact on the spatial distribution of carbon dioxide uptake and release across regions and continents is significant. To estimate the consumption and release of carbon by humans over the landscape, we developed a carbon budget for humans in the United States. The budget was derived from food commodity intake data for the US and from algorithms representing the metabolic processing of carbon by humans. Data on consumption, respiration, and waste of carbon by humans were distributed over the US using geospatial population data with a resolution of ~450 × 450 m. The average adult in the US contains about 21 kg C and consumes about 67 kg C year−1 which is balanced by the annual release of about 59 kg C as expired CO2, 7 kg C as feces and urine, and less than 1 kg C as flatus, sweat, and aromatic compounds. In 2000, an estimated 17.2 Tg C were consumed by the US population and 15.2 Tg C were expired to the atmosphere as CO2. Historically, carbon stock in the US human population has increased between 1790 and 2006 from 0.06 Tg to 5.37 Tg. Displacement and release of total harvested carbon per capita in the US is nearly 12% of per capita fossil fuel emissions. Humans are using, storing, and transporting carbon about the Earth’s surface. Inclusion of these carbon dynamics in regional carbon budgets can improve our understanding of carbon sources and sinks.

Nitrate has long been thought to be chemically unreactive in soil. This view was challenged by the report of an apparently abiotic process whereby nitrate (NO3 −) is incorporated into organic compounds (Dail et al. 2001). In Colman et al. (2007), we examined how common this process might be by testing for it in 45 soils collected from across a range of ecosystem types. We found no evidence of this process occurring in any of the soils, but found evidence of an analytical artifact that creates the appearance of incorporation. We suggested that prior evidence of this process might be due in part or in total to this analytical artifact. Davidson et al. (2008), however, challenged our results and conclusions, suggesting that we failed to observe the abiotic incorporation because we eliminated the anaerobic microsites they argue are necessary for the process. We address the criticisms, and show that they actually raise questions about the robustness of the only study to have reported abiotic NO3 − incorporation in sterile soils. We argue that this area of research needs new artifact-free experiments if the controversy is going to be resolved.