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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.

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.

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.

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.

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.

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.

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 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.