Estimating Ecosystem Nitrogen Addition by a Leguminous Tree: A Mass Balance Approach Using a Woody Encroachment Chronosequence

Difficulty in quantifying rates of biological N fixation (BNF), especially over long time scales, remains a major impediment to defining N budgets in many ecosystems. To estimate N additions from BNF, we applied a tree-scale N mass balance approach to a well-characterized chronosequence of woody legume (Prosopis glandulosa) encroachment into subtropical grasslands. We defined spatially discrete single Prosopis clusters (aged 28–99 years), and for each calculated BNF as the residual of: soil N (0–30 cm), above- and below-ground biomass N, wet and dry atmospheric N deposition, N trace gas and N₂ loss, leaching loss, and baseline grassland soil N at time of establishment. Contemporary BNF for upland savanna woodland was estimated at 10.9 ± 1.8 kg N ha^?1 y^?1, equal to a total of 249 ± 60 kg N ha^?1 over about 130 years of encroachment at the site. Though these BNF values are lower than previous estimates for P. glandulosa, this likely reflects lower plant density as well as low water availability at this site. Uncertainty in soil and biomass parameters affected BNF estimates by 6–11%, with additional sensitivity of up to 18% to uncertainty in other scaling parameters. Differential N deposition (higher rates of dry N deposition to Prosopis canopies versus open grasslands) did not explain N accrual beneath trees; iterations that represented this scenario reduced estimated BNF estimates by a maximum of 1.5 kg N ha^?1 y^?1. We conclude that in this relatively well-constrained system, small-scale mass balance provides a reasonable method of estimating BNF and could provide an opportunity to cross-calibrate alternative estimation approaches.     

Locus-specific ribosomal RNA gene silencing in nucleolar dominance

The silencing of one parental set of rRNA genes in a genetic hybrid is an epigenetic phenomenon known as nucleolar dominance. We showed previously that silencing is restricted to the nucleolus organizer regions (NORs), the loci where rRNA genes are tandemly arrayed, and does not spread to or from neighboring protein-coding genes. One hypothesis is that nucleolar dominance is the net result of hundreds of silencing events acting one rRNA gene at a time. A prediction of this hypothesis is that rRNA gene silencing should occur independent of chromosomal location. An alternative hypothesis is that the regulatory unit in nucleolar dominance is the NOR, rather than each individual rRNA gene, in which case NOR localization may be essential for rRNA gene silencing. To test these alternative hypotheses, we examined the fates of rRNA transgenes integrated at ectopic locations. The transgenes were accurately transcribed in all independent transgenic Arabidopsis thaliana lines tested, indicating that NOR localization is not required for rRNA gene expression. Upon crossing the transgenic A. thaliana lines as ovule parents with A. lyrata to form F1 hybrids, a new system for the study of nucleolar dominance, the endogenous rRNA genes located within the A. thaliana NORs are silenced. However, rRNA transgenes escaped silencing in multiple independent hybrids. Collectively, our data suggest that rRNA gene activation can occur in a gene-autonomous fashion, independent of chromosomal location, whereas rRNA gene silencing in nucleolar dominance is locus-dependent.     

A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes

Viral lysis of microbial hosts releases organic matter that can then be assimilated by nontargeted microorganisms. Quantitative estimates of virus-mediated recycling of carbon in marine waters, first established in the late 1990s, were originally extrapolated from marine host and virus densities, host carbon content and inferred viral lysis rates. Yet, these estimates did not explicitly incorporate the cascade of complex feedbacks associated with virus-mediated lysis. To evaluate the role of viruses in shaping community structure and ecosystem functioning, we extend dynamic multitrophic ecosystem models to include a virus component, specifically parameterized for processes taking place in the ocean euphotic zone. Crucially, we are able to solve this model analytically, facilitating evaluation of model behavior under many alternative parameterizations. Analyses reveal that the addition of a virus component promotes the emergence of complex communities. In addition, biomass partitioning of the emergent multitrophic community is consistent with well-established empirical norms in the surface oceans. At steady state, ecosystem fluxes can be probed to characterize the effects that viruses have when compared with putative marine surface ecosystems without viruses. The model suggests that ecosystems with viruses will have (1) increased organic matter recycling, (2) reduced transfer to higher trophic levels and (3) increased net primary productivity. These model findings support hypotheses that viruses can have significant stimulatory effects across whole-ecosystem scales. We suggest that existing efforts to predict carbon and nutrient cycling without considering virus effects are likely to miss essential features of marine food webs that regulate global biogeochemical cycles.     

Detection of Coccidioides immitis in Kern County, California, by multiplex PCR

Coccidioides immitis is a fungal human pathogen endemic to semiarid soils in southern California and Baja California (Mexico). Results of culture-dependent detection of C. immitis in the past indicated a spotty distribution and unreliable prediction of C. immitis growth sites and accumulation sites. In this project we investigated bulk soil samples for the presence of the pathogen in nonagricultural loamy soils at nine different locations around Bakersfield, Kern County, California, for almost 2 y (2008-2009). To detect the pathogen we used a multiplex PCR method with optimized soil handling and storage, DNA extraction procedure and PCR protocol. With this method we were able to detect C. immitis in 8.42% of our samples in 2008 (n = 285), mostly from early spring to early summer. In 2009 however the percentage of samples positive for C. immitis from the same sites declined to 2.68% (n = 261). We also were able to distinguish C. immitis growth sites from accumulation sites. One site close to a recreation area (Lake Webb, Buena Vista Lake Basin), not previously known to support the growth of C. immitis, was identified as a strong growth site of the fungus. The cultivation-independent method in this study together with soil parameters can be used to predict and confirm C. immitis growth sites and might be a valuable tool for public health institutions.     

Recent advances of novel targeted therapy in non-small cell lung cancer

Lung cancer is the leading cause of cancer deaths world-wide. Recent advances in cancer biology have led to the identification of new targets in neoplastic cells and the development of novel targeted therapies. At this time, two targeted agents are approved by the FDA in advanced non-small cell lung cancer (NSCLC): the epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) erlotinib, and the anitangiogenic bevacizumab. A third agent, cetuximab, which was recently shown to enhance survival when used with cisplatin and vinorelbine as first line therapy for advanced NSCLC, will likely be approved by regulatory agencies. With more than 500 molecularly targeted agents under development, the prospects of identifying novel therapies that benefit individual patients with lung cancer are bright.     

The future of the β-lactams

In the 80 years since their discovery the β-lactam antibiotics have progressed through structural generations, each in response to the progressive evolution of bacterial resistance mechanisms. The generational progression was driven by the ingenious, but largely empirical, manipulation of structure by medicinal chemists. Nonetheless, the true creative force in these efforts was Nature, and as the discovery of new β-lactams from Nature has atrophied while at the same time multi-resistant and opportunistic bacterial pathogens have burgeoned, the time for empirical drug discovery has passed. We concisely summarize recent developments with respect to bacterial resistance, the identity of the new β-lactams, and the emerging non-empirical strategies that will ensure that this incredible class of antibiotics has a future.     

Field Characterization of Potential Reference Sediments in the Gulf of Mexico: Chemical and Biological Quality

Baseline information on the chemical and biological quality of sediments is provided for six coastal locations in the northern Gulf of Mexico, which were considered possible candidates for regional reference areas. Chemical quality, toxicity and benthic community composition were determined for sediments collected three times from each of 12 sites during an approximate one-year period. Potential contaminants in the usually sand-dominated sediments exceeded individual threshold effects level guidelines proposed for Florida coastal areas in approximately 31% of the samples collected from 8 of 12 sites. No probable effects level guidelines were exceeded. Acute toxicity occurred in 16% or less of the sediment samples and no significant chronic toxicity was observed to the infaunal amphipod, Leptocheirus plumulosus. Approximately, 11% and 17% of the sediments were classified as poor or marginal, based on low benthic taxa abundance and diversity index values, respectively. Sediment quality at many sites was less degraded than that for nearby coastal areas receiving point and non-point source contaminants, which suggests their suitability to serve as reference sediments although further confirmation is recommended. In a broader context, the results of this survey reflect the complexity in field verification of reference conditions for near-coastal sediments. This is attributable largely to the natural variability in their physical, biological, and chemical characteristics and to the lack of biocriteria for benthic macro and meiofauna.     

Indoor air quality in schools: exposure to fungal allergens

This study examined indoor air quality within schools in Kansas City, Spokane, Santa Fe, and Orlando. Air sampling was undertaken with both Andersen Single Stage Samplers and Burkard Personal Air Samplers. The data show a wide range of indoor exposures ranging from less than 100 colony forming units (CFU/m³) for viable fungi and 100 spores/m³ for total spores in Spokane and Santa Fe to concentrations over 6000 CFU/m³ for viable fungi and 15 000 spores/m³ for total fungi in Orlando and Kansas City, respectively. In the majority of sites the indoor airspora reflected the outdoor taxa withCladosporium the most abundant genus identified; however, several indoor locations had elevated levels ofPenicillium andAspergillus indicating possible sources of indoor contamination. Airborne basidiospores and smut spores were also fairly abundant in the schools and were among the top five taxa identified. The data also indicated that the airborne concentrations vary significantly during the day and between classrooms within each school. Continued studies in schools are needed to fully assess both the exposure levels and the clinical significance to atopic children allergic to these spores.     

The APG8/12-activating enzyme APG7 is required for proper nutrient recycling and senescence in Arabidopsis thaliana

The vacuole/lysosome serves an important recycling function during starvation and senescence in eukaryotes via a process called autophagy. Here bulk cytosolic constituents and organelles become sequestered in specialized autophagic vesicles, which then deliver their cargo to the vacuole for degradation. In yeasts, genetic screens have identified two novel post-translational modification pathways remarkably similar to ubiquitination that are required for autophagy. From searches of the Arabidopsis genome, we have identified gene families encoding proteins related to both the APG8 and -12 polypeptide tags and orthologs for all components required for their attachment. A single APG7 gene encodes the ATP-dependent activating enzyme that initiates both conjugation pathways. Phenotypic analysis of an APG7 disruption indicates that it is not essential for normal growth and development in Arabidopsis. However, the apg7-1 mutant is hypersensitive to nutrient limiting conditions and displays premature leaf senescence. mRNAs for both APG7 and APG8 preferentially accumulate as leaves senesce, suggesting that both conjugation pathways are up-regulated during the senescence syndrome. These findings show that the APG8/12 conjugation pathways have been conserved in plants and may have important roles in autophagic recycling, especially during situations that require substantial nitrogen and carbon mobilization.     

Spectroscopic evidence for site-specific cellular activity in the tubular gland in human intestine

The intestinal crypts contain mucus-secreting goblet cells in large numbers. In the tubular gland (crypt), the cells are generated at the bottom and end their life cycle at the top. Recently, FTIR microspectroscopy (FTIR-MC) has been applied in biology and medicine. The characterization of various cellular types using FTIR-MC and its subsequent application for the diagnosis of cancer is becoming a reality. In this report, we investigate the differential cellular activity in the normal tubular gland using FTIR-MC. Our results indicate that the absorbance for the cells in the bottom of the crypt is always higher than those in the upper portion. There are spectral pattern changes and frequency shifts for cells at the bottom and top sites of the normal crypt. Also, the comparison of a normal crypt with a malignant one has been made. This is the first spectroscopic evidence in the literature showing the difference in the cellular activity at different sites in the tubular gland. The reasons for our observations and their implications are discussed.