Variability and robustness in T cell activation from regulated heterogeneity in protein levels

In T cells, the stochasticity of protein expression could contribute to the useful diversification of biological functions within a clonal population or interfere with accurate antigen discrimination. Combining computer modeling and single-cell measurements, we examined how endogenous variation in the expression levels of signaling proteins might affect antigen responsiveness during T cell activation. We found that the CD8 co-receptor fine-tunes activation thresholds, whereas the soluble hematopoietic phosphatase 1 (SHP-1) digitally regulates cell responsiveness. Stochastic variation in the expression of these proteins generates substantial diversity of activation within a clonal population of T cells, but co-regulation of CD8 and SHP-1 levels ultimately limits this very diversity. These findings reveal how eukaryotic cells can draw on regulated variation in gene expression to achieve phenotypic variability in a controlled manner.     

Disorder-enhanced transport in photonic quasicrystals

Quasicrystals are aperiodic structures with rotational symmetries forbidden to conventional periodic crystals; examples of quasicrystals can be found in aluminum alloys, polymers, and even ancient Islamic art. Here, we present direct experimental observation of disorder-enhanced wave transport in quasicrystals, which contrasts directly with the characteristic suppression of transport by disorder. Our experiments are carried out in photonic quasicrystals, where we find that increasing disorder leads to enhanced expansion of the beam propagating through the medium. By further increasing the disorder, we observe that the beam progresses through a regime of diffusive-like transport until it finally transitions to Anderson localization and the suppression of transport. We study this fundamental phenomenon and elucidate its origins by relating it to the basic properties of quasicrystalline media in the presence of disorder.     

Conservation genetics of a rare Gerbil species: a comparison of the population genetic structures and demographic histories of the locally rare Pygmy Gerbil and the common Anderson's Gerbil

Background  

One of the major challenges in evolutionary biology is identifying rare species and devising management plans to protect them while also sustaining their genetic diversity. However, in attempting a broad understanding of rarity, single-species studies provide limited insights because they do not reveal whether the factors that affect rare species differ from those that affect more common species. To illustrate this important concept and to arrive at a better understanding of the form of rarity characterizing the rare Gerbillus henleyi, we explored its population genetic structure alongside that of the locally common Gerbillus andersoni allenbyi. We trapped gerbils in several locations in Israel's western and inner Negev sand dunes. We then extracted DNA from ear samples, and amplified two mitochondrial sequences: the control region (CR) and the cytochrome oxidase 2 gene (CO2).     

Integration of geospatial and cattle nutrition information to estimate paddock grazing capacity in Northern US prairie

Spatiotemporal variability in forage quantity and quality requires that regular assessment is needed of the capacity for grasslands to support livestock nutritional requirements. Current methods for estimating grazing capacity are typically production-based and lack the forage quality data necessary to match nutrients in forage with livestock requirements in real time. This paper describes a method for estimating short-term grazing capacity for small (1–20 ha) paddocks using cattle nutrition and high spatial resolution forage data in Geographic Information Systems (GIS) for mixed-grass prairie. We define grazing capacity as the number of days a specific paddock will support the nutritional requirements of beef cattle. We integrate previously published methods for estimating cattle nutritional requirements, forage quality (crude protein) and forage quantity (phytomass) to estimate grazing capacity based on current standing-crop. The model utilizes high-resolution (<30-m) satellite imagery or field data to estimate short-term grazing capacity for small paddocks. Three versions of the model were evaluated on one paddock under cattle use in 2007. One version was parameterized using data collected on June 22 from the Landsat Thematic Mapper (TM), one version was parameterized using data collected June 23 from the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER), and one version was parameterized using data collected June 20 from field clippings. TM and ASTER versions underestimated grazing capacity by four days while the field version overestimated grazing capacity by one day. Results suggest integration of cattle nutrition and forage data in GIS could assist with stocking rate adjustments, but additional trials are needed.     

A Novel Method for Combined Biowaste Stabilization and Production of Nitrate-Rich Liquid Fertilizer for Use in Organic Horticulture

A novel system for organic waste stabilization and reuse, combined with production of nitrate-rich liquid fertilizer was developed by manure digestion followed by volatilization of ammonia-rich gas (originating in manure extract) and its nitrification and recovery. This approach has several advantages, including biowaste stabilization and high recovery (over 60%) of manure N mainly as nitrate which is a better N form for many plants as compared to ammonium as the sole fertilizer N. Moreover, the potential utilization of different wastes as N sources in organic horticulture is possible as well as removal of suspended particles and microorganisms (including pathogens) that might otherwise clog the irrigation system and pose health risks, respectively. In a pilot-scale study, the system yielded several hundred liters of nitrate-rich (ca. 11 g N L⁻¹) liquid fertilizer using guano as substrate. In a fertilization experiment, lettuce fertigated with the nitrate-rich extract exhibited better growth and quality compared to the common organic practice of fertigation with guano extract. The resulting stabilized biowaste was estimated as “low-risk” according to current guidelines and may be used for liming or land application.     

Perchlorate biodegradation in contaminated soils and the deep unsaturated zone

In the United States, perchlorate has been officially recognized as an environmental contaminant. In Israel, widespread perchlorate contamination has been found in the 40-m deep vadose zone near an ammonium perchlorate manufacturing plant north of Tel Aviv, above the central part of Israel's coastal aquifer, with peak concentrations of 1200 mg kg_sediment^?1. In this study, we examined the perchlorate-reduction potential by native microbial communities along this deep contaminated vadose zone profile. We analyzed the effect of various concentrations of nitrate on perchlorate reduction and determined whether perchlorate concentrations in the profile are toxic to the native microbial population. All experiments were performed in soil slurries with sediments taken from the contaminated site. Perchlorate was reduced to chloride in three (1, 15 and 35 m) of the four examined sediment samples taken from different depths (1, 15, 20, and 35 m below surface). No activity was observed in the sediment sample from 20 m below land surface, suggesting low viable microbial communities and water content, and high perchlorate concentrations. In the presence of nitrate, the lag time for perchlorate degradation was inversely correlated to nitrate concentration. We found no perchlorate degradation as long as nitrate was present in the system, and perchlorate degradation initiated only after all the nitrate had been reduced. Nitrate-reduction rates were correlated to the initial concentrations of nitrate and no lag period was observed for nitrate reduction. Viable microbial populations were observed at both high concentrations (10,000 mg l^?1 and 20,000 mg l^?1) and with no addition of perchlorate, at levels of 2.35 × 10⁵, 4.01 × 10⁵, and 3.41 × 10³ CFU ml^?1, respectively; these results were well correlated to those found by PCR amplification analysis of chlorite dismutase. We suggest that the microbial community has adapted to the conditions of high perchlorate concentrations in the unsaturated zone over 30 years of exposure. When no external carbon source was added to the slurry of soil from land surface, all perchlorate was removed after 134 days of incubation. The average perchlorate-reduction rate using natural organic matter as a carbon source was 0.45 mg day^?1, while the average rate using acetate as an external carbon source was 7.2 mg day^?1.