Analyzing highly variable potency data using a linear mixed-effects measurement error model

A house standard lot is tested along with experimental samples in a variable TCID₅₀ assay in order to monitor and control assay performance. Instead of being simply a control, it is proposed to use this lot as a calibration standard to reduce the systematic variability in the assay caused by acknowledged sources of variability such as the age of the cells used in the assay and interlaboratory differences. Because of this new proposal, the consistency of the relationship between the test sample and the house standard is assessed within the acceptance range of the house standard. A linear mixed-effects measurement error model is proposed for the data. The slope curve is then used to assess the dynamic relationship between the sample and the house standard within the house standard range. It is shown with these analyses that the sample and the house standard have uniformly good agreement within the house standard range.     

Porous tubing for use in monitoring soil CO2 concentrations

The composition of the soil atmosphere is an indicator of biological processes, and soil CO₂ gradients have been used to estimate CO₂ efflux from the surface. Soil atmosphere samplers, constructed with gas-permeable materials, have been used to quantify soil CO₂ concentrations. The type of material used can influence the perceived real-time concentrations of CO₂ in the soil. Previous works have not directly compared different types of materials under the same conditions. The objective of this study was to determine the diffusion coefficient (D) and time of 95% equilibrium (t_eq) of CO₂ through several materials, and to evaluate the effect of long-term soil burial (183 days) on diffusion characteristics. Materials tested included silicone, expanded Teflon (ePTFE), and ultra high molecular weight polyethylene (PE) tubing. The D of each material was determined using a closed-loop system consisting of a CO₂-enriched (7800 ppm) chamber, a CO₂ analyzer and an inner tube (experimental tubing) placed inside the chamber. Air was re-circulated through the inner tube, and as CO₂ diffused from the chamber into the tubing, the analyzer recorded the increase in concentration. The silicone tubes had values of D ranging from 8.64 to 5.80×10⁻⁶ cm² s⁻¹ with corresponding t_eq between 3.9 and 9.7 h. Diffusion coefficients of the ePTFE (1.25×10⁻⁴ cm² s⁻¹) and PE (7.70×10⁻⁴ cm² s⁻¹) materials were 2 orders of magnitude greater, with t_eq<6 min. Exposure to the soil environment for 183 days did not visibly deteriorate the materials or significantly affect the D or t_eq values. Use of the ePTFE or PE materials, over the silicone materials, may allow for better characterization of dynamic CO₂ concentrations in the soil based on the greater D and lesser t_eq values of these materials.     

Organic C and N stabilization in a forest soil: Evidence from sequential density fractionation

In mineral soil, organic matter (OM) accumulates mainly on and around surfaces of silt- and clay-size particles. When fractionated according to particle density, C and N concentration (per g fraction) and C/N of these soil organo-mineral particles decrease with increasing particle density across soils of widely divergent texture, mineralogy, location, and management. The variation in particle density is explained potentially by two factors: (1) a decrease in the mass ratio of organic to mineral phase of these particles, and (2) variations in density of the mineral phase. The first explanation implies that the thickness of the organic accumulations decreases with increasing particle density. The decrease in C/N can be explained at least partially by especially stable sorption of nitrogenous N-containing compounds (amine, amide, and pyrrole) directly to mineral surfaces, a phenomenon well documented both empirically and theoretically. These peptidic compounds, along with ligand-exchanged carboxylic compounds, could then form a stable inner organic layer onto which other organics could sorb more readily than onto the unconditioned mineral surfaces (“onion” layering model).To explore mechanisms underlying this trend in C concentration and C/N with particle density, we sequentially density fractionated an Oregon andic soil at 1.65, 1.85, 2.00, 2.28, and 2.55 g cm⁻³ and analyzed the six fractions for measures of organic matter and mineral phase properties.All measures of OM composition showed either: (1) a monotonic change with density, or (2) a monotonic change across the lightest fractions, then little change over the heaviest fractions. Total C, N, and lignin phenol concentration all decreased monotonically with increasing density, and ¹⁴C mean residence time (MRT) increased with particle density from ca. 150 years to >980 years in the four organo-mineral fractions. In contrast, C/N, ¹³C and ¹⁵N concentration all showed the second pattern. All these data are consistent with a general pattern of an increase in extent of microbial processing with increasing organo-mineral particle density, and also with an “onion” layering model.X-ray diffraction before and after separation of magnetic materials showed that the sequential density fractionation (SDF) isolated pools of differing mineralogy, with layer-silicate clays dominating in two of the intermediate fractions and primary minerals in the heaviest two fractions. There was no indication that these differences in mineralogy controlled the differences in density of the organo-mineral particles in this soil. Thus, our data are consistent with the hypothesis that variation in particle density reflects variation in thickness of the organic accumulations and with an “onion” layering model for organic matter accumulation on mineral surfaces. However, the mineralogy differences among fractions made it difficult to test either the layer-thickness or “onion” layering models with this soil. Although SDF isolated pools of distinct mineralogy and organic-matter composition, more work will be needed to understand mechanisms relating the two factors.     

Estimation of genetic components of variation for salt tolerance in chickpea using the generation mean analysis

Chickpea (Cicer arietinum L.) is known to be salt-sensitive and in many regions of the world its yields are restricted by salinity. Recent identification of large variation in chickpea yield under salinity, if genetically controlled, offers an opportunity to develop cultivars with improved salt tolerance. Two chickpea land races, ICC 6263 (salt sensitive) and ICC 1431 (salt tolerant), were inter-crossed to study gene action involved in different agronomic traits under saline and control conditions. The generation mean analysis in six populations, viz. P₁, P₂, F₁, F₂, BC₁P₁ and BC₁P₂, revealed significant gene interactions for days to flowering, days to maturity, and stem Na and K concentrations in control and saline treatments, as well as for 100-seed weight under salinity. Seed yield, pods per plant, seeds per plant, and stem Cl concentration were controlled by additive effects under saline conditions. Broad-sense heritability values (>0.5) for most traits were generally higher in saline than in control conditions, whereas the narrow-sense heritability values for yield traits, and stem Na and K concentrations, were lower in saline than control conditions. The influence of the sensitive parent was higher on the expression of different traits; the additive and dominant genes acted in opposite directions which led to lower heritability estimates in early generations. These results indicate that selection for yield under salinity would be more effective in later filial generations after gene fixation.     

Remote sensing and in situ-based estimates of evapotranspiration for subirrigated meadow,dry valley,and upland dune ecosystems in the semi-arid sand hills of Nebraska,USA

Water consumed through evapotranspiration (ET) impacts local and regional hydrologic regimes on various spatial and temporal scales. Estimating ET in the Great Plains is a prerequisite for effective regional water resource management of the Ogallala (High Plains) Aquifer, which supplies vital water resources in the form of irrigation for extensive agricultural production. The Sand Hills region of Nebraska is one of the largest grass-stabilized eolian (windblown) sand dune formations in the world, with an area of roughly 50,000–60,000 km² that supports a system of five major land cover types: (1) lakes, (2) wetlands (with lakes, ~5%), (3) subirrigated meadows (water table is within ~1 m of surface; ~10%), (4) dry valleys (water table is 1–10 m below surface; ~20%), and (5) upland dunes (water table is more than 10 m below surface; ~65%). Fully understanding the hydrologic regime of these different ecosystems is a fundamental challenge in regional water resource assessment. The surface energy and water balances were analyzed using Bowen Ratio Energy Balance Systems (BREBS) at three locations: (1) a meadow, (2) a valley, and (3) an upland dune. Measurement of the energy budget by BREBS, in concert with Landsat remote sensing image processing for 2004 reveals strong spatial gradients between sites in latent heat flux that are associated with undulating topographic relief. We find that daily estimates of ET from BREBS measurements and remote sensing agree well, with an uncertainty within 1 mm, which is encouraging when applying remote sensing results across such a broad spatial scale and undulating topography.     

Conserved structure for single-stranded telomeric DNA recognition

The essential Cdc13 protein in the yeast Saccharomyces cerevisiae is a single-stranded telomeric DNA binding protein required for chromosome end protection and telomere replication. Here we report the solution structure of the Cdc13 DNA binding domain in complex with telomeric DNA. The structure reveals the use of a single OB (oligonucleotide/oligosaccharide binding) fold augmented by an unusually large loop for DNA recognition. This OB fold is structurally similar to OB folds found in the ciliated protozoan telomere end-binding protein, although no sequence similarity is apparent between them. The common usage of an OB fold for telomeric DNA interaction demonstrates conservation of end-protection mechanisms among eukaryotes.     

Microscopic view of structural phase transitions induced by shock waves

Multimillion-atom molecular-dynamics simulations are used to investigate the shock-induced phase transformation of solid iron. Above a critical shock strength, many small close-packed grains nucleate in the shock-compressed body-centered cubic crystal growing on a picosecond time scale to form larger, energetically favored grains. A split two-wave shock structure is observed immediately above this threshold, with an elastic precursor ahead of the lagging transformation wave. For even higher shock strengths, a single, overdriven wave is obtained. The dynamics and orientation of the developing close-packed grains depend on the shock strength and especially on the crystallographic shock direction. Orientational relations between the unshocked and shocked regions are similar to those found for the temperature-driven martensitic transformation in iron and its alloys.     

Bidirectional transmembrane signaling by cytoplasmic domain separation in integrins

Although critical for development, immunity, wound healing, and metastasis, integrins represent one of the few classes of plasma membrane receptors for which the basic signaling mechanism remains a mystery. We investigated cytoplasmic conformational changes in the integrin LFA-1 (alphaLbeta2) in living cells by measuring fluorescence resonance energy transfer between cyan fluorescent protein-fused and yellow fluorescent protein-fused alphaL and beta2 cytoplasmic domains. In the resting state these domains were close to each other, but underwent significant spatial separation upon either intracellular activation of integrin adhesiveness (inside-out signaling) or ligand binding (outside-in signaling). Thus, bidirectional integrin signaling is accomplished by coupling extracellular conformational changes to an unclasping and separation of the alpha and beta cytoplasmic domains, a distinctive mechanism for transmitting information across the plasma membrane.     

Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation

Maintenance of genomic methylation patterns is mediated primarily by DNA methyltransferase-1 (DNMT1). We have solved structures of mouse and human DNMT1 composed of CXXC, tandem bromo-adjacent homology (BAH1/2), and methyltransferase domains bound to DNA-containing unmethylated CpG sites. The CXXC specifically binds to unmethylated CpG dinucleotide and positions the CXXC-BAH1 linker between the DNA and the active site of DNMT1, preventing de novo methylation. In addition, a loop projecting from BAH2 interacts with the target recognition domain (TRD) of the methyltransferase, stabilizing the TRD in a retracted position and preventing it from inserting into the DNA major groove. Our studies identify an autoinhibitory mechanism, in which unmethylated CpG dinucleotides are occluded from the active site to ensure that only hemimethylated CpG dinucleotides undergo methylation.     

Protein displacement by DExH/D "RNA helicases" without duplex unwinding

Members of the DExH/D superfamily of nucleic acid-activated nucleotide triphosphatases are essential for virtually all aspects of RNA metabolism, including pre-messenger RNA splicing, RNA interference, translation, and nucleocytoplasmic trafficking. Physiological substrates for these enzymes are thought to be regions of double-stranded RNA, because several DExH/D proteins catalyze strand separation in vitro. These "RNA helicases" can also disrupt RNA-protein interactions, but it is unclear whether this activity is coupled to duplex unwinding. Here we demonstrate that two unrelated DExH/D proteins catalyze protein displacement independently of duplex unwinding. Therefore, the essential functions of DExH/D proteins are not confined to RNA duplexes but can be exerted on a wide range of ribonucleoprotein substrates.