Anatomic Demarcation by Positional Variation in Fibroblast Gene Expression Programs

Fibroblasts are ubiquitous mesenchymal cells with many vital functions during development, tissue repair, and disease. Fibroblasts from different anatomic sites have distinct and characteristic gene expression patterns, but the principles that govern their molecular specialization are poorly understood. Spatial organization of cellular differentiation may be achieved by unique specification of each cell type; alternatively, organization may arise by cells interpreting their position along a coordinate system. Here we test these models by analyzing the genome-wide gene expression profiles of primary fibroblast populations from 43 unique anatomical sites spanning the human body. Large-scale differences in the gene expression programs were related to three anatomic divisions: anterior-posterior (rostral-caudal), proximal-distal, and dermal versus nondermal. A set of 337 genes that varied according to these positional divisions was able to group all 47 samples by their anatomic sites of origin. Genes involved in pattern formation, cell-cell signaling, and matrix remodeling were enriched among this minimal set of positional identifier genes. Many important features of the embryonic pattern of HOX gene expression were retained in fibroblasts and were confirmed both in vitro and in vivo. Together, these findings suggest that site-specific variations in fibroblast gene expression programs are not idiosyncratic but rather are systematically related to their positional identities relative to major anatomic axes

Improving Gate-Level Simulation of Quantum Circuits

Simulating quantum computation on a classical computer is a difficult problem. The matrices representing quantum gates, and the vectors modeling qubit states grow exponentially with an increase in the number of qubits. However, by using a novel data structure called the Quantum Information Decision Diagram (QuIDD) that exploits the structure of quantum operators, a useful subset of operator matrices and state vectors can be represented in a form that grows polynomially with the number of qubits. This subset contains, but is not limited to, any equal superposition of n qubits, any computational basis state, n-qubit Pauli matrices, and n-qubit Hadamard matrices. It does not, however, contain the discrete Fourier transform (employed in Shor's algorithm) and some oracles used in Grover's algorithm. We first introduce and motivate decision diagrams and QuIDDs. We then analyze the runtime and memory complexity of QuIDD operations. Finally, we empirically validate QuIDD-based simulation by means of a general-purpose quantum computing simulator QuIDDPro implemented in C++. We simulate various instances of Grover's algorithm with QuIDDPro, and the results demonstrate that QuIDDs asymptotically outperform all other known simulation techniques. Our simulations also show that well-known worst-case instances of classical searching can be circumvented in many specific cases by data compression techniques.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/45525/1/11128_2004_Article_482625.pd

Validation of rice blast resistance genes in barley using a QTL mapping population and near-isolines

There are prior reports of Pyricularia grisea-the causal agent of blast of rice-causing disease in barley. In order to determine the specificity of this resistance in barley, we extended our previous mapping efforts to include blast isolates from barley and rice grown in Thailand and we assessed two resistance phenotypes: leaf blast (LB) and neck blast (NB). The largest-effect resistance QTL, on chromosome I H, was associated with NB and LB and is located in a region rich in resistance genes, including QTL conferring resistance to stripe rust (incited by Puccinia striiformis f. sp. hordei) and the mildew (Blumeria graminis f. sp. hordei) resistance gene Mla. The LB, NB and mildew resistance alleles trace to one parent (Baronesse) whereas the stripe rust resistance allele traces to the other parent (BCD47) of the mapping population. Baronesse is the susceptible recurrent parent of a set of near-isogenic lines (NILs) for three stripe rust resistance QTL, including one on 1H. Unigene (EST) derived single nucleotide polymorphism haplotypes of these NILs were aligned with the blast mapping population QTL using Mla as an anchor. Baronesse and all NILs without the 1H introgression were resistant to LB and NB. However, two NILs with the I H introgression were resistant to LB and NB. Both are resistant to stripe rust. Therefore, the QTL conferring resistance to stripe rust is separable by recombination from the blast resistance QTL

Evaluating the impact of new observational constraints on P-S/IVOC emissions, multi-generation oxidation, and chamber wall losses on SOA modeling for Los Angeles, CA

Secondary organic aerosol (SOA) is an important contributor to fine particulate matter (PM) mass in polluted regions, and its modeling remains poorly constrained. A box model is developed that uses recently published literature parameterizations and data sets to better constrain and evaluate the formation pathways and precursors of urban SOA during the CalNex 2010 campaign in Los Angeles. When using the measurements of intermediate-volatility organic compounds (IVOCs) reported in Zhao et al. (2014) and of semivolatile organic compounds (SVOCs) reported in Worton et al. (2014) the model is biased high at longer photochemical ages, whereas at shorter photochemical ages it is biased low, if the yields for VOC oxidation are not updated. The parameterizations using an updated version of the yields, which takes into account the effect of gas-phase wall losses in environmental chambers, show model–measurement agreement at longer photochemical ages, even though some low bias at short photochemical ages still remains. Furthermore, the fossil and non-fossil carbon split of urban SOA simulated by the model is consistent with measurements at the Pasadena ground site. Multi-generation oxidation mechanisms are often employed in SOA models to increase the SOA yields derived from environmental chamber experiments in order to obtain better model–measurement agreement. However, there are many uncertainties associated with these aging mechanisms. Thus, SOA formation in the model is compared to data from an oxidation flow reactor (OFR) in order to constrain SOA formation at longer photochemical ages than observed in urban air. The model predicts similar SOA mass at short to moderate photochemical ages when the aging mechanisms or the updated version of the yields for VOC oxidation are implemented. The latter case has SOA formation rates that are more consistent with observations from the OFR though. Aging mechanisms may still play an important role in SOA chemistry, but the additional mass formed by functionalization reactions during aging would need to be offset by gasphase fragmentation of SVOCs. All the model cases evaluated in this work show a large majority of the urban SOA (70–83 %) at Pasadena coming from the oxidation of primary SVOCs (P-SVOCs) and primary IVOCs (P-IVOCs). The importance of these two types of precursors is further supported by analyzing the percentage of SOA formed at long photochemical ages (1.5 days) as a function of the precursor rate constant. The P-SVOCs and P-IVOCs have rate constants that are similar to highly reactive VOCs that have been previously found to strongly correlate with SOA formation potential measured by the OFR. Finally, the volatility distribution of the total organic mass (gas and particle phase) in the model is compared against measurements. The total SVOC mass simulated is similar to the measurements, but there are important differences in the measured and modeled volatility distributions. A likely reason for the difference is the lack of particle-phase reactions in the model that can oligomerize and/or continue to oxidize organic compounds even after they partition to the particle phase

First cryo-scanning electron microscopy images and X-ray microanalyses of mucoromycotinian fine root endophytes in vascular plants

Aims. Arbuscule-producing fine root endophytes (FRE) (previously incorrectly Glomus tenue) were recently placed within subphylum Mucoromycotina; the first report of arbuscules outside subphylum Glomeromycotina. Here, we aimed to estimate nutrient concentrations in plant and fungal structures of FRE and to test the utility of cryo-scanning electron microscopy (cryoSEM) for studying these fungi. Methods. To do so, we used replicated cryoSEM and X-ray microanalysis of heavily colonized roots of Trifolium subterraneum. Results. Intercellular hyphae and hyphae in developed arbuscules were consistently very thin; 1.35 ± 0.03 µm and 0.99 ± 0.03 µm in diameter, respectively (mean ± SE). Several intercellular hyphae were often adjacent to each other forming ‘hyphal ropes’. Developed arbuscules showed higher phosphorus concentrations than senesced arbuscules and non-colonized structures. Senesced arbuscules showed greatly elevated concentrations of calcium and magnesium. Conclusions. While uniformly thin hyphae and hyphal ropes are distinct features of FRE, the morphology of fully developed arbuscules, elevated phosphorus in fungal structures, and accumulation of calcium with loss of structural integrity in senesced arbuscules are similar to glomeromycotinian fungi. Thus, we provide evidence that FRE may respond to similar host-plant signals or that the host plant may employ a similar mechanism of association with FRE and AMF

Erythropoietin Treatment in Traumatic Brain Injury: Operation Brain Trauma Therapy

Experimental studies targeting traumatic brain injury (TBI) have reported that erythropoietin (EPO) is an endogenous neuroprotectant in multiple models. In addition to its neuroprotective effects, it has also been shown to enhance reparative processes including angiogenesis and neurogenesis. Based on compelling pre-clinical data, EPO was tested by the Operation Brain Trauma Therapy (OBTT) consortium to evaluate therapeutic potential in multiple TBI models along with biomarker assessments. Based on the pre-clinical TBI literature, two doses of EPO (5000 and 10,000 IU/kg) were tested given at 15 min after moderate fluid percussion brain injury (FPI), controlled cortical impact (CCI), or penetrating ballistic-like brain injury (PBBI) with subsequent behavioral, histopathological, and biomarker outcome assessments. There was a significant benefit on beam walk with the 5000 IU dose in CCI, but no benefit on any other motor task across models in OBTT. Also, no benefit of EPO treatment across the three TBI models was noted using the Morris water maze to assess cognitive deficits. Lesion volume analysis showed no treatment effects after either FPI or CCI; however, with the 5000 IU/kg dose of EPO, a paradoxical increase in lesion volume and percent hemispheric tissue loss was seen after PBBI. Biomarker assessments included measurements of glial fibrillary acidic protein (GFAP) and ubiquitin C-terminal hydrolase-L1 (UCH-L1) in blood at 4 or 24 h after injury. No treatment effects were seen on biomarker levels after FPI, whereas treatment at either dose exacerbated the increase in GFAP at 24 h in PBBI but attenuated 24-4 h delta UCH-L1 levels at high dose in CCI. Our data indicate a surprising lack of efficacy of EPO across three established TBI models in terms of behavioral, histopathological, and biomarker assessments. Although we cannot rule out the possibility that other doses or more prolonged treatment could show different effects, the lack of efficacy of EPO reduced enthusiasm for its further investigation in OBTT

Trait convergence in photosynthetic nutrient-use efficiency along a 2-million year dune chronosequence in a global biodiversity hotspot

The Jurien Bay dune chronosequence in south-western Australia's biodiversity hotspot comprises sites differing in nutrient availability, with phosphorus (P) availability declining strongly with increasing soil age. We have explored the exceptionally high photosynthetic Pause efficiency (PPUE) of Proteaceae in this region, triggering the question what the PPUE of co-occurring species in other families might be along the Jurien Bay chronosequence. We explored how traits associated with PPUE, photosynthetic nitrogen (N)-use efficiency (PNUE) and leaf respiration might converge along the chronosequence, and whether Proteaceae and non-Proteaceae species differ in leaf traits associated with nutrient use. Seven to 10 species were sampled at three sites differing in nutrient availability (ranging from N- to P- limited). Measurements of leaf light-saturated photosynthesis and dark respiration were integrated with measurements of total N and P concentration in both mature and senesced leaves, and leaf mass per unit area (LMA). Contrary to what is known for other chronosequences, rates of photosynthesis and respiration did not decrease with increasing soil age and LMA along the Jurien Bay chronosequence. However, they increased when expressed per unit leaf P. Both N and P were used much more efficiently for photosynthesis on nutrient-poor sites, in both Proteaceae and non-Proteaceae species. Proteaceae had the fastest rate of photosynthesis per unit leaf P, followed by species that preferentially allocate P to mesophyll cells, rather than epidermal cells. Synthesis. Our results show that with declining soil P availability, photosynthetic P-use efficiency of all investigated species from different families increased. Plants growing on the oldest, most nutrient-impoverished soils exhibited similar rates of CO2 exchange as plants growing on more nutrient-rich younger soils, and extraordinarily high photosynthetic P-use efficiency. This indicates convergence in leaf traits related to photosynthetic nutrient use on severely P-impoverished sites.Australian Research Council, Grant/Award Number: CE140100008, DP130100005, DP0985685, DP110101120 and DP0986823; University of Western Australi