Development of a Research Platform for Dissecting Phenotype–Genotype Associations in Rice (Oryza spp.)

We present an overview of a research platform that provides essential germplasm, genotypic and phenotypic data and analytical tools for dissecting phenotype–genotype associations in rice. These resources include a diversity panel of 400 Oryza sativa and 100 Oryza rufipogon accessions that have been purified by single seed descent, a custom-designed Affymetrix array consisting of 44,100 SNPs, an Illumina GoldenGate assay consisting of 1,536 SNPs, and a suite of low-resolution 384-SNP assays for the Illumina BeadXpress Reader that are designed for applications in breeding, genetics and germplasm management. Our long-term goal is to empower basic research discoveries in rice by linking sequence diversity with physiological, morphological, and agronomic variation. This research platform will also help increase breeding efficiency by providing a database of diversity information that will enable researchers to identify useful DNA polymorphisms in genes and germplasm of interest and convert that information into cost-effective tools for applied plant improvement.     

Plant-soil biodiversity relationships and nutrient retention in agricultural riparian zones of the Sacramento Valley,California

Forested riparian buffers in California historically supported high levels of biodiversity, but human activities have degraded these ecosystems over much of their former range. This study examined plant communities, belowground biodiversity and indicators of multiple ecosystem functions of riparian areas across an agricultural landscape in the Sacramento Valley of California, USA. Plant, nematode and soil microbial communities and soil physical and chemical properties were studied along 50-m transects at 20 sites that represented the different land use, soil and vegetation types in the landscape. Riparian zones supported greater plant diversity and nearly twice as much total carbon (C) per hectare compared to adjacent land managed for agricultural uses, but had generally lower soil microbial and nematode diversity and abundance. When woody plant communities were present in the riparian zone, plant diversity and species richness were higher, and soil nitrate and plant-available phosphorus levels were lower. Belowground diversity and community structure, however, appeared to depend more on plant productivity (as inferred by vegetation cover) than plant diversity or species richness. Greater plant species richness, nematode food web structure, total microbial biomass, woody C storage and lower soil nitrate and phosphorus loading were correlated with higher visual riparian health assessment scores, offering the possibility of managing these riparian habitats to provide multiple ecosystem functions.     

The effect of tree architecture on conduit diameter and frequency from small distal roots to branch tips in Betula pendula, Picea abies and Pinus sylvestris

We studied the effect of tree architecture on xylem anatomy in three Betula pendula Roth., three Picea abies (L.) H. Karst. and three Pinus sylvestris (L.) trees (mean age 35 years). First, the analysis of conduit anatomy in different tree parts showed that conduits tapered and their frequency increased from roots (≥ 2 mm) to stem, from stem to branches and further to leaf petioles in B. pendula. Conduit anatomy in lateral and main roots, as well as lateral and main branches, significantly differed from each other in all the studied species. The increase in conduit diameter and decrease in frequency from the pith to the bark were clear aboveground, but variable patterns were observed belowground. In the leaf petioles of B. pendula, conduit diameter increased and conduit frequency decreased with increasing individual leaf area. Second, the results concerning the scaling of conduit diameter were compared with the predictions of the general vascular scaling model (WBE model) and Murray's law. The scaling parameter values at the tree level corresponded with the predictions of the WBE model in all the studied trees except for one tree of both conifer species. However, the scaling parameter values changed from one tree compartment to another rather than remaining uniform inside a tree, as assumed by the WBE model. The assumptions of the WBE model of a constant conductivity ratio, constant tapering and an unchanged total number of conduits were not fulfilled. When the conductivity ratio and relative tapering were plotted together, the results aboveground corresponded quite well with Murray's law: the conductivity ratio increased when relative tapering decreased. Our results support the theory that trees adjust both their macro- and microstructure to maximize their water transport efficiency, but also to prevent embolism and ensure mechanical safety.     

Enrichment of low-abundance proteins from bovine and porcine serum samples for proteomic studies

One of the main applications of serum proteomics is the identification of new biomarkers for animal disease or animal production. However, potential obstacles to these studies are the poor performance of affinity serum depletion methods based on human antigens when using animal samples, and loss of minor serum components bound to albumin and other proteins. In the present study, we have analyzed the efficiency and reproducibility of the ProteoMiner® beads with bovine and porcine serum samples, and compared to a traditional immunoaffinity-based albumin and IgG depletion system specific for human samples. The ProteoMiner kit is based on the use of a combinatorial peptide binding library and intends to enrich low-abundance proteins.     

Variant-specific and diminishing immune responses towards the highly variable MSP2(P44) outer membrane protein of Anaplasma phagocytophilum during persistent infection in lambs

Anaplasma phagocytophilum is the causative agent of tick-borne fever in small ruminants and has been identified as the zoonotic agent of human granulocytic anaplasmosis. The Norwegian strains of the rickettsia are naturally persistent in lambs and represent a suitable experimental system for analyzing the mechanisms of persistence. Variation of the outer membrane protein MSP2(P44) by recombination of variable pseudogene segments into an expression site is believed to play a key role in persistence of the organism. The goal of the present study was to analyze the dynamics of the immune response towards A. phagocytophilum and MSP2(P44) during persistent infection of lambs. Responses to the hypervariable region of MSP2(P44) were detected shortly after appearance of the respective variants in cyclic rickettsemic peaks, consistent with a process of antigenic variation. In addition, there was a diminishing antibody response to MSP2(P44) and to other A. phagocytophilum antigens overall with time of infection, that was not associated with clearance of the infection.     

Effect of the span length of Granier-type thermal dissipation probes on sap flux density measurements

? Granier-type thermal dissipation sensors measure sap flux density (u) by using the temperature difference between the heater and the reference probe. To detect u correctly, heat must not be transferred to the reference probe by thermal conduction. The distance across which heat can be transferred by conduction is important for the span length of a sensor and spacing of a number of sensors.

? To validate span lengths and spacing of sensors, we used numerical simulations to calculate the potential distance across which heat can be transferred by conduction. We compared measurements with an original and a modified sensor for a Japanese red pine (Pinus densiflora) from December 2004 to May 2005. The span length of the original and the modified sensor is 15 and 4 cm, respectively.

? Numerical simulations showed that span length and spacing of Granier sensors should be more than 10 cm for trees in which u ceases for a few hours before the predawn period. The modified sensor underestimated u by 18–46% in winter (December–March) because its reference temperature was increased by heat transferred by conduction. The modified sensor measured u correctly in warm seasons, and only underestimated the annual amount of transpiration by 6%.

     

The pharmacological activity of wheat bran polysaccharides

(Glucurono)arabinoxylans were extracted from the wheat bran with acetate buffer in the first step (WBH1) and with dilute alkali in the second step (WBH2). In both samples xylose and arabinose dominated, accompanied with smaller amounts of galactose, glucose, mannose and uronic acids mainly in WBH1. WBH1 was free of protein and with low content of phenolic compounds. Fraction WBH2 contained relatively low levels of proteins and about 4.5% of the total phenolic. When tested for antitussive activity, the (glucurono)arabinoxylans exhibited comparable cough-suppressing effect with centrally acting codeine. The observed effects of bronchoconstriction are limiting practical application of WBH2.     

Time course differential gene expression in response to porcine circovirus type 2 subclinical infection

This study was aimed at characterizing the potential differences in gene expression in piglets inoculated with Porcine circovirus type 2 (PCV2), the essential causative agent of postweaning multisystemic wasting syndrome. Seven-day-old caesarean-derived, colostrum-deprived piglets were distributed into two groups: control (n = 8) and pigs inoculated with 10^5.2 TCID₅₀ of the Burgos PCV2 isolate (n = 16). One control and three inoculated pigs were necropsied on days 1, 2, 5, and 8 post-infection (p.i.). The remaining pigs (four of each group) were sequentially bled on days 0, 7, 14, 21, and 29 p.i. (necropsy). Total RNA from the mediastinal lymph node (MLN) and lysed whole blood (LWB) samples were hybridized to Affymetrix Porcine GeneChip^®. Forty-three probes were differentially expressed (DE) in MLN samples (FDR < 0.1, fold change > 2) and were distributed into three clusters: globally down-regulated genes, and up-regulated genes at early (first week p.i.) and late (day 29 p.i.) stages of infection. In LWB samples, maximal differences were observed at day 7 p.i., with 54 probes DE between control and inoculated pigs. Main Gene Ontology biological processes assigned to up-regulated genes were related to the immune response. Six common genes were found in both types of samples, all of which belonged to the interferon signaling antiviral effector pathway. Down-regulated genes were mainly related to cell adhesion and migration in MLN, and cellular organization and biogenesis in LWB. Microarray results were validated by quantitative real-time PCR. This study provides, for the first time, the characterization of the early and late molecular events taking place in response to a subclinical PCV2 infection.     

Changes of very low-density lipoprotein concentration in hepatic blood from cows with fasting-induced hepatic lipidosis

The purpose of this study was to evaluate changes of very low-density lipoprotein (VLDL) components in hepatic blood (HB) from 5 nonlactating nonpregnant cows fasted from days 0 to 3 and subsequently refed to day 10 and, in addition, to assess those of other lipoproteins. Increased phospholipid concentrations in each lipoprotein after the start of fasting suggested their availability for the surface lipids of lipoproteins. Although the VLDL-triglyceride (TG) concentration in HB from all cows increased on day 1, the value on day 4 became similar to that on day 0. However, the concentration on day 10 was significantly increased. In all cows, the decreased ratio of the VLDL-TG concentration in HB to the non-esterified fatty acids (NEFA) concentration in portal blood (PB) on day 4 appeared to reflect relatively decreased secretion of TG as VLDL by NEFA excessively mobilized to the liver via PB. The markedly increased ratio on day 10 was considered to contribute to the improvement of hepatic lipidosis.     

3-[4-(1H-Indol-3-yl)-1,3-thiazol-2-yl]-1H-pyrrolo[2,3-b]pyridines,Nortopsentin Analogues with Antiproliferative Activity

A new series of nortopsentin analogues, in which the imidazole ring of the natural product was replaced by thiazole and the indole unit bound to position 2 of the thiazole ring was substituted by a 7-azaindole moiety, was efficiently synthesized. Two of the new nortopsentin analogues showed good antiproliferative effect against the totality of the NCI full panel of human tumor cell lines (~60) having GI₅₀ values ranging from low micromolar to nanomolar level. The mechanism of the antiproliferative effect of these derivatives, investigated on human hepatoma HepG2 cells, was pro-apoptotic, being associated with externalization of plasma membrane phosphatidylserine and mitochondrial dysfunction. Moreover, the compounds induced a concentration-dependent accumulation of cells in the subG0/G1phase, while confined viable cells in G2/M phase.