Candidate Gene Sequence Analyses toward Identifying -Type Resistance to.

is one of three genetic loci conferring strain-specific resistance to (SMV). The locus has been mapped to a 154-kb region on chromosome 14, containing a cluster of five nucleotide-binding leucine-rich repeat (NB-LRR) resistance genes. High sequence similarity between the candidate genes challenges fine mapping of the locus. Among the five, Glyma14g38533 showed the highest transcript abundance in 1 to 3 h of SMV-G7 inoculation. Comparative sequence analyses were conducted with the five candidate NB-LRR genes from susceptible (-type) soybean [ (L.) Merr.] cultivar Williams 82, resistant (-type) cultivar Hwangkeum, and resistant lines L29 and RRR. Sequence comparisons revealed that Glyma14g38533 had far more polymorphisms than the other candidate genes. Interestingly, Glyma14g38533 gene from -type lines exhibited 150 single-nucleotide polymorphism (SNP and six insertion-deletion (InDel) markers relative to -type line, Furthermore, the polymorphisms identified in three -type lines were highly conserved. Several polymorphisms were validated in 18 -type resistant and six -type susceptible lines and were found associated with their disease response. The majority of the polymorphisms were located in LRR domain encoding region, which is involved in pathogen recognition via protein-protein interactions. These findings associating Glyma14g38533 with -type resistance to SMV suggest it is the most likely candidate gene for .

19-core MCF transmission system using EDFA with shared core pumping coupled via free-space optics.

We report the development of a space division multiplexed (SDM) transmission system consisting of a 19-core fiber and 19-core Erbium-doped fiber amplifier (EDFA). A new 19-core fiber with an improved core arrangement was employed to achieve a low aggregated inter-core crosstalk of -42 dB at 1550 nm over 30 km. The EDFA uses shared free-space optics for pump beam combining and isolation, thus is SDM transparent and has some potential for cost reduction. 19.6 dB to 23.3 dB gain and 6.0 dB to 7.0 dB noise figure were obtained for each SDM channel at 1550 nm. System feasibility for SDM transmission over 1200 km was demonstrated with 100 Gb/s PDM-QPSK signals.

Exercise-induced cardioprotection is mediated by a bloodborne, transferable factor.

Exercise protects against myocardial ischemia-reperfusion (I-R) injury but the mechanism remains unclear. Protection can be transferred from a remotely preconditioned human donor to an isolated perfused rabbit heart using a dialysate of plasma. We hypothesized that physical exercise preconditioning also confers cardioprotection through a humorally mediated effector dependent on opioid receptor activation. Thirteen male volunteers performed vigorous exercise (four 2-minute bouts of high-intensity exercise) and 1 week later they underwent remote ischemic preconditioning (four cycles of 5 min upper limb ischemia and reperfusion). Dialysates were prepared from blood collected before (control) and after the two interventions. Isolated rabbit hearts were perfused with the dialysates without and with co-administration of naloxone (opioid receptor antagonist) prior to 40 min regional ischemia and 2 h reperfusion. Exercise and remote ischemic preconditioning (rIPC) reduced infarct size from 60 ± 5 to 35 ± 5 % and from 57 ± 7 to 27 ± 3 % of the area at risk, respectively (p < 0.05 and < 0.01). Furthermore, post-ischemic left ventricular developed pressure was improved compared with controls (p = 0.08 for exercise and p = 0.04 for rIPC). Co-perfusion with naloxone abrogated the protective effects of exercise and remote ischemic preconditioned dialysates. In conclusion, high-intensity exercise preconditioning elicits cardioprotection through a humorally mediated dependent on opioid receptor activation, similar to rIPC.

Influence of androgens on gene expression in the BALB/c mouse submandibular gland.

Androgens have profound effects on the murine submandibular gland. Our objective was to determine the nature and extent of androgen control of gene expression in the submandibular gland, and to explore the degree to which this might account for known sex differences. Orchiectomized male BALB/c mice were treated with placebo- or testosterone-containing hormone pellets for 14 days. Glands were collected, and total RNA was isolated. Samples were analyzed for differentially expressed mRNAs by CodeLink microarrays, and the data were evaluated with GeneSifter. Androgens significantly (p < 0.05) influenced the expression of over 1300 genes, and many (n = 366) of the genes differentially regulated by androgen treatment were also differentially expressed in males compared with the females in our previous study. These findings support our hypotheses that testosterone extensively influences gene expression in the male submandibular gland, and that many of the sex differences are due to androgens.

Genome-wide expression profiling of human blood reveals biomarkers for Huntington's disease.

Huntington's disease (HD) is an autosomal dominant disorder caused by an expansion of glutamine repeats in ubiquitously distributed huntingtin protein. Recent studies have shown that mutant huntingtin interferes with the function of widely expressed transcription factors, suggesting that gene expression may be altered in a variety of tissues in HD, including peripheral blood. Affymetrix and Amersham Biosciences oligonucleotide microarrays were used to analyze global gene expression in blood samples of HD patients and matched controls. We identified 322 mRNAs that showed significantly altered expression in HD blood samples, compared with controls (P < 0.0005), on two different microarray platforms. A subset of up-regulated mRNAs selected from this group was able to distinguish controls, presymptomatic individuals carrying the HD mutation, and symptomatic HD patients. In addition, early presymptomatic subjects showed gene expression profiles similar to those of controls, whereas late presymptomatic subjects showed altered expression that resembled that of symptomatic HD patients. These elevated mRNAs were significantly reduced in HD patients involved in a dose-finding study of the histone deacetylase inhibitor sodium phenylbutyrate. Furthermore, expression of the marker genes was significantly up-regulated in postmortem HD caudate, suggesting that alterations in blood mRNAs may reflect disease mechanisms observed in HD brain. In conclusion, we identified changes in blood mRNAs that clearly distinguish HD patients from controls. These alterations in mRNA expression correlate with disease progression and response to experimental treatment. Such markers may provide clues to the state of HD and may be of predictive value in clinical trials.

Sex-related differences in gene expression in salivary glands of BALB/c mice.

Sex-related differences exist in the structure and function of the major glands in a variety of species. Moreover, many of these variations appear to be unique to each tissue. We hypothesized that this sexual dimorphism is due, at least in part, to gland-specific differences in gene expression between males and females. Glands were collected from male and female BALB/c mice (n = 5/sex/experiment), and total RNA was isolated. Samples were analyzed for differentially expressed mRNAs with CodeLink microarrays, and data were evaluated by GeneSifter. Our results demonstrate that significant (P < 0.05) sex-related differences exist in the expression of numerous genes in the major salivary glands, and many of these differences were tissue-specific. These findings support our hypothesis that sex-related differences in the salivary glands are due, at least in part, to tissue-specific variations in gene expression.

Exact, convergent periodic-orbit expansions of individual energy eigenvalues of regular quantum graphs.

We present exact, explicit, convergent periodic-orbit expansions for individual energy levels of regular quantum graphs in the paper. One simple application is the energy levels of a particle in a piecewise constant potential. Since the classical ray trajectories (including ray splitting) in such systems are strongly chaotic, this result provides an explicit quantization of a classically chaotic system.

Correcting for signal saturation errors in the analysis of microarray data.

A variety of technical errors have arisen in data analysis when using cDNA or oligonucleotide microarrays. One of the most insidious problems is the saturation of the hybridization signal of high-abundant transcripts. This problem arises from the truncation of the laser fluorescence signal. When the hybridization signal on the microarray is very strong, this truncation can result in serious consequences that may not be readily apparent to the user. As an illustration of this problem, two subclasses of normal human tissue samples (six liver and six lung samples) were analyzed with GeneChip probe arrays to evaluate the patterns of expression for approximately 7000 human genes. Five of these data sets were found to suffer from signal truncation. This caused several tissues to be incorrectly classified using hierarchical clustering. To rectify this problem so that the gene expression data could be properly compared and clustered, we developed a "filtering" procedure that identifies a subset of genes least affected by the signal saturation. This filtering procedure can be obtained at www.hugeindex.org.

Explicitly solvable cases of one-dimensional quantum chaos.

We identify a set of quantum graphs with unique and precisely defined spectral properties called regular quantum graphs. Although chaotic in their classical limit with positive topological entropy, regular quantum graphs are explicitly solvable. The proof is constructive: we present exact, convergent periodic orbit expansions for individual energy levels, thus obtaining an analytical solution for the spectrum of regular quantum graphs that is complete, explicit, and exact.

EBP2 is a member of the yeast RRB regulon, a transcriptionally coregulated set of genes that are required for ribosome and rRNA biosynthesis.

In an effort to identify sets of yeast genes that are coregulated across various cellular transitions, gene expression data sets derived from yeast cells progressing through the cell cycle, sporulation, and diauxic shift were analyzed. A partitioning algorithm was used to divide each data set into 24 clusters of similar expression profiles, and the membership of the clusters was compared across the three experiments. A single cluster of 189 genes from the cell cycle experiment was found to share 65 genes with a cluster of 159 genes from the sporulation data set. Many of these genes were found to be clustered in the diauxic-shift experiment as well. The overlapping set was enriched for genes required for rRNA biosynthesis and included genes encoding RNA helicases, subunits of RNA polymerases I and III, and rRNA processing factors. A subset of the 65 genes was tested for expression by a quantitative-relative reverse transcriptase PCR technique, and they were found to be coregulated after release from alpha factor arrest, heat shock, and tunicamycin treatment. Promoter scanning analysis revealed that the 65 genes within this ribosome and rRNA biosynthesis (RRB) regulon were enriched for two motifs: the 13-base GCGATGAGATGAG and the 11-base TGAAAAATTTT consensus sequences. Both motifs were found to be important for promoting gene expression after release from alpha factor arrest in a test rRNA processing gene (EBP2), which suggests that these consensus sequences may function broadly in the regulation of a set of genes required for ribosome and rRNA biosynthesis.

Exact trace formulas for a class of one-dimensional ray-splitting systems.

Using quantum graph theory we establish that the ray-splitting trace formula proposed by Couchman et al. [Phys. Rev. A 46, 6193 (1992)] is exact for a class of one-dimensional ray-splitting systems. Important applications in combinatorics are suggested.

A compendium of gene expression in normal human tissues.

This study creates a compendium of gene expression in normal human tissues suitable as a reference for defining basic organ systems biology. Using oligonucleotide microarrays, we analyze 59 samples representing 19 distinct tissue types. Of approximately 7,000 genes analyzed, 451 genes are expressed in all tissue types and designated as housekeeping genes. These genes display significant variation in expression levels among tissues and are sufficient for discerning tissue-specific expression signatures, indicative of fundamental differences in biochemical processes. In addition, subsets of tissue-selective genes are identified that define key biological processes characterizing each organ. This compendium highlights similarities and differences among organ systems and different individuals and also provides a publicly available resource (Human Gene Expression Index, the HuGE Index, http://www.hugeindex.org) for future studies of pathophysiology.

Dimensional complexity of EEG waveforms in neuroleptic-free schizophrenic patients and normal control subjects.

Dimensional complexity reflects the number of independent variables contributing to a dynamic process. EEG epochs recorded from 12 neuroleptic-free schizophrenic patients and 11 normal control subjects were Laplacian-filtered to highlight activity specific to prefrontal and parietal areas, and dimensional complexity measures of the resulting signals were then derived. Complexity of EEG waveforms generated by schizophrenic patients was depressed relative to that of normal subjects, especially in left frontal and right parietal regions. These data suggest that complexity of underlying is also reduced.

Order and chaos in semiconductor microstructures.

The semiclassical theory of ballistic electron transport in semiconductor microstructures provides a description of the quantum conductance fluctuations in terms of the classical distributions for the lengths and directed areas of the scattering trajectories. Because the classical dynamics differs for integrable (circular) and chaotic (stadium) scattering domains, experimental measurements of the conductance of these microstructures provide a unique probe of the quantum properties of classically regular and chaotic systems. To advance these theoretical and experimental studies we compare geometrical formulas for the classical distributions of lengths and areas with numerical simulations for microstructures examined in recent experiments, we assess the effects of lead size and placement, and we provide a critical analysis of the role of scattering "noise" on the classical and semiclassical predictions. Finally, we present a detailed comparison of the semiclassical theory with recent experimental measurements of the conductance fluctuations in circular- and stadium-shaped microstructures.

Chaotic scattering, unstable periodic orbits, and fluctuations in quantum transport.

The field of quantum chaos has recently focused attention on the quantum description of chaotic scattering processes. The new physical intuition, analytical methods, and numerical tools developed in the study of the quantum behavior of classically chaotic bound systems, like quantum billiards or atoms in strong fields, has led to exciting new predictions for the scattering of electromagnetic waves in curved waveguides, electrons in mesoscopic wires, and atoms off molecules. After a brief review of recent progress in the field of quantum chaos, this paper focuses on specific results relating to ballistic electron transport in small, mesoscopic devices. Several specific geometries are suggested for experimental studies of this "game" of quantum pinball with explicit predictions for the fluctuations in the electrical conductivity as functions of the electron Fermi energy and of an applied magnetic field.