Dynamic Patterns of Transcript Abundance of Transposable Element Families in Maize.

Transposable Elements (TEs) are mobile elements that contribute the majority of DNA sequences in the maize genome. Due to their repetitive nature, genomic studies of TEs are complicated by the difficulty of properly attributing multi-mapped short reads to specific genomic loci. Here, we utilize a method to attribute RNA-seq reads to TE families rather than particular loci in order to characterize transcript abundance for TE families in the maize genome. We applied this method to assess per-family expression of transposable elements in >800 published RNA-seq libraries representing a range of maize development, genotypes, and hybrids. While a relatively small proportion of TE families are transcribed, expression is highly dynamic with most families exhibiting tissue-specific expression. A large number of TE families were specifically detected in pollen and endosperm, consistent with reproductive dynamics that maintain silencing of TEs in the germ line. We find that B73 transcript abundance is a poor predictor of TE expression in other genotypes and that transcript levels can differ even for shared TEs. Finally, by assessing recombinant inbred line and hybrid transcriptomes, complex patterns of TE transcript abundance across genotypes emerged. Taken together, this study reveals a dynamic contribution of TEs to maize transcriptomes

Crystal growth, Structure Determination and Magnetism of a New Hexagonal Rhodate: Ba9Rh8O24

Single crystals of Ba9Rh8O24, grown from a molten potassium carbonate flux, crystallize in the spacegroup R¯3c with lattice parameters of a = 10.0899(4) and c = 41.462(2) Å. Magnetic measurements on oriented single crystals reveal the existence of magnetic anisotrop

Structure Determination of Ba\u3csub\u3e8\u3c/sub\u3eCoRh\u3csub\u3e6\u3c/sub\u3eO\u3csub\u3e21\u3c/sub\u3e, a New Member of the 2H-Perovskite Related Oxides

Single crystals of Ba8CoRh6O21 were grown out of a potassium carbonate flux. The structure was solved by a general method using the superspace group approach. The superspace group employed was R3m(00γ)0s with a = 10.0431(1) Å, c1 = 2.5946(1) Å and c2 = 4.5405(1) Å, V = 226.60(1) Å3. Ba8CoRh6O21 represents the first example of an m = 5, n = 3 member of the A3n+3mA\u27nB3m+nO9m+6n family of 2H hexagonal perovskite related oxides and contains chains consisting of six consecutive RhO6 octahedra followed by one distorted CoO6 trigonal prism. These chains in turn are separated from each other by [Ba]∞ chains

The Origin of Magnetic Interactions in Ca3Co2O6

We investigate the microscopic origin of the ferromagnetic and antiferromagnetic spin exchange couplings in the quasi one-dimensional cobalt compound Ca3Co2O6. In particular, we establish a local model which stabilizes a ferromagnetic alignment of the S=2 spins on the cobalt sites with trigonal prismatic symmetry, for a sufficiently strong Hund's rule coupling on the cobalt ions. The exchange is mediated through a S=0 cobalt ion at the octahedral sites of the chain structure. We present a strong coupling evaluation of the Heisenberg coupling between the S=2 Co spins on a separate chain. The chains are coupled antiferromagnetically through super-superexchange via short O-O bonds.Comment: 5 Pages, 3 Figures; added anisotropy term in eq. 9; extended discussion of phase transitio

Hybrid Decay: A Transgenerational Epigenetic Decline in Vigor and Viability Triggered in Backcross Populations of Teosinte with Maize.

In the course of generating populations of maize with teosinte chromosomal introgressions, an unusual sickly plant phenotype was noted in individuals from crosses with two teosinte accessions collected near Valle de Bravo, Mexico. The plants of these Bravo teosinte accessions appear phenotypically normal themselves and the F1 plants appear similar to typical maize × teosinte F1s. However, upon backcrossing to maize, the BC1 and subsequent generations display a number of detrimental characteristics including shorter stature, reduced seed set, and abnormal floral structures. This phenomenon is observed in all BC individuals and there is no chromosomal segment linked to the sickly plant phenotype in advanced backcross generations. Once the sickly phenotype appears in a lineage, normal plants are never again recovered by continued backcrossing to the normal maize parent. Whole-genome shotgun sequencing reveals a small number of genomic sequences, some with homology to transposable elements, that have increased in copy number in the backcross populations. Transcriptome analysis of seedlings, which do not have striking phenotypic abnormalities, identified segments of 18 maize genes that exhibit increased expression in sickly plants. A de novo assembly of transcripts present in plants exhibiting the sickly phenotype identified a set of 59 upregulated novel transcripts. These transcripts include some examples with sequence similarity to transposable elements and other sequences present in the recurrent maize parent (W22) genome as well as novel sequences not present in the W22 genome. Genome-wide profiles of gene expression, DNA methylation, and small RNAs are similar between sickly plants and normal controls, although a few upregulated transcripts and transposable elements are associated with altered small RNA or methylation profiles. This study documents hybrid incompatibility and genome instability triggered by the backcrossing of Bravo teosinte with maize. We name this phenomenon "hybrid decay" and present ideas on the mechanism that may underlie it

Clinically relevant characteristics associated with early treatment drug use versus abstinence

Background: This study describes early treatment drug use status and associated clinical characteristics in a diverse sample of patients entering outpatient substance abuse psychosocial counseling treatment. The goal is to more fully characterize those entering treatment with and without active use of their primary drug in order to better understand associated treatment needs and resilience factors. Methods: We examined baseline data from a NIDA Clinical Trials Network (CTN) study (Web-delivery of Treatment for Substance Use) with an all-comers sample of patients (N = 494) entering 10 outpatient treatment centers. Patients were categorized according to self-identified primary drug of abuse (alcohol, cocaine/stimulants, opioids, marijuana) and by baseline drug use status (positive/negative) based on urine testing or self-reports of recent use (alcohol). Characteristics were examined by primary drug and early use status. Results: Classified as drug-negative were 84%, 76%, 62%, and 33% of primary opioid, stimulant, alcohol, and marijuana users; respectively. Drug-positive versus -negative patients did not differ on demographics or rates of substance abuse/dependence diagnoses. However, those negative for active use had better physical and mental health profiles, were less likely to be using a secondary drug, and were more likely to be attending 12-step self-help meetings. Conclusions: Early treatment drug abstinence is common among substance users entering outpatient psychosocial counseling programs, regardless of primary abused drug. Abstinence (by negative UA) is associated with better health and mental health profiles, less secondary drug use, and more days of 12-step attendance. These data highlight differential treatment needs and resiliencies associated with early treatment drug use status. Trial registration: NCT01104805

Transposable elements contribute to activation of maize genes in response to abiotic stress. PLoS Genet

Abstract Transposable elements (TEs) account for a large portion of the genome in many eukaryotic species. Despite their reputation as ''junk'' DNA or genomic parasites deleterious for the host, TEs have complex interactions with host genes and the potential to contribute to regulatory variation in gene expression. It has been hypothesized that TEs and genes they insert near may be transcriptionally activated in response to stress conditions. The maize genome, with many different types of TEs interspersed with genes, provides an ideal system to study the genome-wide influence of TEs on gene regulation. To analyze the magnitude of the TE effect on gene expression response to environmental changes, we profiled gene and TE transcript levels in maize seedlings exposed to a number of abiotic stresses. Many genes exhibit up-or down-regulation in response to these stress conditions. The analysis of TE families inserted within upstream regions of up-regulated genes revealed that between four and nine different TE families are associated with up-regulated gene expression in each of these stress conditions, affecting up to 20% of the genes up-regulated in response to abiotic stress, and as many as 33% of genes that are only expressed in response to stress. Expression of many of these same TE families also responds to the same stress conditions. The analysis of the stress-induced transcripts and proximity of the transposon to the gene suggests that these TEs may provide local enhancer activities that stimulate stress-responsive gene expression. Our data on allelic variation for insertions of several of these TEs show strong correlation between the presence of TE insertions and stress-responsive upregulation of gene expression. Our findings suggest that TEs provide an important source of allelic regulatory variation in gene response to abiotic stress in maize

Specific heat and magnetization study on single crystals of a frustrated, quasi one-dimensional oxide: Ca3Co2O6

Specific heat and magnetization measurements have been carried out under a range of magnetic fields on single crystals of Ca3Co2O6. This compound is composed of Ising magnetic chains that are arranged on a triangular lattice. The intrachain and interchain couplings are ferromagnetic and antiferromagnetic, respectively. This situation gives rise to geometrical frustration, that bears some similarity to the classical problem of a two-dimensional Ising triangular antiferromagnet. This paper reports on the ordering process at low-T and the possibility of one-dimensional features at high-T.Comment: 7 pages, 6 figures, accepted for publication in PR

Crystal structure, electronic, and magnetic properties of the bilayered rhodium oxide Sr3Rh2O7

The bilayered rhodium oxide Sr3Rh2O7 was synthesized by high-pressure and high-temperature heating techniques. The single-phase polycrystalline sample of Sr3Rh2O7 was characterized by measurements of magnetic susceptibility, electrical resistivity, specific heat, and thermopower. The structural characteristics were investigated by powder neutron diffraction study. The rhodium oxide Sr3Rh2O7 [Bbcb, a = 5.4744(8) A, b = 5.4716(9) A, c = 20.875(2) A] is isostructural to the metamagnetic metal Sr3Ru2O7, with five 4d electrons per Rh, which is electronically equivalent to the hypothetic bilayered ruthenium oxide, where one electron per Ru is doped into the Ru-327 unit. The present data show the rhodium oxide Sr3Rh2O7 to be metallic with enhanced paramagnetism, similar to Sr3Ru2O7. However, neither manifest contributions from spin fluctuations nor any traces of a metamagnetic transition were found within the studied range from 2 K to 390 K below 70 kOe.Comment: To be published in PR