Rare earth elements distribution in the river sediments of Ditrău Alkaline massif, Eastern Carpathians.

Ditrău Alkaline Massif is one of the few syenitic Massifs in Europe subjected to mining exploration in the past, located in the Eastern Carpathians, Romania. The heterogenous petrography includes acid to ultrabasic rocks such as syenites, hornblendites, and diorites, making it the defining feature of the Massif. In this study, we analyze the river bed sediments of two rivers, Ditrău and Jolotca, draining the Ditrău Alkaline Massif to determine their geochemical composition, with particular interest in Rare Earth Elements.

Regional Analysis of the Brain Transcriptome in Mice Bred for High and Low Methamphetamine Consumption.

Transcriptome profiling can broadly characterize drug effects and risk for addiction in the absence of drug exposure. Modern large-scale molecular methods, including RNA-sequencing (RNA-Seq), have been extensively applied to alcohol-related disease traits, but rarely to risk for methamphetamine (MA) addiction. We used RNA-Seq data from selectively bred mice with high or low risk for voluntary MA intake to construct coexpression and cosplicing networks for differential risk.

Space Radiation Alters Genotype-Phenotype Correlations in Fear Learning and Memory Tests.

Behavioral and cognitive traits have a genetic component even though contributions from individual genes and genomic loci are in many cases modest. Changes in the environment can alter genotype-phenotype relationships. Space travel, which includes exposure to ionizing radiation, constitutes environmental challenges and is expected to induce not only dramatic behavioral and cognitive changes but also has the potential to induce physical DNA damage.

Cross-species molecular dissection across alcohol behavioral domains.

This review summarizes the proceedings of a symposium presented at the "Alcoholism and Stress: A Framework for Future Treatment Strategies" conference held in Volterra, Italy on May 9-12, 2017. Psychiatric diseases, including alcohol-use disorders (AUDs), are influenced through complex interactions of genes, neurobiological pathways, and environmental influences. A better understanding of the common neurobiological mechanisms underlying an AUD necessitates an integrative approach, involving a systematic assessment of diverse species and phenotype measures.

Regional Differences and Similarities in the Brain Transcriptome for Mice Selected for Ethanol Preference From HS-CC Founders.

The high genetic complexity found in heterogeneous stock (HS-CC) mice, together with selective breeding, can be used to detect new pathways and mechanisms associated with ethanol preference and excessive ethanol consumption. We predicted that these pathways would provide new targets for therapeutic manipulation. Previously (Colville et al.

Network-Based Predictors of Progression in Head and Neck Squamous Cell Carcinoma.

The heterogeneity in head and neck squamous cell carcinoma (HNSCC) has made reliable stratification extremely challenging. Behavioral risk factors such as smoking and alcohol consumption contribute to this heterogeneity. To help elucidate potential mechanisms of progression in HNSCC, we focused on elucidating patterns of gene interactions associated with tumor progression.

Gender-Specific Effects of Selection for Drinking in the Dark on the Network Roles of Coding and Noncoding RNAs.

Background: Transcriptional differences between heterogeneous stock mice and high drinking-in-the-dark selected mouse lines have previously been described based on microarray technology coupled with network-based analysis. The network changes were reproducible in 2 independent selections and largely confined to 2 distinct network modules; in contrast, differential expression appeared more specific to each selected line. This study extends these results by utilizing RNA-Seq technology, allowing evaluation of the relationship between genetic risk and transcription of noncoding RNA (ncRNA); we additionally evaluate sex-specific transcriptional effects of selection.

Alignment of the transcriptome with individual variation in animals selectively bred for High Drinking-In-the-Dark (HDID).

Among animals at risk for excessive ethanol consumption such as the HDID selected mouse lines, there is considerable individual variation in the amount of ethanol consumed and the associated blood ethanol concentrations (BECs). For the HDID lines, this variation occurs even though the residual genetic variation associated with the DID phenotype has been largely exhausted and thus is most likely associated with epigenetic factors. Here we focus on the question of whether the genes associated with individual variation in HDID-1 mice are different from those associated with selection (risk) (Iancu et al.

On the relationships in rhesus macaques between chronic ethanol consumption and the brain transcriptome.

This is the first description of the relationship between chronic ethanol self-administration and the brain transcriptome in a non-human primate (rhesus macaque). Thirty-one male animals self-administered ethanol on a daily basis for over 12 months. Gene transcription was quantified with RNA-Seq in the central nucleus of the amygdala (CeA) and cortical Area 32.

Enhanced functional connectivity involving the ventromedial hypothalamus following methamphetamine exposure.

Methamphetamine (MA) consumption causes disruption of many biological rhythms including the sleep-wake cycle. This circadian effect is seen shortly following MA exposure and later in life following developmental MA exposure. MA phase shifts, entrains the circadian clock and can also alter the entraining effect of light by currently unknown mechanisms.

Cosplicing network analysis of mammalian brain RNA-Seq data utilizing WGCNA and Mantel correlations.

Across species and tissues and especially in the mammalian brain, production of gene isoforms is widespread. While gene expression coordination has been previously described as a scale-free coexpression network, the properties of transcriptome-wide isoform production coordination have been less studied. Here we evaluate the system-level properties of cosplicing in mouse, macaque, and human brain gene expression data using a novel network inference procedure.

Dual-trait selection for ethanol consumption and withdrawal: genetic and transcriptional network effects.

Background: Data from C57BL/6J (B6) × DBA/2J (D2) F2 intercrosses (B6xD2 F2 ), standard and recombinant inbred strains, and heterogeneous stock mice indicate that a reciprocal (or inverse) genetic relationship exists between alcohol consumption and withdrawal severity. Furthermore, some genetic studies have detected reciprocal quantitative trait loci (QTLs) for these traits. We used a novel mouse model developed by simultaneous selection for both high alcohol consumption/low withdrawal and low alcohol consumption/high withdrawal and analyzed the gene expression and genome-wide genotypic differences.

Coexpression and cosplicing network approaches for the study of mammalian brain transcriptomes.

Next-generation sequencing experiments have demonstrated great potential for transcriptome profiling. While transcriptome sequencing greatly increases the level of biological detail, system-level analysis of these high-dimensional datasets is becoming essential. We illustrate gene network approaches to the analysis of transcriptional data, with particular focus on the advantage of RNA-Seq technology compared to microarray platforms.

Introduction to sequencing the brain transcriptome.

High-throughput next-generation sequencing is now entering its second decade. However, it was not until 2008 that the first report of sequencing the brain transcriptome appeared (Mortazavi, Williams, Mccue, Schaeffer, & Wold, 2008). These authors compared short-read RNA-Seq data for mouse whole brain with microarray results for the same sample and noted both the advantages and disadvantages of the RNA-Seq approach.

The genetics of gene expression in complex mouse crosses as a tool to study the molecular underpinnings of behavior traits.

Complex Mus musculus crosses provide increased resolution to examine the relationships between gene expression and behavior. While the advantages are clear, there are numerous analytical and technological concerns that arise from the increased genetic complexity that must be considered. Each of these issues is discussed, providing an initial framework for complex cross study design and planning.

Differential network analysis reveals genetic effects on catalepsy modules.

We performed short-term bi-directional selective breeding for haloperidol-induced catalepsy, starting from three mouse populations of increasingly complex genetic structure: an F2 intercross, a heterogeneous stock (HS) formed by crossing four inbred strains (HS4) and a heterogeneous stock (HS-CC) formed from the inbred strain founders of the Collaborative Cross (CC). All three selections were successful, with large differences in haloperidol response emerging within three generations. Using a custom differential network analysis procedure, we found that gene coexpression patterns changed significantly; importantly, a number of these changes were concordant across genetic backgrounds.

Selection for drinking in the dark alters brain gene coexpression networks.

Background: Heterogeneous stock (HS/NPT) mice have been used to create lines selectively bred in replicate for elevated drinking in the dark (DID). Both selected lines routinely reach a blood ethanol (EtOH) concentration (BEC) of 1.00 mg/ml or greater at the end of the 4-hour period of access in Day 2.

Detection of expression quantitative trait Loci in complex mouse crosses: impact and alleviation of data quality and complex population substructure.

Complex Mus musculus crosses, e.g., heterogeneous stock (HS), provide increased resolution for quantitative trait loci detection.

Role of mGluR4 in acquisition of fear learning and memory.

Group III metabotropic glutamate receptors (mGluRs), which are generally located presynaptically, modulate synaptic transmission by regulating neurotransmitter release. Previously we showed enhanced amygdala-dependent cued fear conditioning in mGluR4(-/-) mice 24 h following training involving two tone-shock pairings. In this study, we assessed the effects of modulating mGluR4 signaling on acquisition and extinction of conditioned fear.

Utilizing RNA-Seq data for de novo coexpression network inference.

Motivation: RNA-Seq experiments have shown great potential for transcriptome profiling. While sequencing increases the level of biological detail, integrative data analysis is also important. One avenue is the construction of coexpression networks.

Gamma oscillations in the auditory cortex of awake rats.

Numerous reports of human electrophysiology have demonstrated gamma (30-150 Hz) frequency oscillations in the auditory cortex during listening. However, only a small number of studies in non-human animals have provided evidence for gamma oscillations during listening. In this report, multi-site recordings from primary auditory cortex (A1) were carried out using a 16-channel microelectrode array in awake rats as they passively listened to tones.

Genetic diversity and striatal gene networks: focus on the heterogeneous stock-collaborative cross (HS-CC) mouse.

Background: The current study focused on the extent genetic diversity within a species (Mus musculus) affects gene co-expression network structure. To examine this issue, we have created a new mouse resource, a heterogeneous stock (HS) formed from the same eight inbred strains that have been used to create the collaborative cross (CC). The eight inbred strains capture > 90% of the genetic diversity available within the species.