The effect of N-Acetyl cysteine on the expression of Fxr (Nr1h4), LXRα (Nr1h3) and Sirt1 genes,oxidative stress,and apoptosis in the liver of rats exposed to different doses of cadmium

Molecular Biology Reports - The aim of this study was to consider the expression of farnesoid X receptor (Fxr), liver X receptor (LXRα) and sirtuin 1 (Sirt1), oxidative stress, inflammation,...     

Fine Mapping and Candidate Gene Prediction of the Quantitative Trait Locus <i>qPL8</i> for Panicle Length in Rice

Rice panicle is the sink organ where assimilation product accumulates, and its morphology determines the rice yield. Panicle length has been suggested as a yield-related trait, but the genetic factor for its control is still limited. In this study, we carried out fine-mapping of qPL8, a QTL identified for panicle length in our previous work. Near isogenic line (NIL) with qPL8 exhibited elongated panicle without obvious effect on other panicle elements. With five key recombinants from NIL population, the locus was finally narrowed down to a 278-kb region, where 44 genes are annotated. By comparing the genomic sequence of two parents, 17 genes were identified with SNPs or InDels variations in the coding region. Expression analysis showed that eight genes were up-regulated in the NIL with qPL8. Considering both the coding variation and expression status, several candidate genes for the locus were identified, and OsMADS37 was raised as the most possible candidate. Interestingly, an expression QTL (eQTL) also resides in the locus, leading to a cluster of gene expression variation in the region. This study will facilitate the application of qPL8 locus in rice breeding for yield potential.     

Mechanisms of lung endothelial barrier disruption induced by cigarette smoke: role of oxidative stress and ceramides

The epithelial and endothelial cells lining the alveolus form a barrier essential for the preservation of the lung respiratory function, which is, however, vulnerable to excessive oxidative, inflammatory, and apoptotic insults. Whereas profound breaches in this barrier function cause pulmonary edema, more subtle changes may contribute to inflammation. The mechanisms by which cigarette smoke (CS) exposure induce lung inflammation are not fully understood, but an early alteration in the epithelial barrier function has been documented. We sought to investigate the occurrence and mechanisms by which soluble components of mainstream CS disrupt the lung endothelial cell barrier function. Using cultured primary rat microvascular cell monolayers, we report that CS induces endothelial cell barrier disruption in a dose- and time-dependent manner of similar magnitude to that of the epithelial cell barrier. CS exposure triggered a mechanism of neutral sphingomyelinase-mediated ceramide upregulation and p38 MAPK and JNK activation that were oxidative stress dependent and that, along with Rho kinase activation, mediated the endothelial barrier dysfunction. The morphological changes in endothelial cell monolayers induced by CS included actin cytoskeletal rearrangement, junctional protein zonula occludens-1 loss, and intercellular gap formation, which were abolished by the glutathione modulator N-acetylcysteine and ameliorated by neutral sphingomyelinase inhibition. The direct application of ceramide recapitulated the effects of CS, by disrupting both endothelial and epithelial cells barrier, by a mechanism that was redox and apoptosis independent and required Rho kinase activation. Furthermore, ceramide induced dose-dependent alterations of alveolar microcirculatory barrier in vivo, measured by two-photon excitation microscopy in the intact rat. In conclusion, soluble components of CS have direct endothelial barrier-disruptive effects that could be ameliorated by glutathione modulators or by inhibitors of neutral sphingomyelinase, p38 MAPK, JNK, and Rho kinase. Amelioration of endothelial permeability may alleviate lung and systemic vascular dysfunction associated with smoking-related chronic obstructive lung diseases.     

Genetic variation in Malaysian oysters: taxonomic ambiguities and evidence of biological invasion

Genetic diversities in two cultured oyster species, Crassostrea iredalei (Faustino 1932) and Crassostrea belcheri (Sowerby 1871) were assessed using a 581-nucleotide fragment of the mtDNA cytochrome oxidase subunit 1 (CO1) gene. A total of 103 C. iredalei individuals and 120 C. belcheri from 12 populations were sampled along the coast of Malaysia. Trees of unique haplotype samples generated based on Neighbor-Joining (NJ) algorithm revealed that many individuals had been misidentified and did not cluster with their presumed species based on morphological identification. BLAST results of DNA sequences showed presence of previously unreported C. madrasensis in Peninsular Malaysian waters (98% maximum identity). The true identity of the Muar (Crassostrea sp.) and Semporna (Saccostrea sp.) populations were unresolved by two BLAST search and showed less than 88% identity with other species in GenBank. Repeated analysis of these two populations using 487 bp of the mitochondrial 16S gene data showed only a maximum identity less than 97%. Hence, the identity of these specimens remains unclear. Evolutionary divergences within presumed species were 0.001–0.011 and 0.034–0.313 between species. Findings from this study have important implications for aquaculture, management and monitoring of cultured populations as well as conservation of wild oyster species in Malaysia.     

A dynamical systems model for combinatorial cancer therapy enhances oncolytic adenovirus efficacy by MEK-inhibition

Oncolytic adenoviruses, such as ONYX-015, have been tested in clinical trials for currently untreatable tumors, but have yet to demonstrate adequate therapeutic efficacy. The extent to which viruses infect targeted cells determines the efficacy of this approach but many tumors down-regulate the Coxsackievirus and Adenovirus Receptor (CAR), rendering them less susceptible to infection. Disrupting MAPK pathway signaling by pharmacological inhibition of MEK up-regulates CAR expression, offering possible enhanced adenovirus infection. MEK inhibition, however, interferes with adenovirus replication due to resulting G1-phase cell cycle arrest. Therefore, enhanced efficacy will depend on treatment protocols that productively balance these competing effects. Predictive understanding of how to attain and enhance therapeutic efficacy of combinatorial treatment is difficult since the effects of MEK inhibitors, in conjunction with adenovirus/cell interactions, are complex nonlinear dynamic processes. We investigated combinatorial treatment strategies using a mathematical model that predicts the impact of MEK inhibition on tumor cell proliferation, ONYX-015 infection, and oncolysis. Specifically, we fit a nonlinear differential equation system to dedicated experimental data and analyzed the resulting simulations for favorable treatment strategies. Simulations predicted enhanced combinatorial therapy when both treatments were applied simultaneously; we successfully validated these predictions in an ensuing explicit test study. Further analysis revealed that a CAR-independent mechanism may be responsible for amplified virus production and cell death. We conclude that integrated computational and experimental analysis of combinatorial therapy provides a useful means to identify treatment/infection protocols that yield clinically significant oncolysis. Enhanced oncolytic therapy has the potential to dramatically improve non-surgical cancer treatment, especially in locally advanced or metastatic cases where treatment options remain limited.     

Proteomics analysis of the ezrin interactome in B cells reveals a novel association with Myo18aα

The molecular regulation of recruitment and assembly of signalosomes near the B cell receptor (BCR) is poorly understood. We have previously demonstrated a role for the ERM family protein ezrin in regulating antigen-dependent lipid raft coalescence in B cells. In this study, we addressed the possibility that ezrin may collaborate with other adaptor proteins to regulate signalosome dynamics at the membrane. Using mass spectrometry-based proteomics analysis, we identified Myo18aα as a novel binding partner of ezrin. Myo18aα is an attractive candidate as it has several protein-protein interaction domains and an intrinsic motor activity. The expression of Myo18aα varied during B cell development in the bone marrow and in mature B cell subsets suggesting functional differences. Interestingly, BCR stimulation increased the association between ezrin and Myo18aα, and induced co-segregation of Myo18aα with the BCR and phosphotyrosine-containing proteins. Our data raise an intriguing possibility that the Myo18aα/ezrin complex may facilitate BCR-mediated signaling by recruiting signaling proteins that are in close proximity of the antigen receptor. Our study is not only significant with respect to understanding the molecular regulation of BCR signaling but also provides a broader basis for understanding the mechanism of action of ezrin in other cellular systems.     

Preference for bridging versus terminal ligands in magnesium dimers

Magnesium dimers play important roles in inorganic and organometallic chemistry. This study evaluates the inherent bridging ability of a range of different ligands in magnesium dimers. In the first part, the Cambridge Structural Database is interrogated to establish the frequency of different types of ligands found in bridging versus terminal positions in two key structural motifs: one in which there are two bridging ligands (the D _2h “Mg₂(μ-X₂)” structure); the other in which there are three bridging ligands (the C _3v “Mg₂(μ-X₃)” structure). The most striking finding from the database search is the overwhelming preference for magnesium dimers possessing two bridging ligands. The most common bridging ligands are C-, N-, and O-based. In the second part, DFT calculations (at the B3LYP/6-311+G(d) level of theory) are carried out to examine a wider range of structural types for dimers consisting of the stoichiometries Mg₂Cl₃R and Mg₂Cl₂R₂, where R = CH₃, SiH₃, NH₂, PH₂, OH, SH, CH₂CH₃, CH=CH₂, C≡CH, Ph, OAc, F and Br. Consistent with the database search, the most stable magnesium dimers are those that contain two bridging ligands. Furthermore, it was demonstrated that the electronic effect of the bridging ligands is important in influencing the stability of the magnesium dimers. The preference for a bridging ligand, which reflects its ability to stabilize a magnesium dimer, follows the order: OH > NH₂ > C≡CH > SH > Ph > Br > PH₂ = CH=CH₂ > CH₂CH₃ > CH₃ > SiH₃. Finally, the role that the ether solvent Me₂O has on the stability of isomeric Mg₂Cl₂Me₂ dimers was studied. It was found that the first solvent molecule stabilizes the dimers, while the second solvent molecule can either have a stabilizing or destabilizing effect, depending on the isomer structure.     

Correlation of LNCR rasiRNAs expression with heterochromatin formation during development of the holocentric insect Spodoptera frugiperda

Repeat-associated small interfering RNAs (rasiRNAs) are derived from various genomic repetitive elements and ensure genomic stability by silencing endogenous transposable elements. Here we describe a novel subset of 46 rasiRNAs named LNCR rasiRNAs due to their homology with one long non-coding RNA (LNCR) of Spodoptera frugiperda. LNCR operates as the intermediate of an unclassified transposable element (TE-LNCR). TE-LNCR is a very invasive transposable element, present in high copy numbers in the S. frugiperda genome. LNCR rasiRNAs are single-stranded RNAs without a prominent nucleotide motif, which are organized in two distinct, strand-specific clusters. The expression of LNCR and LNCR rasiRNAs is developmentally regulated. Formation of heterochromatin in the genomic region where three copies of the TE-LNCR are embedded was followed by chromatin immunoprecipitation (ChIP) and we observed this chromatin undergo dynamic changes during development. In summary, increased LNCR expression in certain developmental stages is followed by the appearance of a variety of LNCR rasiRNAs which appears to correlate with subsequent accumulation of a heterochromatic histone mark and silencing of the genomic region with TE-LNCR. These results support the notion that a repeat-associated small interfering RNA pathway is linked to heterochromatin formation and/or maintenance during development to establish repression of the TE-LNCR transposable element. This study provides insights into the rasiRNA silencing pathway and its role in the formation of fluctuating heterochromatin during the development of one holocentric organism.     

Considering transposable element diversification in de novo annotation approaches

Transposable elements (TEs) are mobile, repetitive DNA sequences that are almost ubiquitous in prokaryotic and eukaryotic genomes. They have a large impact on genome structure, function and evolution. With the recent development of high-throughput sequencing methods, many genome sequences have become available, making possible comparative studies of TE dynamics at an unprecedented scale. Several methods have been proposed for the de novo identification of TEs in sequenced genomes. Most begin with the detection of genomic repeats, but the subsequent steps for defining TE families differ. High-quality TE annotations are available for the Drosophila melanogaster and Arabidopsis thaliana genome sequences, providing a solid basis for the benchmarking of such methods. We compared the performance of specific algorithms for the clustering of interspersed repeats and found that only a particular combination of algorithms detected TE families with good recovery of the reference sequences. We then applied a new procedure for reconciling the different clustering results and classifying TE sequences. The whole approach was implemented in a pipeline using the REPET package. Finally, we show that our combined approach highlights the dynamics of well defined TE families by making it possible to identify structural variations among their copies. This approach makes it possible to annotate TE families and to study their diversification in a single analysis, improving our understanding of TE dynamics at the whole-genome scale and for diverse species.