LncRNA and mRNA integration network reconstruction reveals novel key regulators in esophageal squamous-cell carcinoma

Many experimental and computational studies have identified key protein coding genes in initiation and progression of esophageal squamous cell carcinoma (ESCC). However, the number of researches that tried to reveal the role of long non-coding RNAs (lncRNAs) in ESCC has been limited. LncRNAs are one of the important regulators of cancers which are transcribed dominantly in the genome and in various conditions. The main goal of this study was to use a systems biology approach to predict novel lncRNAs as well as protein coding genes associated with ESCC and assess their prognostic values. By using microarray expression data for mRNAs and lncRNAs from a large number of ESCC patients, we utilized “Weighted Gene Co-expression Network Analysis” (WGCNA) method to make a big coding-non-coding gene co-expression network, and discovered important functional modules. Gene set enrichment and pathway analysis revealed major biological processes and pathways involved in these modules. After selecting some protein coding genes involved in biological processes and pathways related to cancer, we used “LncTar”, a computational tool to predict potential interactions between these genes and lncRNAs. By combining interaction results with Pearson correlations, we introduced some novel lncRNAs with putative key regulatory roles in the network. Survival analysis with Kaplan-Meier estimator and Log-rank test statistic confirmed that most of the introduced genes are associated with poor prognosis in ESCC. Overall, our study reveals novel protein coding genes and lncRNAs associated with ESCC, along with their predicted interactions. Based on the promising results of survival analysis, these genes can be used as good estimators of patients' survival, or even can be analyzed further as new potential signatures or targets for the therapy of ESCC disease.     

The prevalence, intensity and viability of hydatid cysts in slaughtered animals in the Ardabil province of Northwest Iran

In a cross-sectional study, a total of 5381 slaughtered animals, namely 928 cattle, 243 buffaloes, 3765 sheep and 445 goats were inspected macroscopically for hydatid cysts in northwest Iran, with prevalence values of 38.3%, 11.9%, 74.4% and 20%, respectively, being recorded. Prevalences were higher in females compared with males, but a significant difference (P < 0.001) was only found in sheep and cattle. Most cases which were condemned were seen in the lungs of sheep (13.4%) indicating that sheep are the most important intermediate hosts for Echinococcus granulosus in this area.     

Molecular detection of Puccinia horiana Henn. the causal agent of Chrysanthemum white rust

Chrysanthemum white rust is one of the most important foliar diseases of pot chrysanthemum and is a quarantine pathogen in many countries. Under conducive environmental conditions, it has the potential to completely destroy susceptible cultivars. This is mainly avoided through frequent preventive fungicide applications. As part of a research program to develop a disease warning system, a molecular detection method was developed. To determine the nucleotide sequence of the nuclear rDNA-ITS (internal transcribed spacer) region of P. horiana, 56 isolates were collected between 2003 and 2006 from diseased commercial chrysanthemum plants from different national and international geographical areas. DNA was isolated from the basidiospores or teliospores from several isolates and the rDNA-ITS region was cloned and sequenced. Based on the limited variability in rDNA-ITS sequence between these isolates, several primer pairs were designed and tested for detection through conventional and real-time PCR. Specificity of detection was cross-checked against a variety of other fungi (saprophytes and other rusts) that may occur in the same environment, and against DNA of healthy chrysanthemum leaves. Using the best primers, the PCR-based methods successfully detected all the P. horiana isolates tested, while no signal was observed with other rust species up to 1 ng non target genomic DNA template. The limit of detection of P. horiana DNA in conventional, nested and real-time PCR was 10 pg, 10 fg and 10 fg, respectively. The DNA extraction method and PCR template concentration were optimized to maximize the recoverability of the pathogen from infected plant tissue. Using the optimized real-time PCR method, the pathogen could be detected in washed plant tissue, 9 hours after inoculation. Hence, this method allows detection of the P. horiana in any part of its latent stage and will also serve as a tool for studying the biology and epidemiology of the pathogen.     

Achieving a High Q-Factor and Tunable Slow-Light via Classical Electromagnetically Induced Transparency (Cl-EIT) in Metamaterials

Plasmonics - We report on our numerical work concerning a 3D planar nano-structure metamaterial exhibiting classical electromagnetically induced transparency (Cl-EIT). The interaction between two...     

Acetylation of C-terminal lysines modulates protein turnover and stability of Connexin-32

Background

The gap junction protein, Connexin32 (Cx32), is expressed in various tissues including liver, exocrine pancreas, gastrointestinal epithelium, and the glia of the central and peripheral nervous system. Gap junction-mediated cell-cell communication and channel-independent processes of Cx32 contribute to the regulation of physiological and cellular activities such as glial differentiation, survival, and proliferation; maintenance of the hepatic epithelium; and axonal myelination. Mutations in Cx32 cause X-linked Charcot–Marie–Tooth disease (CMT1X), an inherited peripheral neuropathy. Several CMT1X causing mutations are found in the cytoplasmic domains of Cx32, a region implicated in the regulation of gap junction assembly, turnover and function. Here we investigate the roles of acetylation and ubiquitination in the C-terminus on Cx32 protein function. Cx32 protein turnover, ubiquitination, and response to deacetylase inhibitors were determined for wild-type and C-terminus lysine mutants using transiently transfected Neuro2A (N2a) cells.

Results

We report here that Cx32 is acetylated in transfected N2a cells and that inhibition of the histone deacetylase, HDAC6, results in an accumulation of Cx32. We identified five lysine acetylation targets in the C-terminus. Mutational analysis demonstrates that these lysines are involved in the regulation of Cx32 ubiquitination and turnover. While these lysines are not required for functional Cx32 mediated cell-cell communication, BrdU incorporation studies demonstrate that their relative acetylation state plays a channel-independent role in Cx32-mediated control of cell proliferation.

Conclusion

Taken together these results highlight the role of post translational modifications and lysines in the C-terminal tail of Cx32 in the fine-tuning of Cx32 protein stability and channel-independent functions.

     

Molecular detection of Puccinia horiana in Chrysanthemum x morifolium through conventional and real-time PCR

Puccinia horiana Henn. is a quarantine organism and one of the most important fungal pathogens of Chrysanthemum x morifolium cultivars grown for cut flower or potted plant production (florist's chrysanthemum) in several regions of the world. Highly specific primer pairs were identified for conventional, nested, and real-time PCR detection of P. horiana based on the specific and sensitive PCR amplification of selected regions in the internal transcribed spacers (ITS1 and ITS2) of the nuclear ribosomal DNA (rDNA). Using these different PCR versions, 10 pg, 10 fg, and 5 fg genomic DNA could be detected, respectively. When using cloned target DNA as template, the detection limits were 5000, 50, and 5 target copies, respectively. These detection limits were not affected by a background of chrysanthemum plant DNA. The DNA extraction method was optimized to maximize the recoverability of the pathogen from infected plant tissue. A CTAB extraction protocol or a selection of commercial DNA extraction methods allowed the use of 10 ng total (plant+pathogen) DNA without interference of PCR inhibitors. Due to the specificity of the primers, SYBR Green I technology enabled reliable real time PCR signal detection. However, an efficient TaqMan probe is available. The lowest proportion of infected plant material that could still be detected when mixed with healthy plant material was 0.001%. The real-time PCR assay could detect as few as eight pure P. horiana basidiospores, demonstrating the potential of the technique for aerial detection of the pathogen. The amount of P. horiana DNA in plant tissue was determined at various time points after basidiospore inoculation. Using the real-time PCR protocol, it was possible to detect the pathogen immediately after the inoculation period, even though the accumulation of pathogen DNA was most pronounced near the end of the latent period. The detection system proved to be accurate and sensitive and could help not only in pathogen diagnosis but also in pathogen monitoring and disease forecasting systems.     

Oxidative Stress Parameters,Trace Elements,and Lipid Profile in Iranian Patients with Gaucher Disease

Biological Trace Element Research - Gaucher disease (GD) is most frequent disorder of glycolipid storage. The glucosylceramide accumulation might lead to oxidative stress and changes in lipid...     

Short-term carbon input increases microbial nitrogen demand,but not microbial nitrogen mining,in a set of boreal forest soils

Rising carbon dioxide (CO₂) concentrations and temperatures are expected to stimulate plant productivity and ecosystem C sequestration, but these effects require a concurrent increase in N availability for plants. Plants might indirectly promote N availability as they release organic C into the soil (e.g., by root exudation) that can increase microbial soil organic matter (SOM) decomposition (“priming effect”), and possibly the enzymatic breakdown of N-rich polymers, such as proteins, into bio-available units (“N mining”). We tested the adjustment of protein depolymerization to changing soil C and N availability in a laboratory experiment. We added easily available C or N sources to six boreal forest soils, and determined soil organic C mineralization, gross protein depolymerization and gross ammonification rates (using ¹⁵N pool dilution assays), and potential extracellular enzyme activities after 1 week of incubation. Added C sources were ¹³C-labelled to distinguish substrate from soil derived C mineralization. Observed effects reflect short-term adaptations of non-symbiotic soil microorganisms to increased C or N availability. Although C input promoted microbial growth and N demand, we did not find indicators of increased N mobilization from SOM polymers, given that none of the soils showed a significant increase in protein depolymerization, and only one soil showed a significant increase in N-targeting enzymes. Instead, our findings suggest that microorganisms immobilized the already available N more efficiently, as indicated by decreased ammonification and inorganic N concentrations. Likewise, although N input stimulated ammonification, we found no significant effect on protein depolymerization. Although our findings do not rule out in general that higher plant-soil C allocation can promote microbial N mining, they suggest that such an effect can be counteracted, at least in the short term, by increased microbial N immobilization, further aggravating plant N limitation.     

Gametic selection,developmental trajectories,and extrinsic heterogeneity in Haldane's rule

Deciphering the genetic and developmental causes of the disproportionate rarity, inviability, and sterility of hybrid males, Haldane's rule, is important for understanding the evolution of reproductive isolation between species. Moreover, extrinsic and prezygotic factors can contribute to the magnitude of intrinsic isolation experienced between species with partial reproductive compatibility. Here, we use the nematodes Caenorhabditis briggsae and C. nigoni to quantify the sensitivity of hybrid male viability to extrinsic temperature and developmental timing, and test for a role of mito‐nuclear incompatibility as a genetic cause. We demonstrate that hybrid male inviability manifests almost entirely as embryonic, not larval, arrest and is maximal at the lowest rearing temperatures, indicating an intrinsic‐by‐extrinsic interaction to hybrid inviability. Crosses using mitochondrial substitution strains that have reciprocally introgressed mitochondrial and nuclear genomes show that mito‐nuclear incompatibility is not a dominant contributor to postzygotic isolation and does not drive Haldane's rule in this system. Crosses also reveal that competitive superiority of X‐bearing sperm provides a novel means by which postmating prezygotic factors exacerbate the rarity of hybrid males. These findings highlight the important roles of gametic, developmental, and extrinsic factors in modulating the manifestation of Haldane's rule.