NFIC mediates m6A mRNA methylation to orchestrate transcriptional and post-transcriptional regulation to represses malignant phenotype of non-small cell lung cancer cells.

BACKGROUND: Multiple genetic and epigenetic regulatory mechanisms are crucial in the development and tumorigenesis process. Transcriptional regulation often involves intricate relationships and networks with post-transcriptional regulatory molecules, impacting the spatial and temporal expression of genes. However, the synergistic relationship between transcription factors and N6-methyladenosine (m6A) modification in regulating gene expression, as well as their influence on the mechanisms underlying the occurrence and progression of non-small cell lung cancer (NSCLC), requires further investigation. The present study aimed to investigate the synergistic relationship between transcription factors and m6A modification on NSCLC. METHODS: The transcription factor NFIC and its potential genes was screened by analyzing publicly available datasets (ATAC-seq, DNase-seq, and RNA-seq). The association of NFIC and its potential target genes were validated through ChIP-qPCR and dual-luciferase reporter assays. Additionally, the roles of NFIC and its potential genes in NSCLC were detected in vitro and in vivo through silencing and overexpression assays. RESULTS: Based on multi-omics data, the transcription factor NFIC was identified as a potential tumor suppressor of NSCLC. NFIC was significantly downregulated in both NSCLC tissues and cells, and when NFIC was overexpressed, the malignant phenotype and total m6A content of NSCLC cells was suppressed, while the PI3K/AKT pathway was inactivated. Additionally, we discovered that NFIC inhibits the expression of METTL3 by directly binding to its promoter region, and METTL3 regulates the expression of KAT2A, a histone acetyltransferase, by methylating the m6A site in the 3'UTR of KAT2A mRNA in NSCLC cells. Intriguingly, NFIC was also found to negatively regulate the expression of KAT2A by directly binding to its promoter region. CONCLUSIONS: Our findings demonstrated that NFIC suppresses the malignant phenotype of NSCLC cells by regulating gene expression at both the transcriptional and post-transcriptional levels. A deeper comprehension of the genetic and epigenetic regulatory mechanisms in tumorigenesis would be beneficial for the development of personalized treatment strategies.

Electron-Induced Nonmonotonic Pressure Dependence of the Lattice Thermal Conductivity of θ-TaN.

Recent theoretical and experimental research suggests that θ-TaN is a semimetal with high thermal conductivity (κ), primarily due to the contribution of phonons (κ_{ph}). By using first-principles calculations, we show a nonmonotonic pressure dependence of the κ of θ-TaN. κ_{ph} first increases until it reaches a maximum at around 60 GPa, and then decreases. This anomalous behavior is a consequence of the competing pressure responses of phonon-phonon and phonon-electron interactions, in contrast to the known materials BAs and BP, where the nonmonotonic pressure dependence is caused by the interplay between different phonon-phonon scattering channels. Although TaN has phonon dispersion features similar to BAs at ambient pressure, its response to pressure is different and an overall stiffening of the phonon branches takes place. Consequently, the relevant phonon-phonon scattering weakens as pressure increases. However, the increased electronic density of states near the Fermi level, and specifically the emergence of additional pockets of the Fermi surface at the high-symmetry L point in the Brillouin zone, leads to a substantial increase in phonon-electron scattering at high pressures, driving a decrease in κ_{ph}. At intermediate pressures (∼20-70 GPa), the κ of TaN surpasses that of BAs. Our Letter provides deeper insight into phonon transport in semimetals and metals where phonon-electron scattering is relevant.

Diversification of JAZ-MYC signaling function in immune metabolism.

Jasmonate (JA) re-programs metabolism to confer resistance to diverse environmental threats. Jasmonate stimulates the degradation of JASMONATE ZIM-DOMAIN (JAZ) proteins that repress the activity of MYC transcription factors. In Arabidopsis thaliana, MYC and JAZ are encoded by 4 and 13 genes, respectively. The extent to which expansion of the MYC and JAZ families has contributed to functional diversification of JA responses is not well understood. Here, we investigated the role of MYC and JAZ paralogs in controlling the production of defense compounds derived from aromatic amino acids (AAAs). Analysis of loss-of-function and dominant myc mutations identified MYC3 and MYC4 as the major regulators of JA-induced tryptophan metabolism. We developed a JAZ family-based, forward genetics approach to screen randomized jaz polymutants for allelic combinations that enhance tryptophan biosynthetic capacity. We found that mutants defective in all members (JAZ1/2/5/6) of JAZ group I over-accumulate AAA-derived defense compounds, constitutively express marker genes for the JA-ethylene branch of immunity and are more resistant to necrotrophic pathogens but not insect herbivores. In defining JAZ and MYC paralogs that regulate the production of amino-acid-derived defense compounds, our results provide insight into the specificity of JA signaling in immunity.

Molecular Mechanism Underlying the Synergetic Effect of Jasmonate on Abscisic Acid Signaling during Seed Germination in Arabidopsis.

Abscisic acid (ABA) is known to suppress seed germination and post-germinative growth of Arabidopsis (Arabidopsis thaliana), and jasmonate (JA) enhances ABA function. However, the molecular mechanism underlying the crosstalk between the ABA and JA signaling pathways remains largely elusive. Here, we show that exogenous coronatine, a JA analog structurally similar to the active conjugate jasmonate-isoleucine, significantly enhances the delayed seed germination response to ABA. Disruption of the JA receptor CORONATINE INSENSITIVE1 or accumulation of the JA signaling repressor JASMONATE ZIM-DOMAIN (JAZ) reduced ABA signaling, while jaz mutants enhanced ABA responses. Mechanistic investigations revealed that several JAZ repressors of JA signaling physically interact with ABSCISIC ACID INSENSITIVE3 (ABI3), a critical transcription factor that positively modulates ABA signaling, and that JAZ proteins repress the transcription of ABI3 and ABI5. Further genetic analyses showed that JA activates ABA signaling and requires functional ABI3 and ABI5. Overexpression of ABI3 and ABI5 simultaneously suppressed the ABA-insensitive phenotypes of the coi1-2 mutant and JAZ-accumulating (JAZ-ΔJas) plants. Together, our results reveal a previously uncharacterized signaling module in which JAZ repressors of the JA pathway regulate the ABA-responsive ABI3 and ABI5 transcription factors to integrate JA and ABA signals during seed germination and post-germinative growth.

A meta-analysis of the risk factors for surgical site infection in patients with colorectal cancer.

The purpose of the meta-analysis was to evaluate and compare the surgical site infection (SSI) risk factors in patients with colorectal cancer (CC). The results of this meta-analysis were analysed, and the odds ratio (OR) and mean difference (MD) with 95% confidence intervals (CIs) were calculated using dichotomous or contentious random or fixed-effect models. For the current meta-analysis, 23 examinations spanning from 2001 to 2023 were included, encompassing 89 859 cases of CC. Clean-contaminated surgical site wounds had significantly lower infections (OR, 0.36; 95% CI, 0.20-0.64, p < 0.001) compared to contaminated surgical site wounds in patients with CCs. Males had significantly higher SSIs (OR, 1.18; 95% CI, 1.12-1.24, p < 0.001) compared to females in patients with CC. American Society of Anesthesiology score ≥3 h had a significantly higher SSI (OR, 1.42; 95% CI, 1.18-1.71, p < 0.001) compared to <3 score in patients with CCs. Body mass index ≥25 had significantly higher SSIs (OR, 1.54; 95% CI, 1.11-2.14, p = 0.01) compared to <25 in patients with CCs. The presence of stoma creation had a significantly higher SSI rate (OR, 2.28; 95% CI, 1.37-3.79, p = 0.001) compared to its absence in patients with CC. Laparoscopic surgery had significantly lower SSIs (OR, 0.68; 95% CI, 0.59-0.78, p < 0.001) compared to open surgery in patients with CC. The presence of diabetes mellitus had a significantly higher SSI rate (OR, 1.24; 95% CI, 1.15-1.33, p < 0.001) compared to its absence in patients with CCs. No significant difference was found in SSI rate in patients with CCs between <3 and ≥3 h of operative time (OR, 1.07; 95% CI, 0.75-1.51, p = 0.72), between the presence and absence of blood transfusion (OR, 1.60; 95% CI, 0.69-3.66, p = 0.27) and between the presence and absence of previous laparotomies (OR, 1.47; 95% CI, 0.93-2.32, p = 0.10). The examined data revealed that contaminated wounds, male sex, an American Society of Anesthesiology score ≥3 h, a body mass index ≥25, stoma creation, open surgery and diabetes mellitus are all risk factors for SSIs in patients with CC. However, operative time, blood transfusion and previous laparotomies were not found to be risk factors for SSIs in patients with CC. However, given that several comparisons had a small number of chosen research, consideration should be given to their values.

Color ghost imaging through the scattering media based on A-cGAN.

Ghost imaging plays an important role in the field of optical imaging. To realize color ghost imaging through the scattering media, we propose a deep learning method with high generation ability. Through our method, we can efficiently reconstruct color images with rich details, in line with human perception and close to the target color pictures. Experimental results show that our method can image through the scattering media with different scattering intensities and achieve good results even at a sampling rate of 0.1.

Fatigue behavior of endodontically treated maxillary premolars with MOD defects under different minimally invasive restorations.

OBJECTIVES: To analyze the stress distribution and subsequent fracture resistance of human maxillary premolars with mesial-occlusal-distal (MOD) defects restored with different minimally invasive restorations. MATERIALS AND METHODS: Seventy non-carious human maxillary premolars were selected and divided into seven groups (n = 10). Ten teeth without further preparation served as control. The remaining teeth were endodontically treated and received three restorative patterns: inlays without cusp coverage (I), onlays with palatal coverage (O), overlays with both buccal and palatal coverage (Ov). Lithium disilicate glass ceramics (EM) and machinable composite resin (LU) were used for restoration. Specimens were tested under cycling loading with tongue direction of 45° for 1.2 × 106 cycles at a 50-N load and 2.0-Hz frequency. The survival time and two fracture mode classifications were assessed. Three-dimensional models of each group were designed. The magnitude and pattern of stresses were analyzed under the same condition of the in vitro test using finite element stress analysis. RESULTS: Although the overlay model pattern produced more favorable stress distribution, three restorative patterns restored with the same material had no difference in survival curves (P > 0.05). Only the survival curve of the EM-Ov group had no statistical difference with that of the control group (P > 0.05). EM groups presented mainly interface adhesive failure, while LU groups were mainly material cohesive failure. CONCLUSION: For the endodontically treated maxillary premolars with MOD defect, the lithium disilicate glass ceramic overlay pattern can reach the best restorative effect. CLINICAL RELEVANCE: Comparing with restorative pattern, restorative material had a greater influence on the minimally invasive restoration of posterior teeth.

Automatic RadLex coding of Chinese structured radiology reports based on text similarity ensemble.

BACKGROUND: Standardized coding of plays an important role in radiology reports' secondary use such as data analytics, data-driven decision support, and personalized medicine. RadLex, a standard radiological lexicon, can reduce subjective variability and improve clarity in radiology reports. RadLex coding of radiology reports is widely used in many countries, but translation and localization of RadLex in China are far from being established. Although automatic RadLex coding is a common way for non-standard radiology reports, the high-accuracy cross-language RadLex coding is hardly achieved due to the limitation of up-to-date auto-translation and text similarity algorithms and still requires further research. METHODS: We present an effective approach that combines a hybrid translation and a Multilayer Perceptron weighting text similarity ensemble algorithm for automatic RadLex coding of Chinese structured radiology reports. Firstly, a hybrid way to integrate Google neural machine translation and dictionary translation helps to optimize the translation of Chinese radiology phrases to English. The dictionary is made up of 21,863 Chinese-English radiological term pairs extracted from several free medical dictionaries. Secondly, four typical text similarity algorithms are introduced, which are Levenshtein distance, Jaccard similarity coefficient, Word2vec Continuous bag-of-words model, and WordNet Wup similarity algorithms. Lastly, the Multilayer Perceptron model has been used to synthesize the contextual, lexical, character and syntactical information of four text similarity algorithms to promote precision, in which four similarity scores of two terms are taken as input and the output presents whether the two terms are synonyms. RESULTS: The results show the effectiveness of the approach with an F1-score of 90.15%, a precision of 91.78% and a recall of 88.59%. The hybrid translation algorithm has no negative effect on the final coding, F1-score has increased by 21.44% and 8.12% compared with the GNMT algorithm and dictionary translation. Compared with the single similarity, the result of the MLP weighting similarity algorithm is satisfactory that has a 4.48% increase compared with the best single similarity algorithm, WordNet Wup. CONCLUSIONS: The paper proposed an innovative automatic cross-language RadLex coding approach to solve the standardization of Chinese structured radiology reports, that can be taken as a reference to automatic cross-language coding.

Probing the Ferromagnetism and Spin Wave Gap in VI3 by Helicity-Resolved Raman Spectroscopy.

Circularly polarized light carries light spin angular momentum, which may lead helicity-resolved Raman scattering to be sensitive to the electronic spin configuration in magnetic materials. Here, we demonstrate that all Raman modes in the 2D ferromagnet VI3 show different scattering intensities to left and right circularly polarized light at low temperatures, which gives direct evidence of the time-reversal symmetry breaking. By measuring the circular polarization of the dominant Raman mode with respect to the temperature and magnetic field, the ferromagnetic (FM) phase transition and hysteresis behavior can be clearly resolved. Besides the lattice excitations, quasielastic scattering is detected in the paramagnetic phase, and it gradually evolves into the acoustic magnon mode at 18.5 cm-1 in the FM state, which gives the spin wave gap that results from large magnetic anisotropy. Our findings demonstrate that helicity-resolved Raman spectroscopy is an effective tool to directly probe the ferromagnetism in 2D magnets.

An Anti-Inflammatory Role for NLRP10 in Murine Cutaneous Leishmaniasis.

The role of the nucleotide-binding domain and leucine-rich repeat containing receptor NLRP10 in disease is incompletely understood. Using three mouse strains lacking the gene encoding NLRP10, only one of which had a coincidental mutation in DOCK8, we documented a role for NLRP10 as a suppressor of the cutaneous inflammatory response to Leishmania major infection. There was no evidence that the enhanced local inflammation was due to enhanced inflammasome activity. NLRP10/DOCK8-deficient mice harbored lower parasite burdens at the cutaneous site of inoculation compared with wild-type controls, whereas NLRP10-deficient mice and controls had similar parasite loads, suggesting that DOCK8 promotes local growth of parasites in the skin, whereas NLRP10 does not. NLRP10-deficient mice developed vigorous adaptive immune responses, indicating that there was not a global defect in the development of Ag-specific cytokine production. Bone marrow chimeras showed that the anti-inflammatory role of NLRP10 was mediated by NLRP10 expressed in resident cells in the skin rather than by bone marrow-derived cells. These data suggest a novel role for NLRP10 in the resolution of local inflammatory responses during L. major infection.

Molecular insight into chymotrypsin inhibitor 2 resisting proteolytic degradation.

Chymotrypsin inhibitor 2 (CI2) is a special serine protease inhibitor which can resist hydrolysis for several days with a rapid equilibrium between the Michaelis complex and acyl-enzyme intermediate. The energies and conformational changes for subtilisin-catalyzed proteolysis of CI2 were examined in this paper for the first time by employing pseudo bond ab initio QM/MM MD simulations. In the acylation reaction, a low-barrier hydrogen bond between His64 and Asp32 in the transition state together with the lack of covalent backbone constraints makes the peptide bonds of CI2 break more easily than in other serine protease inhibitors. After acyl-enzyme formation, molecular dynamics simulations showed that the access of hydrolytic water to the active site requires partial dissociation of the leaving group. However, retention of the leaving group mainly by the intra- and inter-molecular H-bonding networks hinders the access of water and retards the deacylation reaction. Instead of the dissociation constant of inhibitors, we suggest employing the free energy at the acyl-enzyme state to predict the relative hydrolysis rates of CI2 mutants, which are testified by the experimental relative hydrolysis rates.

Effect and mechanism of mGluR6 on the biological function of rat embryonic neural stem cells.

Here, we investigated the effects and molecular mechanisms of metabotropic glutamate receptor 6 (mGluR6) on rat embryonic neural stem cells (NSCs). Overexpression of mGluR6 significantly promoted the proliferation of NSCs and increased the diameter of neutrospheres after treatment for 24 h, 48 h and 72 h. Overexpression of mGluR6 promoted G1 to S phase transition, with significantly decreased cell ratio in G1/G0 phase but significantly increased cell ratio in S phase. Additionally, mGluR6 overexpression for 48 h decreased the early and late apoptosis significantly. Moreover, overexpression of mGluR6 significantly increased the expression of p-ERK1/2, Cyclin D1 and CDK2, while the expression of p-p38 was significantly decreased. On the contrary, these effects of mGluR6 overexpression were reversed by mGluR6 knockdown. In conclusion, mGluR6 promotes the proliferation of NSCs by activation of ERK1/2-Cyclin D1/CDK2 signaling pathway and inhibits the apoptosis of NSCs by blockage of the p38 MAPK signaling pathway.

Proteomic Screening for Serum Biomarkers for Cervical Cancer and Their Clinical Significance.

BACKGROUND The present study aimed to determine serum markers for cervical cancer (CC) and to provide valuable references for clinical diagnosis and treatment. MATERIAL AND METHODS Serum samples were collected from age-matched healthy control women, and from female CC patients before and after surgery. Serum biomarkers were selected by comparing serum peptides profiles among the 3 groups by magnetic bead-based weak cation - exchange chromatography fractionation combined with matrix-assisted laser desorption/ionization-time of flight mass spectrometry. Probable serum biomarkers for cervical cancer were then further identified by liquid chromatography-electrospray ionization-tandem mass spectrometry system and the identified proteins were verified by enzyme-linked immunosorbent assay (ELISA). RESULTS Three peptide biomarkers were identified for distinguishing CC patients from normal individuals, and distinguishing preoperative CC patients from postoperative CC patients. Of these 3 identified protein peptide regions, 2 peptide regions - TKT (Peak 2, 2435.63 m/z, 499-524) and FGA (Peak 4, 2761.79 m/z, 603-629) - were identified as upregulated markers, and peptide region of APOA1 (Peak 9, 2575.3 m/z, 245-260) was identified as a downregulated biomarker in preoperative CC patients compared with healthy women. CONCLUSIONS The present study provides a new method for identifying potential serum biomarkers for CC patients.

Matrine Suppresses Reactive Oxygen Species (ROS)-Mediated MKKs/p38-Induced Inflammation in Oxidized Low-Density Lipoprotein (ox-LDL)-Stimulated Macrophages.

BACKGROUND The objective of this study was to study the anti-inflammatory effect and possibly involved molecular mechanisms of matrine on oxidized low-density lipoprotein (ox-LDL)-exposed macrophages. MATERIAL AND METHODS Cultured human macrophages (THP-1 cell line) were exposed to ox-LDL at final concentrations of 0, 25, 50, and 100 µg/mL. Several cells were then treated with matrine at serial diluted concentrations. 2,7-Dichlorodi-hydrofluorescein diacetate (DCFH-DA) staining was used to evaluate reactive oxygen species (ROS) production; a colorimetric method was used to determine the cellular antioxidant capacity; production of pro-inflammatory cytokines interleukin (IL)18 and tumor necrosis factor (TNF)alpha were determined by enzyme-linked immunosorbent assay (ELISA); and immunoblot assay was used to assess the relative protein phosphorylation and expression. RESULTS ox-LDL exposure significantly elevated intracellular ROS level and supernatant IL18 and TNFalpha concentrations, but impaired total antioxidant capacity (TAC) of macrophages. The relative phosphorylations of MAPK kinase kinases (MKK)6, MKK3, and p38 mitogen-activated protein kinases (MAPK) were increased by ox-LDL exposure. The expression levels of IL18 and TNFalpha were also increased in ox-LDL-treated macrophages. The matrine treatment reduced intracellular ROS level and supernatant IL18 and TNFalpha concentrations and increased TAC in a concentration- dependent manner. The relative phosphorylations of MKK6, MKK3, and p38 MAPK were reduced after matrine administration. Moreover, the expression levels of IL18 and TNFalpha were also decreased by matrine treatment, in a concentration-dependent manner. CONCLUSIONS ox-LDL increases inflammatory response in macrophages by activating the ROS-mediated MKKs/p38 MAPK-induced inflammatory signaling pathway. Matrine suppresses ox-LDL-induced inflammatory by inhibiting the MKKs/p38 MAPK signaling pathway.

Gene regulatory divergence between locally adapted ecotypes in their native habitats.

Local adaptation is a key driver of ecological specialization and the formation of new species. Despite its importance, the evolution of gene regulatory divergence among locally adapted populations is poorly understood, especially how that divergence manifests in nature. Here, we evaluate gene expression divergence and allele-specific gene expression responses for locally adapted coastal perennial and inland annual accessions of the yellow monkeyflower, Mimulus guttatus, in a field reciprocal transplant experiment. Overall, 6765 (73%) of surveyed genes were differentially expressed between coastal and inland habitats, while 7213 (77%) were differentially expressed between the coastal perennial and inland annual accessions. Cis-regulatory variation was pervasive, affecting 79% (5532) of differentially expressed genes. We detected trans effects for 52% (3611) of differentially expressed genes. Expression plasticity of alleles across habitats (G × E interactions) appears to be relatively common (affecting 18% of transcripts) and could minimize fitness trade-offs at loci that contribute to local adaptation. We also found evidence that at least one chromosomal inversion may act as supergene by holding together haplotypes of differentially expressed genes, but this pattern depends on habitat context. Our results highlight multiple key patterns regarding the relationship between gene expression and the evolution of locally adapted populations.

Insights into charge carrier dynamics in organo-metal halide perovskites: from neat films to solar cells.

Organo-metal halide perovskites have recently obtained world-wide attention as promising solar cell materials. They have broad and strong light absorption along with excellent carrier transport properties which partially explain their record power conversion efficiencies above 22%. However, the basic understanding of the underlying physical mechanisms is still limited and there remain large discrepancies among reported transport characteristics of perovskite materials. Notably, the carrier mobility of perovskite samples either in thin films or within solar cells obtained using different techniques can vary by up to 7-8 orders of magnitude. This tutorial review aims to offer insights into the scope, advantages, limitations and latest developments of the techniques that have been applied for studying charge carrier dynamics in perovskites. We summarize a comprehensive set of measurements including (1) time-resolved laser spectroscopies (transient absorption, time-resolved photoluminescence, terahertz spectroscopy and microwave conductivity); (2) electrical transient techniques (charge extraction by linearly increasing voltage and time-of-flight); and (3) steady-state methods (field-effect transistor, Hall effect and space charge limited current). Firstly, the basics of the above measurements are described. We then comparatively summarize the charge carrier characteristics of perovskite-based neat films, bilayer films and solar cells. Finally, we compare the different approaches in evaluating the key parameters of transport dynamics and unravel the reasons for the large discrepancies among these methods. We anticipate that this tutorial review will serve as the entry point for understanding the experimental results from the above techniques and provide insights into charge carrier dynamics in perovskite materials and devices.

Pooled ecotype sequencing reveals candidate genetic mechanisms for adaptive differentiation and reproductive isolation.

The early stages of speciation are often characterized by the formation of partially reproductively isolated ecotypes, which evolve as a by-product of divergent selective forces that are endemic to different habitats. Identifying the genomic regions, genes and ultimately functional polymorphisms that are involved in the processes of ecotype formation is inherently challenging, as there are likely to be many different loci involved in the process. To localize candidate regions of the genome contributing to ecotype formation, we conducted whole-genome pooled sequencing (pool-seq) with 47 coastal perennial and 50 inland annual populations of the yellow monkeyflower, Mimulus guttatus. Coastal perennial and inland annual ecotypes of M. guttatus have previously been shown to be ecologically reproductively isolated and highly locally adapted to their respective habitats. Our pool-seq results found allelic differentiation between the ecotypes for two chromosomal inversions, suggesting that frequencies of inversion heterokaryotypes are strongly differentiated between the ecotypes. Further, there were elevated levels of nonsynonymous change across chromosomal inversions. Across the genome, we identified multiple strong candidate genes potentially driving the morphological, life history and salt tolerance differences between the ecotypes. Several candidate genes coincide with previously identified quantitative trait locus regions and also show a signature of recent natural selection. Overall, the results of our study add to growing support for a major role of chromosomal inversions in adaptation and speciation and provide new insights into the genetic mechanisms underlying classic plant ecotype adaptations to wet and dry habitats.

Inter-regulation of the unfolded protein response and auxin signaling.

The unfolded protein response (UPR) is a signaling network triggered by overload of protein-folding demand in the endoplasmic reticulum (ER), a condition termed ER stress. The UPR is critical for growth and development; nonetheless, connections between the UPR and other cellular regulatory processes remain largely unknown. Here, we identify a link between the UPR and the phytohormone auxin, a master regulator of plant physiology. We show that ER stress triggers down-regulation of auxin receptors and transporters in Arabidopsis thaliana. We also demonstrate that an Arabidopsis mutant of a conserved ER stress sensor IRE1 exhibits defects in the auxin response and levels. These data not only support that the plant IRE1 is required for auxin homeostasis, they also reveal a species-specific feature of IRE1 in multicellular eukaryotes. Furthermore, by establishing that UPR activation is reduced in mutants of ER-localized auxin transporters, including PIN5, we define a long-neglected biological significance of ER-based auxin regulation. We further examine the functional relationship of IRE1 and PIN5 by showing that an ire1 pin5 triple mutant enhances defects of UPR activation and auxin homeostasis in ire1 or pin5. Our results imply that the plant UPR has evolved a hormone-dependent strategy for coordinating ER function with physiological processes.

Targeted inhibition of prostate cancer metastases with an RNA aptamer to prostate-specific membrane antigen.

Cell-targeted therapies (smart drugs), which selectively control cancer cell progression with limited toxicity to normal cells, have been developed to effectively treat some cancers. However, many cancers such as metastatic prostate cancer (PC) have yet to be treated with current smart drug technology. Here, we describe the thorough preclinical characterization of an RNA aptamer (A9g) that functions as a smart drug for PC by inhibiting the enzymatic activity of prostate-specific membrane antigen (PSMA). Treatment of PC cells with A9g results in reduced cell migration/invasion in culture and metastatic disease in vivo. Importantly, A9g is safe in vivo and is not immunogenic in human cells. Pharmacokinetic and biodistribution studies in mice confirm target specificity and absence of non-specific on/off-target effects. In conclusion, these studies provide new and important insights into the role of PSMA in driving carcinogenesis and demonstrate critical endpoints for the translation of a novel RNA smart drug for advanced stage PC.

Characteristics and significance of intergenic polyadenylated RNA transcription in Arabidopsis.

The Arabidopsis (Arabidopsis thaliana) genome is the most well-annotated plant genome. However, transcriptome sequencing in Arabidopsis continues to suggest the presence of polyadenylated (polyA) transcripts originating from presumed intergenic regions. It is not clear whether these transcripts represent novel noncoding or protein-coding genes. To understand the nature of intergenic polyA transcription, we first assessed its abundance using multiple messenger RNA sequencing data sets. We found 6,545 intergenic transcribed fragments (ITFs) occupying 3.6% of Arabidopsis intergenic space. In contrast to transcribed fragments that map to protein-coding and RNA genes, most ITFs are significantly shorter, are expressed at significantly lower levels, and tend to be more data set specific. A surprisingly large number of ITFs (32.1%) may be protein coding based on evidence of translation. However, our results indicate that these "translated" ITFs tend to be close to and are likely associated with known genes. To investigate if ITFs are under selection and are functional, we assessed ITF conservation through cross-species as well as within-species comparisons. Our analysis reveals that 237 ITFs, including 49 with translation evidence, are under strong selective constraint and relatively distant from annotated features. These ITFs are likely parts of novel genes. However, the selective pressure imposed on most ITFs is similar to that of randomly selected, untranscribed intergenic sequences. Our findings indicate that despite the prevalence of ITFs, apart from the possibility of genomic contamination, many may be background or noisy transcripts derived from "junk" DNA, whose production may be inherent to the process of transcription and which, on rare occasions, may act as catalysts for the creation of novel genes.