Description: Miniature inverted-repeat transposable elements (MITEs) are prevalent in eukaryotic species including plants. MITE families vary dramatically and usually cannot be identified based on homology. In this study, we de novo identified MITEs from 41 plant species, using computer programs MITE Digger, MITE-Hunter and/or Repetitive Sequence with Precise Boundaries (RSPB). MITEs were found in all, but one ( Cyanidioschyzon merolae ), species. Combined with the MITEs identified previously from the rice genome, 〉2.3 million sequences from 3527 MITE families were obtained from 41 plant species. In general, higher plants contain more MITEs than lower plants, with a few exceptions such as papaya, with only 538 elements. The largest number of MITEs is found in apple, with 237 302 MITE sequences. The number of MITE sequences in a genome is significantly correlated with genome size. A series of databases (plant MITE databases, P-MITE), available online at http://pmite.hzau.edu.cn/django/mite/ , was constructed to host all MITE sequences from the 41 plant genomes. The databases are available for sequence similarity searches (BLASTN), and MITE sequences can be downloaded by family or by genome. The databases can be used to study the origin and amplification of MITEs, MITE-derived small RNAs and roles of MITEs on gene and genome evolution.

Description: The C-terminal extension of prokaryotic leucyl-tRNA synthetase (LeuRS) has been shown to make contacts with the tertiary structure base pairs of tRNA Leu as well as its long variable arm. However, the precise role of the flexibly linked LeuRS C-terminal domain (CTD) in aminoacylation and editing processes has not been clarified. In this study, we carried out aspartic acid scanning within the CTD of Mycobacterium tuberculosis LeuRS ( Mtb LeuRS) and studied the effects on tRNA Leu -binding capacity and enzymatic activity. Several critical residues were identified to impact upon the interactions between LeuRS and tRNA Leu due to their contributions in the maintenance of structural stability or a neutral interaction interface between the CTD platform and tRNA Leu elbow region. Moreover, we propose Arg921 as a crucial recognition site for the tRNA Leu long variable arm in aminoacylation and tRNA-dependent pre-transfer editing. We also show here the CTD flexibility conferred by Val910 in regulation of LeuRS–tRNA Leu interaction. Taken together, our results suggest the structural importance of the CTD in modulating precise interactions between LeuRS and tRNA Leu during the quality control of leucyl-tRNA Leu synthesis. This system for the investigation of the interactions between Mtb LeuRS and tRNA Leu provides a platform for the development of novel antitubercular drugs.

Description: Background Gliomas are based on a genetic abnormality and present with a dismal prognosis. MicroRNAs (miRNAs) are considered to be important mediators of gene expression in glioma tissues. Methods Real-time PCR was used to analyze the expression of microRNA-423-5p (miR-423-5p) in human glioma samples and normal brain tissue. Apoptosis, cell cycle, proliferation, immunostaining, transwell, in vitro 2D and 3D migration, and chemosensitivity assays were performed to assess the phenotypic changes in glioma cells overexpressing miRNA-423-5p. Western blotting was used to determine the expression of inhibitor of growth 4 (ING-4)in glioma tissues, and a luciferase reporter assay was conducted to confirm whether ING-4 is a direct target of miR-423-5p. Western blotting was used to identify the potential signaling pathways that are affected in glioma cell growth by miR-423-5p. Xenograft tumors were examined in vivo for the carcinogenic effects of miR-423-5p in glioma tissues. Results We first reported that miR-423-5p expression was increased in gliomas and was a potential tumor promoter via targeting ING-4. The overexpression of miR-423-5p resulted in upregulation of important signaling molecules such as p-AKT and p-ERK1/2. In clinical samples, miR-423-5p was dysregulated, and a corresponding alteration in ING-4 expression was observed ( P = .0207). Furthermore, the overexpression of miR-423-5p strengthened glioma cell proliferation, angiogenesis, and invasion. Finally, miR-423-5p overexpression also strengthened GBM neurosphere formation and rendered glioma cells resistant to temozolomide (TMZ). Conclusion This study establishes that miR-423-5p functions as an oncogene in glioma tissues by suppressing ING-4 and suggests that it has therapeutic potential for glioma.

Description: Aims Numerous studies have showed that the balance between negative and positive plant–plant interactions shifted along environmental gradients. But little is known how the positive or negative plant–plant interactions varied with temporal fluctuating habitat conditions and plant ontogenetic phases. Methods In a 2-year experiment, the four perennial grasses ( Kobresia humilis , Stipa aliena , Elymus nutans and Saussurea superba ) were grown under four interaction treatments (no root or shoot interaction, only shoot interaction, only root interaction, root and shoot interaction). Intensity of above- and belowground interactions is proposed to vary with the fluctuation of seasonal climatic conditions and soil available nutrients. Here we report measurements of above- and belowground interactions during entire growing season. Correlation between plant interaction intensity and seasonal soil available N as well as habitat climate conditions was also performed. Important findings Our experiment found that root interactions had negative effect on plant growth for the four species during growing season. However, both negative and positive shoot interactions occurred among the four species. Despite there being shoot facilitative effect for E. nutans and S. superba , the full interaction was negative, suggested that root interaction take more important role on plant growth than that of shoot interaction. The interaction between root and shoot effect varied as a function of species identity and growth phases. The weak correlation of plant interaction intensity to habitat environmental factors suggested that plant ontogenetic characteristics may be primary factors causing temporal variation in plant interaction.

Description: Background Oxaliplatin-related neurotoxicity is the main limitation for its continuation in adjuvant and palliative chemotherapy for patients with colorectal cancer. The purpose of this meta-analysis was to determine the efficacy of calcium and magnesium (Ca/Mg) infusions in oxaliplatin-induced neurotoxicity. Methods Two independent authors conducted database searches of the literature to find clinical-controlled trials analyzing Ca/Mg infusions in oxaliplatin-induced neurotoxicity. The keywords used to search were oxaliplatin, neurotoxicity, calcium, magnesium, neuropathy, and peripheral. Clinical studies that included at least one primary or secondary event were eligible for the analysis, where primary events were incidences of acute and cumulative neurotoxicity, and secondary events were the total doses and cycles of oxaliplatin, response rate (RR), overall survival (OS), and progression-free survival (PFS). Odds ratios (ORs) and weighted mean differences (MD) were analyzed using models of fixed and random effects. Results This meta-analysis comprised four prospective randomized clinical trials and three retrospective clinical trials involving 1170 colorectal cancer patients, of which 802 received Ca/Mg infusions (Ca/Mg group) and 368 did not (control group). According to the National Cancer Institute-Common Terminology Criteria for Adverse Events, the incidence of grade 3 acute neurotoxicity in those who received Ca/Mg was significantly lower than that of the control group (OR = 0.26; 95% confidence interval (CI), 0.11 to 0.62; P  = 0.0002). The total rate of cumulative neurotoxicity, and that of grade 3 in particular, was significantly lower in the Ca/Mg group than in the control group (OR = 0.42; 95% CI 0.26–0.65; P  = 0.0001; OR = 0.60; 95% CI 0.39–0.92; P  = 0.02, respectively). The differences in total doses and cycles of oxaliplatin were also significant between the Ca/Mg and control group (MD = 246.73 mg/m 2 ; 95% CI 3.01–490.45; P  = 0.05; MD = 1.55; 95% CI 0.46–2.63; P  = 0.005, respectively). No significant differences were found in median PFS (MD = 0.71 month; 95% CI –0.59–2.01; P  = 0.29), median OS (MD = 0.10 month; 95% CI –0.41–0.61; P  = 0.70) or RRs (OR = 0.82; 95% CI 0.61–1.10; P  = 0.18). Conclusion Ca/Mg infusions tend to decrease the incidence of oxaliplatin-induced acute and cumulative neurotoxicity and thus enhance patients' tolerance to oxaliplatin, without significantly altering the efficacy of chemotherapy.

Description: Aims Pulmonary arterial hypertension, a chronic lung disease, remains an unacceptable prognosis despite significant advances in conventional therapies. Stem cell therapy represents a novel and effective modality. This study was aimed to add new insight in gender differences of bone marrow-derived mesenchymal stem cells on therapy against pulmonary arterial hypertension and the underlying mechanism. Methods and results By in vivo experiments, we showed for the first time female bone marrow-derived mesenchymal stem cells possessed a better therapeutic potential against monocrotaline-induced pulmonary arterial hypertension in C57BL/6J mice compared with male counterparts. In vitro experiments demonstrated superior function of female bone marrow-derived mesenchymal stem cells in cell proliferation, migration and [Ca 2+ ] i kinetics. Moreover, we unexpectedly found that, compared with male ones, female bone marrow-derived mesenchymal stem cells had a higher expression level of glyceraldehyde-3-phosphate dehydrogenase and manipulations of its expression in female or male bone marrow-derived mesenchymal stem cells profoundly affected their cellular behaviours and therapeutic efficacies against pulmonary arterial hypertension. Conclusion Our results suggest that glyceraldehyde-3-phosphate dehydrogenase plays a critical role in determining the superior functions of female bone marrow-derived mesenchymal stem cells in cell therapy against pulmonary arterial hypertension by regulating [Ca 2+ ] i signal-associated cellular behaviours.

Description: PIWI-interacting RNA (piRNA) silences the transposons in germlines or induces epigenetic modifications in the invertebrates. However, its function in the mammalian somatic cells remains unknown. Here we demonstrate that a piRNA derived from Growth Arrest Specific 5, a tumor-suppressive long non-coding RNA, potently upregulates the transcription of tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL), a proapoptotic protein, by inducing H3K4 methylation/H3K27 demethylation. Interestingly, the PIWIL1/4 proteins, which bind with this piRNA, directly interact with WDR5, resulting in a site-specific recruitment of the hCOMPASS-like complexes containing at least MLL3 and UTX (KDM6A). We have indicated a novel pathway for piRNAs to specially activate gene expression. Given that MLL3 or UTX are frequently mutated in various tumors, the piRNA/MLL3/UTX complex mediates the induction of TRAIL, and consequently leads to the inhibition of tumor growth.

Description: Mitochondrial dysfunction plays important roles in Parkinson's disease (PD) and the degradation of the damaged mitochondria by the mitochondria quality control system is important for dopaminergic (DA) neuronal survival. BNIP3L/Nix is a mitochondrial outer membrane protein that is required for the selective clearance of mitochondria. Here, we found that the mitochondrial protein BNIP3L acts downstream of the PINK1/PARK2 pathway to induce mitophagy. BNIP3L is a substrate of PARK2 to drive PARK2-mediated mitophagy. The ubiquitination of BNIP3L by PARK2 recruits NBR1 to mitochondria, thereby targeting mitochondria for degradation. BNIP3L rescues mitochondrial defects in pink1 mutant Drosophila but not in park mutant Drosophila, indicating that the clearance of mitochondria induced by BNIP3L depends on the presence of PARK2. In cells intoxicated with mitochondrial complex I inhibitors rotenone, 6-OHDA or MPP + , the disrupted mitochondria are not appropriately eliminated by mitophagy due to the improper degradation of BNIP3L. Thus, our study demonstrates that BNIP3L, as a substrate of PARK2, promotes mitophagy in the PINK1/PARK2 pathway associated with PD pathogenesis.

Description: Motivation: One of the most promising applications of biosynthetic methods is to produce chemical products of high value from the ready-made chemicals. To explore the biosynthetic potentials of a chemical as a synthesis precursor, biosynthetic databases and related chemoinformatics tools are urgently needed. In the present work, a web-based tool, BioSynther, is developed to explore the biosynthetic potentials of precursor chemicals using BKM-react, Rhea, and more than 50 000 in-house RxnFinder reactions manually curated. BioSynther allows researchers to explore biosynthetic potentials, through so far known biochemical reactions, step by step interactively, which could be used as a useful tool in metabolic engineering and synthetic biology. Availability and implementation : BioSynther is available at: http://www.lifemodules.org/BioSynther/ . Contact : hu_qn@tib.cas.cn . Supplementary information: Supplementary data are available at Bioinformatics online.

Description: The Hippo signaling pathway regulates cellular proliferation and survival, thus exerting profound effects on normal cell fate and tumorigenesis. Dysfunction of the Hippo pathway components has been linked with breast cancer stem cell regulation, as well as breast tumor progression and metastasis. TAZ, a key component of the Hippo pathway, is highly expressed in triple negative breast cancer; however, the associations of genetic variations in this important pathway with breast cancer risk remain largely unexplored. Here, we analyzed 8309 germline variants in 15 genes from the Hippo pathway with a total of 3663 cases and 4687 controls from the African American Breast Cancer Epidemiology and Risk Consortium. Odds ratios (ORs) were estimated using logistic regression for overall breast cancer, by estrogen receptor (ER) status (1983 ER positive and 1098 ER negative), and for case-only analyses by ER status. The Hippo signaling pathway was significantly associated with ER-negative breast cancer (pathway level P = 0.02). Gene-based analyses revealed that CDH1 was responsible for the pathway association ( P 〈 0.01), with rs4783673 in CDH1 statistically significant after gene-level adjustment for multiple comparisons ( P = 9.2 x 10 –5 , corrected P = 0.02). rs142697907 in PTPN14 was associated with ER-positive breast cancer and rs2456773 in CDK1 with ER-negativity in case-only analysis after gene-level correction for multiple comparisons (corrected P 〈 0.05). In conclusion, common genetic variations in the Hippo signaling pathway may contribute to both ER-negative and ER+ breast cancer risk in AA women.