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https://www.readbyqxmd.com/read/28922802/succession-of-arbuscular-mycorrhizal-fungi-along-a-52-year-agricultural-recultivation-chronosequence
#1
Julien Roy, Rüdiger Reichel, Nicolas Brüggemann, Stefan Hempel, Matthias C Rillig
Arbuscular mycorrhizal (AM) fungi provide a range of functions in natural and managed ecosystems. However, the trajectory of AM fungal diversity after land degradation is poorly known. We studied the succession of AM fungi along an agricultural recultivation chronosequence after open-cast mining near Cologne, Germany. We used high-throughput sequencing of the large-subunit ribosomal RNA genes to characterize the soil AM fungal communities of 10 agricultural fields spanning 52 years of recultivation. During three years, soils are recultivated with a legume, and then converted to agriculture to be later returned to local farmers implementing conventional agriculture...
September 1, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28922229/micrornas-as-clinical-biomarkers-and-therapeutic-tools-in-perioperative-medicine
#2
Simone Kreth, Max Hübner, Ludwig Christian Hinske
Over the past decade, evolutionarily conserved, noncoding small RNAs-so-called microRNAs (miRNAs)-have emerged as important regulators of virtually all cellular processes. miRNAs influence gene expression by binding to the 3'-untranslated region of protein-coding RNA, leading to its degradation and translational repression. In medicine, miRNAs have been revealed as novel, highly promising biomarkers and as attractive tools and targets for novel therapeutic approaches. miRNAs are currently entering the field of perioperative medicine, and they may open up new perspectives in anesthesia, critical care, and pain medicine...
September 14, 2017: Anesthesia and Analgesia
https://www.readbyqxmd.com/read/28918038/strategies-for-in%C3%A2-vivo-screening-and-mitigation-of-hepatotoxicity-associated-with-antisense-drugs
#3
Piotr J Kamola, Klio Maratou, Paul A Wilson, Kay Rush, Tanya Mullaney, Tom McKevitt, Paula Evans, Jim Ridings, Probash Chowdhury, Aude Roulois, Ann Fairchild, Sean McCawley, Karen Cartwright, Nigel J Gooderham, Timothy W Gant, Kitty Moores, Stephen A Hughes, Mark R Edbrooke, Kenneth Clark, Joel D Parry
Antisense oligonucleotide (ASO) gapmers downregulate gene expression by inducing enzyme-dependent degradation of targeted RNA and represent a promising therapeutic platform for addressing previously undruggable genes. Unfortunately, their therapeutic application, particularly that of the more potent chemistries (e.g., locked-nucleic-acid-containing gapmers), has been hampered by their frequent hepatoxicity, which could be driven by hybridization-mediated interactions. An early de-risking of this liability is a crucial component of developing safe, ASO-based drugs...
September 15, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28917667/amyloid-%C3%AE-42-clearance-and-neuroprotection-mediated-by-x-box-binding-protein-1-signaling-decline-with-aging-in-the-drosophila-brain
#4
María S Marcora, Lautaro F Belfiori-Carrasco, Nadia I Bocai, Laura Morelli, Eduardo M Castaño
The unfolded protein response (UPR) may be pathogenically related to Alzheimer's disease. Yet, the effects of chronic amyloid-β42 (Aβ42) accumulation and UPR activation upon neurotoxicity remain unclear. Here, we show that neuronal Aβ42 expression in Drosophila activated the inositol-requiring protein-1/X-box binding protein 1 (XBP1) UPR branch before the onset of behavioral impairment and persisted with aging. Early upregulation of hsc3/BiP, a target of XBP1 and activating transcription factor 6 pathways, was also sustained in old animals...
August 24, 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/28915706/the-role-of-autophagy-in-hepatocellular-carcinoma-friend-or-foe
#5
REVIEW
Lian Liu, Jia-Zhi Liao, Xing-Xing He, Pei-Yuan Li
Autophagy is an evolutionarily conserved lysosome-dependent catabolic process which degrades cell's components in order to recycle substrates to exert optimally and adapt to tough circumstances. It is a critical cellular homeostatic mechanism with stress resistance, immunity, antiaging, and pro-tumor or anti-tumor effects. Among these, the role of autophagy in cancer is the most eye-catching that is not immutable but dynamic and highly complex. Basal autophagy acts as a tumor suppressor by maintaining genomic stability in normal cells...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28912886/the-ph-triggered-triblock-nanocarrier-enabled-highly-efficient-sirna-delivery-for-cancer-therapy
#6
Lili Du, Junhui Zhou, Lingwei Meng, Xiaoxia Wang, Changrong Wang, Yuanyu Huang, Shuquan Zheng, Liandong Deng, Huiqing Cao, Zicai Liang, Anjie Dong, Qiang Cheng
Small interfering RNA (siRNA) therapies have been hampered by lack of delivery systems in the past decades. Nowadays, a few promising vehicles for siRNA delivery have been developed and it is gradually revealed that enhancing siRNA release from endosomes into cytosol is a very important factor for successful delivery. Here, we designed a novel pH-sensitive nanomicelle, PEG-PTTMA-P(GMA-S-DMA) (PTMS), for siRNA delivery. Owing to rapid hydrolysis in acidic environment, PTMS NPs underwent hydrophobic-to-hydrophilic transition in endosomes that enabled combination of proton sponge effect and raised osmotic pressure in endosomes, resulting in vigorous release of siRNAs from endosomes into cytosol...
2017: Theranostics
https://www.readbyqxmd.com/read/28911210/a20-an-essential-component-of-the-ubiquitin-editing-protein-complex-is-a-negative-regulator-of-inflammation-in-human-myometrium-and-foetal-membranes
#7
Martha Lappas
STUDY QUESTION: Does A20 regulate mediators involved in the terminal processes of human labour in primary myometrial and amnion cells? SUMMARY ANSWER: A20 is a nuclear factor-kappa B (NF-κB) responsive gene that acts as a negative regulator of NF-κB-induced expression of pro-labour mediators. WHAT IS KNOWN ALREADY: Inflammation is commonly implicated in spontaneous preterm birth and the processes involved in rupture of foetal membranes and uterine contractions...
September 1, 2017: Molecular Human Reproduction
https://www.readbyqxmd.com/read/28904816/regulation-of-hnrnpa1-by-micrornas-controls-the-mir-18a-k-ras-axis-in-chemotherapy-resistant-ovarian-cancer
#8
Cristian Rodriguez-Aguayo, Paloma Del C Monroig, Roxana S Redis, Emine Bayraktar, Maria I Almeida, Cristina Ivan, Enrique Fuentes-Mattei, Mohammed H Rashed, Arturo Chavez-Reyes, Bulent Ozpolat, Rahul Mitra, Anil K Sood, George A Calin, Gabriel Lopez-Berestein
The regulation of microRNA (miRNA) biogenesis, function and degradation involves a range of mechanisms, including interactions with RNA-binding proteins. The potential contribution of regulatory miRNAs to the expression of these RNA interactor proteins that could control other miRNAs expression is still unclear. Here we demonstrate a regulatory circuit involving oncogenic and tumor-suppressor miRNAs and an RNA-binding protein in a chemotherapy-resistant ovarian cancer model. We identified and characterized miR-15a-5p and miR-25-3p as negative regulators of hnRNPA1 expression, which is required for the processing of miR-18a-3p, an inhibitor of the K-RAS oncogene...
2017: Cell Discovery
https://www.readbyqxmd.com/read/28903064/isolation-and-characterization-of-peroxiredoxin-1-gene-of-dunaliella-salina
#9
Fanghua Gong, Jing Wang, Jie Li
Peroxiredoxin 1 (Prdx1) is a ubiquitously expressed protein in eukaryotic cells, and plays an important role in cell proliferation, differentiation, apoptosis, and redox signaling. Although Prdx1 has been better studied in yeasts and humans, only few Prdx1 genes have been cloned in green algae. The microalga Dunaliella salina (D. salina) is a model for the study of a variety of human cilia-related diseases. In this study, a suppression subtractive hybridization cDNA library of D. salina was constructed, and 6 flagellum-associated genes including D...
September 10, 2017: Gene
https://www.readbyqxmd.com/read/28900156/dual-roles-of-two-isoforms-of-autophagy-related-gene-atg10-in-hcv-subgenomic-replicon-mediated-autophagy-flux-and-innate-immunity
#10
Qiong Zhao, Zhan-Ying Hu, Jing-Pu Zhang, Jian-Dong Jiang, Yuan-Yuan Ma, Jian-Rui Li, Zong-Gen Peng, Jin-Hua Chen
Autophagy and immune response are two defense systems that human-body uses against viral infection. Previous studies documented that some viral mechanisms circumvented host immunity mechanisms and hijacked autophagy for its replication and survival. Here, we focus on interactions between autophagy mechanism and innate-immune-response in HCV-subgenomic replicon cells to find a mechanism linking the two pathways. We report distinct effects of two autophagy-related protein ATG10s on HCV-subgenomic replication...
September 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28899899/dual-function-of-upf3b-in-early-and-late-translation-termination
#11
Gabriele Neu-Yilik, Etienne Raimondeau, Boris Eliseev, Lahari Yeramala, Beate Amthor, Aurélien Deniaud, Karine Huard, Kathrin Kerschgens, Matthias W Hentze, Christiane Schaffitzel, Andreas E Kulozik
Nonsense-mediated mRNA decay (NMD) is a cellular surveillance pathway that recognizes and degrades mRNAs with premature termination codons (PTCs). The mechanisms underlying translation termination are key to the understanding of RNA surveillance mechanisms such as NMD and crucial for the development of therapeutic strategies for NMD-related diseases. Here, we have used a fully reconstituted in vitro translation system to probe the NMD proteins for interaction with the termination apparatus. We discovered that UPF3B (i) interacts with the release factors, (ii) delays translation termination and (iii) dissociates post-termination ribosomal complexes that are devoid of the nascent peptide...
September 12, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28899357/comparative-transcriptome-analysis-provides-clues-to-molecular-mechanisms-underlying-blue-green-eggshell-color-in-the-jinding-duck-anas-platyrhynchos
#12
Zhepeng Wang, Guohua Meng, Yun Bai, Ruifang Liu, Yu Du, Lihong Su
BACKGROUND: In birds, blue-green eggshell color (BGEC) is caused by biliverdin, a bile pigment derived from the degradation of heme and secreted in the eggshell by the shell gland. Functionally, BGEC might promote the paternal investment of males in the nest and eggs. However, little is known about its formation mechanisms. Jinding ducks (Anas platyrhynchos) are an ideal breed for research into the mechanisms, in which major birds lay BGEC eggs with minor individuals laying white eggs...
September 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28898812/formation-of-hydroxylated-and-methoxylated-polychlorinated-biphenyls-by-bacillus-subtilis-new-insights-into-microbial-metabolism
#13
Jianteng Sun, Lili Pan, Lizhong Zhu
The detoxification and degradation of polychlorinated biphenyls (PCBs) have been studied. However, little information is available about the biological mechanisms involved in the metabolism of hydroxylated polychlorinated biphenyls (OH-PCBs) and methoxylated polychlorinated biphenyls (MeO-PCBs) by specific microorganism. In this study, the simultaneous formation of OH-PCB (major metabolite) and MeO-PCB (minor metabolite) was found in Bacillus subtilis after exposure to PCB. Interconversion between MeO-PCB and OH-PCB was also observed and the demethylation ratio of MeO-PCB was higher than the methylation ratio of OH-PCB...
September 9, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28898802/nucleases-activities-during-french-bean-leaf-aging-and-dark-induced-senescence
#14
Rocío Lambert, Francisco Antonio Quiles, Gregorio Gálvez-Valdivieso, Pedro Piedras
During leaf senescence resources are managed, with nutrients mobilized from older leaves to new sink tissues. The latter implies a dilemma in terms of resource utilization, the leaf senescence should increase seed quality whereas delay in senescence should improve the seed yield. Increased knowledge about nutrient recycling during leaf senescence could lead to advances in agriculture and improved seed quality. Macromolecules mobilized during leaf senescence include proteins and nucleic acids. Although nucleic acids have been less well studied than protein degradation, they are possible reservoirs of nitrogen and phosphorous...
September 7, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28895406/identification-of-potential-key-genes-associated-with-diffuse-large-b-cell-lymphoma-based-on-microarray-gene-expression-profiling
#15
X Luo, F Shi, H Qiu, Y Tong, X Gao
The study aimed to screen potential key genes, and their targeted miRNAs and transcription factors (TFs) that were related to diffuse large B-cell lymphoma (DLBCL), and explore potential therapeutic targets for the progression of DLBCL. Dataset GSE56315 extracted from human tonsils was downloaded from Gene Expression Omnibus. Limma package was used to identify differential expression genes (DEG) between DLBCL and normal human tonsils samples, and the function and pathway enrichment analyses were performed. Then, functional interaction (FI) networks analyses of DEGs were implemented, and modules were extracted...
September 12, 2017: Neoplasma
https://www.readbyqxmd.com/read/28894100/structural-basis-for-the-bidirectional-activity-of-bacillus-nanornase-nrna
#16
Brad J Schmier, Claudiu M Nelersa, Arun Malhotra
NanoRNAs are RNA fragments 2 to 5 nucleotides in length that are generated as byproducts of RNA degradation and abortive transcription initiation. Cells have specialized enzymes to degrade nanoRNAs, such as the DHH phosphoesterase family member NanoRNase A (NrnA). This enzyme was originally identified as a 3' → 5' exonuclease, but we show here that NrnA is bidirectional, degrading 2-5 nucleotide long RNA oligomers from the 3' end, and longer RNA substrates from the 5' end. The crystal structure of Bacillus subtilis NrnA reveals a dynamic bi-lobal architecture, with the catalytic N-terminal DHH domain linked to the substrate binding C-terminal DHHA1 domain via an extended linker...
September 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28893654/strain-specific-association-of-soybean-dwarf-virus-small-subgenomic-rna-with-virus-particles
#17
Thanuja Thekke-Veetil, Nancy K McCoppin, Leslie L Domier
Soybean dwarf virus (SbDV) produces a large subgenomic RNA (LsgRNA) for expression of structural and movement proteins and a small subgenomic RNA (SsgRNA) that does not contain an open reading frame. Sucrose gradient-purified SbDV virions from soybean plants systemically infected with SbDV by aphids and Nicotiana benthamiana leaves agroinfiltrated with infectious clones of two red clover SbDV isolates encapsidated genomic RNA and were associated with SsgRNA in a strain-specific manner. The LsgRNA was protected from RNase degradation, but not packaged into virions as indicated by its presence primarily in ELISA-negative fractions near the tops of sucrose gradients even in mutants that did not express coat protein...
September 8, 2017: Virus Research
https://www.readbyqxmd.com/read/28892259/cellulose-production-is-coupled-to-sensing-of-the-pyrimidine-biosynthetic-pathway-via-c-di-gmp-production-by-the-dgcq-protein-of-escherichia-coli
#18
Elio Rossi, Sara Motta, Alessandro Aliverti, Federica Cossu, Louise Gourlay, Pierluigi Mauri, Paolo Landini
Production of cellulose, a stress response-mediated process in enterobacteria, is modulated in Escherichia coli by the activity of the two pyrimidine nucleotide biosynthetic pathways, namely, the de novo biosynthetic pathway, and the salvage pathway, which relies on the environmental availability of pyrimidine nitrogenous bases. We had previously reported that prevalence of the salvage over the de novo pathway triggers cellulose production via synthesis of the second messenger c-di-GMP by the DgcQ (YedQ) diguanylate cyclase...
September 11, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28892041/guide-bound-structures-of-an-rna-targeting-a-cleaving-crispr-cas13a-enzyme
#19
Gavin J Knott, Alexandra East-Seletsky, Joshua C Cofsky, James M Holton, Emeric Charles, Mitchell R O'Connell, Jennifer A Doudna
CRISPR adaptive immune systems protect bacteria from infections by deploying CRISPR RNA (crRNA)-guided enzymes to recognize and cut foreign nucleic acids. Type VI-A CRISPR-Cas systems include the Cas13a enzyme, an RNA-activated RNase capable of crRNA processing and single-stranded RNA degradation upon target-transcript binding. Here we present the 2.0-Å resolution crystal structure of a crRNA-bound Lachnospiraceae bacterium Cas13a (LbaCas13a), representing a recently discovered Cas13a enzyme subtype. This structure and accompanying biochemical experiments define the Cas13a catalytic residues that are directly responsible for crRNA maturation...
September 11, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28891815/rna-binding-protein-zfp36l1-maintains-posttranscriptional-regulation-of-bile-acid-metabolism
#20
Elizabeth J Tarling, Bethan L Clifford, Joan Cheng, Pauline Morand, Angela Cheng, Ellen Lester, Tamer Sallam, Martin Turner, Thomas Q de Aguiar Vallim
Bile acids function not only as detergents that facilitate lipid absorption but also as signaling molecules that activate the nuclear receptor farnesoid X receptor (FXR). FXR agonists are currently being evaluated as therapeutic agents for a number of hepatic diseases due to their lipid-lowering and antiinflammatory properties. FXR is also essential for maintaining bile acid homeostasis and prevents the accumulation of bile acids. Elevated bile acids activate FXR, which in turn switches off bile acid synthesis by reducing the mRNA levels of bile acid synthesis genes, including cholesterol 7α-hydroxylase (Cyp7a1)...
September 11, 2017: Journal of Clinical Investigation
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