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https://www.readbyqxmd.com/read/28933595/phosphoproteome-based-kinase-activity-profiling-reveals-the-critical-role-of-map2k2-and-plk1-in-neuronal-autophagy
#1
Lei-Lei Chen, Yong-Bo Wang, Ju-Xian Song, Wan-Kun Deng, Jia-Hong Lu, Li-Li Ma, Chuan-Bin Yang, Min Li, Yu Xue
Recent studies have demonstrated that dysregulation of macroautophagy/autophagy may play a central role in the pathogenesis of neurodegenerative disorders, and the induction of autophagy protects against the toxic insults of aggregate-prone proteins by enhancing their clearance. Thus, autophagy has become a promising therapeutic target against neurodegenerative diseases. In this study, quantitative phosphoproteomic profiling together with a computational analysis was performed to delineate the phosphorylation signalling networks regulated by 2 natural neuroprotective autophagy enhancers, corynoxine (Cory) and corynoxine B (Cory B)...
September 21, 2017: Autophagy
https://www.readbyqxmd.com/read/28930607/transcriptomics-in-amyotrophic-lateral-sclerosis
#2
Marios G Krokidis, Panagiotis Vlamos
Amyotrophic lateral sclerosis (ALS) is an adult-onset, incurable neurodegenerative disease characterized by the selective death of upper and lowers motor neurons in the spinal cord, brainstem and motor cortex, which ultimately leads to paralysis and death within 2-3 years of onset. ALS is poorly understood, although multiple studies have been proposed to explain the pathophysiological mechanisms of the disorder. The development of microarray technology, for simultaneous analysis of the transcriptional expression of thousands of genes, has provided new possibilities to get better insights into the pathogenesis of ALS, and most important, potential new candidate targets for novel treatments...
January 1, 2018: Frontiers in Bioscience (Elite Edition)
https://www.readbyqxmd.com/read/28920958/the-n-6-methyladenosine-m-6-a-forming-enzyme-mettl3-controls-myeloid-differentiation-of-normal-hematopoietic-and-leukemia-cells
#3
Ly P Vu, Brian F Pickering, Yuanming Cheng, Sara Zaccara, Diu Nguyen, Gerard Minuesa, Timothy Chou, Arthur Chow, Yogesh Saletore, Matthew MacKay, Jessica Schulman, Christopher Famulare, Minal Patel, Virginia M Klimek, Francine E Garrett-Bakelman, Ari Melnick, Martin Carroll, Christopher E Mason, Samie R Jaffrey, Michael G Kharas
N(6)-methyladenosine (m(6)A) is an abundant nucleotide modification in mRNA that is required for the differentiation of mouse embryonic stem cells. However, it remains unknown whether the m(6)A modification controls the differentiation of normal and/or malignant myeloid hematopoietic cells. Here we show that shRNA-mediated depletion of the m(6)A-forming enzyme METTL3 in human hematopoietic stem/progenitor cells (HSPCs) promotes cell differentiation, coupled with reduced cell proliferation. Conversely, overexpression of wild-type METTL3, but not of a catalytically inactive form of METTL3, inhibits cell differentiation and increases cell growth...
September 18, 2017: Nature Medicine
https://www.readbyqxmd.com/read/28919899/emerging-roles-and-landscape-of-translating-mrnas-in-plants
#4
REVIEW
Gaurav Sablok, Jonathan J Powell, Kemal Kazan
Plants use a wide range of mechanisms to adapt to different environmental stresses. One of the earliest responses displayed under stress is rapid alterations in stress responsive gene expression that has been extensively analyzed through expression profiling such as microarrays and RNA-sequencing. Recently, expression profiling has been complemented with proteome analyses to establish a link between transcriptional and the corresponding translational changes. However, proteome profiling approaches have their own technical limitations...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28917040/studying-selenoprotein-mrna-translation-using-rna-seq-and-ribosome-profiling
#5
Brian K Dalley, Lisa Baird, Michael T Howard
Deep sequencing of ribosome protected mRNA footprints, also called ribosome profiling or Ribo-Seq, is a relatively new methodology well suited to address questions regarding the mechanisms and efficiency of protein expression. Specifically, the ability of this technique to quantify ribosome abundance with codon resolution enables experiments aimed at studying many aspects of translation, including gene-specific translational efficiency, translation of regulatory upstream short open reading frames, sites of ribosome pausing, and most importantly for selenoproteins, the efficiency by which UGA codons are redefined to encode selenocysteine...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28914802/phylogenetic-analysis-and-antimicrobial-profiles-of-cultured-emerging-opportunistic-pathogens-phyla-actinobacteria-and-proteobacteria-identified-in-hot-springs
#6
Jocelyn Leonie Jardine, Akebe Luther King Abia, Vuyo Mavumengwana, Eunice Ubomba-Jaswa
Hot spring water may harbour emerging waterborne opportunistic pathogens that can cause infections in humans. We have investigated the diversity and antimicrobial resistance of culturable emerging and opportunistic bacterial pathogens, in water and sediment of hot springs located in Limpopo, South Africa. Aerobic bacteria were cultured and identified using 16S ribosomal DNA (rDNA) gene sequencing. The presence of Legionella spp. was investigated using real-time polymerase chain reaction. Isolates were tested for resistance to ten antibiotics representing six different classes: β-lactam (carbenicillin), aminoglycosides (gentamycin, kanamycin, streptomycin), tetracycline, amphenicols (chloramphenicol, ceftriaxone), sulphonamides (co-trimoxazole) and quinolones (nalidixic acid, norfloxacin)...
September 15, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28911333/profiling-bacterial-communities-by-minion-sequencing-of-ribosomal-operons
#7
Lee J Kerkhof, Kevin P Dillon, Max M Häggblom, Lora R McGuinness
BACKGROUND: An approach utilizing the long-read capability of the Oxford Nanopore MinION to rapidly sequence bacterial ribosomal operons of complex natural communities was developed. Microbial fingerprinting employs domain-specific forward primers (16S rRNA subunit), reverse primers (23S rRNA subunit), and a high-fidelity Taq polymerase with proofreading capabilities. Amplicons contained both ribosomal subunits for broad-based phylogenetic assignment (~ 3900 bp of sequence), plus the intergenic spacer (ITS) region (~ 300 bp) for potential strain-specific identification...
September 15, 2017: Microbiome
https://www.readbyqxmd.com/read/28911071/prediction-of-pathological-response-to-neoadjuvant-treatment-in-rectal-cancer-with-a-two-protein-immunohistochemical-score-derived-from-stromal-gene-profiling
#8
S Gonçalves-Ribeiro, R Sanz-Pamplona, A Vidal, X Sanjuan, N Guillen Díaz-Maroto, A Soriano, J Guardiola, N Albert, M Martínez-Villacampa, I López, C Santos, J Serra-Musach, R Salazar, G Capellà, A Villanueva, D G Molleví
Background: Preoperative chemoradiotherapy followed by surgical mesorectal resection is the standard of care for locally advanced rectal carcinomas. Yet, predicting that patients will respond to treatment remains an unmet clinical challenge. Experimental design: Using laser-capture microdissection we isolated RNA from stroma and tumour glands from prospective pre-treatment samples (n = 15). Transcriptomic profiles were obtained hybridising PrimeView Affymetrix arrays...
September 1, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28905707/-candidatus-phytoplasma-wodyetiae-a-new-taxon-associated-with-yellow-decline-disease-of-foxtail-palm-wodyetia-bifurcata-in-malaysia
#9
Neda Naderali, Naghmeh Nejat, Ganesan Vadamalai, Robert E Davis, Wei Wei, Nigel A Harrison, LihLing Kong, Jugah Kadir, Yee-How Tan, Yan Zhao
Landscape-grown foxtail palm (Wodyetia bifurcata A. K. Irvine) trees displaying symptoms of severe foliar chlorosis, stunting, general decline and mortality reminiscent of coconut yellow decline disease were observed in Bangi, Malaysia, during 2012. DNA samples from foliage tissues of 15 symptomatic palms were analysed by employing a nested PCR assay primed by phytoplasma universal ribosomal RNA operon primer pairs, P1/P7 followed by R16F2n/R2. The assay yielded amplicons of a single band of 1.25 kb from DNA samples of 11 symptomatic palms...
September 14, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28903954/quantity-and-source-of-dietary-protein-influence-metabolite-production-by-gut-microbiota-and-rectal-mucosa-gene-expression-a-randomized-parallel-double-blind-trial-in-overweight-humans
#10
Martin Beaumont, Kevin Joseph Portune, Nils Steuer, Annaïg Lan, Victor Cerrudo, Marc Audebert, Florent Dumont, Giulia Mancano, Nadezda Khodorova, Mireille Andriamihaja, Gheorghe Airinei, Daniel Tomé, Robert Benamouzig, Anne-Marie Davila, Sandrine Paule Claus, Yolanda Sanz, François Blachier
Background: Although high-protein diets (HPDs) are frequently consumed for body-weight control, little is known about the consequences for gut microbiota composition and metabolic activity and for large intestine mucosal homeostasis. Moreover, the effects of HPDs according to the source of protein need to be considered in this context.Objective: The objective of this study was to evaluate the effects of the quantity and source of dietary protein on microbiota composition, bacterial metabolite production, and consequences for the large intestinal mucosa in humans...
September 13, 2017: American Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/28903409/acetyl-lupeolic-acid-inhibits-akt-signaling-and-induces-apoptosis-in-chemoresistant-prostate-cancer-cells-in-vitro-and-in-vivo
#11
Claudia Schmidt, Cornelia Loos, Lu Jin, Michael Schmiech, Christoph Q Schmidt, Menna El Gaafary, Tatiana Syrovets, Thomas Simmet
The triterpenoid acetyl-lupeolic acid (ac-LA) isolated from the oleogum resin of Boswellia carterii reduced the viability of a panel of cancer cell lines more efficiently than lupeol. There was no detectable intracellular conversion of ac-LA to lupeol and vice versa. In contrast to docetaxel, ac-LA did not induce selection of treatment-resistant cancer cells. By various parameters including DNA fragmentation, ac-LA was shown to induce apoptosis in androgen-independent PC-3 cells, whereas in MDA-MB-231 breast cancer cells, ac-LA led to cell accumulation in the G2/M phase of the cell cycle, but not to apoptosis...
August 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28901441/profiling-of-differentially-expressed-genes-in-adipose-tissues-of-multiple-symmetric-lipomatosis
#12
Ke Chen, Linghao Wang, Wenjun Yang, Changfa Wang, Gui Hu, Zhaohui Mo
Multiple symmetric lipomatosis (MSL) is a rare disorder characterized by aberrant multiple and symmetric subcutaneous adipose tissue accumulation in the face, neck, shoulders, back, chest and abdomen, severely affecting the quality of life of patients. At present, precise MSL etiology and pathogenesis remain to be elucidated. The present study first utilized a digital gene expression technique with a next‑generation sequencing platform to profile differentially expressed genes in three cases of MSL vs. normal control tissue...
September 7, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28900741/occurrence-and-distribution-of-antibiotic-resistance-genes-in-water-supply-reservoirs-in-jingjinji-area-china
#13
Kai Zhang, Zhi-Guang Niu, Zhiwei Lv, Ying Zhang
Jingjinji area occupies important position in developing of the Chinese economy, while there exists a sharp conflict between economic growth and limited water resources in this area. To ensure the safety of water consumption of cities in Jingjinji area, we investigated the abundance of three classes of antibiotic resistance genes (ARGs) in water and sediment of six water supply reservoirs in this area. The results showed that the detection frequency of sul1, tetM and ermB were 100%. However, the content ranges of these genes were different (10(-5) to 10(-2)/16S gene copies for sul1, 10(-5) to 10(-3)/16S gene copies for ermB, and 10(-5) to 10(-3)/16S gene copies for tetM)...
September 12, 2017: Ecotoxicology
https://www.readbyqxmd.com/read/28894921/structural-and-functional-variability-in-root-associated-bacterial-microbiomes-of-cd-zn-hyperaccumulator-sedum-alfredii
#14
Jipeng Luo, Qi Tao, Keren Wu, Jinxing Li, Jie Qian, Yongchao Liang, Xiaoe Yang, Tingqiang Li
Interactions between roots and microbes affect plant's resistance to abiotic stress. However, the structural and functional variation of root-associated microbiomes and their effects on metal accumulation in hyperaccumulators remain poorly understood. Here, we characterize the root-associated microbiota of a hyperaccumulating (HP) and a non-hyperaccumulating (NHP) genotype of Sedum alfredii by 16S ribosomal RNA gene profiling. We show that distinct microbiomes are observed in four spatially separable compartments: the bulk soil, rhizosphere, rhizoplane, and endosphere...
September 11, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28894789/impact-of-the-mk-vi-skinsuit-on-skin-microbiota-of-terrestrial-volunteers-and-an-international-space-station-bound-astronaut
#15
Richard A Stabler, Helena Rosado, Ronan Doyle, David Negus, Philip A Carvil, Juan G Kristjánsson, David A Green, Rafael Franco-Cendejas, Cadi Davies, Andreas Mogensen, Jonathan Scott, Peter W Taylor
Microgravity induces physiological deconditioning due to the absence of gravity loading, resulting in bone mineral density loss, atrophy of lower limb skeletal and postural muscles, and lengthening of the spine. SkinSuit is a lightweight compression suit designed to provide head-to-foot (axial) loading to counteract spinal elongation during spaceflight. As synthetic garments may impact negatively on the skin microbiome, we used 16S ribosomal RNA (rRNA) gene amplicon procedures to define bacterial skin communities at sebaceous and moist body sites of five healthy male volunteers undergoing SkinSuit evaluation...
2017: NPJ Microgravity
https://www.readbyqxmd.com/read/28894161/microbial-communities-in-placentas-from-term-normal-pregnancy-exhibit-spatially-variable-profiles
#16
Lindsay A Parnell, Catherine M Briggs, Bin Cao, Omar Delannoy-Bruno, Andrew E Schrieffer, Indira U Mysorekar
The placenta is the principal organ nurturing the fetus during pregnancy and was traditionally considered to be sterile. Recent work has suggested that the placenta harbours microbial communities, however the location and possible function of these microbes remain to be confirmed and elucidated. Here, we employed genomic DNA sequencing of multiple variable (V) regions of the bacterial 16S ribosomal gene, to interrogate microbial profiles in term pregnancies, from the basal plate, which is in direct contact with maternal uterine, endothelial, and immune cells; placental villi, which are bathed in maternal blood, and fetal membranes, which encapsulate the amniotic cavity...
September 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28887370/genome-reprogramming-in-saccharomyces-cerevisiae-upon-nonylphenol-exposure
#17
Ceyhun Bereketoglu, Kazim Yalcin Arga, Serpil Eraslan, Bulent Mertoglu
Bioaccumulative environmental estrogen, nonylphenol (NP; 4-nonylphenol), is widely used as a non-ionic surfactant and can affect human health. Since genomes of Saccharomyces cerevisiae and higher eukaryotes share many structural and functional similarities, we investigated subcellular effects of NP on S. cerevisiae BY4742 cells by analyzing genome-wide transcriptional profiles. We examined effects of low (1 mg/L NP) and high (5 mg/L NP) inhibitory concentration exposures for 120 or 180 min. After 120 and 180 min of 1 mg/L NP exposure, 187 (63 downregulated, 124 upregulated) and 103 genes (56 downregulated, 47 upregulated), respectively, were differentially expressed...
September 8, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28887122/blastocystis-subtypes-detected-in-long-tailed-macaques-in-thailand-further-evidence-of-cryptic-host-specificity
#18
Kotchaphon Vaisusuk, Weerachai Saijuntha, Sutthira Sedlak, Thongchit Thanchomnang, Warayutt Pilap, Warong Suksavate, Christen Rune Stensvold, Chairat Tantrawatpan
Blastocystis is an enteric parasitic protist with a widespread distribution in a variety of human and non-human hosts and supposedly a source of zoonotic transmission. This study aimed to determine the frequency and distribution of Blastocystis subtypes in free-ranging Macaca fascicularis (long-tailed macaques, LTMs) in Thailand. A total of 628 faecal samples were collected from free-ranging LTMs inhabiting fourteen tourist attraction sites in Thailand. Fresh faecal samples were individually cultured in Jones' medium, and Blastocystis-positive samples were subtyped using nuclear small subunit ribosomal DNA (SSU rDNA) sequencing...
September 5, 2017: Acta Tropica
https://www.readbyqxmd.com/read/28887026/beyond-read-counts-ribo-seq-data-analysis-to-understand-the-functions-of-the-transcriptome
#19
REVIEW
Lorenzo Calviello, Uwe Ohler
By mapping the positions of millions of translating ribosomes in the cell, ribosome profiling (Ribo-seq) has established its role as a powerful tool to study gene expression. Several laboratories have introduced modifications to the experimental protocol and expanded the repertoire of biochemical methods to study translation transcriptome-wide. However, the diversity of protocols highlights a need for standardization. At the same time, different computational analysis strategies have used Ribo-seq data to identify the set of translated sequences with high confidence...
September 5, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28886561/zinc-protects-against-cadmium-induced-toxicity-by-regulating-oxidative-stress-ions-homeostasis-and-protein-synthesis
#20
Jingmei Pan, Xinhe Huang, Yuxing Li, Ming Li, Ning Yao, Zhengdong Zhou, Xueru Li
The widespread environmental toxin cadmium (Cd) is associated with numerous human diseases. The essential trace element zinc (Zn) strongly counteracts Cd-induced toxicity; however, the mechanism is incompletely understood. Here, we conducted RNA sequencing and bioinformatics analyses to determine the global gene expression profiles of yeast cells exposed to Cd or Cd plus Zn. We identified 912 Cd-induced and 627 Cd plus Zn-induced differentially expressed genes (DEGs). Adding Zn during Cd exposure efficiently reversed the expression of 92...
August 21, 2017: Chemosphere
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