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https://www.readbyqxmd.com/read/29082417/vibrational-spectroscopy-combined-with-transcriptomic-analysis-for-investigation-of-bacterial-responses-towards-acid-stress
#1
Mya M Hlaing, Bayden R Wood, Don McNaughton, Julian I Rood, Edward M Fox, Mary Ann Augustin
The ability of bacteria to tolerate acid stress plays an important role in their growth and survival. In particular, aciduric bacteria have several survival systems that prevent cell damage from acid stress. In this study, the effect of the bacterial stress induced by pre-adaptation at different pH values on the cellular macromolecules of Lactobacillus plantarum was investigated using Raman spectroscopy and Fourier transform infrared spectroscopy. The expression of key genes was also quantified to provide understanding of the transcriptional response of the cells to lethal acid stress conditions...
October 29, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29075180/evaluating-the-autonomy-of-the-drosophila-circadian-clock-in-dissociated-neuronal-culture
#2
Virginie Sabado, Ludovic Vienne, Emi Nagoshi
Circadian behavioral rhythms offer an excellent model to study intricate interactions between the molecular and neuronal mechanisms of behavior. In mammals, pacemaker neurons in the suprachiasmatic nucleus (SCN) generate rhythms cell-autonomously, which are synchronized by the network interactions within the circadian circuit to drive behavioral rhythms. However, whether this principle is universal to circadian systems in animals remains unanswered. Here, we examined the autonomy of the Drosophila circadian clock by monitoring transcriptional and post-transcriptional rhythms of individual clock neurons in dispersed culture with time-lapse microscopy...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/29052189/cell-type-specific-profiling-of-chromatin-modifications-and-associated-proteins
#3
Ana Karina Morao, Erwann Caillieux, Vincent Colot, François Roudier
Progression of a cell along a differentiation path is characterized by changes in gene expression profiles. Alterations of these transcriptional programs result from cell type-specific transcription factors that act in a dynamic chromatin environment. Understanding the precise contribution of these molecular factors during the differentiation process requires accessing specific cell types within a developing organ. This chapter describes a streamlined and alternative version of INTACT, a method enabling the isolation of specific cell populations by affinity-purification of tagged nuclei and the subsequent analysis of gene expression, transcription factor binding profiles, as well as chromatin state at a genome-wide scale...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29046457/hiv-1-infection-of-primary-cd4-t-cells-regulates-the-expression-of-specific-herv-k-hml-2-elements
#4
George R Young, Sandra N Terry, Lara Manganaro, Alvaro Cuesta-Dominguez, Gintaras Deikus, Dabeiba Bernal-Rubio, Laura Campisi, Ana Fernandez-Sesma, Robert Sebra, Viviana Simon, Lubbertus C F Mulder
Endogenous retroviruses (ERVs) occupy extensive regions of the human genome. Although many of these retroviral elements have lost their ability to replicate, those whose insertion took place more recently, such as the HML-2 group of HERV-K elements, still retain intact open reading frames and the capacity to produce certain viral RNA and/or proteins. Transcription of these ERVs is, however, tightly regulated by dedicated epigenetic control mechanisms. Nonetheless, it has been reported that some pathologic states, such as viral infections and certain cancers, coincide with ERV expression suggesting transcriptional reawakening is possible...
October 18, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29030127/a-method-for-the-isolation-and-enrichment-of-purified-bovine-milk-exosomes
#5
Kanchan Vaswani, Yong Qin Koh, Fatema B Almughlliq, Hassendrini N Peiris, Murray D Mitchell
Exosomes are nanovesicles that play important roles in intercellular communication as they carry information to target cells. Isolation of high purity exosomes will aid in studying the exosomal cargo and quantity as well as how cell-specific messages are carried. We describe a new method incorporating size exclusion chromatography (SEC) to enrich milk-derived exosomes from extracellular vesicles (EVs). This involved the initial isolation of EVs from bovine milk via milk processing and ultracentrifugation; followed by a new method to enrich exosomes using SEC...
October 10, 2017: Reproductive Biology
https://www.readbyqxmd.com/read/28960179/effects-of-orally-ingested-arsenic-on-respiratory-epithelial-permeability-to-bacteria-and-small-molecules-in-mice
#6
Michael W Henderson, Jennifer H Madenspacher, Gregory S Whitehead, Seddon Y Thomas, Jim J Aloor, Kymberly M Gowdy, Michael B Fessler
BACKGROUND: Arsenic exposure via drinking water impacts millions of people worldwide. Although arsenic has been associated epidemiologically with increased lung infections, the identity of the lung cell types targeted by peroral arsenic and the associated immune mechanisms remain poorly defined. OBJECTIVES: We aimed to determine the impact of peroral arsenic on pulmonary antibacterial host defense. METHODS: Female C57BL/6 mice were administered drinking water with 0, 250 ppb, or 25 ppm sodium arsenite for 5 wk and then challenged intratracheally with Klebsiella pneumoniae, Streptococcus pneumoniae, or lipopolysaccharide...
September 28, 2017: Environmental Health Perspectives
https://www.readbyqxmd.com/read/28956755/nuclear-transcriptomes-at-high-resolution-using-retooled-intact
#7
Mauricio Reynoso, Germain Pauluzzi, Kaisa Kajala, Sean Cabanlit, Joel Velasco, Jérémie Bazin, Roger Deal, Neelima Sinha, Siobhan M Brady, Julia Bailey-Serres
Isolated nuclei provide access to early steps in gene regulation involving chromatin as well as transcript production and processing. Here we describe transfer of the Isolation of Nuclei from TAgged specific Cell Types (INTACT) to the monocot rice (Oryza sativa L.). The purification of biotinylated nuclei was redesigned by replacing the outer nuclear envelope-targeting domain of the Nuclear Tagging Fusion (NTF) protein with an outer nuclear envelope-anchored domain. This modified NTF was combined with codon optimized E...
September 27, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28910620/ctag-paperclip-reveals-alternative-polyadenylation-promotes-cell-type-specific-protein-diversity-and-shifts-araf-isoforms-with-microglia-activation
#8
Hun-Way Hwang, Yuhki Saito, Christopher Y Park, Nathalie E Blachère, Yoko Tajima, John J Fak, Ilana Zucker-Scharff, Robert B Darnell
Alternative polyadenylation (APA) is increasingly recognized to regulate gene expression across different cell types, but obtaining APA maps from individual cell types typically requires prior purification, a stressful procedure that can itself alter cellular states. Here, we describe a new platform, cTag-PAPERCLIP, that generates APA profiles from single cell populations in intact tissues; cTag-PAPERCLIP requires no tissue dissociation and preserves transcripts in native states. Applying cTag-PAPERCLIP to profile four major cell types in the mouse brain revealed common APA preferences between excitatory and inhibitory neurons distinct from astrocytes and microglia, regulated in part by neuron-specific RNA-binding proteins NOVA2 and PTBP2...
September 13, 2017: Neuron
https://www.readbyqxmd.com/read/28886250/dectin-2-is-a-c-type-lectin-receptor-that-recognizes-pneumocystis-and-participates-in-innate-immune-responses
#9
Theodore J Kottom, Deanne M Hebrink, Paige E Jenson, Paige L Marsolek, Marcel Wüthrich, Huafeng Wang, Bruce Klein, Sho Yamasaki, Andrew H Limper
Pneumocystis remains an important fungal pathogen causing life-threatening pneumonia in patients with AIDS and malignancy. Lung fungal pathogens are recognized by C-type Lectin Receptors (CLRs), which bind specific ligands and stimulate innate immune responses. Previously, a role for the CLR Dectin-1 has been shown to mediate immune responses to Pneumocystis spp. For this reason, we investigated a potential role for Dectin-2. Rats with Pneumocystis pneumonia (PCP) exhibited elevated Dectin-2 mRNA levels. Soluble Dectin-2 CRD fusions protein showed binding to intact Pneumocystis carinii (Pc) and to native Pneumocystis major surface glycoprotein/glycoprotein A (Msg/gpA)...
September 8, 2017: American Journal of Respiratory Cell and Molecular Biology
https://www.readbyqxmd.com/read/28866327/beyond-quality-control-the-role-of-nonsense-mediated-mrna-decay-nmd-in-regulating-gene-expression
#10
REVIEW
Sofia Nasif, Lara Contu, Oliver Mühlemann
Nonsense-mediated mRNA decay (NMD) has traditionally been described as a quality control system that rids cells of aberrant mRNAs with crippled protein coding potential. However, transcriptome-wide profiling of NMD deficient cells identified a plethora of seemingly intact mRNAs coding for functional proteins as NMD targets. This led to the view that NMD constitutes an additional post-transcriptional layer of gene expression control involved in the regulation of many different biological pathways. Here, we review our current knowledge about the role of NMD in embryonic development and tissue-specific cell differentiation...
September 1, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28860943/biochemical-and-histological-alterations-induced-by-the-smoke-of-allethrin-based-mosquito-coil-on-mice-model
#11
M Abdulla Al-Mamun, M Ataur Rahman, M Habibur Rahman, K M F Hoque, Z Ferdousi, Mohammad Nurul Matin, M Abu Reza
BACKGROUND: Mosquito coil (MC) emits insecticide upon burning which provides limited protection against lethal mosquito borne diseases. However, apart from killing the insect, toxicities associated with the inhalation of these insecticides poses severe health hazards. However, the use of MC is increasing day by day in third world countries in particular but, yet to receive enough attention of both policy maker and general public. The current study was aimed to assess the MC smoke induced damage of pulmonary and hepatic tissues along with observing the alterations of several blood biochemical parameters in mice model...
2017: BMC Clinical Pathology
https://www.readbyqxmd.com/read/28839250/pharmacological-profile-and-efficiency-in-vivo-of-diflapolin-the-first-dual-inhibitor-of-5-lipoxygenase-activating-protein-and-soluble-epoxide-hydrolase
#12
Ulrike Garscha, Erik Romp, Simona Pace, Antonietta Rossi, Veronika Temml, Daniela Schuster, Stefanie König, Jana Gerstmeier, Stefanie Liening, Markus Werner, Heiner Atze, Sandra Wittmann, Christina Weinigel, Silke Rummler, Gerhard K Scriba, Lidia Sautebin, Oliver Werz
Arachidonic acid (AA) is metabolized to diverse bioactive lipid mediators. Whereas the 5-lipoxygenase-activating protein (FLAP) facilitates AA conversion by 5-lipoxygenase (5-LOX) to pro-inflammatory leukotrienes (LTs), the soluble epoxide hydrolase (sEH) degrades anti-inflammatory epoxyeicosatrienoic acids (EETs). Accordingly, dual FLAP/sEH inhibition might be advantageous drugs for intervention of inflammation. We present the in vivo pharmacological profile and efficiency of N-[4-(benzothiazol-2-ylmethoxy)-2-methylphenyl]-N'-(3,4-dichlorophenyl)urea (diflapolin) that dually targets FLAP and sEH...
August 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28771188/apigenin-impacts-the-growth-of-the-gut-microbiota-and-alters-the-gene-expression-of-enterococcus
#13
Minqian Wang, Jenni Firrman, Liqing Zhang, Gustavo Arango-Argoty, Peggy Tomasula, LinShu Liu, Weidong Xiao, Kit Yam
Apigenin is a major dietary flavonoid with many bioactivities, widely distributed in plants. Apigenin reaches the colon region intact and interacts there with the human gut microbiota, however there is little research on how apigenin affects the gut bacteria. This study investigated the effect of pure apigenin on human gut bacteria, at both the single strain and community levels. The effect of apigenin on the single gut bacteria strains Bacteroides galacturonicus, Bifidobacterium catenulatum, Lactobacillus rhamnosus GG, and Enterococcus caccae, was examined by measuring their anaerobic growth profiles...
August 3, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28766291/comprehensive-identification-of-mrna-polyadenylation-sites-by-paperclip
#14
Hun-Way Hwang, Robert B Darnell
We discuss a newly developed method to profile mRNA polyadenylation (pA) sites in an unbiased manner, PAPERCLIP (Poly(A) binding Protein-mediated mRNA 3'End Retrieval by CrossLinking ImmunoPrecipitation). Based on the well-established CLIP (crosslinking immunoprecipitation) technique, PAPERCLIP utilizes the poly(A) binding protein (PABP) as a biological filter to selectively retrieve mRNA 3' end fragments by immunoprecipitation from ultraviolet (UV) irradiated tissues or cultured cells. The mRNA fragments are subsequently extracted from the immunoprecipitated PABP:RNA complexes to generate a cDNA library, which goes through two rounds of purification before the final amplification by real-time polymerase chain reaction (PCR)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28765873/classification-of-cancer-cell-lines-using-matrix-assisted-laser-desorption-ionization-time%C3%A2-of%C3%A2-flight-mass-spectrometry-and-statistical-analysis
#15
Vlad Serafim, Ajit Shah, Maria Puiu, Nicoleta Andreescu, Dorina Coricovac, Alexander Nosyrev, Demetrios A Spandidos, Aristides M Tsatsakis, Cristina Dehelean, Iulia Pinzaru
Over the past decade, matrix-assisted laser desorption/ionization time‑of‑flight mass spectrometry (MALDI‑TOF MS) has been established as a valuable platform for microbial identification, and it is also frequently applied in biology and clinical studies to identify new markers expressed in pathological conditions. The aim of the present study was to assess the potential of using this approach for the classification of cancer cell lines as a quantifiable method for the proteomic profiling of cellular organelles...
October 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28764802/mesenchymal-stem-cells-derived-from-inflamed-dental-pulpal-and-gingival-tissue-a-potential-application-for-bone-formation
#16
Laura Tomasello, Rodolfo Mauceri, Antonina Coppola, Maria Pitrone, Giuseppe Pizzo, Giuseppina Campisi, Giuseppe Pizzolanti, Carla Giordano
BACKGROUND: Chronic periodontal disease is an infectious disease consisting of prolonged inflammation of the supporting tooth tissue and resulting in bone loss. Guided bone regeneration procedures have become common and safe treatments in dentistry, and in this context dental stem cells would represent the ideal solution as autologous cells. In this study, we verified the ability of dental pulp mesenchymal stem cells (DPSCs) and gingival mesenchymal stem cells (GMSCs) harvested from periodontally affected teeth to produce new mineralized bone tissue in vitro, and compared this to cells from healthy teeth...
August 1, 2017: Stem Cell Research & Therapy
https://www.readbyqxmd.com/read/28744713/genome-wide-analysis-of-gene-expression-profiling-revealed-that-cop9-signalosome-is-essential-for-correct-expression-of-fe-homeostasis-genes-in-arabidopsis
#17
Seckin Eroglu, Emre Aksoy
In plant cells, either excess or insufficient iron (Fe) concentration triggers stress responses, therefore it is strictly controlled. Proteasome-mediated degradation through ubiquitination of Fe homeostasis proteins has just become the focus of research in recent years. Deactivating ubiquitin ligases, COP9 signalosome has a central importance in the translational control of various stress responses. The aim of the study was to investigate COP9 signalosome in Fe deficiency response of Strategy I plants. In silico analysis of a set of Fe-deficiency-responsive genes was conducted against the transcriptome of Arabidopsis csn mutant lines using Genevestigator software...
October 2017: Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine
https://www.readbyqxmd.com/read/28741179/activation-of-liver-x-receptor-inhibits-oct2-mediated-organic-cation-transport-in-renal-proximal-tubular-cells
#18
Teerasak Wongwan, Suticha Kittayaruksakul, Nithi Asavapanumas, Varanuj Chatsudthipong, Sunhapas Soodvilai
Liver X receptor (LXR) is transcriptional factor that plays an important role in the regulation of energy metabolism such as cholesterol, lipid, and glucose metabolism as well as membrane transporters and channels. Using both in vitro and in vivo models, LXR regulation of the expression and function of renal organic cation transporter 2 (OCT2) was observed. Synthetic LXR agonist (GW3965) and endogenous LXR agonist (22R-hydroxycholesterol) significantly reduced the uptake of (3)H-MPP(+), a prototypic substrate of OCT2, in both OCT2- Chinese hamster ovary K1 and human renal proximal tubular cells (RPTEC/TERT1)...
July 25, 2017: Pflügers Archiv: European Journal of Physiology
https://www.readbyqxmd.com/read/28693997/lectin-from-canavalia-villosa-seeds-a-glucose-mannose-specific-protein-and-a-new-tool-for-inflammation-studies
#19
Claudia F Lossio, Cleane G Moreira, Renata M F Amorim, Clareane S Nobre, Mayara T L Silva, Cornevile C Neto, Vanir R Pinto-Junior, Ivanice B Silva, Julia Campos, Ana Maria S Assreuy, Benildo S Cavada, Kyria S Nascimento
With important carbohydrate binding properties, lectins are proteins able to decipher the glycocode, and as such, they can be used in bioassays involving cell-cell communication, protein targeting, inflammation, and hypernociception, among others. In this study, a new glucose/mannose-specific lectin from Canavalia villosa seeds (Cvill) was isolated by a single affinity chromatography step in a Sephadex(®) G-50 column, with a purification yield of 19.35mg of lectin per gram of powdered seed. Analysis of intact protein by mass spectrometry showed the lectin is composed of three polypeptide chains, including a 25...
December 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28629195/candida-albicans-impairments-induced-by-peppermint-and-clove-oils-at-sub-inhibitory-concentrations
#20
Katarzyna Rajkowska, Anna Otlewska, Alina Kunicka-Styczyńska, Agnieszka Krajewska
Members of Candida species cause significant health problems, inducing various types of superficial and deep-seated mycoses in humans. In order to prevent from Candida sp. development, essential oils are more and more frequently applied, due to their antifungal activity, low toxicity if used appropriately, and biodegrability. The aim of the study was to characterize the early alterations in Candida albicans metabolic properties in relation to proteins and chromosomal DNA profiles, after treatment with peppermint and clove oils at sub-inhibitory concentrations...
June 19, 2017: International Journal of Molecular Sciences
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