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https://www.readbyqxmd.com/read/28213537/ketoacylsynthase-domains-of-a-pufa-synthase-in-thraustochytrium-can-effectively-function-as-stand-alone-enzymes-in-escherichia-coli
#1
Xi Xie, Dauenpen Meesapyodsuk, Xiao Qiu
Thraustochytrium sp. 26185 accumulates a high level of docosahexaenoic acid (DHA), a nutritionally important ω-3 very long chain unsaturated fatty acid (VLCPUFA) synthesized primarily by polyunsaturated fatty acid (PUFA) synthase, a Type I polyketide synthase-like mega-enzyme. The PUFA synthase in this species comprises three large subunits each with multiple catalytic domains. It was hypothesized that among these domains, ketoacylsynthase (KS) domains might be critical for catalyzing the condensation of specific unsaturated acyl-ACPs with malonyl-ACP, whereby retaining double bonds in an extended acyl chain...
February 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28210928/bacterial-resistance-to-arsenic-protects-against-protist-killing
#2
Xiuli Hao, Xuanji Li, Chandan Pal, Jon Hobman, D G Joakim Larsson, Quaiser Saquib, Hend A Alwathnani, Barry P Rosen, Yong-Guan Zhu, Christopher Rensing
Protists kill their bacterial prey using toxic metals such as copper. Here we hypothesize that the metalloid arsenic has a similar role. To test this hypothesis, we examined intracellular survival of Escherichia coli (E. coli) in the amoeba Dictyostelium discoideum (D. discoideum). Deletion of the E. coli ars operon led to significantly lower intracellular survival compared to wild type E. coli. This suggests that protists use arsenic to poison bacterial cells in the phagosome, similar to their use of copper...
February 16, 2017: Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine
https://www.readbyqxmd.com/read/28210761/the-evolutionary-loss-of-rnai-key-determinants-in-kinetoplastids-as-a-multiple-sporadic-phenomenon
#3
Andrey V Matveyev, João M P Alves, Myrna G Serrano, Vladimir Lee, Ana M Lara, William A Barton, André G Costa-Martins, Stephen M Beverley, Erney P Camargo, Marta M G Teixeira, Gregory A Buck
We screened the genomes of a broad panel of kinetoplastid protists for genes encoding proteins associated with the RNA interference (RNAi) system using probes from the Argonaute (AGO1), Dicer1 (DCL1), and Dicer2 (DCL2) genes of Leishmania brasiliensis and Crithidia fasciculata. We identified homologs for all the three of these genes in the genomes of a subset of these organisms. However, several of these organisms lacked evidence for any of these genes, while others lacked only DCL2. The open reading frames encoding these putative proteins were structurally analyzed in silico...
February 16, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28203518/inositol-1-4-5-trisphosphate-receptor-determines-intracellular-ca-2-concentration-in-trypanosoma-cruzi-throughout-its-life-cycle
#4
Muneaki Hashimoto, Motomichi Doi, Nagomi Kurebayashi, Koji Furukawa, Hiroko Hirawake-Mogi, Yoshihiro Ohmiya, Takashi Sakurai, Toshihiro Mita, Katsuhiko Mikoshiba, Takeshi Nara
Regulation of intracellular Ca(2+) concentration ([Ca(2+)]i) is vital for eukaryotic organisms. Recently, we identified a Ca(2+) channel (TcIP 3R) associated with intracellular Ca(2+) stores in Trypanosoma cruzi, the parasitic protist that causes Chagas disease. In this study, we measured [Ca(2+)]i during the parasite life cycle and determined whether TcIP 3R is involved in the observed variations. Parasites expressing R-GECO1, a red fluorescent, genetically encoded Ca(2+) indicator for optical imaging that fluoresces when bound to Ca(2+), were produced...
December 2016: FEBS Open Bio
https://www.readbyqxmd.com/read/28192241/molecular-cloning-mrna-expression-and-characterization-of-membrane-bound-hemoglobin-in-oriental-river-prawn-macrobrachium-nipponense
#5
Shengming Sun, Fujun Xuan, Hongtuo Fu, Jian Zhu, Xianping Ge, Xugan Wu
Most hemoglobins are respiratory proteins and are ubiquitous in animals, bacteria, fungi, protists, and plants. In this study, we describe a membrane-bound hemoglobin in the oriental river prawn Macrobrachium nipponense (MnHb), which also expresses hemocyanin. MnHb cDNA was cloned using the rapid amplification of cDNA ends (RACE) approach, which afforded a 1201bp gene encoding a 193 amino acid polypeptide. Bioinformatic evaluation suggested MnHb is membrane anchored by N-myristoylation, and immunofluorescence confirmed its location in the membrane of chief cells in the gill...
February 10, 2017: Comparative Biochemistry and Physiology. Part A, Molecular & Integrative Physiology
https://www.readbyqxmd.com/read/28188662/population-genetics-of-reef-coral-endosymbionts-symbiodinium-dinophyceae
#6
D J Thornhill, E J Howells, D C Wham, T D Steury, S R Santos
Symbiodinium is a diverse genus of unicellular dinoflagellate symbionts associating with various marine protists and invertebrates. Although the broad-scale diversity and phylogenetics of the Symbiodinium complex is well established, there have been surprisingly few data on fine-scale population structure and biogeography of these dinoflagellates. Yet population level processes contribute strongly to the biology of Symbiodinium, including how anthropogenic-driven global climate change impacts these symbionts and their host associations...
February 11, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28182670/killing-of-diverse-eye-pathogens-acanthamoeba-spp-fusarium-solani-and-chlamydia-trachomatis-with-alcohols
#7
Yousuf Aqeel, Raquel Rodriguez, Aparajita Chatterjee, Robin R Ingalls, John Samuelson
BACKGROUND: Blindness is caused by eye pathogens that include a free-living protist (Acanthamoeba castellanii, A. byersi, and/or other Acanthamoeba spp.), a fungus (Fusarium solani), and a bacterium (Chlamydia trachomatis). Hand-eye contact is likely a contributor to the spread of these pathogens, and so hand washing with soap and water or alcohol-based hand sanitizers (when water is not available) might reduce their transmission. Recently we showed that ethanol and isopropanol in concentrations present in hand sanitizers kill walled cysts of Giardia and Entamoeba, causes of diarrhea and dysentery, respectively...
February 9, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28178320/variations-in-the-structural-and-functional-diversity-of-zooplankton-over-vertical-and-horizontal-environmental-gradients-en-route-to-the-arctic-ocean-through-the-fram-strait
#8
Marta Gluchowska, Emilia Trudnowska, Ilona Goszczko, Anna Maria Kubiszyn, Katarzyna Blachowiak-Samolyk, Waldemar Walczowski, Slawomir Kwasniewski
A multi-scale approach was used to evaluate which spatial gradient of environmental variability is the most important in structuring zooplankton diversity in the West Spitsbergen Current (WSC). The WSC is the main conveyor of warm and biologically rich Atlantic water to the Arctic Ocean through the Fram Strait. The data set included 85 stratified vertical zooplankton samples (obtained from depths up to 1000 metres) covering two latitudinal sections (76°30'N and 79°N) located across the multi-path WSC system...
2017: PloS One
https://www.readbyqxmd.com/read/28174578/extracellular-alkalinization-as-a-defense-response-in-potato-cells
#9
Natalia Moroz, Karen R Fritch, Matthew J Marcec, Diwaker Tripathi, Andrei Smertenko, Kiwamu Tanaka
A quantitative and robust bioassay to assess plant defense response is important for studies of disease resistance and also for the early identification of disease during pre- or non-symptomatic phases. An increase in extracellular pH is known to be an early defense response in plants. In this study, we demonstrate extracellular alkalinization as a defense response in potatoes. Using potato suspension cell cultures, we observed an alkalinization response against various pathogen- and plant-derived elicitors in a dose- and time-dependent manner...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28171698/differential-gene-expression-in-five-isolates-of-the-clam-pathogen-quahog-parasite-unknown-qpx
#10
Ewelina Rubin, Arnaud Tanguy, Emmanuelle Pales Espinosa, Bassem Allam
Quahog parasite unknown (QPX) is a thraustochytrid protist that infects the hard clam, Mercenaria mercenaria, causing significant economic losses along the northeastern coasts of North America. Previous investigations noted differences in growth dynamics and virulence in QPX cells from different geographic locations. In order to probe the molecular determinants for these variations, we investigated the transcriptomic profiles of five geographically-distinct QPX isolates using custom 15K 60-mer oligonucleotide arrays...
February 7, 2017: Journal of Eukaryotic Microbiology
https://www.readbyqxmd.com/read/28166371/lineage-specific-and-highly-derived-gene-sequences-among-amoebozoa-revealed-by-the-comparative-analysis-of-transcriptomes-from-twelve-amoebozoan-species
#11
Natalya I Bondarenko, Anton S Bondarenko, Alexey V Smirnov
Amoebozoa represent a difficult group for traditional morphology-based taxonomy. Molecular approaches, such as gene sequencing and DNA barcoding have greatly enhanced our knowledge on the diversity of these organisms. However, metagenomic studies of Amoebozoa still did not provide as impressive results as they did among some other groups of protists. In environmental DNA surveys done on fragments of SSU rDNA gene and other traditional DNA barcodes, Amoebozoa genes normally constitute a minor part of the total gene diversity and represent only the most abundant lineages...
February 6, 2017: Journal of Eukaryotic Microbiology
https://www.readbyqxmd.com/read/28161848/eukaryotic-molecular-diversity-at-different-steps-of-the-wastewater-treatment-plant-process-reveals-more-phylogenetic-novel-lineages
#12
Rakia Chouari, Marie Leonard, Moez Bouali, Sonda Guermazi, Naima Rahli, Ines Zrafi, Loïc Morin, Abdelghani Sghir
Wastewater microbiota represents important actors of organic depollution. Nowadays, some species used as bioindicators of the effluent quality are still identified by microscopy. In the present study, we investigated eukaryotic diversity at the different steps of the treatment process of a wastewater treatment plant (aerobic, anaerobic, clarifier basins and anaerobic digester) using the 18S rRNA gene sequencing approach. Of the 1519 analysed sequences, we identified 160 operational taxonomic units. Interestingly, 56...
March 2017: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28148211/chemical-defense-by-erythrolactones-in-the-euryhaline-ciliated-protist-pseudokeronopsis-erythrina
#13
Federico Buonanno, Andrea Anesi, Graziano Di Giuseppe, Graziano Guella, Claudio Ortenzi
Pseudokeronopsis erythrina produces three new secondary metabolites, erythrolactones A2, B2 and C2, and their respective sulfate esters (A1, B1, C1), the structures of which have been recently elucidated on the basis of NMR spectroscopic data coupled to high resolution mass measurements (HR-MALDI-TOF). An analysis of the discharge of the protozoan pigment granules revealed that the non-sulfonated erythrolactones are exclusively stored in these cortical organelles, which are commonly used by a number of ciliates as chemical weapons in offense/defense interactions with prey and predators...
February 2017: Zoological Science
https://www.readbyqxmd.com/read/28138991/predators-regulate-prey-species-sorting-and-spatial-distribution-in-microbial-landscapes
#14
George Livingston, Kayoko Fukumori, Diogo B Provete, Masanobu Kawachi, Noriko Takamura, Mathew A Leibold
1.The role of predation in determining the metacommunity assembly model of prey communities is understudied relative to that of interspecific competition among prey. Previous work on metacommunity dynamics of competing species has shown that sorting by habitat patch type and spatial patterning can be affected by disturbances. 2.Microcosms offer a useful model system to test the effect of multi-trophic interactions and disturbance on metacommunity dynamics. Here, we investigated the potential role of predators in enhancing or disrupting sorting and spatial pattern among prey in experimental landscapes...
January 31, 2017: Journal of Animal Ecology
https://www.readbyqxmd.com/read/28130230/metashot-an-accurate-workflow-for-taxon-classification-of-host-associated-microbiome-from-shotgun-metagenomic-data
#15
B Fosso, M Santamaria, M D'Antonio, D Lovero, G Corrado, E Vizza, N Passaro, A R Garbuglia, M R Capobianchi, M Crescenzi, G Valiente, G Pesole
: Shotgun metagenomics by high-throughput sequencing may allow deep and accurate characterization of host-associated total microbiomes, including bacteria, viruses, protists and fungi. However, the analysis of such sequencing data is still extremely challenging in terms of both overall accuracy and computational efficiency, and current methodologies show substantial variability in misclassification rate and resolution at lower taxonomic ranks or are limited to specific life domains (e...
January 27, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28127581/dataset-for-distribution-of-sider2-elements-in-the-leishmania-major-genome-and-transcriptome
#16
Jose M Requena, Alberto Rastrojo, Esther Garde, Manuel C López, M Carmen Thomas, Begoña Aguado
This paper contains data related to the research article entitled "Genomic cartography and proposal of nomenclature for the repeated, interspersed elements of the Leishmania major SIDER2 family and identification of SIDER2-containing transcripts" [1]. SIDER2 elements are repeated sequences, derived from, nowadays, extinct retrotransposons, that populate the genomes of protist of the genera Leishmania. This dataset (Supplementary file 1), an inventory of 1100 SIDER2 elements, was generated by surveying the L...
April 2017: Data in Brief
https://www.readbyqxmd.com/read/28118891/differential-interactions-between-the-nematocyst-bearing-mixotrophic-dinoflagellate-paragymnodinium-shiwhaense-and-common-heterotrophic-protists-and-copepods-killer-or-prey
#17
Hae Jin Jeong, Jae Seong Kim, Kyung Ha Lee, Kyeong Ah Seong, Yeong Du Yoo, Nam Seon Kang, Tae Hoon Kim, Jae Yoon Song, Ji Eun Kwon
To investigate interactions between the nematocyst-bearing mixotrophic dinoflagellate Paragymnodinium shiwhaense and different heterotrophic protist and copepod species, feeding by common heterotrophic dinoflagellates (Oxyrrhis marina and Gyrodinium dominans), naked ciliates (Strobilidium sp. approximately 35μm in cell length and Strombidinopsis sp. approximately 100μm in cell length), and calanoid copepods Acartia spp. (A. hongi and A. omorii) on P. shiwhaense was explored. In addition, the feeding activities of P...
February 2017: Harmful Algae
https://www.readbyqxmd.com/read/28117696/a-glimpse-of-nucleo-cytoplasmic-large-dna-virus-biodiversity-through-the-eukaryotic-genomics-window
#18
Lucie Gallot-Lavallée, Guillaume Blanc
The nucleocytoplasmic large DNA viruses (NCLDV) are a group of extremely complex double-stranded DNA viruses, which are major parasites of a variety of eukaryotes. Recent studies showed that certain eukaryotes contain fragments of NCLDV DNA integrated in their genome, when surprisingly many of these organisms were not previously shown to be infected by NCLDVs. We performed an update survey of NCLDV genes hidden in eukaryotic sequences to measure the incidence of this phenomenon in common public sequence databases...
January 20, 2017: Viruses
https://www.readbyqxmd.com/read/28111206/de-novo-assembly-and-characterization-of-the-transcriptome-of-the-newly-described-dinoflagellate-ansanella-granifera-spotlight-on-flagellum-associated-genes
#19
Se Hyeon Jang, Hae Jin Jeong, Jae Kyung Chon, Sung Yeon Lee
Many dinoflagellates are known to cause red tides and often outgrow non-motile diatoms and motile small flagellates through active vertical migration between well-lit surface and eutrophic deep waters and/or by locating and ingesting prey cells. Their flagella play important roles in these two critical behaviors. However, the structural and functional genes of dinoflagellate flagella are very little known. Thus, a de novo assembly and characterization of the transcriptome of the fast-swimming dinoflagellate Ansanella granifera were conducted and its flagellum genes were compared with those of other dinoflagellates, motile small flagellates, and non-motile protist species...
January 19, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28104494/thoughts-on-interactions-between-pgrmc1-and-diverse-attested-and-potential-hydrophobic-ligands
#20
REVIEW
Michael A Cahill, Amy E Medlock
Progesterone Receptor Membrane Component 1 (PGRMC1) is located in many different subcellular locations with many different attested and probably location-specific functions. PGRMC1 was recently identified in the mitochondrial outer membrane where it interacts with ferrochelatase, the last enzyme in the heme synthetic pathway. It has been proposed that PGRMC1 may act as a chaperone to shuttle newly synthesized heme from the mitochondrion to cytochrome P450 (cyP450) enzymes. Here we consider potential roles that PGRMC1 may play in transferring heme, and other small hydrophobic ligands such as cholesterol and steroids, between the hydrophobic compartment of the membrane lipid bilayer interior to aqueous proteins, and perhaps to the membranes of other organelles...
January 16, 2017: Journal of Steroid Biochemistry and Molecular Biology
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