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https://www.readbyqxmd.com/read/28644833/quantifying-the-web-browser-ecosystem
#1
Sela Ferdman, Einat Minkov, Ron Bekkerman, David Gefen
Contrary to the assumption that web browsers are designed to support the user, an examination of a 900,000 distinct PCs shows that web browsers comprise a complex ecosystem with millions of addons collaborating and competing with each other. It is possible for addons to "sneak in" through third party installations or to get "kicked out" by their competitors without user involvement. This study examines that ecosystem quantitatively by constructing a large-scale graph with nodes corresponding to users, addons, and words (terms) that describe addon functionality...
2017: PloS One
https://www.readbyqxmd.com/read/28642272/networks-underpinning-symbiosis-revealed-through-cross-species-eqtl-mapping
#2
Yuelong Guo, Sylwia Fudali, Jacinta Gimeno, Peter DiGennaro, Stella Chang, Valerie M Williamson, David McK Bird, Dahlia M Nielsen
Organisms engage in extensive cross-species molecular dialogue, yet the underlying molecular actors are known for only a few interactions. Many techniques have been designed to uncover genes involved in signaling between organisms. Typically, these focus on only one of the partners. We developed an expression quantitative trait locus (eQTL) mapping-based approach to identify cause-and-effect relationships between genes from two partners engaged in an interspecific interaction. We demonstrated the approach by assaying expression of ninety-eight isogenic plants (Medicago truncatula), each inoculated with a genetically distinct line of the diploid parasitic nematode Meloidogyne hapla With this design, systematic differences in gene expression across host plants could be mapped to genetic polymorphisms of their infecting parasites...
June 22, 2017: Genetics
https://www.readbyqxmd.com/read/28630336/the-red-queen-and-king-in-finite-populations
#3
Carl Veller, Laura K Hayward, Christian Hilbe, Martin A Nowak
In antagonistic symbioses, such as host-parasite interactions, one population's success is the other's loss. In mutualistic symbioses, such as division of labor, both parties can gain, but they might have different preferences over the possible mutualistic arrangements. The rates of evolution of the two populations in a symbiosis are important determinants of which population will be more successful: Faster evolution is thought to be favored in antagonistic symbioses (the "Red Queen effect"), but disfavored in certain mutualistic symbioses (the "Red King effect")...
June 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28628918/bifidobacterium-rich-fecal-donor-may-be-a-positive-predictor-for-successful-fecal-microbiota-transplantation-in-patients-with-irritable-bowel-syndrome
#4
Shinta Mizuno, Tatsuhiro Masaoka, Makoto Naganuma, Taishiro Kishimoto, Momoko Kitazawa, Shunya Kurokawa, Moeko Nakashima, Kozue Takeshita, Wataru Suda, Masaru Mimura, Masahira Hattori, Takanori Kanai
BACKGROUND/AIMS: Dysbiosis is associated with various systemic disorders including irritable bowel syndrome (IBS). Fecal microbiota transplantation (FMT) might restore intestinal microbial balance. The study aimed to determine the safety and efficacy of FMT in IBS patients, as well as also positive predictors for FMT. METHODS: This was a single-arm, open-label study. Eligible patients were diagnosed based on Rome III Diagnostic Criteria. Fecal materials were administered to the patient via colonoscopy...
June 21, 2017: Digestion
https://www.readbyqxmd.com/read/28628098/short-chain-alkanes-fuel-mussel-and-sponge-cycloclasticus-symbionts-from-deep-sea-gas-and-oil-seeps
#5
Maxim Rubin-Blum, Chakkiath Paul Antony, Christian Borowski, Lizbeth Sayavedra, Thomas Pape, Heiko Sahling, Gerhard Bohrmann, Manuel Kleiner, Molly C Redmond, David L Valentine, Nicole Dubilier
Cycloclasticus bacteria are ubiquitous in oil-rich regions of the ocean and are known for their ability to degrade polycyclic aromatic hydrocarbons (PAHs). In this study, we describe Cycloclasticus that have established a symbiosis with Bathymodiolus heckerae mussels and poecilosclerid sponges from asphalt-rich, deep-sea oil seeps at Campeche Knolls in the southern Gulf of Mexico. Genomic and transcriptomic analyses revealed that, in contrast to all previously known Cycloclasticus, the symbiotic Cycloclasticus appears to lack the genes needed for PAH degradation...
June 19, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28622919/diet-of-arbuscular-mycorrhizal-fungi-bread-and-butter
#6
REVIEW
Mélanie K Rich, Eva Nouri, Pierre-Emmanuel Courty, Didier Reinhardt
Most plants entertain mutualistic interactions known as arbuscular mycorrhiza (AM) with soil fungi (Glomeromycota) which provide them with mineral nutrients in exchange for reduced carbon from the plant. Mycorrhizal roots represent strong carbon sinks in which hexoses are transferred from the plant host to the fungus. However, most of the carbon in AM fungi is stored in the form of lipids. The absence of the type I fatty acid synthase (FAS-I) complex from the AM fungal model species Rhizophagus irregularis suggests that lipids may also have a role in nutrition of the fungal partner...
June 13, 2017: Trends in Plant Science
https://www.readbyqxmd.com/read/28622658/how-effectors-promote-beneficial-interactions
#7
REVIEW
Hiroki Miwa, Shin Okazaki
Beneficial microbes such as rhizobia possess effector proteins that are secreted into the host cytoplasm where they modulate host-signaling pathways. Among these effectors, type 3 secreted effectors (T3Es) of rhizobia play roles in promoting nitrogen-fixing nodule symbiosis, suppressing host defenses and directly activating symbiosis-related processes. Rhizobia use the same strategy as pathogenic bacteria to suppress host defenses such as targeting the MAPK cascade. In addition, rhizobial T3E can promote root nodule symbiosis by directly activating Nod factor signaling, which bypasses Nod factor perception...
June 13, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28621804/long-term-evolution-of-viruses-a-janus-faced-balance
#8
REVIEW
Arshan Nasir, Kyung Mo Kim, Gustavo Caetano-Anollés
The popular textbook image of viruses as noxious and selfish genetic parasites greatly underestimates the beneficial contributions of viruses to the biosphere. Given the crucial dependency of viruses to reproduce in an intracellular environment, viruses that engage in excessive killing (lysis) can drive their cellular hosts to extinction and will not survive. The lytic mode of virus propagation must, therefore, be tempered and balanced by non-lytic modes of virus latency and symbiosis. Here, we review recent bioinformatics and metagenomic studies to argue that viral endogenization and domestication may be more frequent mechanisms of virus persistence than lysis...
June 16, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28618146/green-alder-alnus-viridis-encroachment-shapes-microbial-communities-in-subalpine-soils-and-impacts-its-bacterial-or-fungal-symbionts-differently
#9
G Schwob, M Roy, S Manzi, T Pommier, M P Fernandez
Since the mid twentieth-century, subalpine grasslands undergo a progressive encroachment by Alnus viridis shrubs. Thanks to its rapid vegetative reproduction, its nitrogen fixing symbiosis with Frankia and its ectomycorrhizal cohorts, green alders are vigorous colonizers that quickly form mosaic of alder patches that evolves into a close canopy shrub community. To better understand how alder encroachment might influence microbial communities in this successional sequence, symbiont distribution, microbial richness and community structure in both soils and nodules were analyzed at three successional stages: grassland, mosaic and forest...
June 15, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28618121/specificity-traits-consistent-with-legume-rhizobia-coevolution-displayed-by-ensifer-meliloti-rhizosphere-colonization
#10
María Eugenia Salas, Mauricio Javier Lozano, José Luis López, Walter Draghi, Javier Serrania, Gonzalo Arturo Torres Tejerizo, Francisco Javier Albicoro, Juliet Fernanda Nilsson, Mariano Pistorio, María Florencia Del Papa, Gustavo Parisi, Anke Becker, Antonio Lagares
Rhizobia are α- and ß-Proteobacteria that associate with legumes in symbiosis to fix atmospheric nitrogen. The chemical communication between roots and rhizobia begins in the rhizosphere. Using signature-tagged-Tn5 mutagenesis (STM) we performed a genome-wide screening for Ensifer meliloti genes that participate in colonizing the rhizospheres of alfalfa and other legumes. The analysis of ca. 6,000 mutants indicated that genes relevant for rhizosphere colonization account for nearly 2% of the rhizobial genome and that most (ca...
June 15, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28616367/correction-the-scavenger-receptor-repertoire-in-six-cnidarian-species-and-its-putative-role-in-cnidarian-dinoflagellate-symbiosis
#11
Emilie F Neubauer, Angela Z Poole, Olivier Detournay, Virginia M Weis, Simon K Davy
[This corrects the article DOI: 10.7717/peerj.2692.].
2017: PeerJ
https://www.readbyqxmd.com/read/28615286/the-physiology-of-phagocytosis-in-the-context-of-mitochondrial-origin
#12
REVIEW
William F Martin, Aloysius G M Tielens, Marek Mentel, Sriram G Garg, Sven B Gould
How mitochondria came to reside within the cytosol of their host has been debated for 50 years. Though current data indicate that the last eukaryote common ancestor possessed mitochondria and was a complex cell, whether mitochondria or complexity came first in eukaryotic evolution is still discussed. In autogenous models (complexity first), the origin of phagocytosis poses the limiting step at eukaryote origin, with mitochondria coming late as an undigested growth substrate. In symbiosis-based models (mitochondria first), the host was an archaeon, and the origin of mitochondria was the limiting step at eukaryote origin, with mitochondria providing bacterial genes, ATP synthesis on internalized bioenergetic membranes, and mitochondrion-derived vesicles as the seed of the eukaryote endomembrane system...
September 2017: Microbiology and Molecular Biology Reviews: MMBR
https://www.readbyqxmd.com/read/28611764/interplay-of-pathogen-induced-defense-responses-and-symbiotic-establishment-in-medicago-truncatula
#13
Tao Chen, Liujian Duan, Bo Zhou, Haixiang Yu, Hui Zhu, Yangrong Cao, Zhongming Zhang
Suppression of host innate immunity appears to be required for the establishment of symbiosis between rhizobia and host plants. In this study, we established a system that included a host plant, a bacterial pathogen and a symbiotic rhizobium to study the role of innate immunity during symbiotic interactions. A pathogenic bacterium, Pseudomonas syringae pv. tomato strain DC3000 (Pst DC3000), was shown to cause chlorosis in Medicago truncatula A17. Sinorhizobium meliloti strain Sm2011 (Sm2011) and Pst DC3000 strain alone induced similar defense responses in M...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28609960/revision-of-the-subgenus-i-niphetoscapha-i-heller-of-i-gymnopholus-i-heller%C3%A2-coleoptera-curculionoidea-entiminae-eupholini-and-a-new-species-with-epizoic-symbiosis-from-west-new-guinea
#14
Alexander Riedel, Agust Kilmaskossu
The subgenus Niphetoscapha Heller 1914 of Gymnopholus Heller 1901 is revised. It is characterized by the morphology of the elytral apex and the asymmetrical tip of the penis. Vestigial wings and a fused elytral suture indicate flightlessness. Gymnopholus (Niphetoscapha) inexspectatus sp. n. is described as new, exhibiting a distinct epizoic symbiosis with algae otherwise known from the subgenus Symbiopholus Gressitt 1966. The four species of Niphetoscapha inhabit the central mountain range of West New Guinea: Gymnopholus audax Gressitt 1966, G...
April 18, 2017: Zootaxa
https://www.readbyqxmd.com/read/28607058/host-secreted-antimicrobial-peptide-enforces-symbiotic-selectivity-in-medicago-truncatula
#15
Qi Wang, Shengming Yang, Jinge Liu, Kata Terecskei, Edit Ábrahám, Anikó Gombár, Ágota Domonkos, Attila Szűcs, Péter Körmöczi, Ting Wang, Lili Fodor, Linyong Mao, Zhangjun Fei, Éva Kondorosi, Péter Kaló, Attila Kereszt, Hongyan Zhu
Legumes engage in root nodule symbioses with nitrogen-fixing soil bacteria known as rhizobia. In nodule cells, bacteria are enclosed in membrane-bound vesicles called symbiosomes and differentiate into bacteroids that are capable of converting atmospheric nitrogen into ammonia. Bacteroid differentiation and prolonged intracellular survival are essential for development of functional nodules. However, in the Medicago truncatula-Sinorhizobium meliloti symbiosis, incompatibility between symbiotic partners frequently occurs, leading to the formation of infected nodules defective in nitrogen fixation (Fix(-))...
June 12, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28607056/microsymbiont-discrimination-mediated-by-a-host-secreted-peptide-in-medicago-truncatula
#16
Shengming Yang, Qi Wang, Elena Fedorova, Jinge Liu, Qiulin Qin, Qiaolin Zheng, Paul A Price, Huairong Pan, Dong Wang, Joel S Griffitts, Ton Bisseling, Hongyan Zhu
The legume-rhizobial symbiosis results in the formation of root nodules that provide an ecological niche for nitrogen-fixing bacteria. However, plant-bacteria genotypic interactions can lead to wide variation in nitrogen fixation efficiency, and it is not uncommon that a bacterial strain forms functional (Fix(+)) nodules on one plant genotype but nonfunctional (Fix(-)) nodules on another. Host genetic control of this specificity is unknown. We herein report the cloning of the Medicago truncatula NFS1 gene that regulates the fixation-level incompatibility with the microsymbiont Sinorhizobium meliloti Rm41...
June 12, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28606864/suppression-of-nf-%C3%AE%C2%BAb-signal-pathway-by-nlrc3-like-protein-in-stony-coral-acropora-aculeus-under-heat-stress
#17
Zhi Zhou, Yibo Wu, Chengkai Zhang, Can Li, Guangmei Chen, Xiaopeng Yu, Xiaowei Shi, Yanlai Xu, Lingui Wang, Bo Huang
Heat stress is the most common factor for coral bleaching, which has increased both in frequency and severity due to global warming. In the present study, the stony coral Acropora aculeus was subjected to acute heat stress and entire transcriptomes were sequenced via the next generation sequencing platform. Four paired-end libraries were constructed and sequenced in two groups, including a control and a heat stress group. A total of 120,319,751 paired-end reads with lengths of 2 × 100 bp were assembled and 55,021 coral-derived genes were obtained...
June 9, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28601651/plant-carbon-nourishment-of-arbuscular-mycorrhizal-fungi
#18
REVIEW
Ronelle Roth, Uta Paszkowski
Reciprocal nutrient exchange between the majority of land plants and arbucular mycorrhizal (AM) fungi is the cornerstone of a stable symbiosis. To date, a dogma in the comprehension of AM fungal nourishment has been delivery of host organic carbon in the form of sugars. More recently a role for lipids as alternative carbon source or as a signalling molecule during AM symbiosis was proposed. Here we review the symbiotic requirement for carbohydrates and lipids across developmental stages of the AM symbiosis...
June 8, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28601211/the-symbiotic-relationship-between-operational-military-medicine-tactical-medicine-and-wilderness-medicine-a-view-through-a-personal-lens
#19
REVIEW
Craig H Llewellyn
There are direct and indirect linkages and a form of symbiosis between operational military medicine from World War II and present wilderness medicine, from the beginnings to contemporary practice, and the more recently evolved field of tactical emergency medical support. Each of these relationships will be explored from the historical perspective of the Department of Military & Emergency Medicine, Uniformed Services University of the Health Sciences from 1982 to the present.
June 2017: Wilderness & Environmental Medicine
https://www.readbyqxmd.com/read/28598263/the-phenylalanine-ammonia-lyase-gene-ljpal1-is-involved-in-plant-defense-responses-to-pathogens-and-plays-diverse-roles-in-lotus-japonicus-rhizobium-symbioses
#20
Yaping Chen, Fengjiao Li, Lu Tian, Mingchao Huang, Rufang Deng, Xueliu Li, Wei Chen, Pingzhi Wu, Meiru Li, Huawu Jiang, Guojiang Wu
Phenylalanine ammonia-lyase (PAL) is important in the biosynthesis of plant secondary metabolites that regulate growth responses. Although its function is well established in various plants, the functional significance of PAL genes in nodulation is poorly understood. Here, we demonstrate that the Lotus japonicus PAL (LjPAL1) gene is induced by Mesorhizobium loti (M. loti) infection and MeJA treatment in roots. LjPAL1 altered PAL activity, leading to changes in lignin contents and thicknesses of cell walls in roots and nodules of transgenic plants, and hence to structural changes in roots and nodules...
June 9, 2017: Molecular Plant-microbe Interactions: MPMI
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