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Molecular ecology

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https://www.readbyqxmd.com/read/28724491/comparison-of-antemortem-and-environmental-samples-for-zebrafish-health-monitoring-and-quarantine
#1
Marcus J Crim, Christian Lawrence, Robert S Livingston, Andrei Rakitin, Shane J Hurley, Lela K Riley
Molecular diagnostic assays offer both exquisite sensitivity and the ability to test a wide variety of sample types. Various types of environmental sample, such as detritus and concentrated water, might provide a useful adjunct to sentinels in routine zebrafish health monitoring. Similarly, antemortem sampling would be advantageous for expediting zebrafish quarantine, without euthanasia of valuable fish. We evaluated the detection of Mycobacterium chelonae, M. fortuitum, M. peregrinum, Pseudocapillaria tomentosa, and Pseudoloma neurophilia in zebrafish, detritus, pooled feces, and filter membranes after filtration of 1000-, 500-, and 150-mL water samples by real-time PCR analysis...
July 1, 2017: Journal of the American Association for Laboratory Animal Science: JAALAS
https://www.readbyqxmd.com/read/28719959/pcr-identification-and-phylogenetic-analysis-of-trichomonas-gallinae-from-domestic-pigeons-in-guangzhou-china
#2
Shen-Ben Qiu, Meng-Na Lv, Xi He, Ya-Biao Weng, Shang-Shu Zou, Xin-Qiu Wang, Rui-Qing Lin
Avian trichomoniasis caused by Trichomonas gallinae is a serious protozoan disease worldwide. The domestic pigeon (Columba livia domestica) is the main host for T. gallinae and plays an important role in the spread of the disease. Based on the internal transcribed spacers of nuclear ribosomal DNA of this parasite, a pair of primers (TgF2/TgR2) was designed and used to develop a PCR assay for the diagnosis of T. gallinae infection in domestic pigeons. This approach allowed the identification of T. gallinae, and no amplicons were produced when using DNA from other common avian pathogens...
June 2017: Korean Journal of Parasitology
https://www.readbyqxmd.com/read/28719406/toward-a-biopsychosocial-ecology-of-the-human-microbiome-brain-gut-axis-and-health
#3
Karl J Maier, Mustafa al'Absi
OBJECTIVE: Rapidly expanding insights to the human microbiome and health suggest that Western medicine is poised for significant evolution, or perhaps revolution - this while the field continues on a trajectory from reductionism to a biopsychosocial (BPS) paradigm recognizing biological, psychological, and social influences on health. The apparent sensitivity of the microbiota to perturbations across BPS domains suggests that a broad and inclusive framework is needed to develop applicable knowledge in this area...
July 18, 2017: Psychosomatic Medicine
https://www.readbyqxmd.com/read/28719191/relationships-between-dissolved-organic-matter-composition-and-photochemistry-in-lakes-of-diverse-trophic-status
#4
Andrew Chapin Maizel, Jing Li, Christina K Remucal
The North Temperate Lakes-Long Term Ecological Research site includes seven lakes in northern Wisconsin that vary in hydrology, trophic status, and landscape position. We examine the molecular composition of dissolved organic matter (DOM) within these lakes using Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) and quantify DOM photochemical activity using probe compounds. Correlations between the relative intensity of individual molecular formulas and reactive species production demonstrate the influence of DOM composition on photochemistry...
July 18, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28718795/novel-molecular-insights-about-lactobacillar-sortase-dependent-piliation
#5
REVIEW
Ingemar von Ossowski
One of the more conspicuous structural features that punctuate the outer cell surface of certain bacterial Gram-positive genera and species is the sortase-dependent pilus. As these adhesive and variable-length protrusions jut outward from the cell, they provide a physically expedient and useful means for the initial contact between a bacterium and its ecological milieu. The sortase-dependent pilus displays an elongated macromolecular architecture consisting of two to three types of monomeric protein subunits (pilins), each with their own specific function and location, and that are joined together covalently by the transpeptidyl activity of a pilus-specific C-type sortase enzyme...
July 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28717020/towards-an-understanding-of-the-molecular-regulation-of-carbon-allocation-in-diatoms-the-interaction-of-energy-and-carbon-allocation
#6
REVIEW
Heiko Wagner, Torsten Jakob, Andrea Fanesi, Christian Wilhelm
In microalgae, the photosynthesis-driven CO2 assimilation delivers cell building blocks that are used in different biosynthetic pathways. Little is known about how the cell regulates the subsequent carbon allocation to, for example, cell growth or for storage. However, knowledge about these regulatory mechanisms is of high biotechnological and ecological importance. In diatoms, the situation becomes even more complex because, as a consequence of their secondary endosymbiotic origin, the compartmentation of the pathways for the primary metabolic routes is different from green algae...
September 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28716740/multilocus-analysis-of-the-catfish-family-trichomycteridae-teleostei-ostariophysi-siluriformes-supporting-a-monophyletic-trichomycterinae
#7
Luz E Ochoa, Fabio F Roxo, Carlos DoNascimiento, Mark H Sabaj, Aléssio Datovo, Michael Alfaro, Claudio Oliveira
Trichomycteridae is the second most diverse family of the order Siluriformes, its members are widely distributed through the freshwaters of Central and South America, exhibiting an exceptional ecological and phenotypic disparity. The most diverse subfamily, Trichomycterinae, represented mainly by the genus Trichomycterus, historically has been recognized as non-monophyletic and various characters used to unite or divide its constituents are repeatedly called into question. No comprehensive molecular phylogenetic hypothesis regarding relationships of trichomycterids has been produced, and the present study is the first extensive phylogeny for the family Trichomycteridae, based on a multilocus dataset of three mitochondrial loci and two nuclear markers (3284 bp total)...
July 14, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28715960/histone-methylation-by-set-domain-proteins-in-fungi
#8
Michael Freitag
Histone-modifying enzymes are responsible for regulating transcription, recombination, DNA repair, DNA replication, chromatid cohesion, and chromosome segregation. Fungi are ideally suited for comparative chromatin biology because sequencing of numerous genomes from many clades is coupled to existing rich methodology that allows truly holistic approaches, integrating evolutionary biology with mechanistic molecular biology and ecology, promising applications in medicine or plant pathology. While genome information is rich, mechanistic studies on histone modifications are largely restricted to two yeasts, Saccharomyces cerevisiae and Schizosaccharomyces pombe, and one filamentous fungus, Neurospora crassa-three species that arguably are not representative of this diverse kingdom...
July 17, 2017: Annual Review of Microbiology
https://www.readbyqxmd.com/read/28713360/cyanobacterial-diversity-in-microbial-mats-from-the-hypersaline-lagoon-system-of-araruama-brazil-an-in-depth-polyphasic-study
#9
Vitor M C Ramos, Raquel Castelo-Branco, Pedro N Leão, Joana Martins, Sinda Carvalhal-Gomes, Frederico Sobrinho da Silva, João G Mendonça Filho, Vitor M Vasconcelos
Microbial mats are complex, micro-scale ecosystems that can be found in a wide range of environments. In the top layer of photosynthetic mats from hypersaline environments, a large diversity of cyanobacteria typically predominates. With the aim of strengthening the knowledge on the cyanobacterial diversity present in the coastal lagoon system of Araruama (state of Rio de Janeiro, Brazil), we have characterized three mat samples by means of a polyphasic approach. We have used morphological and molecular data obtained by culture-dependent and -independent methods...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28713343/the-bacterial-ecosystem-of-mother-s-milk-and-infant-s-mouth-and-gut
#10
Elena Biagi, Sara Quercia, Arianna Aceti, Isadora Beghetti, Simone Rampelli, Silvia Turroni, Giacomo Faldella, Marco Candela, Patrizia Brigidi, Luigi Corvaglia
The progressive building of the infants' gut microbiota is pivotal for educating their immune system. Human breast milk is among the first sources of microbes for the assembly of the infant's microbiota, but research struggles to give a demonstration for the origin of bacteria in milk. Aiming at contributing to the knowledge on assembly of the mother's milk and infant's microbiome, here we characterized the oral, gut and milk ecosystems in a homogeneous cohort of 36 healthy mother-infants pairs, by 16S rRNA next-generation sequencing...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28712045/dynamics-of-soil-bacterial-communities-over-a-vegetation-season-relate-to-both-soil-nutrient-status-and-plant-growth-phenology
#11
Davide Francioli, Elke Schulz, François Buscot, Thomas Reitz
Soil microorganisms regulate element cycling and plant nutrition, mediate co-existence of neighbors, and stabilize plant communities. Many of these effects are dependent upon environmental conditions and, in particular, on nutrient quality and availability in soils. In this context, we set up a pot experiment in order to examine the combined effects of soil nutrient availability and microbial communities on plant-soil interactions and to investigate assemblage rules for soil bacterial communities under changed nutrient conditions...
July 15, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28711820/integrated-metagenomics-and-molecular-ecological-network-analysis-of-bacterial-community-composition-during-the-phytoremediation-of-cadmium-contaminated-soils-by-bioenergy-crops
#12
Zhaojin Chen, Yuan Zheng, Chuanyu Ding, Xuemin Ren, Jian Yuan, Feng Sun, Yuying Li
Two energy crops (maize and soybean) were used in the remediation of cadmium-contaminated soils. These crops were used because they are fast growing, have a large biomass and are good sources for bioenergy production. The total accumulation of cadmium in maize and soybean plants was 393.01 and 263.24μg pot(-1), respectively. The rhizosphere bacterial community composition was studied by MiSeq sequencing. Phylogenetic analysis was performed using 16S rRNA gene sequences. The rhizosphere bacteria were divided into 33 major phylogenetic groups according to phyla...
July 13, 2017: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/28710809/the-uvb-photoreceptor-uvr8-mediates-accumulation-of-uv-absorbing-pigments-but-not-changes-in-plant-morphology-under-outdoor-conditions
#13
A Coffey, Els Prinsen, M A K Jansen, James Conway
UVB radiation is biologically active; in plants, it can induce a range of molecular, biochemical, morphological and developmental responses. Although much progress has been made in elucidating UVB perception and signalling pathways under controlled laboratory conditions, understanding of the adaptive, ecological role of UVB responses is still very limited. In this study, we looked at the functional role of UVR8 under outdoor light conditions, by studying growth, photosynthetic competence and accumulation of UV absorbing pigments in a mutant lacking functional UVR8 protein...
July 14, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/28710258/the-evolution-and-ecology-of-resistance-in-cancer-therapy
#14
Robert Gatenby, Joel Brown
Despite continuous deployment of new treatment strategies and agents over many decades, most disseminated cancers remain fatal. Cancer cells, through their access to the vast information of human genome, have a remarkable capacity to deploy adaptive strategies for even the most effective treatments. We note there are two critical steps in the clinical manifestation of treatment resistance. The first, which is widely investigated, requires deployment of a mechanism of resistance that usually involves increased expression of molecular machinery necessary to eliminate the cytotoxic effect of treatment...
July 14, 2017: Cold Spring Harbor Perspectives in Medicine
https://www.readbyqxmd.com/read/28706319/redefinition-of-genus-malenchus-andr%C3%A3-ssy-1968-tylenchomorpha-tylenchidae-with-additional-data-on-ecology
#15
Xue Qing, Wim Bert
Malenchus is the second specious genus in Tylenchidae. In the presented study, we examined 22 populations including 12 type/paratype species. Detailed morphology was recovered using light microscopy, scanning- and transmission- electron microscopy. All population and type slides were recorded as picture and video vouchers, which are available online. We have compared inter- or intraspecific variations and extracted taxonomically informative traits. Amended definitions of the Malenchus as well as the closely related Ottolenchus were given based on a combination of morphology and recent molecular data, and their phylogeny were analyzed in a context of Tylenchidae...
June 2017: Journal of Nematology
https://www.readbyqxmd.com/read/28704705/a-new-parasitic-chytrid-staurastromyces-oculus-rhizophydiales-staurastromycetaceae-fam-nov-infecting-the-freshwater-desmid-staurastrum-sp
#16
Silke Van den Wyngaert, Kensuke Seto, Keilor Rojas-Jimenez, Maiko Kagami, Hans-Peter Grossart
Chytrids are a diverse group of ubiquitous true zoosporic fungi. The recent molecular discovery of a large diversity of undescribed chytrids has raised awareness on their important, but so far understudied ecological role in aquatic ecosystems. In the pelagic zone, of both freshwater and marine ecosystems, many chytrid species have been morphologically described as parasites on almost all major groups of phytoplankton. However, the majority of these parasitic chytrids has rarely been isolated and lack DNA sequence data, resulting in a large proportion of "dark taxa" in databases...
May 13, 2017: Protist
https://www.readbyqxmd.com/read/28702013/nitrogen-fixation-aligns-with-nifh-abundance-and-expression-in-two-coral-trophic-functional-groups
#17
Claudia Pogoreutz, Nils Rädecker, Anny Cárdenas, Astrid Gärdes, Christian Wild, Christian R Voolstra
Microbial nitrogen fixation (diazotrophy) is a functional trait widely associated with tropical reef-building (scleractinian) corals. While the integral role of nitrogen fixation in coral nutrient dynamics is recognized, its ecological significance across different coral functional groups remains yet to be evaluated. Here we set out to compare molecular and physiological patterns of diazotrophy (i.e., nifH gene abundance and expression as well as nitrogen fixation rates) in two coral families with contrasting trophic strategies: highly heterotrophic, free-living members of the family Fungiidae (Pleuractis granulosa, Ctenactis echinata), and mostly autotrophic coral holobionts with low heterotrophic capacity (Pocilloporidae: Pocillopora verrucosa, Stylophora pistillata)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28700322/molecular-epidemiology-of-avian-poxvirus-in-the-oriental-turtle-dove-streptopelia-orientalis-and-the-biting-midge-culicoides-arakawae-in-the-republic-of-korea
#18
Hae Rim Lee, Bon-Sang Koo, Jong-Taek Kim, Heung-Chul Kim, Myung-Soon Kim, Terry A Klein, Man-Seok Shin, Sanghun Lee, Eun-Ok Jeon, Kyung-Cheol Min, Seung Baek Lee, Yeonji Bae, In-Pil Mo
A total of 600 wild birds were analyzed for the causes of mortality in the Republic of Korea (ROK) from 2011 to 2013. Avian poxvirus (APV) infections were identified as the primary cause of mortality in 39% (29/74) Oriental Turtle Doves (Streptopelia orientalis). At necropsy, all 29 S. orientalis birds, of which, 76% (22/29) were juveniles, had severe diphtheritic lesions in their oral and nasal cavities and on their eyelids, which were the lesions of APV that resulted in mortality. We detected APV infection by chorioallantoic membrane inoculation and molecular study of the partial region of the P4b gene...
July 12, 2017: Journal of Wildlife Diseases
https://www.readbyqxmd.com/read/28696285/early-paleocene-landbird-supports-rapid-phylogenetic-and-morphological-diversification-of-crown-birds-after-the-k-pg-mass-extinction
#19
Daniel T Ksepka, Thomas A Stidham, Thomas E Williamson
Evidence is accumulating for a rapid diversification of birds following the K-Pg extinction. Recent molecular divergence dating studies suggest that birds radiated explosively during the first few million years of the Paleocene; however, fossils from this interval remain poorly represented, hindering our understanding of morphological and ecological specialization in early neoavian birds. Here we report a small fossil bird from the Nacimiento Formation of New Mexico, constrained to 62.221-62.517 Ma. This partial skeleton represents the oldest arboreal crown group bird known...
July 10, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28694102/evolution-of-dmsp-dimethylsulfoniopropionate-biosynthesis-pathway-origin-and-phylogenetic-distribution-in-polyploid-spartina-poaceae-chloridoideae
#20
Hélène Rousseau, Mathieu Rousseau-Gueutin, Xavier Dauvergne, Julien Boutte, Gaëlle Simon, Nathalie Marnet, Alain Bouchereau, Solène Guiheneuf, Jean-Pierre Bazureau, Jérôme Morice, Stéphane Ravanel, Francisco Cabello-Hurtado, Abdelkader Ainouche, Armel Salmon, Jonathan F Wendel, Malika L Ainouche
DMSP (dimethylsulfoniopropionate) is an ecologically important sulfur metabolite commonly produced by marine algae and by some higher plant lineages, including the polyploid salt marsh genus Spartina (Poaceae). The molecular mechanisms and genes involved in the DMSP biosynthesis pathways are still unknown. In this study, we performed comparative analyses of DMSP amounts and molecular phylogenetic analyses to decipher the origin of DMSP in Spartina that represents one of the major source of terrestrial DMSP in coastal marshes...
July 7, 2017: Molecular Phylogenetics and Evolution
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