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Molecular ecology

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https://www.readbyqxmd.com/read/29786924/reproductive-ecology-of-ocotea-catharinensis-an-endangered-tree-species
#1
Tiago Montagna, Juliano Zago da Silva, Tiago Georg Pickart, Maurício Sedrez Dos Reis
Ocotea catharinensis (Lauraceae) is an endangered tree species from the Brazilian Atlantic Rainforest. Currently, little is known about the reproductive ecology of this species. Aiming to propose conservation measures, we described aspects related to phenology, floral biology, pollination, seed dispersal, and mating system of O. catharinensis. We conducted phenological observations in 62 individuals for two years. In one reproductive event, we evaluated nectar production, stigmatic receptivity, and pollen viability...
May 22, 2018: Plant Biology
https://www.readbyqxmd.com/read/29783718/functional-genomics-approaches-to-studying-symbioses-between-legumes-and-nitrogen-fixing-rhizobia
#2
REVIEW
Martina Lardi, Gabriella Pessi
Biological nitrogen fixation gives legumes a pronounced growth advantage in nitrogen-deprived soils and is of considerable ecological and economic interest. In exchange for reduced atmospheric nitrogen, typically given to the plant in the form of amides or ureides, the legume provides nitrogen-fixing rhizobia with nutrients and highly specialised root structures called nodules. To elucidate the molecular basis underlying physiological adaptations on a genome-wide scale, functional genomics approaches, such as transcriptomics, proteomics, and metabolomics, have been used...
May 18, 2018: High-throughput
https://www.readbyqxmd.com/read/29783680/-copaifera-of-the-neotropics-a-review-of-the-phytochemistry-and-pharmacology
#3
REVIEW
Rafaela da Trindade, Joyce Kelly da Silva, William N Setzer
The oleoresin of Copaifera trees has been widely used as a traditional medicine in Neotropical regions for thousands of years and remains a popular treatment for a variety of ailments. The copaiba resins are generally composed of a volatile oil made up largely of sesquiterpene hydrocarbons, such as β-caryophyllene, α-copaene, β-elemene, α-humulene, and germacrene D. In addition, the oleoresin is also made up of several biologically active diterpene acids, including copalic acid, kaurenoic acid, alepterolic acid, and polyalthic acid...
May 18, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29782705/wild-gwas-association-mapping-in-natural-populations
#4
Anna W Santure, Dany Garant
The increasing affordability of sequencing and genotyping technologies has transformed the field of molecular ecology in recent decades. By correlating marker variants with trait variation using association analysis, large-scale genotyping and phenotyping of individuals from wild populations has enabled the identification of genomic regions that contribute to phenotypic differences among individuals. Such 'gene mapping' studies are enabling us to better predict evolutionary potential and the ability of populations to adapt to challenges, such as changing environment...
May 21, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29781421/molecular-phylogeny-based-on-six-nuclear-genes-suggests-that-echinococcus-granulosus-sensu-lato-genotypes-g6-g7-and-g8-g10-can-be-regarded-as-two-distinct-species
#5
Teivi Laurimäe, Liina Kinkar, Epp Moks, Thomas Romig, Rihab A Omer, Adriano Casulli, Gérald Umhang, Guna Bagrade, Malik Irshadullah, Mitra Sharbatkhori, Hossein Mirhendi, Francisco Ponce-Gordo, Silvia V Soriano, Antonio Varcasia, Mohammad Rostami-Nejad, Vanessa Andresiuk, Urmas Saarma
Tapeworms of the species complex of Echinococcus granulosus sensu lato (s. l.) are the cause of a severe zoonotic disease - cystic echinococcosis, which is listed among the most severe parasitic diseases in humans and is prioritized by the World Health Organization. A stable taxonomy of E. granulosus s. l. is essential to the medical and veterinary communities for accurate and effective communication of the role of different species in this complex on human and animal health. E. granulosus s. l. displays high genetic diversity and has been divided into different species and genotypes...
May 21, 2018: Parasitology
https://www.readbyqxmd.com/read/29780369/identification-and-removal-of-contaminant-sequences-from-ribosomal-gene-databases-lessons-from-the-census-of-deep-life
#6
Cody S Sheik, Brandi Kiel Reese, Katrina I Twing, Jason B Sylvan, Sharon L Grim, Matthew O Schrenk, Mitchell L Sogin, Frederick S Colwell
Earth's subsurface environment is one of the largest, yet least studied, biomes on Earth, and many questions remain regarding what microorganisms are indigenous to the subsurface. Through the activity of the Census of Deep Life (CoDL) and the Deep Carbon Observatory, an open access 16S ribosomal RNA gene sequence database from diverse subsurface environments has been compiled. However, due to low quantities of biomass in the deep subsurface, the potential for incorporation of contaminants from reagents used during sample collection, processing, and/or sequencing is high...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29778490/the-molecular-allergology-of-subtropical-grass-pollen
#7
Thina Kailaivasan, Janet M Davies
Grass pollens are amongst the most important aeroallergen sources world-wide triggering allergic rhinoconjunctivitis and asthma in sensitised patients. Much of what we know about the allergen components of grasses is informed by research on pollen of temperate (Pooideae) species that are abundant in the temperate climate zones. However, climate changes are altering the biogeographical distribution as well as timing and allergenicity of grass pollens. This provides an impetus for better understanding of the contribution of subtropical subfamilies of grasses to pollen allergy globally...
May 16, 2018: Molecular Immunology
https://www.readbyqxmd.com/read/29777837/bacteriophage-research-what-we-have-learnt-and-what-still-needs-to-be-addressed
#8
Andrew M Kropinski
Research on bacteriophages has significantly enhanced our understanding of molecular biology, the genomes of prokaryotic cells, and viral ecology. Phages and lysins offer a viable alternative to the declining utility of antibiotics in this post-antibiotic era. They also provide ideal teaching tools for genomics and bioinformatics. This article touches on the first 100 years of phage research with the author commenting on what he thinks are the highlights, and what needs to be addressed.
May 16, 2018: Research in Microbiology
https://www.readbyqxmd.com/read/29776375/range-wide-genetic-analysis-of-dermacentor-variabilis-and-its-francisella-like-endosymbionts-demonstrates-phylogeographic-concordance-between-both-taxa
#9
Emily L Kaufman, Nathan E Stone, Glen A Scoles, Crystal M Hepp, Joseph D Busch, David M Wagner
BACKGROUND: The American dog tick, Dermacentor variabilis, is an important vector of pathogens to humans, wildlife and domestic animals in North America. Although this tick species is widely distributed in the USA and Canada, knowledge of its range-wide phylogeographic patterns remains incomplete. METHODS: We carried out a phylogenetic analysis of D. variabilis using samples collected from 26 USA states and five Canadian provinces. Tick samples (n = 1053 in total) originated from two main sources: existing archives (2000-2011), and new collections made from 2012 to 2013...
May 18, 2018: Parasites & Vectors
https://www.readbyqxmd.com/read/29774016/taxon-function-decoupling-as-an-adaptive-signature-of-lake-microbial-metacommunities-under-a-chronic-polymetallic-pollution-gradient
#10
Bachar Cheaib, Malo Le Boulch, Pierre-Luc Mercier, Nicolas Derome
Adaptation of microbial communities to anthropogenic stressors can lead to reductions in microbial diversity and disequilibrium of ecosystem services. Such adaptation can change the molecular signatures of communities with differences in taxonomic and functional composition. Understanding the relationship between taxonomic and functional variation remains a critical issue in microbial ecology. Here, we assessed the taxonomic and functional diversity of a lake metacommunity system along a polymetallic pollution gradient caused by 60 years of chronic exposure to acid mine drainage (AMD)...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29772751/what-we-do-not-know-about-fungal-cell-adhesion-molecules
#11
REVIEW
Peter N Lipke
There has been extensive research on structure and function of fungal cell adhesion molecules, but the most of the work has been about adhesins in Candida albicans and Saccharomyces cerevisiae. These yeasts are members of a single ascomycete order, and adhesion molecules from the six other fungal phyla are only sparsely described in the literature. In these other phyla, most of the research is at the cellular level, rather than at the molecular level, so there has been little characterization of the adhesion molecules themselves...
May 17, 2018: Journal of Fungi (Basel, Switzerland)
https://www.readbyqxmd.com/read/29772096/signatures-of-diversifying-selection-and-convergence-acting-on-passerine-toll-like-receptor-4-in-an-evolutionary-context
#12
Tereza Králová, Tomáš Albrecht, Josef Bryja, David Hořák, Arild Johnsen, Jan T Lifjeld, Marian Novotný, Ondřej Sedláček, Hana Velová, Michal Vinkler
Positive selection acting on Toll-like receptors (TLRs) has been recently investigated to reveal evolutionary mechanisms of host-pathogen molecular co-adaptation. Much of this research, however, has focused mainly on the identification of sites predicted to be under positive selection, bringing little insight into the functional differences and similarities among species and a limited understanding of convergent evolution in the innate immune molecules. In this study we provide evidence of phenotypic variability in the avian TLR4 ligand-binding region (LBR), the direct interface between host and pathogen molecular structures...
May 17, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29769131/echinococcus-multilocularis-and-echinococcus-shiquicus-in-a-small-mammal-community-on-the-eastern-tibetan-plateau-host-species-composition-molecular-prevalence-and-epidemiological-implications
#13
Xu Wang, Jiayu Liu, Qingqiu Zuo, Zhiqiang Mu, Xiaodong Weng, Xiaohui Sun, Junyao Wang, Belgees Boufana, Philip S Craig, Patrick Giraudoux, Francis Raoul, Zhenghuan Wang
BACKGROUND: The eastern part of the Tibetan Plateau is now recognized as an endemic region with the highest reported human infection rates in the world of human alveolar echinococcosis (AE) caused by Echinococcus multilocularis. Existing epidemiological studies on AE have mainly focused on the synanthropic environment, while basic parasitological and ecological aspects in wildlife host species remain largely unknown, especially for small mammal hosts. Therefore, we examined small mammal host species composition, occurrence, and the prevalence of both E...
May 16, 2018: Parasites & Vectors
https://www.readbyqxmd.com/read/29765380/the-complete-plastome-sequences-of-seven-species-in-gentiana-sect-kudoa-gentianaceae-insights-into-plastid-gene-loss-and-molecular-evolution
#14
Shan-Shan Sun, Peng-Cheng Fu, Xiao-Jun Zhou, Yan-Wei Cheng, Fa-Qi Zhang, Shi-Long Chen, Qing-Bo Gao
The chloroplast (cp) genome is useful in the study of phylogenomics, molecular dating, and molecular evolution. Gentiana sect. Kudoa is a predominantly alpine flowering plant that is valued for its contributions to medicine, ecology, and horticulture. Previous evolutionary studies showed that the plastid gene loss pattern and intra-sectional phylogenetics in sect. Kudoa are still unclear. In this study, we compared 11 Gentiana plastomes, including 7 newly sequenced plastomes from sect. Kudoa , to represent its three serious: ser...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29765021/prospective-surveillance-for-influenza-virus-in-chinese-swine-farms
#15
Benjamin D Anderson, Mai-Juan Ma, Guo-Lin Wang, Zhen-Qiang Bi, Bing Lu, Xian-Jun Wang, Chuang-Xin Wang, Shan-Hui Chen, Yan-Hua Qian, Shao-Xia Song, Min Li, Teng Zhao, Meng-Na Wu, Laura K Borkenhagen, Wu-Chun Cao, Gregory C Gray
Pork production in China is rapidly increasing and swine production operations are expanding in size and number. However, the biosecurity measures necessary to prevent swine disease transmission, particularly influenza. viruses (IAV) that can be zoonotic, are often inadequate. Despite this risk, few studies have attempted to comprehensively study IAV ecology in swine production settings. Here, we present environmental and animal sampling data collected in the first year of an ongoing five-year prospective epidemiological study to assess IAV ecology as it relates to swine workers, their pigs, and the farm environment...
May 16, 2018: Emerging Microbes & Infections
https://www.readbyqxmd.com/read/29764730/molecular-detection-of-the-human-pathogen-rickettsia-parkeri-strain-atlantic-rainforest-in-amblyomma-ovale-ticks-in-argentina
#16
Daniela Lamattina, Evelina Luisa Tarragona, Santiago Nava
Human rickettsioses caused by Rickettsia parkeri strain Atlantic rainforest in Brazil motivated the analysis of Amblyomma ovale ticks in Misiones province, a similar ecological region in northeastern Argentina. During 2010-2017, 393 A. ovale ticks were collected from domestic and wild animals and from vegetation, and 177 were pooled for rickettsial detection by PCR targeting the gltA, ompA and ompB genes. A sample consisting of a pool of two A. ovale adults collected on Nasua nasua was positive for Rickettsia parkeri strain Atlantic rainforest...
May 5, 2018: Ticks and Tick-borne Diseases
https://www.readbyqxmd.com/read/29761037/uncovering-the-hidden-players-in-lepidoptera-biology-the-heritable-microbial-endosymbionts
#17
Anne Duplouy, Emily A Hornett
The Lepidoptera is one of the most widespread and recognisable insect orders. Due to their remarkable diversity, economic and ecological importance, moths and butterflies have been studied extensively over the last 200 years. More recently, the relationship between Lepidoptera and their heritable microbial endosymbionts has received increasing attention. Heritable endosymbionts reside within the host's body and are often, but not exclusively, inherited through the female line. Advancements in molecular genetics have revealed that host-associated microbes are both extremely prevalent among arthropods and highly diverse...
2018: PeerJ
https://www.readbyqxmd.com/read/29761036/sponge-community-of-the-western-black-sea-shallow-water-caves-diversity-and-spatial-distribution
#18
Alexander Ereskovsky, Oleg A Kovtun, Konstantin K Pronin, Apostol Apostolov, Dirk Erpenbeck, Viatcheslav Ivanenko
Marine caves possess unique biocoenotic and ecological characteristics. Sessile benthic species such as sponges associated with cave habitats typically show a marked zonation from the cave entrance towards the end of the cave. We describe three semi-submerged karstic caves of 50 to 83 m length and 936 to 2,291 m3 volume from the poorly explored cavernicolous fauna of North-East Bulgaria. We surveyed sponge diversity and spatial variability. Eight demosponge species were identified based on morphological and molecular data, of which six are known from the adjacent open sea waters of the Black Sea...
2018: PeerJ
https://www.readbyqxmd.com/read/29760889/measuring-inferential-importance-of-taxa-using-taxon-influence-indices
#19
John S S Denton, Eric W Goolsby
Assessing the importance of different taxa for inferring evolutionary history is a critical, but underutilized, aspect of systematics. Quantifying the importance of all taxa within a dataset provides an empirical measurement that can establish a ranking of extant taxa for ecological study and/or quantify the relative importance of newly announced or redescribed specimens to enable the disentangling of novelty and inferential influence. Here, we illustrate the use of taxon influence indices through analysis of both molecular and morphological datasets, introducing a modified Bayesian approach to the taxon influence index that accounts for model and topological uncertainty...
May 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29757994/bioinformatics-meets-virology-the-european-virus-bioinformatics-center-s-second-annual-meeting
#20
Bashar Ibrahim, Ksenia Arkhipova, Arno C Andeweg, Susana Posada-Céspedes, François Enault, Arthur Gruber, Eugene V Koonin, Anne Kupczok, Philippe Lemey, Alice C McHardy, Dino P McMahon, Brett E Pickett, David L Robertson, Richard H Scheuermann, Alexandra Zhernakova, Mark P Zwart, Alexander Schönhuth, Bas E Dutilh, Manja Marz
The Second Annual Meeting of the European Virus Bioinformatics Center (EVBC), held in Utrecht, Netherlands, focused on computational approaches in virology, with topics including (but not limited to) virus discovery, diagnostics, (meta-)genomics, modeling, epidemiology, molecular structure, evolution, and viral ecology. The goals of the Second Annual Meeting were threefold: (i) to bring together virologists and bioinformaticians from across the academic, industrial, professional, and training sectors to share best practice; (ii) to provide a meaningful and interactive scientific environment to promote discussion and collaboration between students, postdoctoral fellows, and both new and established investigators; (iii) to inspire and suggest new research directions and questions...
May 14, 2018: Viruses
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