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Molecular ecology

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https://www.readbyqxmd.com/read/28239926/documenting-dna-in-the-dust
#1
M T P Gilbert
I bought a robotic vacuum cleaner this summer and set it to work. Although my initial expectations were not high, my robot (christened Buddy) finished its cleaning cycle, and then insistently demanded that I empty its dust collection box. As I took the box out, my jaw dropped. I live in a modern house, we don't have pets, and I like to think that I keep it reasonably dust free. But, there was much dust in that box. And when I ran it again 2 days later, the same thing happened. And indeed, every 2 days, Buddy dutifully goes to work, and sucks up a similarly impressive quantity...
February 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28239874/habitat-segregation-and-cryptic-adaptation-of-species-of-periophthalmus-gobioidei-gobiidae
#2
G Polgar, S Zaccara, M Babbucci, F Fonzi, C M Antognazza, N Ishak, Z Sulaiman, G Crosa
A study was conducted on the habitat distribution of four sympatric species of Periophthalmus (the silver-lined mudskipper Periophthalmus argentilineatus, the slender mudskipper Periophthalmus gracilis, the kalolo mudskipper Periophthalmus kalolo and the Malacca mudskipper Periophthalmus malaccensis) from northern Sulawesi. Molecular phylogenetic reconstructions based on one mtDNA marker (16S) were used to validate the morphological taxa, identifying five molecular clades. Periophthalmus argentilineatus includes two molecular species, which are named Periophthalmus argentilineatus clades F and K...
February 27, 2017: Journal of Fish Biology
https://www.readbyqxmd.com/read/28236169/triazole-resistance-in-aspergillus-species-an-emerging-problem
#3
Rocio Garcia-Rubio, Manuel Cuenca-Estrella, Emilia Mellado
Aspergillus species are ubiquitous fungal saprophytes found in diverse ecological niches worldwide. Among them, Aspergillus fumigatus is the most prevalent and is largely responsible for the increased incidence of invasive aspergillosis with high mortality rates in some immunocompromised hosts. Azoles are the first-line drugs in treating diseases caused by Aspergillus spp. However, increasing reports in A. fumigatus azole resistance, both in the clinical setting and in the environment, are threatening the effectiveness of clinical and agricultural azole drugs...
February 24, 2017: Drugs
https://www.readbyqxmd.com/read/28231407/co-occurrence-and-hybridization-of-anther-smut-pathogens-specialized-on-dianthus-hosts
#4
Elsa Petit, Casey Silver, Amandine Cornille, Pierre Gladieux, Lisa Rosenthal, Emily Bruns, Sarah Yee, Janis Antonovics, Tatiana Giraud, Michael E Hood
Host specialization has important consequences for the diversification and ecological interactions of obligate pathogens. The anther-smut disease of natural plant populations, caused by Microbotryum fungi, has been characterized by specialized host-pathogen interactions, which contribute in part to the isolation among these numerous fungal species. This study investigated the molecular variation of Microbotryum pathogens within the geographic and host-specific distributions on wild Dianthus species in southern European Alps...
February 23, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28231394/adaptive-divergence-in-wine-yeasts-and-their-wild-relatives-suggests-a-prominent-role-for-introgressions-and-rapid-evolution-at-non-coding-sites
#5
Pedro Almeida, Raquel Barbosa, Douda Bensasson, Paula Gonçalves, José Paulo Sampaio
In Saccharomyces cerevisiae, the main yeast in wine fermentation, the opportunity to examine divergence at the molecular level between a domesticated lineage and its wild counterpart arose recently due to the identification of the closest relatives of wine strains, a wild population associated with Mediterranean oaks. Since genomic data is available for a considerable number of representatives belonging to both groups, we used population genomics to estimate the degree and distribution of nucleotide variation between wine yeasts and their closest wild relatives...
February 23, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28229023/toxgen-an-improved-reference-database-for-the-identification-of-type-b-trichothecene-genotypes-in-fusarium
#6
Tomasz Kulik, Kessy Abarenkov, Maciej Buśko, Katarzyna Bilska, Anne D van Diepeningen, Anna Ostrowska-Kołodziejczak, Katarzyna Krawczyk, Balázs Brankovics, Sebastian Stenglein, Jakub Sawicki, Juliusz Perkowski
Type B trichothecenes, which pose a serious hazard to consumer health, occur worldwide in grains. These mycotoxins are produced mainly by three different trichothecene genotypes/chemotypes: 3ADON (3-acetyldeoxynivalenol), 15ADON (15-acetyldeoxynivalenol) and NIV (nivalenol), named after these three major mycotoxin compounds. Correct identification of these genotypes is elementary for all studies relating to population surveys, fungal ecology and mycotoxicology. Trichothecene producers exhibit enormous strain-dependent chemical diversity, which may result in variation in levels of the genotype's determining toxin and in the production of low to high amounts of atypical compounds...
2017: PeerJ
https://www.readbyqxmd.com/read/28226232/the-epigenome-and-transcriptional-dynamics-of-fruit-ripening
#7
James Giovannoni, Cuong Nguyen, Betsy Ampofo, Silin Zhong, Zhangjun Fei
Fruit has evolved myriad forms that facilitate seed dispersal in varied environmental and ecological contexts. Because fleshy fruits become attractive and nutritious to seed-dispersing animals, the transition from unripe to ripe fruit represents a dramatic shift in survival strategy-from protecting unripe fruit against damaging animals to making it appealing to those same animals once ripened. For optimal fitness, ripening therefore must be tightly controlled and coordinated with seed development. Fruits, like many vegetative tissues of plants that contribute to human diets, are also subject to decay, which is enhanced as a consequence of the ripening transition...
February 22, 2017: Annual Review of Plant Biology
https://www.readbyqxmd.com/read/28224003/darwinism-for-the-genomic-age-connecting-mutation-to-diversification
#8
Xia Hua, Lindell Bromham
A growing body of evidence suggests that rates of diversification of biological lineages are correlated with differences in genome-wide mutation rate. Given that most research into differential patterns of diversification rate have focused on species traits or ecological parameters, a connection to the biochemical processes of genome change is an unexpected observation. While the empirical evidence for a significant association between mutation rate and diversification rate is mounting, there has been less effort in explaining the factors that mediate this connection between genetic change and species richness...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28219758/resolving-relationships-at-the-animal-fungal-divergence-a-molecular-phylogenetic-study-of-the-protist-trichomycetes-ichthyosporea-eccrinida
#9
Nicole K Reynolds, Matthew E Smith, Eric D Tretter, Justin Gause, Dustin Heeney, Matías J Cafaro, James F Smith, Stephen J Novak, William A Bourland, Merlin M White
Trichomycetes is a group of microorganisms that was considered a class of fungi comprising four orders of commensal, gut-dwelling endosymbionts obligately associated with arthropods. Since molecular phylogenies revealed two of those orders (Amoebidiales and Eccrinales = "protist trichos") to be closely related to members of the protist class Ichthyosporea (= Mesomycetozoea), trichomycetes have been considered an ecological association of both early-diverging fungi and protists. Understanding of the taxonomy, evolution, and diversity of the protist trichos is lacking largely due to the difficulties inherent in species collection that have contributed to undersampling and understudy...
February 17, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28219522/molecular-assessment-of-the-bacterial-community-associated-with-cassava-manihot-esculenta-crantz-cultivation-in-cameroon
#10
Papa Saliou Sarr, Akifumi Sugiyama, Aime Didier Boyogueno Begoude, Kazufumi Yazaki, Shigeru Araki, Eiji Nawata
Bacterial communities play an important role in nutrient cycles and plant development. Their distribution and activity may depend on location and environmental heterogeneity. This study characterized soil bacterial communities in cassava fields of Eastern (Andom) and Southern (Bityili) Cameroon using molecular tools. In both sites, two improved varieties (TMS-96/1414; TMS-92/0326) and a local variety (Local) were grown in a randomized block design. Composite bulk soils were collected at 10months after planting from cassava plots...
April 2017: Microbiological Research
https://www.readbyqxmd.com/read/28218960/evolutionary-genetics-of-host-shifts-in-herbivorous-insects-insights-from-the-age-of-genomics
#11
Kim L Vertacnik, Catherine R Linnen
Adaptation to different host taxa is a key driver of insect diversification. Herbivorous insects are classic models for ecological and evolutionary research, but it is recent advances in sequencing, statistics, and molecular technologies that have cleared the way for investigations into the proximate genetic mechanisms underlying host shifts. In this review, we discuss how genome-scale data are revealing-at resolutions previously unimaginable-the genetic architecture of host-use traits, the causal loci underlying host shifts, and the predictability of host-use evolution...
February 2017: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/28218791/development-and-validation-of-the-first-ssr-markers-for-mimosa-scabrella-benth
#12
F A Saiki, A P Bernardi, M S Reis, H Faoro, E M Souza, F O Pedrosa, A Mantovani, A F Guidolin
Mimosa scabrella Benth., popularly known as ''bracatinga'', is a pioneer and endemic species of Brazil, occurring in Mixed Ombrophilous Forest associated with Brazilian Atlantic Rainforest biomes. It is a fast-growing tree of the Fabaceae family that facilitates the dynamics of ecological succession. SSR development, when there is no genome sequence, is time and labor intensive and there are no molecular markers for M. scabrella. We developed and validated the first microsatellite markers for this tetraploid species, evaluating mother trees and progenies...
February 16, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28217877/high-resolution-sequencing-reveals-unexplored-archaeal-diversity-in-freshwater-wetland-soils
#13
Adrienne B Narrowe, Jordan C Angle, Rebecca A Daly, Kay C Stefanik, Kelly C Wrighton, Christopher S Miller
Despite being key contributors to biogeochemical processes, archaea are frequently outnumbered by bacteria, and consequently are underrepresented in combined molecular surveys. Here, we demonstrate an approach to concurrently survey the archaea alongside the bacteria with high-resolution 16S rRNA gene sequencing, linking these community data to geochemical parameters. We applied this integrated analysis to hydric soils sampled across a model methane-emitting freshwater wetland. Geochemical profiles, archaeal communities, and bacterial communities were independently correlated with soil depth and water cover...
February 20, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28217773/finding-food-how-marine-invertebrates-use-chemical-cues-to-track-and-select-food
#14
REVIEW
Michiya Kamio, Charles D Derby
Benthic marine invertebrates sense molecules from other organisms and use these molecules to find and evaluate the organisms as sources of food. These processes depend on the detection and discrimination of molecules carried in sea water around and in the mouths of these animals. To understand these processes, researchers have studied how molecules released from food distribute in the sea water as a plume, how animals respond to the plume, the molecular identity of the attractants in the plume, the effect of turbulence on food-searching success, and how animals evaluate the quality of food and make decisions to eat or not...
February 20, 2017: Natural Product Reports
https://www.readbyqxmd.com/read/28216337/identification-and-gene-expression-of-multiple-peptidoglycan-recognition-proteins-pgrps-in-the-deep-sea-mussel-bathymodiolus-azoricus-involvement-in-symbiosis
#15
Camille Détrée, François H Lallier, Arnaud Tanguy, Jean Mary
The relationship between the deep-sea mussel Bathymodiolus azoricus and its thiotrophic (SOX) and methanotrophic (MOX) symbionts has been ecologically and functionally well studied. Endosymbiosis is common in deep-sea hydrothermal vent fauna, yet little is known about the molecular mechanisms underlying the regulation of interactions between host and symbionts. In this study we focused on a group of pattern recognition receptors (PRR), called PGRPs that are able to recognize the peptidoglycan of bacterial cell wall...
February 12, 2017: Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology
https://www.readbyqxmd.com/read/28213546/environmental-surveillance-of-norovirus-genogroups-i-and-ii-for-sensitive-detection-of-epidemic-variants
#16
Shinobu Kazama, Takayuki Miura, Yoshifumi Masago, Yoshimitsu Konta, Kentaro Tohma, Takafumi Manaka, Xiaofang Liu, Daisuke Nakayama, Takashi Tanno, Mayuko Saito, Hitoshi Oshitani, Tatsuo Omura
Sewage samples have been investigated to study the level of noroviruses concentration in sewage or the genotypes of noroviruses circulating in human populations. However, the statistical relationship between the concentration of the virus and the number of infected individuals, and the clinical importance of genotypes or strains detected in sewage are unclear. In this study, we carried out both environmental and clinical surveillance of noroviruses for three years: 2013-2016. We performed cross-correlation analysis between the concentrations of norovirus GI or GII in sewage samples collected weekly and the number of gastroenteritis cases...
February 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28212379/distribution-and-abundance-of-key-vectors-of-rift-valley-fever-and-other-arboviruses-in-two-ecologically-distinct-counties-in-kenya
#17
Rosemary Sang, Samwel Arum, Edith Chepkorir, Gladys Mosomtai, Caroline Tigoi, Faith Sigei, Olivia Wesula Lwande, Tobias Landmann, Hippolyte Affognon, Clas Ahlm, Magnus Evander
BACKGROUND: Rift Valley fever (RVF) is a mosquito-borne viral zoonosis of ruminants and humans that causes outbreaks in Africa and the Arabian Peninsula with significant public health and economic consequences. Humans become infected through mosquito bites and contact with infected livestock. The virus is maintained between outbreaks through vertically infected eggs of the primary vectors of Aedes species which emerge following rains with extensive flooding. Infected female mosquitoes initiate transmission among nearby animals, which amplifies virus, thereby infecting more mosquitoes and moving the virus beyond the initial point of emergence...
February 17, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28211246/dna-amplification-in-the-field-move-over-pcr-here-comes-lamp
#18
Patricia L M Lee
It would not be an exaggeration to say that among molecular technologies, it is PCR (polymerase chain reaction) that underpins the discipline of molecular ecology as we know it today. With PCR, it has been possible to target the amplification of particular fragments of DNA, which can then be analysed in a multitude of ways. The capability of PCR to amplify DNA from a mere handful of copies further means that conservationists and ecologists are able to sample DNA unobtrusively and with minimal disturbance to the environment and the organisms of interest...
March 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28209121/evolution-of-toll-like-receptors-in-the-context-of-terrestrial-ungulates-and-cetaceans-diversification
#19
Edson Ishengoma, Morris Agaba
BACKGROUND: Toll-like receptors (TLRs) are the frontline actors in the innate immune response to various pathogens and are expected to be targets of natural selection in species adapted to habitats with contrasting pathogen burdens. The recent publication of genome sequences of giraffe and okapi together afforded the opportunity to examine the evolution of selected TLRs in broad range of terrestrial ungulates and cetaceans during their complex habitat diversification. Through direct sequence comparisons and standard evolutionary approaches, the extent of nucleotide and protein sequence diversity in seven Toll-like receptors (TLR2, TLR3, TLR4, TLR5, TLR7, TLR9 and TLR10) between giraffe and closely related species was determined...
February 16, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28208885/study-on-distribution-of-scorpions-to-provide-prevention-and-interventions-in-combating-scorpionism-in-poldokhtar-county-lorestan-province-iran
#20
Mansour Nazari, Rastgar Hassan
INTRODUCTION: Scorpions are arthropods of medical importance classified in the class Arachnida, inhabiting hot and dry environments. All scorpions have a venomous sting and several thousand people die each year from scorpion stings, but this mortality is due to the venom of about 25 species located in northern Africa, the Middle East, India, Mexico and parts of South America. Poldokhtar County belongs to one of the southern cities of Lorestan Province, providing suitable habitats for many different species of scorpions due to its specific climatic conditions...
December 2016: Journal of Clinical and Diagnostic Research: JCDR
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