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https://www.readbyqxmd.com/read/28813483/muroid-rodent-phylogenetics-900-species-tree-reveals-increasing-diversification-rates
#1
Scott J Steppan, John J Schenk
We combined new sequence data for more than 300 muroid rodent species with our previously published sequences for up to five nuclear and one mitochondrial genes to generate the most widely and densely sampled hypothesis of evolutionary relationships across Muroidea. An exhaustive screening procedure for publically available sequences was implemented to avoid the propagation of taxonomic errors that are common to supermatrix studies. The combined data set of carefully screened sequences derived from all available sequences on GenBank with our new data resulted in a robust maximum likelihood phylogeny for 900 of the approximately 1,620 muroids...
2017: PloS One
https://www.readbyqxmd.com/read/28813451/schistosoma-mansoni-reinfection-analysis-of-risk-factors-by-classification-and-regression-tree-cart-modeling
#2
Andréa Gazzinelli, Roberta Oliveira-Prado, Leonardo Ferreira Matoso, Bráulio M Veloso, Gisele Andrade, Helmut Kloos, Jeffrey M Bethony, Renato M Assunção, Rodrigo Correa-Oliveira
Praziquantel (PZQ) is an effective chemotherapy for schistosomiasis mansoni and a mainstay for its control and potential elimination. However, it does not prevent against reinfection, which can occur rapidly in areas with active transmission. A guide to ranking the risk factors for Schistosoma mansoni reinfection would greatly contribute to prioritizing resources and focusing prevention and control measures to prevent rapid reinfection. The objective of the current study was to explore the relationship among the socioeconomic, demographic, and epidemiological factors that can influence reinfection by S...
2017: PloS One
https://www.readbyqxmd.com/read/28813430/reprogramming-human-gallbladder-cells-into-insulin-producing-%C3%AE-like-cells
#3
Feorillo Galivo, Eric Benedetti, Yuhan Wang, Carl Pelz, Jonathan Schug, Klaus H Kaestner, Markus Grompe
The gallbladder and cystic duct (GBCs) are parts of the extrahepatic biliary tree and share a common developmental origin with the ventral pancreas. Here, we report on the very first genetic reprogramming of patient-derived human GBCs to β-like cells for potential autologous cell replacement therapy for type 1 diabetes. We developed a robust method for large-scale expansion of human GBCs ex vivo. GBCs were reprogrammed into insulin-producing pancreatic β-like cells by a combined adenoviral-mediated expression of hallmark pancreatic endocrine transcription factors PDX1, MAFA, NEUROG3, and PAX6 and differentiation culture in vitro...
2017: PloS One
https://www.readbyqxmd.com/read/28813429/the-impact-of-tree-age-on-biomass-growth-and-carbon-accumulation-capacity-a-retrospective-analysis-using-tree-ring-data-of-three-tropical-tree-species-grown-in-natural-forests-of-suriname
#4
Michael Köhl, Prem R Neupane, Neda Lotfiomran
The world's forests play a pivotal role in the mitigation of global climate change. By photosynthesis they remove CO2 from the atmosphere and store carbon in their biomass. While old trees are generally acknowledged for a long carbon residence time, there is no consensus on their contribution to carbon accumulation due to a lack of long-term individual tree data. Tree ring analyses, which use anatomical differences in the annual formation of wood for dating growth zones, are a retrospective approach that provides growth patterns of individual trees over their entire lifetime...
2017: PloS One
https://www.readbyqxmd.com/read/28813413/polylox-barcoding-reveals-haematopoietic-stem-cell-fates-realized-in-vivo
#5
Weike Pei, Thorsten B Feyerabend, Jens Rössler, Xi Wang, Daniel Postrach, Katrin Busch, Immanuel Rode, Kay Klapproth, Nikolaus Dietlein, Claudia Quedenau, Wei Chen, Sascha Sauer, Stephan Wolf, Thomas Höfer, Hans-Reimer Rodewald
Developmental deconvolution of complex organs and tissues at the level of individual cells remains challenging. Non-invasive genetic fate mapping has been widely used, but the low number of distinct fluorescent marker proteins limits its resolution. Much higher numbers of cell markers have been generated using viral integration sites, viral barcodes, and strategies based on transposons and CRISPR-Cas9 genome editing; however, temporal and tissue-specific induction of barcodes in situ has not been achieved. Here we report the development of an artificial DNA recombination locus (termed Polylox) that enables broadly applicable endogenous barcoding based on the Cre-loxP recombination system...
August 16, 2017: Nature
https://www.readbyqxmd.com/read/28813177/how-single-cell-genomics-is-changing-evolutionary-and-developmental-biology
#6
John C Marioni, Detlev Arendt
The recent flood of single-cell data not only boosts our knowledge of cells and cell types, but also provides new insight into development and evolution from a cellular perspective. For example, assaying the genomes of multiple cells during development reveals developmental lineage trees-the kinship lineage-whereas cellular transcriptomes inform us about the regulatory state of cells and their gradual restriction in potency-the Waddington lineage. Beyond that, the comparison of single-cell data across species allows evolutionary changes to be tracked at all stages of development from the zygote, via different kinds of stem cells, to the differentiating cells...
August 16, 2017: Annual Review of Cell and Developmental Biology
https://www.readbyqxmd.com/read/28813103/nutrition-facts-and-limits-for-micronutrients-in-tree-species-used-in-urban-forestry
#7
Flávia G K Brun, Eleandro J Brun, Dionatan Gerber, Denise A Szymczak, Eduardo K Londero, Evandro A Meyer, Márcio C Navroski
There is a huge lack of researches that evaluate the nutritional limits in tree species used in urban forestry, especially in terms of micronutrients. This study aimed to establish limits and range of micronutrients levels for the proper development of tree species utilized in urban forestry. The study was conducted in the city of Santa Maria-RS-Brazil. Through forest inventory, 23 forest species present in urban forest were selected, and 05 vegetative branches of each tree were collected, in which the contents of B, Cu, Fe, Mn and Zn were analyzed...
August 14, 2017: Anais da Academia Brasileira de Ciências
https://www.readbyqxmd.com/read/28812792/a-case-for-open-network-health-systems-systems-as-networks-in-public-mental-health
#8
Michael Grant Rhodes, Marten W de Vries
Increases in incidents involving so-called confused persons have brought attention to the potential costs of recent changes to public mental health (PMH) services in the Netherlands. Decentralized under the (Community) Participation Act (2014), local governments must find resources to compensate for reduced central funding to such services or "innovate." But innovation, even when pressure for change is intense, is difficult. This perspective paper describes experience during and after an investigation into a particularly violent incident and murder...
January 8, 2017: International Journal of Health Policy and Management
https://www.readbyqxmd.com/read/28812701/contentious-relationships-in-phylogenomic-studies-can-be-driven-by-a-handful-of-genes
#9
Xing-Xing Shen, Chris Todd Hittinger, Antonis Rokas
Phylogenomic studies have resolved countless branches of the tree of life, but remain strongly contradictory on certain, contentious relationships. Here, we use a maximum likelihood framework to quantify the distribution of phylogenetic signal among genes and sites for 17 contentious branches and 6 well-established control branches in plant, animal and fungal phylogenomic data matrices. We find that resolution in some of these 17 branches rests on a single gene or a few sites, and that removal of a single gene in concatenation analyses or a single site from every gene in coalescence-based analyses diminishes support and can alter the inferred topology...
April 10, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812675/spatial-complementarity-in-tree-crowns-explains-overyielding-in-species-mixtures
#10
Laura J Williams, Alain Paquette, Jeannine Cavender-Bares, Christian Messier, Peter B Reich
Deciphering the mechanisms that link biodiversity with ecosystem functions is critical to understanding the consequences of changes in biodiversity. The hypothesis that complementarity and selection effects drive relationships between biodiversity and ecosystem functions is well accepted, and an approach to statistically untangle the relative importance of these effects has been widely applied. In contrast, empirical demonstrations of the biological mechanisms that underlie these relationships remain rare. Here, on the basis of a field experiment with young trees, we provide evidence that one form of complementarity in plant communities-complementarity among crowns in canopy space-is a mechanism, related to light interception and use, that links biodiversity with ecosystem productivity...
March 1, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812652/parasites-dominate-hyperdiverse-soil-protist-communities-in-neotropical-rainforests
#11
Frédéric Mahé, Colomban de Vargas, David Bass, Lucas Czech, Alexandros Stamatakis, Enrique Lara, David Singer, Jordan Mayor, John Bunge, Sarah Sernaker, Tobias Siemensmeyer, Isabelle Trautmann, Sarah Romac, Cédric Berney, Alexey Kozlov, Edward A D Mitchell, Christophe V W Seppey, Elianne Egge, Guillaume Lentendu, Rainer Wirth, Gabriel Trueba, Micah Dunthorn
High animal and plant richness in tropical rainforest communities has long intrigued naturalists. It is unknown if similar hyperdiversity patterns are reflected at the microbial scale with unicellular eukaryotes (protists). Here we show, using environmental metabarcoding of soil samples and a phylogeny-aware cleaning step, that protist communities in Neotropical rainforests are hyperdiverse and dominated by the parasitic Apicomplexa, which infect arthropods and other animals. These host-specific parasites potentially contribute to the high animal diversity in the forests by reducing population growth in a density-dependent manner...
March 20, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812635/divergent-plant-soil-feedbacks-could-alter-future-elevation-ranges-and-ecosystem-dynamics
#12
Michael E Van Nuland, Joseph K Bailey, Jennifer A Schweitzer
Plant-soil feedbacks (PSF) are important interactions that may influence range dynamics in a changing world. What remains largely unknown is the generality of plant-soil biotic interactions across populations and the potential role of specific soil biota, both of which are key for understanding how PSF might change future communities and ecosystems. We combined landscape-level field observations and experimental soil treatments to test whether a dominant tree alters soil environments to impact its own performance and range shifts towards higher elevations...
April 28, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812617/improved-tree-ring-archives-will-support-earth-system-science
#13
Flurin Babst, Benjamin Poulter, Paul Bodesheim, Miguel D Mahecha, David C Frank
No abstract text is available yet for this article.
January 24, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812612/phylogenomics-constrained-gene-tree-inference
#14
Siavash Mirarab
No abstract text is available yet for this article.
January 13, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812610/genome-wide-interrogation-advances-resolution-of-recalcitrant-groups-in-the-tree-of-life
#15
Dahiana Arcila, Guillermo Ortí, Richard Vari, Jonathan W Armbruster, Melanie L J Stiassny, Kyung D Ko, Mark H Sabaj, John Lundberg, Liam J Revell, Ricardo Betancur-R
Much progress has been achieved in disentangling evolutionary relationships among species in the tree of life, but some taxonomic groups remain difficult to resolve despite increasing availability of genome-scale data sets. Here we present a practical approach to studying ancient divergences in the face of high levels of conflict, based on explicit gene genealogy interrogation (GGI). We show its efficacy in resolving the controversial relationships within the largest freshwater fish radiation (Otophysi) based on newly generated DNA sequences for 1,051 loci from 225 species...
January 13, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28811890/beyond-temperature-coupling-effects-of-temperature-on-ectotherm-signaling-and-mate-choice-and-the-implications-for%C3%A2-communication-in-multispecies-assemblages
#16
Laurel B Symes, Rafael L Rodríguez, Gerlinde Höbel
Many organisms share communication channels, generating complex signaling environments that increase the risk of signal interference. Variation in abiotic conditions, such as temperature, may further exacerbate signal interference, particularly in ectotherms. We tested the effects of temperature on the pulse rate of male signals in a community of Oecanthus tree crickets, and for one focal species we also assessed its effect on female pulse rate preferences and motivation to seek mates. We confirm prior findings of temperature-dependent signals that result in increasing signal similarity at lower temperatures...
August 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28811882/seasonal-changes-in-leaf-chemistry-and-leaf-selection-of-the-japanese-giant-flying-squirrel-upon-two-tree-species
#17
Mutsumi Ito, Noriko Tamura, Fumio Hayashi
Tree leaves are important food sources for arboreal herbivores, such as primates, rodents, and marsupials. These animals do not eat leaves randomly in habitats with many tree species but rather choose based on the chemical components of leaves, such as sugars, fibers, proteins, and toxins. However, the effects of the microscale distribution of these chemicals within each leaf have not been examined for these animals. The giant flying squirrels Petaurista leucogenys are entirely arboreal, nocturnal herbivores, usually feeding on leaves and dropping leaf debris on the ground after partially consuming them...
August 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28811799/diversity-physiochemical-and-phylogenetic-analyses-of-bacteria-isolated-from-various-drinking-water-sources
#18
Neveen H Eid, Huda A Al Doghaither, Taha A Kumosani, Munazza Gull
OBJECTIVE: To evaluate the indigenous bacterial strains of drinking water from the most commercial water types including bottled and filtered water that are currently used in Saudi Arabia. METHODS: Thirty randomly selected commercial brands of bottled water were purchased from Saudi local markets. Moreover, samples from tap water and filtered water were collected in sterilized glass bottles and stored at 4°C. Biochemical analyses including pH, temperature, lactose fermentation test (LAC), indole test (IND), methyl red test (MR), Voges-Proskauer test (VP), urease test (URE), catalase test (CAT), aerobic and anaerobic test (Ae/An) were measured...
May 2017: Pakistan Journal of Medical Sciences Quarterly
https://www.readbyqxmd.com/read/28811761/incidence-rates-of-major-diseases-of-kiwiberry-in-2015-and-2016
#19
Gyoung Hee Kim, Deok Ryong Kim, Sook-Young Park, Young Sun Lee, Jae Sung Jung, Young Jin Koh
Incidence rates of diseases in kiwiberry orchards were investigated monthly from late June to late September in Gwangyang and Boseong in 2015 and 2016. The impact of postharvest fruit rot was investigated during ripening after harvest. Bacterial canker was only observed on one single tree in 2015, but black rot, powdery mildew, leaf spot and blight, and postharvest fruit rot diseases were problematic throughout the study period in both 2015 and 2016. Incidence rates of the diseases varied with kiwiberry cultivar, region and sampling time...
August 2017: Plant Pathology Journal
https://www.readbyqxmd.com/read/28811753/characterization-of-the-rosellinia-necatrix-transcriptome-and-genes-related-to-pathogenesis-by-single-molecule-mrna-sequencing
#20
Hyeongmin Kim, Seung Jae Lee, Ick-Hyun Jo, Jinsu Lee, Wonsil Bae, Hyemin Kim, Kyungho Won, Tae Kyung Hyun, Hojin Ryu
White root rot disease, caused by the pathogen Rosellinia necatrix, is one of the world's most devastating plant fungal diseases and affects several commercially important species of fruit trees and crops. Recent global outbreaks of R. necatrix and advances in molecular techniques have both increased interest in this pathogen. However, the lack of information regarding the genomic structure and transcriptome of R. necatrix has been a barrier to the progress of functional genomic research and the control of this harmful pathogen...
August 2017: Plant Pathology Journal
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