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Pavlina Sasheva, Ueli Grossniklaus
Over the last years, it has become increasingly clear that environmental influences can affect the epigenomic landscape and that some epigenetic variants can have heritable, phenotypic effects. While there are a variety of methods to perform genome-wide analyses of DNA methylation in model organisms, this is still a challenging task for non-model organisms without a reference genome. Differentially methylated region-representational difference analysis (DMR-RDA) is a sensitive and powerful PCR-based technique that isolates DNA fragments that are differentially methylated between two otherwise identical genomes...
2017: Methods in Molecular Biology
Xianbo Liu, Xiangjin Wei, Zhonghua Sheng, Guiai Jiao, Shaoqing Tang, Ju Luo, Peisong Hu
Polycomb group (PcG) proteins have been shown to affect growth and development in plants. To further elucidate their role in these processes in rice, we isolated and characterized a rice mutant which exhibits dwarfism, reduced seed setting rate, defective floral organ, and small grains. Map-based cloning revealed that abnormal phenotypes were attributed to a mutation of the Fertilization Independent Endosperm 2 (OsFIE2) protein, which belongs to the PcG protein family. So we named the mutant as osfie2-1. Histological analysis revealed that the number of longitudinal cells in the internodes decreased in osfie2-1, and that lateral cell layer of the internodes was markedly thinner than wild-type...
2016: PloS One
Antoine Prandota Trzcinski, Lily Ganda, Chinagarn Kunacheva, Dong Qing Zhang, Li Leonard Lin, Guihe Tao, Yingjie Lee, Wun Jern Ng
In light of global warming mitigation efforts, increasing sludge disposal costs, and need for reduction in the carbon footprint of wastewater treatment plants, innovation in treatment technology has been tailored towards energy self-sufficiency. The AB process is a promising technology for achieving maximal energy recovery from wastewaters with minimum energy expenditure and therefore inherently reducing excess sludge production. Characterization of this novel sludge and its comparison with the more conventional B-stage sludge are necessary for a deeper understanding of AB treatment process design...
October 2016: Water Science and Technology: a Journal of the International Association on Water Pollution Research
Jinpu Jia, Chunjuan Bi, Xue Guo, Xueping Wang, Xiaoxiao Zhou, Zhenlou Chen
Road dusts and agricultural soil samples were collected from eight sites close to steel mills, chemical plants, and municipal solid waste incinerator in suburban Shanghai. Sixteen polycyclic aromatic hydrocarbons (PAHs) in the United States Environmental Protection Agency (US EPA) priority controlled list were analyzed quantitatively using GC-MS. The total PAH concentrations ranged from 0.79 to 6.2 μg g(-1) in road dust samples with a mean value of 2.38 μg g(-1) and 0.26 to 0.54 μg g(-1) in agricultural soils with an average of 0...
October 14, 2016: Environmental Science and Pollution Research International
Johan Asplund, David A Wardle
Lichens occur in most terrestrial ecosystems; they are often present as minor contributors, but in some forests, drylands and tundras they can make up most of the ground layer biomass. As such, lichens dominate approximately 8% of the Earth's land surface. Despite their potential importance in driving ecosystem biogeochemistry, the influence of lichens on community processes and ecosystem functioning have attracted relatively little attention. Here, we review the role of lichens in terrestrial ecosystems and draw attention to the important, but often overlooked role of lichens as determinants of ecological processes...
October 11, 2016: Biological Reviews of the Cambridge Philosophical Society
Wanlong Li, Ghana S Challa, Huilan Zhu, Wenjie Wei
Chromosomal rearrangements (CRs) play important roles in karyotype diversity and speciation. While many CR breakpoints have been characterized at the sequence level in yeast, insects and primates, little is known about the structure of evolutionary CR breakpoints in plant genomes, which are much more dynamic in genome size and sequence organization. Here, we report identification of breakpoints of a translocation between chromosome arms 4L and 5L of Triticeae, which is fixed in several species including diploid wheat and rye, by comparative mapping and comparative analysis of the draft genome and chromosome survey sequences of the Triticeae species...
October 11, 2016: G3: Genes—Genomes—Genetics
Nete Kodahl, Renate Müller, Henrik Lütken
Plant transformation with the wild type Ri plasmid T-DNA of Agrobacterium rhizogenes is a promising method for breeding of compact plants and has been the subject of numerous studies. However, knowledge concerning the isolated functions of single genes and ORFs from the plasmid is limited. The rolB and ORF13 oncogenes of A. rhizogenes show considerable promise in plant breeding, but have not been comprehensively studied. Detailed information regarding the morphological impact of specific genes of the Ri plasmid will allow for optimized targeted breeding of plants transformed with the wild type Ri plasmid T-DNA...
November 2016: Plant Science: An International Journal of Experimental Plant Biology
Xianzong Wang, Xiaolin Liu
BACKGROUND: Horizontal transfer (HT) of genetic materials is increasingly being found in both animals and plants and mainly concerns transposable elements (TEs). Many crustaceans have big genome sizes and are thus likely to harbor high TE contents. Their habitat might offer them ample opportunities to exchange genetic materials with organisms that are ecologically close but taxonomically distant to them. RESULTS: In this study, we analyzed the transcriptome of Pacific white shrimp (Litopenaeus vannamei), an important economic crustacean, to explore traces of HT events...
October 7, 2016: BMC Evolutionary Biology
Mónica Fernández-Aparicio, Fernando Flores, Diego Rubiales
Broomrape weeds (Orobanche and Phelipanche spp.) are root holoparasites that feed off a wide range of important crops. Among them, Orobanche crenata attacks legumes complicating their inclusion in cropping systems along the Mediterranean area and West Asia. The detrimental effect of broomrape parasitism in crop yield can reach up to 100% depending on infection severity and the broomrape-crop association. This work provides field data of the consequences of O. crenata infection severity in three legume crops, i...
2016: Frontiers in Plant Science
Wenyi Wang, Mengyun Xu, Xuejiao Liu, Jumin Tu
Eukaryotic translation initiation factor 3 (eIF3) is a large protein complex that participates in most translation initiation processes. While eIF3 has been well characterized, less is known about the roles of individual eIF3 subunits, particularly in plants. Here, we identified and characterized OseIF3e in rice (Oryza sativa L.). OseIF3e was constitutively expressed in various tissues, but most strongly in vigorously growing organs. Transgenic OseIF3e-silenced rice plants showed inhibited growth in seedling and vegetative stages...
2016: Frontiers in Plant Science
Satoru Wakabayashi, Naoya Sawamura, André Voelzmann, Meike Broemer, Toru Asahi, Michael Hoch
Cereblon (CRBN) is a substrate receptor of the E3 ubiquitin ligase complex that is highly conserved in animals and plants. CRBN proteins have been implicated in various biological processes such as development, metabolism, learning and memory formation and their impairment has been linked to autosomal recessive non-syndromic intellectual disability and cancer. Furthermore, human CRBN was identified as the primary target of thalidomide teratogenicity. Data on functional analysis of CRBN family members in vivo is, however, still scarce...
October 4, 2016: Journal of Biological Chemistry
Gbadamassi G O Dossa, Ekananda Paudel, Kunfang Cao, Douglas Schaefer, Rhett D Harrison
Organic matter decomposition represents a vital ecosystem process by which nutrients are made available for plant uptake and is a major flux in the global carbon cycle. Previous studies have investigated decomposition of different plant parts, but few considered bark decomposition or its role in decomposition of wood. However, bark can comprise a large fraction of tree biomass. We used a common litter-bed approach to investigate factors affecting bark decomposition and its role in wood decomposition for five tree species in a secondary seasonal tropical rain forest in SW China...
October 4, 2016: Scientific Reports
Kalpana Nanjareddy, Lourdes Blanco, Manoj Kumar Arthikala, Xochitl Alvarado-Affantranger, Carmen Quinto, Federico Sanchez, Miguel Lara
The target of rapamycin (TOR) protein kinase regulates metabolism, growth and life span in yeast, animals and plants in coordination with nutrient status and environmental conditions. The nutrient-dependent nature of TOR functionality makes this kinase a putative regulator of symbiotic associations involving nutrient acquisition. However, TOR's role in these processes remains to be understood. Here, we uncovered the role of TOR during the Phaseolus vulgaris-Rhizobium symbiotic interaction. TOR was expressed in all tested Phaseolus tissues, with higher expression levels in the root meristems and senesced nodules...
October 3, 2016: Plant Physiology
Khadiza Khatun, Arif Hasan Khan Robin, Jong-In Park, Chang Kil Kim, Ki-Byung Lim, Min-Bae Kim, Do-Jin Lee, Ill Sup Nou, Mi-Young Chung
The actin depolymerizing factor (ADF) proteins have growth, development, defense-related and growth regulatory functions in plants. The present study used genome-wide analysis to investigate ADF family genes in tomato. Eleven tomato ADF genes were identified and differential expression patterns were found in different organs. SlADF6 was preferentially expressed in roots, suggesting its function in root development. SlADF1, SlADF3 and SlADF10 were predominately expressed in the flowers compared to the other organs and specifically in the stamen compared to other flower parts, indicating their potential roles in pollen development...
2016: Genes
Bruna Marques Dos Santos, Tiago Santana Balbuena
: Photosynthetic organisms may be drastically affected by the future climate projections of a considerable increase in CO2 concentrations. Growth under a high concentration of CO2 could stimulate carbon assimilation-especially in C3-type plants. We used a proteomics approach to test the hypothesis of an increase in the abundance of the enzymes involved in carbon assimilation in Eucalyptus urophylla plants grown under conditions of high atmospheric CO2. Our strategy allowed the profiling of all Calvin-Benson cycle enzymes and associated protein species...
September 24, 2016: Journal of Proteomics
Izabela Pawlaczyk-Graja, Sebastian Balicki, Rafał Ziewiecki, Mária Matulová, Peter Capek, Roman Gancarz
A macromolecular complex has been isolated from the dried flowering parts of medicinal plant Sanguisorba officinalis L. (So) by multi-step extraction procedure, including that with extraction by organic solvents to degrease the plant material, then with hot alkali, followed by neutralization, partitioning with organic solvents and dialysis. The complex was purified by size-exclusion chromatography into five fractions labeled as So1-So5. Individual fractions differed in the chemical composition and molecular weight distribution patterns...
September 21, 2016: International Journal of Biological Macromolecules
Anália Lúcia Vieira Pacheco, Mateus Francisco Pagliarini, Gilberto Bernardo de Freitas, Ricardo Henrique Silva Santos, José Eduardo Serrão, José Cola Zanuncio
The use of organic foods has been increased in the world. Organic fertilizers, like cattle manure, have emerged as an important component of the organic system production. The production, mass, size, and mineral composition of passion fruit pulp were evaluated when treated with a mineral fertilizer (control) (MIN) or cattle manure at a single dose equivalent to potassium fertilizer (ORG) or double dose (2×ORG). The production and the numbers of fruits of plants treated with MIN and 2×ORG was higher than with ORG...
February 15, 2017: Food Chemistry
Patricia L Gillis, Rodney McInnis, Joseph Salerno, Shane R de Solla, Mark R Servos, Erin M Leonard
The substantial increase in urbanization worldwide has resulted in higher emissions of wastewater to riverine systems near urban centers, which often impairs aquatic populations and communities. This study examined the effect of urbanization on freshwater mussel populations, including Species at Risk in two rivers receiving wastewater. The influence of anthropogenic activities was assessed in a watershed in the Laurentian Great Lakes basin, one that historically supported one of the most diverse mussel faunas in Canada...
September 20, 2016: Science of the Total Environment
Jacob Heilmann-Clausen, Pietro K Maruyama, Hans Henrik Bruun, Dimitar Dimitrov, Thomas Laessøe, Tobias Guldberg Frøslev, Bo Dalsgaard
Woody plants host diverse communities of associated organisms, including wood-inhabiting fungi. In this group, host effects on species richness and interaction network structure are not well understood, especially not at large geographical scales. We investigated ecological, historical and evolutionary determinants of fungal species richness and network modularity, that is, subcommunity structure, across woody hosts in Denmark, using a citizen science data set comprising > 80 000 records of > 1000 fungal species on 91 genera of woody plants...
September 23, 2016: New Phytologist
Mohammed Al Mamun, Luca Albergante, Alberto Moreno, James T Carrington, J Julian Blow, Timothy J Newman
The replication of DNA is initiated at particular sites on the genome called replication origins (ROs). Understanding the constraints that regulate the distribution of ROs across different organisms is fundamental for quantifying the degree of replication errors and their downstream consequences. Using a simple probabilistic model, we generate a set of predictions on the extreme sensitivity of error rates to the distribution of ROs, and how this distribution must therefore be tuned for genomes of vastly different sizes...
September 27, 2016: Proceedings of the National Academy of Sciences of the United States of America
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