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New Phytologist

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https://www.readbyqxmd.com/read/30521109/loop-assembly-a-simple-and-open-system-for-recursive-fabrication-of-dna-circuits
#1
Bernardo Pollak, Ariel Cerda, Mihails Delmans, Simón Álamos, Tomás Moyano, Anthony West, Rodrigo A Gutiérrez, Nicola Patron, Fernán Federici, Jim Haseloff
High efficiency methods for DNA assembly have enabled routine assembly of synthetic DNAs of increased size and complexity. However, these techniques require customisation, elaborate vector sets or serial manipulations for the different stages of assembly. We have developed Loop assembly based on a recursive approach to DNA fabrication. The system makes use of two Type IIS restriction endonucleases and corresponding vector sets for efficient and parallel assembly of large DNA circuits. Standardised level 0 parts can be assembled into circuits containing 1, 4, 16 or more genes by looping between the two vector sets...
December 6, 2018: New Phytologist
https://www.readbyqxmd.com/read/30521089/methane-production-and-emissions-in-trees-and-forests
#2
Kristofer R Covey, Yale University, J Patrick Megonigal
Forest ecosystem methane (CH4 ) research has focused on soils, but trees are also important sources and sinks in forest CH4 budgets. Living and dead trees transport and emit CH4 produced in soils; living trees and deadwood emit CH4 produced inside trees by microorganisms; and trees produce CH4 through an abiotic photochemical process. Here, we review the state of the science on the production, consumption, transport, and emission of CH4 by living and dead trees, and the spatial and temporal dynamics of these processes across hydrologic gradients inclusive of wetland and upland ecosystems...
December 6, 2018: New Phytologist
https://www.readbyqxmd.com/read/30511456/the-rin-regulated-small-auxin-up-rna-saur69-is-involved-in-the-unripe-to-ripe-phase-transition-of-tomato-fruit-via-enhancing-sensitivity-to-ethylene
#3
Jun-Hye Shin, Isabelle Mila, Mingchun Liu, Maria Aurineide Rodrigues, Teva Vernoux, Julien Pirrello, Mondher Bouzayen
Ethylene is the main hormone controlling climacteric fruit ripening; however, the mechanisms underlying the developmental transition leading to initiation of the ripening process remain elusive although the presumed role of active hormone interplay has been often postulated. To unravel the putative role of auxin in the unripe-to-ripe transition, we investigated the dynamics of auxin activity in tomato fruit and addressed the physiological significance of Sl-SAUR69, previously identified as RIN target gene, using reverse genetics approaches...
December 3, 2018: New Phytologist
https://www.readbyqxmd.com/read/30507001/n-2-fixation-in-free-floating-filaments-of-trichodesmium-is-higher-than-in-transiently-suboxic-colony-microenvironments
#4
Meri Eichner, Silke Thoms, Björn Rost, Wiebke Mohr, Soeren Ahmerkamp, Helle Ploug, Marcel Mm Kuypers, Dirk de Beer
To understand the role of micrometer-scale oxygen (O2 ) gradients in facilitating dinitrogen (N2 ) fixation, we characterized O2 dynamics in the microenvironment around free-floating trichomes and colonies of Trichodesmium erythraeum IMS101. Diurnal and spatial variability in O2 concentrations in the bulk medium, within colonies, along trichomes and within single cells were determined using O2 optodes, microsensors and model calculations. Carbon (C) and N2 fixation as well as O2 evolution and uptake under different O2 concentrations were analyzed by stable isotope incubations and membrane inlet mass spectrometry...
December 3, 2018: New Phytologist
https://www.readbyqxmd.com/read/30506801/the-enigmatic-loss-of-light-independent-chlorophyll-biosynthesis-from-an-antarctic-green-alga-in-a-light-limited-environment
#5
Marina Cvetkovska, Shane Orgnero, Norman P A Hüner, David Roy Smith
Chlorophyll production is a complicated, multifaceted process. Indeed, the cyanobacterial progenitor of chloroplasts bestowed eukaryotic plants and algae with two distinct nonhomologous enzymes for reducing protochlorophyllide to chlorophyllide (the penultimate step of chlorophyll a biosynthesis): light-dependent (LPOR) and light-independent protochlorophyllide oxidoreductase (DPOR) (Armstrong, 1998; Fujita & Bauer, 2003; Reinbothe et al., 2010). This article is protected by copyright. All rights reserved...
December 3, 2018: New Phytologist
https://www.readbyqxmd.com/read/30506685/cotton-fiber-elongation-requires-the-transcription-factor-ghmyb212-to-regulate-sucrose-transportation-into-expanding-fibers
#6
Wenjie Sun, Zhengyin Gao, Jun Wang, Yiqun Huang, Yun Chen, Jianfu Li, Mengli Lv, Jin Wang, Ming Luo, Kaijing Zuo
Cotton is white gold over the globe and composed of fiber cells derived from outer integument of cotton ovules. Fiber elongation uses sucrose as direct carbon source. The molecular mechanism transcriptionally controlling sucrose transport from ovules into elongating fibers remains elusive. It was investigated here that GhMYB212 is involved in the regulation of sucrose transportion into expanding fibers. GhMYB212 RNAi plants (GhMYB212i) accumulated less sucrose and glucose in developing fibers, and had shorter fibers and lower lint index...
December 3, 2018: New Phytologist
https://www.readbyqxmd.com/read/30500990/autoimmunity-and-effector-recognition-in-arabidopsis-thaliana-can-be-uncoupled-by-mutations-in-the-rrs1-r-immune-receptor
#7
Toby E Newman, Jungmin Lee, Simon J Williams, Sera Choi, Morgan K Halane, Jun Zhou, Peter Solomon, Bostjan Kobe, Jonathan D G Jones, Cécile Segonzac, Kee Hoon Sohn
Plant nucleotide-binding leucine-rich repeat (NLR) disease resistance proteins recognize specific pathogen effectors and activate a cellular defense program. In Arabidopsis thaliana (Arabidopsis) Resistance to Ralstonia solanacearum 1 (RRS1-R) and Resistance to Pseudomonas syringae 4 (RPS4) function together to recognize the unrelated bacterial effectors PopP2 and AvrRps4. In the plant cell nucleus, the RRS1-R/RPS4 complex binds to and signals the presence of AvrRps4 or PopP2. The exact mechanism underlying NLR signaling and immunity activation remains to be elucidated...
November 30, 2018: New Phytologist
https://www.readbyqxmd.com/read/30489637/zmpbf-and-zmgamyb-transcription-factors-independently-transactivate-the-promoter-of-the-maize-zea-mays-%C3%AE-carotene-hydroxylase-2-gene
#8
Xin Jin, Chao Bai, Ludovic Bassie, Carmina Nogareda, Ignacio Romagosa, Richard M Twyman, Paul Christou, Changfu Zhu
The maize (Zea mays) enzyme β-carotene hydroxylase 2 (ZmBCH2) controls key steps in the conversion of β-carotene to zeaxanthin in the endosperm. The ZmBCH2 has an endosperm-preferred and developmentally regulated expression profile but the detailed regulatory mechanism is unknown. To gain insight into the regulation of ZmBCH2, we isolated 2036 bp of the 5'-flanking region which contains the 263-bp 5'-untranslated region (5'-UTR) including the first intron. We linked this to the β-glucuronidase reporter gene gusA...
November 29, 2018: New Phytologist
https://www.readbyqxmd.com/read/30485455/sequential-regiospecific-gem-diprenylation-of-tetrahydroxyxanthone-by-prenyltransferases-from-hypericum-sp
#9
Mohamed Nagia, Mariam Gaid, Eline Biedermann, Tobias Fiesel, Islam El-Awaad, Robert Hänsch, Ute Wittstock, Ludger Beerhues
Polyprenylated acylphloroglucinol derivatives, such as xanthones, are plant natural products with interesting pharmacological properties. They are difficult to synthesise chemically. Biotechnological production is desirable but requires the understanding of the biosynthetic pathways. cDNAs encoding membrane-bound aromatic prenyltransferase (aPT) enzymes from Hypericum sampsonii seedlings (HsPT8px and HsPTpat) and Hypericum calycinum cell cultures (HcPT8px and HcPTpat) were cloned and expressed in Saccharomyces cerevisiae and Nicotiana benthamiana, respectively...
November 28, 2018: New Phytologist
https://www.readbyqxmd.com/read/30485448/phylogenomics-of-endogonaceae-and-evolution-of-mycorrhizas-within-mucoromycota
#10
Ying Chang, Alessandro Desirò, Hyunsoo Na, Laura Sandor, Anna Lipzen, Alicia Clum, Kerrie Barry, Igor V Grigoriev, Francis M Martin, Jason E Stajich, Matthew E Smith, Gregory Bonito, Joseph W Spatafora
Endogonales (Mucoromycotina), composed of Endogonaceae and Densosporaceae, is the only known non-Dikarya order with ectomycorrhizal members. They also form mycorrhizal-like association with some non-Spermatophyte plants. It has been recently proposed that Endogonales were among the earliest mycorrhizal partners with land plants. It remains unknown whether Endogonales possess genomes with mycorrhizal-lifestyle signatures and whether Endogonales originated around the same time as land plants did. We sampled sporocarp tissue from four Endogonaceae collections and performed shotgun genome sequencing...
November 28, 2018: New Phytologist
https://www.readbyqxmd.com/read/30485444/long-distance-pollen-dispersal-during-recent-colonization-favors-a-rapid-but-partial-recovery-of-genetic-diversity-in-picea-sitchensis
#11
Joane S Elleouet, Sally N Aitken
Tree species in the northern hemisphere are currently subject to rapid anthropogenic climate change and are shifting their ranges in response. This prompts questions about the mechanisms allowing tree populations to respond quickly to selection pressures when establishing into new areas. Focusing on the northern expanding range edge of Picea sitchensis, a widespread conifer of western North America, we ask how genetic structure and diversity develop during colonization, and assess the role of demographic history in shaping the evolutionary trajectory of an establishing population...
November 28, 2018: New Phytologist
https://www.readbyqxmd.com/read/30485443/the-macroecology-and-macroevolution-of-plant-species-at-risk
#12
T Jonathan Davies
Current rates of extinction are unprecedented in human history. The fossil record and newer molecular phylogenies illuminate historical patterns of speciation and extinction. They reveal both spectacular radiations and the characteristic features of mass extinction events in our geological past. The IUCN Red List provides insight into present-day species declines. There is emerging synthesis that species at risk are nonrandomly distributed across space and phylogeny. This pattern may be explained by geographical variation in driver intensity and species differential sensitivities...
November 28, 2018: New Phytologist
https://www.readbyqxmd.com/read/30484867/bicellular-pollen-1-is-a-modulator-of-dna-replication-and-pollen-development-in-arabidopsis
#13
Yan-Ping Long, Dong-Jiang Xie, Yan-Yan Zhao, Dong-Qiao Shi, Wei-Cai Yang
During male gametogenesis in Arabidopsis, the haploid microspore undergoes an asymmetric division to produce a vegetative and a generative cell, the latter continues to divide symmetrically to form two sperms. This simple system couples cell cycle with cell fate specification. Here we addressed the role of DNA replication in male gametogenesis using a mutant bicellular pollen 1 (bice1) which produces bicellular, rather than tricellular pollen grains as in wild-type plant at anthesis. The mutation prolonged DNA synthesis of the generative cell, which resulted in about 40% pollen grains arrested at two nucleate stage...
November 28, 2018: New Phytologist
https://www.readbyqxmd.com/read/30481367/biome-evolution-of-a-crucial-ecological-and-biogeographical-concept
#14
Ladislav Mucina
Biome is and remains a key community ecological and biogeographical concept and as such profited from overall progress of community ecology which was punctuated by two major innovations: shifting focus from pure pattern description to understanding functionality, changing approach from observational to explanatory and, most importantly, from descriptive to predictive. The functional focus enabled development of mechanistic and function-focused predictive and retrodictive modelling; it also shaped the current understanding of the concept of biome as a dynamic biological entity having many faces, deep roots in evolutionary past, and undergoing changes...
November 27, 2018: New Phytologist
https://www.readbyqxmd.com/read/30472753/oxidosqualene-cyclase-and-cyp716-enzymes-contribute-to-the-triterpene-structural-diversity-in-the-medicinal-tree-banaba
#15
Sandeep, Rajesh Chandra Misra, Chandan Singh Chanotiya, Pradipto Mukhopadhyay, Sumit Ghosh
Pentacyclic triterpenes (PCTs) represent a major class of bioactive metabolites in banaba (Lagerstroemia speciosa) leaves; however, biosynthetic enzymes and their involvement in temporal accumulation of PCTs are still not studied. We employed an integrated approach involving transcriptomics, metabolomics and gene function analysis to identify oxidosqualene cyclases (OSCs) and cytochrome P450 monooxygenases (P450s) that catalyzed sequential cyclization and oxidative reactions towards PCT scaffold diversification...
November 24, 2018: New Phytologist
https://www.readbyqxmd.com/read/30471231/monkeyflowers-mimulus-new-model-for-plant-developmental-genetics-and-evo-devo
#16
REVIEW
Yao-Wu Yuan
Contents Summary I. Introduction II. The system III. Regulation of carotenoid pigmentation IV. Formation of periodic pigmentation patterns V. Developmental genetics of corolla tube formation and elaboration VI. Molecular basis of floral trait variation underlying pollinator shift VII. Outlook Acknowledgements References SUMMARY: Monkeyflowers (Mimulus) have long been recognized as a classic ecological and evolutionary model system. However, only recently has it been realized that this system also holds great promise for studying the developmental genetics and evo-devo of important plant traits that are not found in well-established model systems such as Arabidopsis...
November 24, 2018: New Phytologist
https://www.readbyqxmd.com/read/30471121/identification-and-characterization-of-the-rice-pre-harvest-sprouting-mutants-involved-in-molybdenum-cofactor-biosynthesis
#17
Xin Liu, Jing Wang, Yang Yu, Lina Kong, Yimei Liu, Zhiqi Liu, Hongyu Li, Piwei Wei, Minglong Liu, Hai Zhou, Qingyu Bu, Jun Fang
In cereal crops, ABA deficiency during seed maturation phase causes pre-harvest sprouting (PHS), and molybdenum cofactor (MoCo) is required for ABA biosynthesis. Here, two rice PHS mutants F254 and F5-1 were characterized. In addition to the PHS, these mutants showed pleiotropic phenotypes such as twisting and slender leaves, and then died when the seedling developed to four or five leaves. Map-based cloning showed that OsCNX6 and OsCNX1 encoding homologs of MoaE and MoeA were responsible for F254 and F5-1 mutants, respectively...
November 24, 2018: New Phytologist
https://www.readbyqxmd.com/read/30461018/a-domestication-associated-reduction-in-k-preferring-hkt-transporter-activity-underlies-maize-shoot-k-accumulation-and-salt-tolerance
#18
Yibo Cao, Xiaoyan Liang, Pan Yin, Ming Zhang, Caifu Jiang
Maize was domesticated from balsas teosinte c. 10000 yr ago. Previous studies have suggested that increased tolerance to environmental stresses have occurred during maize domestication. However, the underlying genetic basis remains largely unknown. We here employ a maize(W22)-teosinte recombinant inbred line (RIL) population to investigate the salt-tolerance aspects of maize domestication. We revealed that ZmHKT2 is a major QTL regulating K+ homeostasis in saline soils. Whilst ZmHKT2 encodes a K+ -preferring HKT family transporter and likely reduces shoot K+ content by removing K+ ions from root-to-shoot flowing xylem sap, ZmHKT2 deficiency increases xylem sap and shoot K+ concentrations, and increases salt tolerance...
November 21, 2018: New Phytologist
https://www.readbyqxmd.com/read/30451299/high-carbon-storage-in-carbon-limited-trees
#19
Raphael Weber, Arthur Gessler, Günter Hoch
The concentrations of nonstructural carbohydrates (NSC) in plant tissues are commonly used as an indicator of total plant carbon (C) supply; but some evidence suggests the possibility for high NSC concentrations during periods of C-limitation. Despite this uncertainty, NSC dynamics have not been investigated experimentally under long-term C-limitation. We exposed saplings of 10 temperate tree species differing in shade tolerance to 6% of ambient sunlight for 3 yr to induce C-limitation, and also defoliated one species, Carpinus betulus, in the third season...
November 19, 2018: New Phytologist
https://www.readbyqxmd.com/read/30451288/cautionary-notes-on-the-use-of-agrobacterium-mediated-transient-gene-expression-upon-sgt1-silencing-in-nicotiana-benthamiana
#20
Gang Yu, Liu Xian, Yuying Sang, Alberto P Macho
The suppressor of the G2 allele of skp1 (SGT1) is an essential component of the plant immune system, required for the induction of disease resistance mediated by many intracellular immune receptors containing nucleotide-binding and leucine-rich repeat domains (NLRs) (Azevedo et al., 2002; Kadota et al., 2010). Accordingly, virus-induced gene silencing (VIGS) of SGT1 in Nicotiana benthamiana is commonly used to test for immune- or SGT1-dependence of hypersensitive response (HR), or HR-like cell death induced by pathogen effectors, elicitors, or heterologous protein overexpression (Supporting table 1)...
November 19, 2018: New Phytologist
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