Impacts of freshwater aquaculture on fish communities: A whole‐ecosystem experimental approach

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Effects of rhizoma peanut cultivars (Arachis glabrata Benth.) on the soil bacterial diversity and predicted function in nitrogen fixation

There is a growing awareness of the importance of soil microorganisms in agricultural management practices. Currently, much less is known about whether different crop cultivar has an effect on the taxonomic structure and diversity, and specific functions of soil bacterial communities. Here, we examined the changes of the diversity and composition and enzyme‐encoding nitrogenase genes in a long‐term field experiment with seven different rhizoma peanut cultivars in southeastern USA, coupling high‐throughput 16S rRNA gene sequencing and the sequence‐based function prediction with Tax4Fun. Of the 32 phyla detected (Proteobacteria class), 13 were dominant: Acidobacteria, Alphaproteobacteria, Actinobacteria, Betaproteobacteria, Bacteroidetes, Verrucomicrobia, Gammaproteobacteria, Deltaproteobacteria, Gemmatimonadetes, Firmicutes, Nitrospirae, Chloroflexi, and Planctomycetes (relative abundance >1%). We found no evidence that the diversity and composition of bacterial communities were significantly different among different cultivars, but the abundance of some dominant bacterial groups that have N‐fixation potentials (at broad or fine taxonomic level) and predicted abundances of some enzyme‐encoding nitrogenase genes showed significant across‐cultivar differences. The nitrogenase genes were notably abundant in Florigraze and Latitude soils while remarkably lower in Arbook and UF_TITO soils when compared with other cultivars, indicating different nitrogen fixation potentials among different cultivars. The findings also suggest that the abundance of certain bacterial taxa and the specific function bacteria perform in ecosystems can have an inherent association. Our study is helpful to understand how microbiological responses and feedback to different plant genotypes through the variation in structure and function of their communities in the rhizosphere.     

LLY-507, a Cell-active,Potent, and Selective Inhibitor of Protein-lysine Methyltransferase SMYD2

SMYD2 is a lysine methyltransferase that catalyzes the monomethylation of several protein substrates including p53. SMYD2 is overexpressed in a significant percentage of esophageal squamous primary carcinomas, and that overexpression correlates with poor patient survival. However, the mechanism(s) by which SMYD2 promotes oncogenesis is not understood. A small molecule probe for SMYD2 would allow for the pharmacological dissection of this biology. In this report, we disclose LLY-507, a cell-active, potent small molecule inhibitor of SMYD2. LLY-507 is >100-fold selective for SMYD2 over a broad range of methyltransferase and non-methyltransferase targets. A 1.63-Å resolution crystal structure of SMYD2 in complex with LLY-507 shows the inhibitor binding in the substrate peptide binding pocket. LLY-507 is active in cells as measured by reduction of SMYD2-induced monomethylation of p53 Lys³⁷⁰ at submicromolar concentrations. We used LLY-507 to further test other potential roles of SMYD2. Mass spectrometry-based proteomics showed that cellular global histone methylation levels were not significantly affected by SMYD2 inhibition with LLY-507, and subcellular fractionation studies indicate that SMYD2 is primarily cytoplasmic, suggesting that SMYD2 targets a very small subset of histones at specific chromatin loci and/or non-histone substrates. Breast and liver cancers were identified through in silico data mining as tumor types that display amplification and/or overexpression of SMYD2. LLY-507 inhibited the proliferation of several esophageal, liver, and breast cancer cell lines in a dose-dependent manner. These findings suggest that LLY-507 serves as a valuable chemical probe to aid in the dissection of SMYD2 function in cancer and other biological processes.     

Whole Exome Sequencing of Distant Relatives in Multiplex Families Implicates Rare Variants in Candidate Genes for Oral Clefts

A dozen genes/regions have been confirmed as genetic risk factors for oral clefts in human association and linkage studies, and animal models argue even more genes may be involved. Genomic sequencing studies should identify specific causal variants and may reveal additional genes as influencing risk to oral clefts, which have a complex and heterogeneous etiology. We conducted a whole exome sequencing (WES) study to search for potentially causal variants using affected relatives drawn from multiplex cleft families. Two or three affected second, third, and higher degree relatives from 55 multiplex families were sequenced. We examined rare single nucleotide variants (SNVs) shared by affected relatives in 348 recognized candidate genes. Exact probabilities that affected relatives would share these rare variants were calculated, given pedigree structures, and corrected for the number of variants tested. Five novel and potentially damaging SNVs shared by affected distant relatives were found and confirmed by Sanger sequencing. One damaging SNV in CDH1, shared by three affected second cousins from a single family, attained statistical significance (P = 0.02 after correcting for multiple tests). Family-based designs such as the one used in this WES study offer important advantages for identifying genes likely to be causing complex and heterogeneous disorders.     

Strategies for rapidly mapping proviral integration sites and assessing cardiogenic potential of nascent human induced pluripotent stem cell clones

Recent methodological advances have improved the ease and efficiency of generating human induced pluripotent stem cells (hiPSCs), but this now typically results in a greater number of hiPSC clones being derived than can be wholly characterized. It is therefore imperative that methods are developed which facilitate rapid selection of hiPSC clones most suited for the downstream research aims. Here we describe a combination of procedures enabling the simultaneous screening of multiple clones to determine their genomic integrity as well as their cardiac differentiation potential within two weeks of the putative reprogrammed colonies initially appearing. By coupling splinkerette-PCR with Ion Torrent sequencing, we could ascertain the number and map the proviral integration sites in lentiviral-reprogrammed hiPSCs. In parallel, we developed an effective cardiac differentiation protocol that generated functional cardiomyocytes within 10 days without requiring line-specific optimization for any of the six independent human pluripotent stem cell lines tested. Finally, to demonstrate the scalable potential of these procedures, we picked 20 nascent iPSC clones and performed these independent assays concurrently. Before the clones required passaging, we were able to identify clones with a single integrated copy of the reprogramming vector and robust cardiac differentiation potential for further analysis.     

Novel H7N9 Influenza Virus Shows Low Infectious Dose,High Growth Rate,and Efficient Contact Transmission in the Guinea Pig Model

The zoonotic outbreak of H7N9 subtype avian influenza virus that occurred in eastern China in the spring of 2013 resulted in 135 confirmed human cases, 44 of which were lethal. Sequencing of the viral genome revealed a number of molecular signatures associated with virulence or transmission in mammals. We report here that, in the guinea pig model, a human isolate of novel H7N9 influenza virus, A/Anhui/1/2013 (An/13), is highly dissimilar to an H7N1 avian isolate and instead behaves similarly to a human seasonal strain in several respects. An/13 was found to have a low 50% infectious dose, grow to high titers in the upper respiratory tract, and transmit efficiently among cocaged guinea pigs. The pH of fusion of the hemagglutinin (HA) and the binding of virus to fixed guinea pig tissues were also examined. The An/13 HA displayed a relatively elevated pH of fusion characteristic of many avian strains, and An/13 resembled avian viruses in terms of attachment to tissues. One important difference was seen between An/13 and both the H3N2 human and the H7N1 avian viruses: when inoculated intranasally at a high dose, only the An/13 virus led to productive infection of the lower respiratory tract of guinea pigs. In sum, An/13 was found to retain fusion and attachment properties of an avian influenza virus but displayed robust growth and contact transmission in the guinea pig model atypical of avian strains and indicative of mammalian adaptation.     

Specificity of the Cyanobacterial Orange Carotenoid Protein: Influences of Orange Carotenoid Protein and Phycobilisome Structures

Cyanobacteria have developed a photoprotective mechanism that decreases the energy arriving at the reaction centers by increasing thermal energy dissipation at the level of the phycobilisome (PB), the extramembranous light-harvesting antenna. This mechanism is triggered by the photoactive Orange Carotenoid Protein (OCP), which acts both as the photosensor and the energy quencher. The OCP binds the core of the PB. The structure of this core differs in diverse cyanobacterial strains. Here, using two isolated OCPs and four classes of PBs, we demonstrated that differences exist between OCPs related to PB binding, photoactivity, and carotenoid binding. Synechocystis PCC 6803 (hereafter Synechocystis) OCP, but not Arthrospira platensis PCC 7345 (hereafter Arthrospira) OCP, can attach echinenone in addition to hydroxyechinenone. Arthrospira OCP binds more strongly than Synechocystis OCP to all types of PBs. Synechocystis OCP can strongly bind only its own PB in 0.8 m potassium phosphate. However, if the Synechocystis OCP binds to the PB at very high phosphate concentrations (approximately 1.4 m), it is able to quench the fluorescence of any type of PB, even those isolated from strains that lack the OCP-mediated photoprotective mechanism. Thus, the determining step for the induction of photoprotection is the binding of the OCP to PBs. Our results also indicated that the structure of PBs, at least in vitro, significantly influences OCP binding and the stabilization of OCP-PB complexes. Finally, the fact that the OCP induced large fluorescence quenching even in the two-cylinder core of Synechococcus elongatus PBs strongly suggested that OCP binds to one of the basal allophycocyanin cylinders.The cyanobacterial Orange Carotenoid Protein (OCP) is a photoactive soluble protein of 35 kD that binds a ketocarotenoid, 3′-hydroxyechinenone (hECN). It is present in the majority of phycobilisome (PB)-containing cyanobacterial strains (Kirilovsky and Kerfeld, 2012, 2013). The PBs are light-harvesting extramembrane complexes formed by a core from which rods radiate. The core and rods are constituted of water-soluble blue and red phycobiliproteins, which covalently attach bilins (for review, see Glazer, 1984; Grossman et al., 1993; MacColl, 1998; Tandeau de Marsac, 2003; Adir, 2005). The OCP was first described by Holt and Krogmann (1981), and its structure was determined in 2003 (Kerfeld et al., 2003). However, its function was discovered only in 2006 (Wilson et al., 2006) and its photoactivity in 2008 (Wilson et al., 2008). The OCP is essential in a photoprotective mechanism that decreases the energy arriving at the reaction centers under high irradiance. Strong light induces thermal dissipation of the energy absorbed by the PBs, resulting in a decrease of PB fluorescence emission and of energy transfer from the PBs to the reaction centers (Wilson et al., 2006). This process, which is light intensity dependent, is induced by blue or green light but not by orange or red light (Rakhimberdieva et al., 2004; Wilson et al., 2006). The absorption of strong blue-green light by the OCP induces changes in the conformation of the carotenoid, converting the inactive orange dark form (OCP^o) into an active red form (OCP^r; Wilson et al., 2008). In OCP^o, the hECN is in an all-trans-configuration (Kerfeld et al., 2003; Polívka et al., 2005). In OCP^r, the apparent conjugation length of the carotenoid increases, resulting in a less distorted, more planar structure (Wilson et al., 2008). Fourier transform infrared spectra showed that conformational changes in the protein are also induced (Wilson et al., 2008) that are essential for the induction of the photoprotective mechanism. Only OCP^r is able to bind to the core of PBs and to induce thermal energy dissipation (Wilson et al., 2008; Punginelli et al., 2009; Gorbunov et al., 2011; Gwizdala et al., 2011). Since the photoactivation of the OCP has a very low quantum yield (0.03; Wilson et al., 2008), the concentration of activated protein is zero in darkness and very low under low-light conditions (Wilson et al., 2008; Gorbunov et al., 2011). Thus, the photoprotective mechanism functions only under high-light conditions.The crystal structures of the Arthrospira maxima OCP and of the Synechocystis PCC 6803 (hereafter Synechocystis) OCP were solved in 2003 and 2010, respectively (Kerfeld et al., 2003; Wilson et al., 2010). These structures, assumed to correspond to the dark OCP^o form, are essentially identical. The OCP consists of an all-α-helical N-terminal domain (residues 1–165), unique to cyanobacteria, and an α-helical/β-sheet C-terminal domain that is a member of the Nuclear Transport Factor2 superfamily (residues 191–320; Synechocystis numbering). Both domains are joined by a linker (residues 166–190; Synechocystis numbering) that appears to be flexible. The hECN molecule spans the N- and C-terminal domains of the protein, with its carbonyl end embedded in and hydrogen bonded to two absolutely conserved residues (Tyr-201 and Trp-288) in the C-terminal domain. The carotenoid is almost entirely buried; only 3.4% of the 3′ hECN is solvent exposed (Kerfeld et al., 2003). Synechocystis OCP can also bind with high-affinity echinenone (ECN) and zeaxanthin. While the ECN OCP is photoactive, the zeaxanthin OCP is photoinactive (Punginelli et al., 2009), indicating the importance of the carotenoid carbonyl group for photoactivity. The largest interface through which the two domains interact and through which the carotenoid passes is stabilized by a small number of hydrogen bonds, including one formed between Arg-155 and Glu-244 (Wilson et al., 2010). This salt bridge stabilizes the closed structure of OCP^o. Upon illumination, protein conformational changes cause the breakage of this bond and the opening of the protein (Wilson et al., 2012). Arg-155, which becomes more exposed upon the separation of the two domains, is essential for the OCP^r binding to the PBs (Wilson et al., 2012).After exposure to high irradiance, when the light intensity decreases, recovery of full antenna capacity and fluorescence requires another protein, the Fluorescence Recovery Protein (FRP; Boulay et al., 2010). The active form of this soluble 13-kD protein is a dimer (Sutter et al., 2013). It interacts with the OCP^r C-terminal domain (Boulay et al., 2010; Sutter et al., 2013). This accelerates the red-to-orange OCP conversion and helps the OCP to detach from the PB (Boulay et al., 2010; Gwizdala et al., 2011).Genes encoding the full-length OCP are found in the vast majority of cyanobacteria but not in all; 90 of 127 genomes recently surveyed contain at least one gene for a full-length OCP (Kirilovsky and Kerfeld, 2013). The genomes of Synechococcus elongatus and Thermosynechococcus elongatus, two cyanobacterial strains used as model organisms in photosynthesis and stress studies, do not contain a full-length ocp gene. These strains also lack FRP and β-carotene ketolase (involved in ketocarotenoid synthesis). As a consequence, these strains lack the OCP-related photoprotective mechanism and are more sensitive to fluctuating light intensities (Boulay et al., 2008).The core of the hemidiscoidal PBs of Synechocystis, the model organism routinely used for the study of the OCP-related photoprotective mechanism, consists of three cylinders, each one formed by four trimers of allophycocyanin (APC; Fig. 1; for review, see Glazer, 1984; Bryant, 1991; Grossman et al., 1993; MacColl, 1998; Adir, 2005). The APC trimers are predominantly assembled from a two-subunit heterodimer, αAPC-βAPC, which binds two phycocyanobilins, one in each subunit. Of the 12 total APC trimers in the PB core, eight are trimers of αAPC-βAPC. These trimers have a maximal emission at 660 nm (APC₆₆₀). The upper cylinder contains only APC₆₆₀ trimers. In contrast, each basal cylinder contains only two APC₆₆₀ trimers. Each basal cylinder also contains the following: (1) a trimer in which one αAPC subunit is replaced by a special αAPC-like subunit called ApcD, and (2) a trimer in which one β-subunit is replaced by ApcF, a βAPC-like subunit, and one α-subunit is replaced by the N-terminal domain of ApcE, an αAPC-like domain (Fig. 1). The trimers containing one or two of these special subunits have a maximal emission at 680 nm (APC₆₈₀). In each cylinder, the two external trimers are stabilized by an 8.7-kD linker protein.Open in a separate windowFigure 1.Schematic orthogonal projections of the various PB cores. In the PBs containing three or five cylinders, the top complete cylinder is formed by four αAPC-βAPC trimers emitting at 660 nm. Each of the basal cylinders of three types of PBs contains two αAPC-βAPC trimers emitting at 660 nm and two trimers emitting at 683 nm. In one of them, one αAPC is replaced by ApcD, and in the other one, αAPC-βAPC is replaced by the dimer ApcF-ApcE. In the five cylinder PBs, two additional semicylinders formed by two αAPC-βAPC trimers are present. In all the cylinders, the two external trimers include an 8.7-kD linker protein (ApcC).The C-terminal part of Synechocystis ApcE contains three interconnected repeated domains of about 120 residues (called Rep domains) that are similar to the conserved domains of rod linkers. Each Rep domain interacts with an APC trimer situated in different cylinders, which stabilizes the core of PB (Zhao et al., 1992; Shen et al., 1993; Ajlani et al., 1995; Ajlani and Vernotte, 1998). The ApcE protein also determines the number of APC cylinders that form the PB core (Capuano et al., 1991, 1993). Indeed, there are PBs containing only the two basal cylinders, as in S. elongatus (ex S. elongatus PCC 7942) and Synechococcus PCC 6301. In these strains, the approximately 72-kD ApcE possesses only two Rep domains. There also exist pentacylindrical cores in which, in addition to the three cylinders existing in Synechocystis PBs, there are two other cylinders, each formed by two APC₆₆₀ trimers, for example in Anabaena variabilis, Anabaena PCC 7120, and Mastigocladus laminosus (Glauser et al., 1992; Ducret et al., 1998). In the pentacylindrical PBs, ApcE (approximately 125 kD) contains four Rep domains (Capuano et al., 1993). Finally, ApcE is also involved in the interaction between the PB and the thylakoids.The bicylindric and tricylindric cores are surrounded by six rods formed generally by three hexamers of the blue phycocyanin (PC) or two PC hexamers and one hexamer containing phycoerythrin or phycoerythrincyanonin. The rods and the hexamers are stabilized by nonchromophorylated linker proteins. A linker protein, L^RC also stabilizes the binding of the rods to the core. The pentacylindric PBs can contain up to eight rods. The quantity and length of rods and the presence of phycoerythrin or phycoerythrocyanin at the periphery of the rods depends on environmental conditions like light intensity or quality (Kipe-Nolt et al., 1982; Glauser et al., 1992).The OCP probably binds to one of the APC₆₆₀ trimers (Tian et al., 2011, 2012; Jallet et al., 2012), and the presence of the rods stabilizes this binding to Synechocystis PBs (Gwizdala et al., 2011). The different structures of PBs in other strains could affect the binding of the OCP. Thus, we undertook a study about the relationship between the structure of PBs and OCP binding in preparation for introducing the OCP-related photoprotective mechanism into S. elongatus using Synechocystis genes. In this study, we used the in vitro reconstitution system developed by Gwizdala et al. (2011) with three different types of isolated PBs: Arthrospira platensis PCC 7345 (hereafter Arthrospira) PBs, having a tricylindrical core like Synechocystis PBs; Anabaena variabilis (hereafter Anabaena) PBs, having a pentacylindrical core; and S. elongatus PCC 7942 (hereafter Synechococcus) PBs, having a bicylindrical core. We also used two different OCPs, the Synechocystis OCP and the Arthrospira OCP. Each OCP was isolated from mutant Synechocystis cells overexpressing one or the other ocp gene with a C-terminal His tag.