Patterns of pigment changes in apple fruits during adaptation to high sunlight and sunscald development

Reflectance spectra of four apple (Malus domestica Borkh.) cultivars were studied and chlorophyll, carotenoid, anthocyanin and flavonoid content in sunlit and shaded peel was determined. In all cases sunlit peel accumulated high amounts of phenolics (flavonoid glycosides). Adaptation to strong sunlight of an apple cultivar with limited potential for anthocyanin biosynthesis (Antonovka) was accompanied by a decrease in chlorophyll and a significant increase in total carotenoid content. The increase in carotenoids also took place in sunlit sides of the Zhigulevskoye fruits, accumulating high amounts of anthocyanins, but chlorophyll content in sunlit peel was higher than that in shaded peel. Significant increases in carotenoids and anthocyanins were detected during fruit ripening when chlorophyll content fell below 1.5–1.8 nmol cm^–2. Chlorophyll in sunlit fruit surfaces of both cultivars was considerably more resistant to photobleaching than in shaded (especially of Zhigulevskoye) sides. Induced by sun irradiation, the photoadaptive responses were cultivar-dependent and expressed at different stages of fruit ripening even after storage in darkness. The development of sunscald symptoms in susceptible apple cultivars (Granny Smith and Renet Simirenko) led to a dramatic loss of chlorophylls and carotenoids, which was similar to that observed during artificial photobleaching. The results suggest that apple fruits exhibit a genetically determined strategy of adaptation of their photoprotective pigments to cope with mediated by reactive oxygen species photodynamic activity of chlorophyll under strong solar irradiation. This includes induction of synthesis and accumulation of flavonoids, anthocyanins and carotenoids that could be expressed, if necessary, at different stages of fruit development     

Complete Genome Sequence of “Candidatus Portiera aleyrodidarum” BT-QVLC,an Obligate Symbiont That Supplies Amino Acids and Carotenoids to Bemisia tabaci

The genome of “Candidatus Portiera aleyrodidarum,” the primary endosymbiont of the whitefly Bemisia tabaci (Mediterranean species), is reported. It presents a reduced genome (357 kb) encoding the capability to synthetize, or participate in the synthesis of, several amino acids and carotenoids, being the first insect endosymbiont capable of supplying carotenoids.     

Role of carotenoids in the phototropic response of corn seedlings

The herbicide, 4 chloro-5-(methylamino)-2-(α,α,α,-trifluoro-m-tolyl)-3 (2H)-pyridazinone (SAN 9789), which blocks the synthesis in higher plants of colored carotenoids but not of flavins, was used to examine the involvement of carotenoids in corn seedling phototropism. It was concluded that “bulk” carotenoids are not the photoreceptor pigment based on the results that increasing concentrations of SAN 9789 (up to 100 micromolar) did not alter the phototropic sensitivity to 380 nanometers light (using geotropism as a control) and did not increase the threshold intensities of fluence response curves for both 380 and 450 nanometers light even though carotenoid content was reduced to 1 to 2% of normal. SAN 9789 treatment, however, did reduce seedling sensitivity toward 450 nanometers light indicating that carotenoids are involved in phototropism. Carotenoids, which are located mainly in the primary leaves, may act in phototropism as an internal screen, enhancing the light intensity gradient across the seedling and thus contributing to the ability of the seedling to perceive light direction. These results indicate that the action spectra for phototropic responses can be significantly affected by the absorbance of screening pigments in vivo thus altering its shape from the in vitro absorption spectrum of the photoreceptor pigment.     

Evaluation of Linkage Disequilibrium Pattern and Association Study on Seed Oil Content in Brassica napus Using ddRAD Sequencing

High-density genetic markers are the prerequisite for understanding linkage disequilibrium (LD) and genome-wide association studies (GWASs) of complex traits in crops. To evaluate the LD pattern in oilseed rape, we sequenced a previous association panel containing 189 B. napus inbred lines using double-digested restriction-site associated DNA (ddRAD) and genotyped 19,327 RAD tags. A total of 15,921 RAD tags were assigned to a published genetic linkage map and the majority (71.1%) of these tags was uniquely mapped to the draft reference genome “Darmor-bzh.” The distance of LD decay was 1,214 kb across the genome at the background level (r² = 0.26), with the distances of LD decay being 405 kb and 2,111 kb in the A and C subgenomes, respectively. A total of 361 haplotype blocks with length > 100 kb were identified in the entire genome. The association panel could be classified into two groups, P1 and P2, which are essentially consistent with the geographical origins of varieties. A large number of group-specific haplotypes were identified, reflecting that varieties in the P1 and P2 groups experienced distinct selection in breeding programs to adapt their different growth habitats. GWAS repeatedly detected two loci significantly associated with oil content of seeds based on the developed SNPs, suggesting that the high-density SNPs were useful for understanding the genetic determinants of complex traits in GWAS.     

Efficient Agrobacterium-mediated genetic transformation method using hypocotyl explants of radish (Raphanus sativus L.)

To investigate the gene function of radish (Raphanus sativus L.), several attempts have been made to generate genetically transformed radish. However, no efficient and relatively simple method for the genetic transformation of radish has been developed to date. In this study, we established an Agrobacterium-mediated genetic transformation method using the hypocotyl-derived explants of radish cultivar “Pirabikku”. Primarily based on the Brassica transformation procedure, we optimized it for radish transformation. Using this system, the transformation efficiency of radish hypocotyl explants by Agrobacterium tumefaciens strain GV3101 harboring pIG121-Hm was 13.3%. The copy number of transfer DNA integrated into the genome was either one or two in the four independent transgenic plants. Two of the four plants exhibited male sterility and did not produce self-pollinated seeds. Examination of the expression of the β-glucuronidase (GUS) gene in T₁ plants from fertile T₀ plants showed that the GUS genes were inherited. The improvement in the genetic transformation in this study might pave the way for accelerated molecular breeding and genetic analysis of radish.     

Kinetic comparison of cytokinin nucleosidase activity isolated from normally ripening and mutant tomato varieties

Kinetic parameters for cytokinin nucleosidase activity which catalyzes the deribosylation of N⁶(Δ²-isopentenyl)adenosine (I⁶Ado) to produce the more “active” free base N⁵(Δ²-isopenetyl)adenine (I⁶Ade) were compared for a normally ripening tomato (Lycopersicon esculentum L.) cultivar Rutgers, and two mutant tomato varieties (Nor and Rin). K_m for nucleosidase activity in Rutgers was lower (K_m = 0.1 millimolar) than that in either Nor (K_m = 0.14 millimolar) or Rin (K_m = 0.13 millimolar).     

Bioactive Compounds of Fruit Parts of Three Eugenia uniflora Biotypes in Four Ripening Stages

Variability of secondary metabolites in edible (peel and pulp) and inedible (seeds) parts of three pitanga varieties, red, red-orange and purple, was investigated during the maturation process. Hydrolysable tannins, anthocyanins, and flavonoids were quantified by HPLC/DAD and carotenoids by absorbance. Peel/pulp showed greater complexity of constituents (carotenoids, anthocyanins, flavonoids, and hydrolysable tannins), while only tannins were identified in seeds, but in quantities of 10 to 100 times greater. The red-orange variety showed the highest levels of phenolic compounds in seeds and peel/pulp, except anthocyanins. The analysis of the principal response curves showed that the pitanga biotype has greater influence on metabolite variation than ripening stages. During peel/pulp maturation, a reduction in the levels of flavonoids and tannins contrasted with an increase in carotenoids and cyanidin-3-O-glucoside in all varieties, whereas in the seeds oenothein B, the major tannin, increased up to 1.32 g/100 g fresh weight. Such marked differences between fruit parts demonstrate that the seeds in stages E3 and E4 are a source of hydrolysable tannins, compounds known for their antitumor activity, while peel/pulp of all varieties in the ripe stage provide natural antioxidants, such as carotenoids and flavonoids. Lastly, the purple biotype can be a rich source of the cyanidin-3-O-glucoside pigment a potent bioactive compound.     

Plastid genome sequencing,identification of nuclear SNP markers,and quality assessment of medicinal rhizomatous herb Polygonatum odoratum (Asparagaceae) cultivars

Polygonatum odoratum (Mill.) Druce (Asparagaceae, Asparagales) is a widely cultivated medicinal herb in China. However, this useful herb is understudied despite being known as a medicinal resource with top grade medical and edible properties since long. In this study, P. odoratum and four cultivars were investigated. The variations in morphological characteristics and vegetative phases of each cultivar were observed. For genetic aspect, the plastid genome of P. odoratum varies in length from 154,569 bp to 155,491 bp, containing a large single‐copy region of 83,486–84,459 bp, a small single‐copy region of 18,292–18,471 bp, and two inverted repeats of 26,302–26,370 bp. A total of 131 genes were predicted, including 85 protein‐coding, 38 tRNA, and eight rRNA genes. Genome comparisons revealed a slight variation in the sequence across the five accessions, but two highly variable regions (trnC‐petN and rpl32‐trnL) were detected when comparing the four different cultivars. For the RAD‐seq markers, a total of 33.64 Gb of clean data, with an average value of 1.08 Gb per sample, were analyzed for the presence of single nucleotide polymorphisms (SNPs). Well‐resolved phylogenies of the P. odoratum cultivars are constructed; the nonmonophyletic relationship in the plastome‐based phylogenetic trees, yet monophyletic form in the RAD‐based linkage map suggested possibility of hybrid cultivar for P. odoratum “Dazhu” (GDDZ), which was further supported by morphological observations. Quality assessment based on the standards of the Chinese Pharmacopoeia on Polygonati Odorati Rhizoma (POR) on the four cultivars used in this study recorded that PORs from P. odoratum “Zhongzhu” (GDZZ) met the minimum criteria for the acceptance as raw material for medicinal drug production. This study has provided insights on the morphological variations, genetic background, and medicinal qualities of P. odoratum cultivars that could be explored for future genetic improvement as well as breeding programs of P. odoratum for POR production.     

Changes in Cytokinin Activities and Mass Spectrometric Analysis of Cytokinins in Root Exudates of Rice Plant (Oryza sativa L.) : Comparison between Cultivars Nipponbare and Akenohoshi

Changes in exudation rate and cytokinin activities in the exudates were measured in two varieties of rice (Oryza sativa L.), cv Nipponbare (a Japanese normal cultivar) and cv Akenohoshi (a high-yielding cultivar). The exudation rates of Akenohoshi, the leaves of which remained green for a longer time, were higher than those of Nipponbare after the booting stage. Cytokinin activities in the exudates of Akenohoshi were higher than those of Nipponbare during the ripening period. Cytokinins in the exudates collected during the middle of the ripening stage were analyzed with mass spectrometry using deuterium-labeled standards. trans-Zeatin, trans-ribosylzeatin, and N⁶-isopentenyladenosine were detected as free cytokinins, and zeatin was detected in the hydrolysates of highly polar fractions (“conjugated zeatin”) in the exudates of both cultivars. Conjugated zeatin was the predominant cytokinin in both cultivars. Therefore, we suggest that conjugated zeatin is an important form of cytokinin during the ripening stage. The level of each of the cytokinins in Akenohoshi was higher than that in Nipponbare. Also, we discuss the correlation between the leaf senescence and cytokinin content in root exudates.     

A Fluorescence-Based Genetic Screen to Study Retinal Degeneration in Drosophila

The Drosophila visual system has been proved to be a powerful genetic model to study eye disease such as retinal degeneration. Here, we describe a genetic method termed “Rh1::GFP ey-flp/hid” that is based on the fluorescence of GFP-tagged major rhodopsin Rh1 in the eyes of living flies and can be used to monitor the integrity of photoreceptor cells. Through combination of this method and ERG recording, we examined a collection of 667 mutants and identified 18 genes that are required for photoreceptor cell maintenance, photoresponse, and rhodopsin synthesis. Our findings demonstrate that this “Rh1::GFP ey-flp/hid” method enables high-throughput F1 genetic screens to rapidly and precisely identify mutations of retinal degeneration.     

Genetic Diversity of African and Worldwide Strains of Ralstonia solanacearum as Determined by PCR-Restriction Fragment Length Polymorphism Analysis of the hrp Gene Region

The genetic diversity among a worldwide collection of 120 strains of Ralstonia solanacearum was assessed by restriction fragment length polymorphism (RFLP) analysis of amplified fragments from the hrp gene region. Five amplified fragments appeared to be specific to R. solanacearum. Fifteen different profiles were identified among the 120 bacterial strains, and a hierarchical cluster analysis distributed them into eight clusters. Each cluster included strains belonging to a single biovar, except for strains of biovars 3 and 4, which could not be separated. However, the biovar 1 strains showed rather extensive diversity since they were distributed into five clusters whereas the biovar 2 and the biovar 3 and 4 strains were gathered into one and two clusters, respectively. PCR-RFLP analysis of the hrp gene region confirmed the results of previous studies which split the species into an “Americanum” division including biovar 1 and 2 strains and an “Asiaticum” division including biovar 3 and 4 strains. However, the present study showed that most of the biovar 1 strains, originating from African countries (Reunion Island, Madagascar, Zimbabwe, and Angola) and being included in a separate cluster, belong to the “Asiaticum” rather than to the “Americanum” division. These African strains could thus have evolved separately from other biovar 1 strains originating from the Americas.     

GABAA Receptors Containing ρ1 Subunits Contribute to In Vivo Effects of Ethanol in Mice

GABA_A receptors consisting of ρ1, ρ2, or ρ3 subunits in homo- or hetero-pentamers have been studied mainly in retina but are detected in many brain regions. Receptors formed from ρ1 are inhibited by low ethanol concentrations, and family-based association analyses have linked ρ subunit genes with alcohol dependence. We determined if genetic deletion of ρ1 in mice altered in vivo ethanol effects. Null mutant male mice showed reduced ethanol consumption and preference in a two-bottle choice test with no differences in preference for saccharin or quinine. Null mutant mice of both sexes demonstrated longer duration of ethanol-induced loss of righting reflex (LORR), and males were more sensitive to ethanol-induced motor sedation. In contrast, ρ1 null mice showed faster recovery from acute motor incoordination produced by ethanol. Null mutant females were less sensitive to ethanol-induced development of conditioned taste aversion. Measurement of mRNA levels in cerebellum showed that deletion of ρ1 did not change expression of ρ2, α2, or α6 GABA_A receptor subunits. (S)-4-amino-cyclopent-1-enyl butylphosphinic acid (“ρ1” antagonist), when administered to wild type mice, mimicked the changes that ethanol induced in ρ1 null mice (LORR and rotarod tests), but the ρ1 antagonist did not produce these effects in ρ1 null mice. In contrast, (R)-4-amino-cyclopent-1-enyl butylphosphinic acid (“ρ2” antagonist) did not change ethanol actions in wild type but produced effects in mice lacking ρ1 that were opposite of the effects of deleting (or inhibiting) ρ1. These results suggest that ρ1 has a predominant role in two in vivo effects of ethanol, and a role for ρ2 may be revealed when ρ1 is deleted. We also found that ethanol produces similar inhibition of function of recombinant ρ1 and ρ2 receptors. These data indicate that ethanol action on GABA_A receptors containing ρ1/ρ2 subunits may be important for specific effects of ethanol in vivo.     

ISCR Elements: Novel Gene-Capturing Systems of the 21st Century?

“Common regions” (CRs), such as Orf513, are being increasingly linked to mega-antibiotic-resistant regions. While their overall nucleotide sequences show little identity to other mobile elements, amino acid alignments indicate that they possess the key motifs of IS91-like elements, which have been linked to the mobility ent plasmids in pathogenic Escherichia coli. Further inspection reveals that they possess an IS91-like origin of replication and termination sites (terIS), and therefore CRs probably transpose via a rolling-circle replication mechanism. Accordingly, in this review we have renamed CRs as ISCRs to give a more accurate reflection of their functional properties. The genetic context surrounding ISCRs indicates that they can procure 5′ sequences via misreading of the cognate terIS, i.e., “unchecked transposition.” Clinically, the most worrying aspect of ISCRs is that they are increasingly being linked with more potent examples of resistance, i.e., metallo-β-lactamases in Pseudomonas aeruginosa and co-trimoxazole resistance in Stenotrophomonas maltophilia. Furthermore, if ISCR elements do move via “unchecked RC transposition,” as has been speculated for ISCR1, then this mechanism provides antibiotic resistance genes with a highly mobile genetic vehicle that could greatly exceed the effects of previously reported mobile genetic mechanisms. It has been hypothesized that bacteria will surprise us by extending their “genetic construction kit” to procure and evince additional DNA and, therefore, antibiotic resistance genes. It appears that ISCR elements have now firmly established themselves within that regimen.     

Enrichment and Genome Sequence of the Group I.1a Ammonia-Oxidizing Archaeon “Ca. Nitrosotenuis uzonensis” Representing a Clade Globally Distributed in Thermal Habitats

The discovery of ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota and the high abundance of archaeal ammonia monooxygenase subunit A encoding gene sequences in many environments have extended our perception of nitrifying microbial communities. Moreover, AOA are the only aerobic ammonia oxidizers known to be active in geothermal environments. Molecular data indicate that in many globally distributed terrestrial high-temperature habits a thaumarchaeotal lineage within the Nitrosopumilus cluster (also called “marine” group I.1a) thrives, but these microbes have neither been isolated from these systems nor functionally characterized in situ yet. In this study, we report on the enrichment and genomic characterization of a representative of this lineage from a thermal spring in Kamchatka. This thaumarchaeote, provisionally classified as “Candidatus Nitrosotenuis uzonensis”, is a moderately thermophilic, non-halophilic, chemolithoautotrophic ammonia oxidizer. The nearly complete genome sequence (assembled into a single scaffold) of this AOA confirmed the presence of the typical thaumarchaeotal pathways for ammonia oxidation and carbon fixation, and indicated its ability to produce coenzyme F₄₂₀ and to chemotactically react to its environment. Interestingly, like members of the genus Nitrosoarchaeum, “Candidatus N. uzonensis” also possesses a putative artubulin-encoding gene. Genome comparisons to related AOA with available genome sequences confirmed that the newly cultured AOA has an average nucleotide identity far below the species threshold and revealed a substantial degree of genomic plasticity with unique genomic regions in “Ca. N. uzonensis”, which potentially include genetic determinants of ecological niche differentiation.     

Interactions between meat intake and genetic variation in relation to colorectal cancer

Meat intake is associated with the risk of colorectal cancer. The objective of this systematic review was to evaluate interactions between meat intake and genetic variation in order to identify biological pathways involved in meat carcinogenesis. We performed a literature search of PubMed and Embase using “interaction”, “meat”, “polymorphisms”, and “colorectal cancer”, and data on meat–gene interactions were extracted. The studies were divided according to whether information on meat intake was collected prospectively or retrospectively. In prospective studies, interactions between meat intake and polymorphisms in PTGS2 (encoding COX-2), ABCB1, IL10, NFKB1, MSH3, XPC (P_int = 0.006, 0.01, 0.04, 0.03, 0.002, 0.01, respectively), but not IL1B, HMOX1, ABCC2, ABCG2, NR1I2 (encoding PXR), NR1H2 (encoding LXR), NAT1, NAT2, MSH6, or MLH1 in relation to CRC were found. Interaction between a polymorphism in XPC and meat was found in one prospective and one case–control study; however, the directions of the risk estimates were opposite. Thus, none of the findings were replicated. The results from this systematic review suggest that genetic variation in the inflammatory response and DNA repair pathway is involved in meat-related colorectal carcinogenesis, whereas no support for the involvement of heme and iron from meat or cooking mutagens was found. Further studies assessing interactions between meat intake and genetic variation in relation to CRC in large well-characterised prospective cohorts with relevant meat exposure are warranted.

Electronic supplementary material

The online version of this article (doi:10.1007/s12263-014-0448-9) contains supplementary material, which is available to authorized users.     

Serum Nutritional Biomarkers and Their Associations with Sleep among US Adults in Recent National Surveys

Background

The associations between nutritional biomarkers and measures of sleep quantity and quality remain unclear.

Methods

Cross-sectional data from the National Health and Nutrition Examination Surveys (NHANES) 2005–2006 were used. We selected 2,459 adults aged 20–85, with complete data on key variables. Five sleep measures were constructed as primary outcomes: (A) Sleep duration; (B) Sleep disorder; (C) Three factors obtained from factor analysis of 15 items and labeled as “Poor sleep-related daytime dysfunction” (Factor 1), “Sleepiness” (Factor 2) and “Sleep disturbance” (Factor 3). Main exposures were serum concentrations of key nutrients, namely retinol, retinyl esters, carotenoids (α-carotene, β-carotene, β-cryptoxanthin, lutein+zeaxanthin, lycopene), folate, vitamin B-12, total homocysteine (tHcy), vitamin C, 25-hydroxyvitamin D (25(OH)D) and vitamin E. Main analyses consisted of multiple linear, logistic and multinomial logit models.

Results

Among key findings, independent inverse associations were found between serum vitamin B-12 and sleep duration, 25(OH)D and sleepiness (as well as insomnia), and between folate and sleep disturbance. Serum total carotenoids concentration was linked to higher odds of short sleep duration (i.e. 5–6 h per night) compared to normal sleep duration (7–8 h per night).

Conclusions

A few of the selected serum nutritional biomarkers were associated with sleep quantity and quality. Longitudinal studies are needed to ascertain temporality and assess putative causal relationships.     

“Candidatus Accumulibacter” Population Structure in Enhanced Biological Phosphorus Removal Sludges as Revealed by Polyphosphate Kinase Genes

We investigated the fine-scale population structure of the “Candidatus Accumulibacter” lineage in enhanced biological phosphorus removal (EBPR) systems using the polyphosphate kinase 1 gene (ppk1) as a genetic marker. We retrieved fragments of “Candidatus Accumulibacter” 16S rRNA and ppk1 genes from one laboratory-scale and several full-scale EBPR systems. Phylogenies reconstructed using 16S rRNA genes and ppk1 were largely congruent, with ppk1 granting higher phylogenetic resolution and clearer tree topology and thus serving as a better genetic marker than 16S rRNA for revealing population structure within the “Candidatus Accumulibacter” lineage. Sequences from at least five clades of “Candidatus Accumulibacter” were recovered by ppk1-targeted PCR, and subsequently, specific primer sets were designed to target the ppk1 gene for each clade. Quantitative real-time PCR (qPCR) assays using “Candidatus Accumulibacter”-specific 16S rRNA and “Candidatus Accumulibacter” clade-specific ppk1 primers were developed and conducted on three laboratory-scale and nine full-scale EBPR samples and two full-scale non-EBPR samples to determine the abundance of the total “Candidatus Accumulibacter” lineage and the relative distributions and abundances of the five “Candidatus Accumulibacter” clades. The qPCR-based estimation of the total “Candidatus Accumulibacter” fraction as a proportion of the bacterial community as measured using 16S rRNA genes was not significantly different from the estimation measured using ppk1, demonstrating the power of ppk1 as a genetic marker for detection of all currently defined “Candidatus Accumulibacter” clades. The relative distributions of “Candidatus Accumulibacter” clades varied among different EBPR systems and also temporally within a system. Our results suggest that the “Candidatus Accumulibacter” lineage is more diverse than previously realized and that different clades within the lineage are ecologically distinct.     

Subcellular Localization of Zinc and Calcium in Bean (Phaseolus vulgaris L.) Tissues

Two bean (Phaseolus vulgaris L.) cultivars differing in growth responses to zinc were examined for differences in uptake and subcellular localization of ⁶⁵Zn during a 15-day growth period. The zinc-sensitive cultivar Sanilac showed initially a much higher rate of absorption, which declined after 24 hours. The zinc-tolerant cultivar Saginaw showed a slow but steady rate of absorption for 10 days. In roots as well as in stem callus tissues of both cultivars, three-fourths of the absorbed ⁶⁵Zn was localized in the “cytoplasmic” supernatant fractions (containing ribosomes and vacuolar sap). Very little (less than 7%) ⁶⁵Zn was localized in the cell wall fraction. There was a much greater proportion of the absorbed ⁶⁵Zn localized in root mitochondria and nuclei of the zinc-sensitive Sanilac than in the zinc-tolerant Saginaw. Stem callus tissues, however, did not show such cultivar differences in zinc accumulation at the sub-cellular level.