Analysis of plastid and nuclear DNA data in plant phylogenetics——evaluation and improvement

Correct combination of plastid(cp)and nuclear(nr)DNA data for plant phylogenetic reconstructions is not a new issue,but with an increasing number of nrDNA loci being used,it is of ever greater practical concern.For accurately reconstructing the phylogeny and evolutionary history of plant groups,correct treatment of phylogenetic incongruence is a vital step in the proper analysis of cpDNA and nrDNA data.We first evaluated the current status of analyzing cpDNA and nrDNA data by searching all articles published in the journal Systematic Botany between 2005 and 2011.Many studies combining cpDNA and nrDNA data did not rigorously assess the combinability of the data sets,or did not address in detail possible reasons for incongruence between the two data sets.By reviewing various methods,we outline a procedure to more accurately analyze and/or combine cpDNA and nrDNA data,which includes four steps:identifying significant incongruence,determining conflicting taxa,providing possible interpretations for incongruence,and reconstructing the phylogeny after treating incongruence.Particular attention is given to explanation of the cause of incongruence.We hope that our procedure will help raise awareness of the importance of rigorous analysis and help identify the cause of incongruence before combining cpDNA and nrDNA data.     

Inheritance and genetic mapping of two nuclear genes involved in nuclear–cytoplasmic incompatibility in peas (Pisum sativum L.)

Genetic analysis was performed to finely map and assess the mode of inheritance of two unlinked nuclear genes Scs1 and Scs2 involved in incompatibility of the nuclear genome of the cultivated pea Pisum sativum subsp. sativum with the cytoplasm of the wild pea of the subspecies P. sativum subsp. elatius, accession VIR320. Based on the segregation of genotypes in the progeny of the test-crosses, we concluded that if the cytoplasm was inherited from the wild pea VIR320, the Scs1 allele from the cultivated pea was gametophyte lethal and sporophyte recessive lethal. The Scs2 allele from the cultivated pea reduced male gametophyte viability. In homozygote, Scs2 from cultivated parent brought about nuclear–cytoplasmic conflict manifested as chlorophyll deficiency, reduction of blade organs, and low pollen fertility of about 20%. In heterozygote, Scs1 and Scs2 genes reduced pollen fertility by ca 50 and 30%, respectively. The Scs1 and Scs2 genes involved in nuclear–cytoplasmic incompatibility were genetically mapped. The distance between the markers bordering Scs1 comprised about 2.5 cM on linkage group III. The map distance between the bordering markers in the neighborhood of Scs2 varied substantially from cross to cross in the range of 2.0–15.1 cM on linkage group V.     

Effect of a small molecule inhibitor of nuclear factor-κB nuclear translocation in a murine model of arthritis and cultured human synovial cells

A small cell-permeable compound, dehydroxymethylepoxyquinomicin (DHMEQ), does not inhibit phosphorylation and degradation of IκB (inhibitor of nuclear factor-κB [NF-κB]) but selectively inhibits nuclear translocation of activated NF-κB. This study aimed to demonstrate the antiarthritic effect of this novel inhibitor of the NF-κB pathway in vivo in a murine arthritis model and in vitro in human synovial cells. Collagen-induced arthritis was induced in mice, and after onset of arthritis the mice were treated with DHMEQ (5 mg/kg body weight per day). Using fibroblast-like synoviocyte (FLS) cell lines established from patients with rheumatoid arthritis (RA), NF-κB activity was examined by electrophoretic mobility shift assays. The expression of molecules involved in RA pathogenesis was determined by RT-PCR, ELISA, and flow cytometry. The proliferative activity of the cells was estimated with tritiated thymidine incorporation. After 14 days of treatment with DHMEQ, mice with collagen-induced arthritis exhibited decreased severity of arthritis, based on the degree of paw swelling, the number of swollen joints, and radiographic and histopathologic scores, compared with the control mice treated with vehicle alone. In RA FLS stimulated with tumor necrosis factor-α, activities of NF-κB components p65 and p50 were inhibited by DHMEQ, leading to suppressed expression of the key inflammatory cytokine IL-6, CC chemokine ligand-2 and -5, matrix metalloproteinase-3, intercellular adhesion molecule-1, and vascular cell adhesion molecule-1. The proliferative activity of the cells was also suppressed. This is the first demonstration of an inhibitor of NF-κB nuclear translocation exhibiting a therapeutic effect on established murine arthritis, and suppression of inflammatory mediators in FLS was thought to be among the mechanisms underlying such an effect.     

Role of nitric oxide and nuclear factor-κB in the CYP2E1 potentiation of tumor necrosis factor α hepatotoxicity in mice

Induction of CYP2E1 by pyrazole (PY) potentiated the hepatotoxicity induced by TNFα in mice. We evaluated the role of nitrosative and oxidative stress and the NF-κB activation pathway in this liver injury. The iNOS inhibitor N-(3-aminomethyl)benzylacetamindine (1400W) or the antioxidant N-acetyl-l-cysteine (NAC) prevented this liver injury. TNFα plus PY treatment triggered radical stress in the liver with increased lipid peroxidation and decreased glutathione and caused mitochondrial damage as reflected by elevated membrane swelling and cytochrome c release. The radical stress and mitochondrial damage were prevented by 1400W and NAC. TNFα plus PY treatment elevated 3-nitrotyrosine adduct formation and induced NOS2 in the liver; 1400W and NAC blocked these changes. A lower extent of liver injury and oxidative stress was found in NOS2^?/? mice treated with TNFα plus PY compared with wild-type controls. Neither 1400W nor NAC modified CYP2E1 activity or protein. Activation of JNK and p38MAPK was weaker in TNFα plus PY-treated NOS2^?/? mice and 1400W and NAC blocked the activation of JNK and p38MAPK in wild-type mice. IKKα/β protein levels were decreased by TNFα plus PY treatment, whereas IκBα and IκBβ protein levels were elevated compared with saline, PY, or TNFα alone. NF-κB DNA binding activity was increased by TNFα alone but lowered by TNFα plus PY. All these changes were blocked by 1400W and NAC. NF-κB activation products such as Bcl-2, Bcl-X_L, cFLIP_S, cFLIP_L, and Mn-SOD were reduced by TNFα plus PY and restored by 1400W or NAC. We conclude that TNFα plus CYP2E1 induces oxidative/nitrosative stress, which plays a role in the activation of JNK or p38MAPK and mitochondrial damage. These effects combine with the blunting of the NF-κB activation pathways and the synthesis of protective factors to cause liver injury.     

Convergent evolution of gigantism in damselflies of Africa and South America? Evidence from nuclear and mitochondrial sequence data

Extreme large body size is rare in modern Zygoptera (damselflies). Only the South and Central American damselfly family Pseudostigmatidae and one African species, Coryphagrion grandis, share the morphological trait of gigantism. By means of phylogenetic analyses using two mitochondrial markers (16S rDNA and ND1) and one nuclear marker (EF1) in combination with an existing morphological data set, we trace the evolution of gigantism in damselflies. Individual and combined data sets were analyzed using the maximum parsimony, minimum evolution and maximum likelihood algorithms. Regardless of the algorithm used and the data set analyzed all principal tree topologies support a monophyly of the damselfly taxa displaying giant body size. This supports the view that the evolution of gigantism in damselflies from Africa and South America is not the result of convergent evolution due to strikingly similar habitat preferences, but rather the result of close genealogical relationship. Because modern odonates evolved before the split of Africa from Gondwanaland, the proposed phylogeny suggests that C. grandis represents a Gondwana relict.     

Perforin-dependent nuclear targeting of granzymes: A central role in the nuclear events of granule-exocytosis-mediated apoptosis?

Programmed cell death, apoptosis, involves very distinctive changes within the target cell nucleus, including margination of the chromatin, DNA fragmentation and breakdown of the nuclear envelope. Cytolytic granule-mediated target cell apoptosis is effected, in part, through synergistic action of the membrane-acting protein perforin and serine proteases, such as granzymes A or B. Recent work using confocal laser scanning microscopy as well as other techniques supports the idea that perforin-dependent translocation of granzymes to the nucleus of target cells plays a central role in effecting the nuclear changes associated with apoptosis. In vitro experiments indicate that granzyme nuclear import follows a novel pathway, being independent of ATP, not inhibitable by non-hydrolysable GTP analogues and involving binding within the nucleus, unlike conventional signal- dependent nuclear protein import. In intact cells, perforin-dependent nuclear entry of granzymes precedes the nuclear events of apoptosis such as DNA fragmentation and nuclear envelope breakdown; prevention of granzyme nuclear translocation through bcl2 overexpression or treatment of target cells with inhibitors of caspase activation blocks these events. Nuclear localization of granzymes thus appears to be central to induction of the nuclear changes associated with cytolytic granule-mediated apoptosis.     

Physiology and pathology of nuclear phospholipase C β1

The existence and function of inositide signaling in the nucleus is well documented and we know that the existence of the inositide cycle inside the nucleus has a biological role. An autonomous lipid-dependent signaling system, independently regulated from its plasma membrane counterpart, acts in the nucleus and modulates cell cycle progression and differentiation.We and others focused on PLCβ1, which is the most extensively investigated PLC isoform in the nuclear compartment. PLCβ1 is a key player in the regulation of nuclear inositol lipid signaling, and, as discussed above, its function could also be involved in nuclear structure because it hydrolyses PtdIns(4,5)P2, a well accepted regulator of chromatin remodelling. The evidence, in a number of patients with myelodysplastic syndromes, that the mono-allelic deletion of PLCβ1 is associated with an increased risk of developing acute myeloid leukemia paves the way for an entirely new field of investigation. Indeed the genetic defect evidenced, in addition to being a useful prognostic tool, also suggests that altered expression of this enzyme could have a role in the pathogenesis of this disease, by causing an imbalance between proliferation and apoptosis. The epigenetics of PLCβ1 expression in MDS has been reviewed as well.     

Daily variation in antioxidant enzymes and lipid peroxidation in lungs of a tropical bird Perdicula asiatica: role of melatonin and nuclear receptor RORα

The wild animals are exposed in nature to more oxidative stress than any laboratory animals. Studies on oxidative stress of brain, liver and kidney are quite common while very less reports are available on respiratory system when it is the most susceptible organ to various stressors. We checked the oxidative stress of lung tissue of a wild seasonally breeding bird Perdicula asiatica by noting down the daily variation in antioxidant enzymes (superoxide dismutase and catalase) levels, lipid peroxidation in terms of malondialdehyde level and total antioxidant status during reproductively active (RAP) and inactive phase (RIP). On the other hand melatonin has been accepted as free radical scavenger acting via receptor (nuclear receptor) or non receptor pathway. To pin point the role of melatonin in regulation of antioxidant enzymes via non receptor mediated pathway in lungs of bird, we checked variation in the nuclear melatonin receptor RORα. Antioxidant enzymes (superoxide dismutase and catalase) exhibited a marked 24h rhythm in lungs being high during night time and coincided almost with the peak of melatonin and total antioxidant status where as malondialdehyde level and nuclear receptor RORα showed inverse relationship with all the above mentioned parameters. These findings suggest that melatonin might be acting as an antioxidant for the free radical load of lung tissue of a tropical bird P. asiatica and its action might be via nuclear receptor RORα.     

“Self-tanning”—a new and important source of stoichiometric error in cytophotometric determination of nuclear DNA content in plants

A Feulgen-densitometric comparison of nuclear DNA contents (C-values) was performed in various plant species (a fern, four gymnosperms, 16 woody and herbaceous angiosperms) after two types of fixation, additive (neutral formaldehyde) and non-additive (methanol-acetic acid, 3:1, MAA). Nuclei from tissues containing a significant amount of polyphenols (of the hydrolysable and non-hydrolysable tannin type) always showed reduced stainability and distorted spectral absorbance curves after MAA-fixation, while after formaldehyde-fixation no evidence for distorted staining was found. No fixation-dependent differences in Feulgen-DNA contents were stated in nuclei from tissues having no polyphenols. Distorted Feulgen-staining is a consequence of cellular self-tanning during fixation. Tanning is impaired by formaldehyde which binds to tannins and inactivates them. The rationale for using formaldehyde as a fixative in Feulgen-cytophotometry can be mainly seen in its capability of eliminating the self-tanning error. Standardization in plant DNA cytophotometry, and recent reports on unorthodox nuclear DNA variation in conifers are critically discussed.The author dedicates this paper, with emotions of respect and gratitude, to emer. O. Prof. DrElisabeth Tschermak-Woess on the occasion of the 70th anniversary of her birthday. She guided his Ph.D. Thesis in the years 1968 to 1972.     

Estrogen receptor β and its domains interact with casein kinase 2, phosphokinase C, and N-myristoylation sites of mitochondrial and nuclear proteins in mouse brain

The localization of estrogen receptor (ER)β in mitochondria suggests ERβ-dependent regulation of genes, which is poorly understood. Here, we analyzed the ERβ interacting mitochondrial as well as nuclear proteins in mouse brain using pull-down assay and matrix-assisted laser desorption ionization mass spectroscopy (MALDI-MS). In the case of mitochondria, ERβ interacted with six proteins of 35-152 kDa, its transactivation domain (TAD) interacted with four proteins of 37-172 kDa, and ligand binding domain (LBD) interacted with six proteins of 37-161 kDa. On the other hand, in nuclei, ERβ interacted with seven proteins of 30-203 kDa, TAD with ten proteins of 31-160 kDa, and LBD with fourteen proteins of 42-179 kDa. For further identification, these proteins were cleaved by trypsin into peptides and analyzed by MALDI-MS using mascot search engine, immunoprecipitation, immunoblotting, and far-Western blotting. To find the consensus binding motifs in interacting proteins, their unique tryptic peptides were analyzed by the motif scan software. All the interacting proteins were found to contain casein kinase (CK) 2, phosphokinase (PK)C phosphorylation, and N-myristoylation sites. These were further confirmed by peptide pull-down assays using specific mutations in the interacting sites. Thus, the present findings provide evidence for the interaction of ERβ with specific mitochondrial and nuclear proteins through consensus CK2, PKC phosphorylation, and N-myristoylation sites, and may represent an essential step toward designing selective ER modulators for regulating estrogen-mediated signaling.     

DNA from Drosophila melanogaster β-heterochromatin binds specifically to nuclear lamins in vitro and the nuclear envelope in situ

A DNA fragment designated λ20pl.4 binds in vitro to polymerized Drosophila melanogaster lamin. In situ hybridization of λ20p1.4 to isolated polytene chromosomes revealed localization at the chromocenter and to the 49 CD region on the right arm of chromosome 2. About 120 copies of sequences homologous to λ20p1.4 were detected per haploid genome. Nucleotide (nt) sequence analysis demonstrates that λ20p1.4 is an A+T-rich, 1327-bp fragment containing four repeated units between nt 595 and 919. Results suggest that lamin interacts with a region of λ20pl.4 between nt 300 and 1000. Confocal immunofluorescence co-localization demonstrates that in situ, the major locus of λ20p1.4 hybridization, the chromocenter, is found juxtaposed to the nuclear envelope (lamina). This is the first demonstration that a DNA sequence that binds specifically to nuclear lamins in vitro, is located at or near the nuclear envelope in situ and, presumably, in vivo.     

Phosphorylation and biosynthesis of high molecular weight proteins of tumor nuclear meatrix

Our previous studies showed a predominance of high molecular weight protein group in tumor nuclear matrices.Contrary to normal cells,proteins of this group are preferentially phosphorylated.Phosphoproteins of hepatoma nuclear matrix are selectively subjected to rapid proteolysis.By alkali treatment and a monoclonal antibody against phosphotyrosyl residue the presence of two high molecular weight bands of phosphotyrosyl-containing proteins was detected in nuclear matrices of tumor but not of normal liver cells.High molecular weight protein group of tumor nuclear matrices revealed also a rapid turnover and preferential incorporation of labeled amino acids selectively inhibited by chloramphenicol.