Orbicules in Flowering Plants: A Phylogenetic Perspective on their Form and Function

Next to pollen, stamens of flowering plants often produce microstructures, called orbicules, lining the locules. Although the existence of orbicules has been known since 1865, their function still remains enigmatic. This paper surveys orbicule distribution throughout angiosperms, including +1,500 entries. We show that orbicules are found all over of flowering plants with an evolutionary trend towards orbicule absence in more derived clades. Orbicules are common in the ANITA-grade and 85 % of the monocots studied produce orbicules, with Orchidaceae, Commelinales and Zingiberales as notable exceptions. Within eudicots, asterids are most densely sampled with 61 % orbicule presence. Asteraceae and the majority of Lamiaceae lack orbicules. For 17 angiosperm orders orbicule distribution data are lacking entirely. We demonstrate that the hypothesized correlation of orbicule presence with non-amoeboid tapetum types holds true. The presence of orbicules is therefore a convenient proxy for tapetum characterization. The potential of orbicules as an a-cellular model system for patterned sporopollenin polymerization is discussed and suitable model plants for future functional orbicule-research are identified.     

Nontransgenic Genome Modification in Plant Cells

Zinc finger nucleases (ZFNs) are a powerful tool for genome editing in eukaryotic cells. ZFNs have been used for targeted mutagenesis in model and crop species. In animal and human cells, transient ZFN expression is often achieved by direct gene transfer into the target cells. Stable transformation, however, is the preferred method for gene expression in plant species, and ZFN-expressing transgenic plants have been used for recovery of mutants that are likely to be classified as transgenic due to the use of direct gene-transfer methods into the target cells. Here we present an alternative, nontransgenic approach for ZFN delivery and production of mutant plants using a novel Tobacco rattle virus (TRV)-based expression system for indirect transient delivery of ZFNs into a variety of tissues and cells of intact plants. TRV systemically infected its hosts and virus ZFN-mediated targeted mutagenesis could be clearly observed in newly developed infected tissues as measured by activation of a mutated reporter transgene in tobacco (Nicotiana tabacum) and petunia (Petunia hybrida) plants. The ability of TRV to move to developing buds and regenerating tissues enabled recovery of mutated tobacco and petunia plants. Sequence analysis and transmission of the mutations to the next generation confirmed the stability of the ZFN-induced genetic changes. Because TRV is an RNA virus that can infect a wide range of plant species, it provides a viable alternative to the production of ZFN-mediated mutants while avoiding the use of direct plant-transformation methods.Methods for genome editing in plant cells have fallen behind the remarkable progress made in whole-genome sequencing projects. The availability of reliable and efficient methods for genome editing would foster gene discovery and functional gene analyses in model plants and the introduction of novel traits in agriculturally important species (Puchta, 2002; Hanin and Paszkowski, 2003; Reiss, 2003; Porteus, 2009). Genome editing in various species is typically achieved by integrating foreign DNA molecules into the target genome by homologous recombination (HR). Genome editing by HR is routine in yeast (Saccharomyces cerevisiae) cells (Scherer and Davis, 1979) and has been adapted for other species, including Drosophila, human cell lines, various fungal species, and mouse embryonic stem cells (Baribault and Kemler, 1989; Venken and Bellen, 2005; Porteus, 2007; Hall et al., 2009; Laible and Alonso-González, 2009; Tenzen et al., 2009). In plants, however, foreign DNA molecules, which are typically delivered by direct gene-transfer methods (e.g. Agrobacterium and microbombardment of plasmid DNA), often integrate into the target cell genome via nonhomologous end joining (NHEJ) and not HR (Ray and Langer, 2002; Britt and May, 2003).Various methods have been developed to indentify and select for rare site-specific foreign DNA integration events or to enhance the rate of HR-mediated DNA integration in plant cells. Novel T-DNA molecules designed to support strong positive- and negative-selection schemes (e.g. Thykjaer et al., 1997; Terada et al., 2002), altering the plant DNA-repair machinery by expressing yeast chromatin remodeling protein (Shaked et al., 2005), and PCR screening of large numbers of transgenic plants (Kempin et al., 1997; Hanin et al., 2001) are just a few of the experimental approaches used to achieve HR-mediated gene targeting in plant species. While successful, these approaches, and others, have resulted in only a limited number of reports describing the successful implementation of HR-mediated gene targeting of native and transgenic sequences in plant cells (for review, see Puchta, 2002; Hanin and Paszkowski, 2003; Reiss, 2003; Porteus, 2009; Weinthal et al., 2010).HR-mediated gene targeting can potentially be enhanced by the induction of genomic double-strand breaks (DSBs). In their pioneering studies, Puchta et al. (1993, 1996) showed that DSB induction by the naturally occurring rare-cutting restriction enzyme I-SceI leads to enhanced HR-mediated DNA repair in plants. Expression of I-SceI and another rare-cutting restriction enzyme (I-CeuI) also led to efficient NHEJ-mediated site-specific mutagenesis and integration of foreign DNA molecules in plants (Salomon and Puchta, 1998; Chilton and Que, 2003; Tzfira et al., 2003). Naturally occurring rare-cutting restriction enzymes thus hold great promise as a tool for genome editing in plant cells (Carroll, 2004; Pâques and Duchateau, 2007). However, their wide application is hindered by the tedious and next to impossible reengineering of such enzymes for novel DNA-target specificities (Pâques and Duchateau, 2007).A viable alternative to the use of rare-cutting restriction enzymes is the zinc finger nucleases (ZFNs), which have been used for genome editing in a wide range of eukaryotic species, including plants (e.g. Bibikova et al., 2001; Porteus and Baltimore, 2003; Lloyd et al., 2005; Urnov et al., 2005; Wright et al., 2005; Beumer et al., 2006; Moehle et al., 2007; Santiago et al., 2008; Shukla et al., 2009; Tovkach et al., 2009; Townsend et al., 2009; Osakabe et al., 2010; Petolino et al., 2010; Zhang et al., 2010). Here too, ZFNs have been used to enhance DNA integration via HR (e.g. Shukla et al., 2009; Townsend et al., 2009) and as an efficient tool for the induction of site-specific mutagenesis (e.g. Lloyd et al., 2005; Zhang et al., 2010) in plant species. The latter is more efficient and simpler to implement in plants as it does not require codelivery of both ZFN-expressing and donor DNA molecules and it relies on NHEJ—the dominant DNA-repair machinery in most plant species (Ray and Langer, 2002; Britt and May, 2003).ZFNs are artificial restriction enzymes composed of a fusion between an artificial Cys₂His₂ zinc-finger protein DNA-binding domain and the cleavage domain of the FokI endonuclease. The DNA-binding domain of ZFNs can be engineered to recognize a variety of DNA sequences (for review, see Durai et al., 2005; Porteus and Carroll, 2005; Carroll et al., 2006). The FokI endonuclease domain functions as a dimer, and digestion of the target DNA requires proper alignment of two ZFN monomers at the target site (Durai et al., 2005; Porteus and Carroll, 2005; Carroll et al., 2006). Efficient and coordinated expression of both monomers is thus required for the production of DSBs in living cells. Transient ZFN expression, by direct gene delivery, is the method of choice for targeted mutagenesis in human and animal cells (e.g. Urnov et al., 2005; Beumer et al., 2006; Meng et al., 2008). Among the different methods used for high and efficient transient ZFN delivery in animal and human cell lines are plasmid injection (Morton et al., 2006; Foley et al., 2009), direct plasmid transfer (Urnov et al., 2005), the use of integrase-defective lentiviral vectors (Lombardo et al., 2007), and mRNA injection (Takasu et al., 2010).In plant species, however, efficient and strong gene expression is often achieved by stable gene transformation. Both transient and stable ZFN expression have been used in gene-targeting experiments in plants (Lloyd et al., 2005; Wright et al., 2005; Maeder et al., 2008; Cai et al., 2009; de Pater et al., 2009; Shukla et al., 2009; Tovkach et al., 2009; Townsend et al., 2009; Osakabe et al., 2010; Petolino et al., 2010; Zhang et al., 2010). In all cases, direct gene-transformation methods, using polyethylene glycol, silicon carbide whiskers, or Agrobacterium, were deployed. Thus, while mutant plants and tissues could be recovered, potentially without any detectable traces of foreign DNA, such plants were generated using a transgenic approach and are therefore still likely to be classified as transgenic. Furthermore, the recovery of mutants in many cases is also dependent on the ability to regenerate plants from protoplasts, a procedure that has only been successfully applied in a limited number of plant species. Therefore, while ZFN technology is a powerful tool for site-specific mutagenesis, its wider implementation for plant improvement may be somewhat limited, both by its restriction to certain plant species and by legislative restrictions imposed on transgenic plants.Here we describe an alternative to direct gene transfer for ZFN delivery and for the production of mutated plants. Our approach is based on the use of a novel Tobacco rattle virus (TRV)-based expression system, which is capable of systemically infecting its host and spreading into a variety of tissues and cells of intact plants, including developing buds and regenerating tissues. We traced the indirect ZFN delivery in infected plants by activation of a mutated reporter gene and we demonstrate that this approach can be used to recover mutated plants.     

Trans-Arctic dispersals and the evolution of a circumpolar marine fish species complex, the capelin (Mallotus villosus)

Trans-Arctic dispersals and population and range expansions during the Pleistocene enhanced opportunities for evolutionary diversification and contributed to the process of speciation within the capelin, a northern marine-fish complex exhibiting a circumpolar distribution. Capelin is composed of four highly divergent and geographically discrete mitochondrial DNA (mtDNA) clades (609 bp; cytochrome b). Two clades occur in the North Atlantic, one associated with Canadian Atlantic waters, including Hudson Bay, and the second distributed from West Greenland to the Barents Sea. Two additional clades occur in the Arctic and northeast Pacific Oceans, representing the most recent divergence within the capelin phylogenetic tree. Judged from mtDNA diversity, capelin populations comprising all clades experienced at least one demographic and spatial reduction-expansion episode during recent Pleistocene glaciations that imprinted their molecular architecture. The large contemporary populations in the northeast Pacific and Arctic Oceans exhibited significant genetic structure whereas no such structure was detected in the equally extensive North Atlantic clades. All clades are characterized by one or two prevalent mtDNA haplotypes distributed over the entire range of the clade. Assuming a Pacific ancestor for capelin, we infer that capelin dispersed on two separate occasions to the North Atlantic. A more recent event resulted in the isolation of eastern Pacific and Arctic clades, with the Arctic clade positioned for a potential third Atlantic invasion, as revealed by the presence of this clade in the Labrador Sea. The Labrador Sea is a potential contact zone for three of the four capelin clades.     

Iron uptake mediated by binding of H-ferritin to the TIM-2 receptor in mouse cells

Ferritin binds specifically and saturably to a variety of cell types, and recently several ferritin receptors have been cloned. TIM-2 is a specific receptor for H ferritin (HFt) in the mouse. TIM-2 is a member of the T cell immunoglobulin and mucin domain containing (TIM) protein family and plays an important role in immunity. The expression of TIM-2 outside of the immune system indicates that this receptor may have broader roles. We tested whether ferritin binding to TIM-2 can serve as an iron delivery mechanism. TIM-2 was transfected into normal (TCMK-1) mouse kidney cells, where it was appropriately expressed on the cell surface. HFt was labeled with (55)Fe and (55)Fe-HFt was incubated with TIM-2 positive cells or controls. (55)Fe-HFt uptake was observed only in TIM-2 positive cells. HFt uptake was also seen in A20 B cells, which express endogenous TIM-2. TIM-2 levels were not increased by iron chelation. Uptake of (55)Fe-HFt was specific and temperature-dependent. HFt taken up by TIM-2 positive cells transited through the endosome and eventually entered a lysosomal compartment, distinguishing the HFt pathway from that of transferrin, the classical vehicle for cellular iron delivery. Iron delivered following binding of HFt to TIM-2 entered the cytosol and became metabolically available, resulting in increased levels of endogenous intracellular ferritin. We conclude that TIM-2 can function as an iron uptake pathway.     

Detrimental effects of environmental tobacco smoke in relation to asthma severity

Background

Environmental tobacco smoke (ETS) has adverse effects on the health of asthmatics, however the harmful consequences of ETS in relation to asthma severity are unknown.

Methods

In a multicenter study of severe asthma, we assessed the impact of ETS exposure on morbidity, health care utilization and lung functions; and activity of systemic superoxide dismutase (SOD), a potential oxidative target of ETS that is negatively associated with asthma severity.

Findings

From 2002–2006, 654 asthmatics (non-severe 366, severe 288) were enrolled, among whom 109 non-severe and 67 severe asthmatics were routinely exposed to ETS as ascertained by history and validated by urine cotinine levels. ETS-exposure was associated with lower quality of life scores; greater rescue inhaler use; lower lung function; greater bronchodilator responsiveness; and greater risk for emergency room visits, hospitalization and intensive care unit admission. ETS-exposure was associated with lower levels of serum SOD activity, particularly in asthmatic women of African heritage.

Interpretation

ETS-exposure of asthmatic individuals is associated with worse lung function, higher acuity of exacerbations, more health care utilization, and greater bronchial hyperreactivity. The association of diminished systemic SOD activity to ETS exposure provides for the first time a specific oxidant mechanism by which ETS may adversely affect patients with asthma.     

Screening for Bacillus subtilis mutants deficient in pressure induced spore germination: identification of ykvU as a novel germination gene

Exposure to high pressure induces germination in spores of Bacillus subtilis. To investigate the mechanisms of this process and to compare the pressure and nutrient induced germination pathways, a random transposon knock-out library of B. subtilis was constructed and screened for clones with a compromised pressure induced germination at 100 MPa. Two mutants were isolated and their transposon insertion was mapped to gerAC and ykvU respectively. While GerAC is required for production of the l-alanine receptor which has been implicated in pressure-induced germination before, YkvU is shown here to be a novel germination determinant in B. subtilis, affecting germination by high (100 MPa) and very high (600 MPa) pressure, by nutrients and by dodecylamine, but not by Ca(2+)-dipicolinic acid.     

Reduction of antigen-induced respiratory abnormalities and airway inflammation in sensitized guinea pigs by a superoxide dismutase mimetic

Reactive oxygen species have been implicated in the pathogenesis of asthma and, in atopic asthmatics, endogenous superoxide dismutase (SOD) enzyme levels are known to decrease. This suggests that replacing a failed endogenous SOD enzyme system with a mimetic of the endogenous enzyme would be beneficial and protective. In this study we demonstrate that removal of superoxide by the SOD mimetic (SODm) M40403 reduces the respiratory and histopathological lung abnormalities due to ovalbumin (OA) aerosol in a model of allergic asthma-like reaction in sensitized guinea pigs. Both respiratory abnormalities and bronchoconstriction in response to OA challenge are nearly absent in na?ve animals, while they sharply became severe in sensitized animals. In addition, OA aerosol induced a reduction of MnSOD activity which was paralleled with bronchiolar lumen reduction, pulmonary air space hyperinflation, mast cell degranulation, eosinophil infiltration, bronchial epithelial cell apoptosis, increase in myeloperoxidase activity, malonyldialdehyde production and 8-hydroxy-2'-deoxyguanosine formation in the lung tissue, as well as elevation of PGD2 in the bronchoalveolar lavage fluid. Treatment with M40403 restored the levels of MnSOD activity and significantly reduced all the above parameters. In summary, our findings support the potential therapeutic use of SOD mimetics in asthma and anaphylactic reactions and account for a critical role for superoxide in acute allergic asthma-like reaction in actively sensitized guinea pig.     

Nutritional composition and digestibility by ocelots (Leopardus pardalis) of whole animals and a commercial diet

Felids are adapted to eat whole prey, but in North American zoos are usually fed processed diets based on muscle meat. We analyzed proximate nutrient composition and digestibility by ocelots of a commercial processed diet and whole animals of five species. The processed diet did not differ significantly from the whole animals in proximate composition, although it was at one end of the range of results for all nutrients. Domestic chicks were significantly lower than all other dietary items tested in digestibility of energy and fat, and lower than rabbits and quail in digestibility of dry matter. There were no other significant differences. These results suggest that the commercial diet tested provides an appropriate nutritional environment for ocelots with respect to proximate constituents. Studies of vitamin and mineral composition and digestibility and comparisons to wild prey species should be conducted to permit a full evaluation. Zoo Biol 29:753–759, 2010. © 2009 Wiley‐Liss, Inc.     

Nitrotyrosine proteome survey in asthma identifies oxidative mechanism of catalase inactivation

Reactive oxygen species and reactive nitrogen species produced by epithelial and inflammatory cells are key mediators of the chronic airway inflammation of asthma. Detection of 3-nitrotyrosine in the asthmatic lung confirms the presence of increased reactive oxygen and nitrogen species, but the lack of identification of modified proteins has hindered an understanding of the potential mechanistic contributions of nitration/oxidation to airway inflammation. In this study, we applied a proteomic approach, using nitrotyrosine as a marker, to evaluate the oxidation of proteins in the allergen-induced murine model of asthma. Over 30 different proteins were targets of nitration following allergen challenge, including the antioxidant enzyme catalase. Oxidative modification and loss of catalase enzyme function were seen in this model. Subsequent investigation of human bronchoalveolar lavage fluid revealed that catalase activity was reduced in asthma by up to 50% relative to healthy controls. Analysis of catalase isolated from asthmatic airway epithelial cells revealed increased amounts of several protein oxidation markers, including chloro- and nitrotyrosine, linking oxidative modification to the reduced activity in vivo. Parallel in vitro studies using reactive chlorinating species revealed that catalase inactivation is accompanied by the oxidation of a specific cysteine (Cys(377)). Taken together, these studies provide evidence of multiple ongoing and profound oxidative reactions in asthmatic airways, with one early downstream consequence being catalase inactivation. Loss of catalase activity likely amplifies oxidative stress, contributing to the chronic inflammatory state of the asthmatic airway.