Hypergravity prevents seed production in <Emphasis Type="Italic">Arabidopsis</Emphasis> by disrupting pollen tube growth

How tightly land plants are adapted to the gravitational force (g) prevailing on Earth has been of interest because unlike many other environmental factors, g presents as a constant force. Ontogeny of mature angiosperms begins with an embryo that is formed after tip growth by a pollen tube delivers the sperm nucleus to the egg. Because of the importance to plant fitness, we have investigated how gravity affects these early stages of reproductive development. Arabidopsis thaliana (L.) Heynh. plants were grown for 13 days prior to being transferred to growth chambers attached to a large diameter rotor, where they were continuously exposed to 2-g or 4-g for the subsequent 11 days. Plants began flowering 1 day after start of the treatments, producing hundreds of flowers for analysis of reproductive development. At 4-g, Arabidopsis flowers self-pollinated normally but did not produce seeds, thus derailing the entire life cycle. Pollen viability and stigma esterase activity were not compromised by hypergravity; however, the growth of pollen tubes into the stigmas was curtailed at 4-g. In vitro pollen germination assays showed that 4-g average tube length was less than half that for 1-g controls. Closely related Brassica rapa L., which produces seeds at 4-g, required forces in excess of 6-g to slow in vitro tube growth to half that at 1-g. The results explain why seed production is absent in Arabidopsis at 4-g and point to species differences with regard to the g-sensitivity of pollen tube growth.     

Habitat Heterogeneity and Associated Microbial Community Structure in a Small-Scale Floodplain Hyporheic Flow Path

The Nyack floodplain is located on the Middle Fork of the Flathead River, an unregulated, pristine, fifth-order stream in Montana, USA, bordering Glacier National Park. The hyporheic zone is a nutritionally heterogeneous floodplain component harboring a diverse array of microbial assemblages essential in fluvial biogeochemical cycling, riverine ecosystem productivity, and trophic interactions. Despite these functions, microbial community structure in pristine hyporheic systems is not well characterized. The current study was designed to assess whether physical habitat heterogeneity within the hyporheic zone of the Nyack floodplain was sufficient to drive bacterial β diversity between three different hyporheic flow path locations. Habitat heterogeneity was assessed by measuring soluble reactive phosphorous, nitrate, dissolved organic carbon, dissolved oxygen, and soluble total nitrogen levels seasonally at surface water infiltration, advection, and exfiltration zones. Significant spatial differences were detected in dissolved oxygen and nitrate levels, and seasonal differences were detected in dissolved oxygen, nitrate, and dissolved organic carbon levels. Denaturing gradient gel electrophoresis (DGGE) and cell counts indicated that bacterial diversity increased with abundance, and DGGE fingerprints covaried with nitrate levels where water infiltrated the hyporheic zone. The ribosomal gene phylogeny revealed that hyporheic habitat heterogeneity was sufficient to drive β diversity between bacterial assemblages. Phylogenetic (P) tests detected sequence disparity between the flow path locations. Small distinct lineages of Firmicutes, Actinomycetes, Planctomycetes, and Acidobacteria defined the infiltration zone and α- and β-proteobacterial lineages delineated the exfiltration and advection zone communities. These data suggest that spatial habitat heterogeneity drives hyporheic microbial community development and that attempts to understand functional differences between bacteria inhabiting nutritionally heterogeneous hyporheic environments might begin by focusing on the biology of these taxa.     

Single-chain variable fragment antibodies selected by phage display against the sporozoite surface antigen P23 Of Cryptosporidium parvum

Cryptosporidium parvum, an apicomplexan parasite transmitted via animal fecal wastes, is the causative agent of cryptosporidiosis. Clones were selected from 2 synthetic na?ve human single-chain variable fragment (scFv) phagemid libraries that bound to the recombinant P23 protein of C. parvum. Panning the Tomlinson I and J phagemid libraries resulted in 6 distinct clones. Two clones had full-length scFv sequences, while the remaining clones were either truncated or missing a section of the heavy chain. Despite these differences, all clones were able to detect both native C. parvum proteins and recombinant P23. None of the selected clones cross-reacted with Escherichia coli, Streptococcus pyogenes, Listeria monocytogenes, Bacillus cereus, Giardia lamblia (cysts or trophozoites), or with S16, another dominant surface antigen on C. parvum sporozoites. Clones expressed as the scFv-gIIIp fusion construct in soluble form detected C. parvum. Panning from na?ve libraries is a useful method for isolation and identification of recombinant antibodies that have the potential for use in pathogen detection and immunotherapy.     

Copper-dependent Recycling of hCTR1, the Human High Affinity Copper Transporter

Copper is an essential co-factor in many important physiological processes, but at elevated levels it is toxic to cells. Thus at both the organism and cellular level mechanisms have evolved to finely tune copper homeostasis. The protein responsible for copper entry from the circulation in most human cells is hCTR1, a small protein (190 amino acid residues) that functions as a trimer in the plasma membrane. In the present work we employ cell surface biotinylation and isotopic copper uptake studies of overexpressed hCTR1 in HEK293 cells to examine the acute (minutes) response of hCTR1 to changes in extracellular copper. We show that within 10 min of exposure to copper at 2.5 μm or higher, plasma membrane hCTR1 levels are reduced (by ∼40%), with a concomitant reduction in copper uptake rates. We are unable to detect any degradation of internalized hCTR1 in the presence of cycloheximide after up to 2 h of exposure to 0–100 μm copper. Using a reversible biotinylation assay, we quantified internalized hCTR1, which increased upon the addition of copper and corresponded to the hCTR1 lost from the surface. In addition, when extracellular copper is then removed, internalized hCTR1 is promptly (within 30 min) recycled to the plasma membrane. We have shown that in the absence of added extracellular copper, there is a small but detectable amount of internalized hCTR1 that is increased in the presence of copper. Similar studies on endogenous hCTR1 show a cell-specific response to elevated extracellular copper. Copper-dependent internalization and recycling of hCTR1 provides an acute and reversible mechanism for the regulation of cellular copper entry.Copper is an essential micronutrient and plays an important function as a co-factor for a number of cellular processes including oxidative phosphorylation, free radical detoxification, neurotransmitter synthesis, iron metabolism, and maturation of connective tissue (1). Copper in excess of cellular requirements is toxic; therefore cells have developed sophisticated mechanisms for regulating copper acquisition and secretion, thus maintaining a critical copper homeostasis (2, 3). In eukaryotes a family of transporters known as the copper transporter (Ctr) proteins mediate cellular copper uptake (4). Ctr proteins are integral membrane proteins that are structurally conserved with three membrane-spanning domains and a number of methionine rich motifs in the N terminus (5). They contain a sequence of conserved cysteine and histidine residues at or close to the C terminus and are predominantly located at the plasma membrane (6). In the yeast, Saccharomyces cerevisiae, the first high affinity copper transporters, yCtr1 and yCtr3, were identified (7, 8), and this facilitated the identification of the human copper transporter gene, hCTR1,² by functional complementation of yeast high affinity copper uptake mutant, ctr1 (9). The mouse CTR1 is 92% identical to hCTR1 (10), and the deletion of mCTR1 results in early embryonic lethality, suggesting an essential role for the high affinity copper transporter in mammalian growth and development (11).hCTR1 has 190 amino acid residues, three membrane-spanning domains, an extracellular N terminus (of 66 amino acids), a large cytoplasmic loop (of 46 amino acid residues), and a short C-terminal tail (of 15 amino acids) and has been shown to form stable dimers and trimers (12–14). The hCTR1 protein has been shown in ⁶⁴Cu uptake experiments to mediate copper transport with a K_m of 1–5 μm and is thought to transport the reduced form, Cu(I) (12, 13, 15). The extracellular N terminus has both N- and O-linked glycosylation at residues Asn¹⁵ and Thr²⁷, respectively (12, 16, 17), and contains two histidine-rich regions and two methionine motifs that are thought to function in copper binding/sensing. Recent studies showed that mutation or deletion of the methionine residues closest to the first transmembrane domain (Met⁴³ and Met⁴⁵) and the conserved methionine residues in the second transmembrane domain (Met¹⁵⁰ and Met¹⁵⁴) had a large inhibitory effect on ⁶⁴Cu uptake (18, 19). Mutational analysis provided no evidence for the tight binding of copper at any specific residues, and it was proposed that hCTR1 provided a pore for the permeation of copper across the membrane (18). Structural confirmation of such a mechanism was provided in the low resolution structure obtained by cryo-electron microscopy studies on recombinant protein (20, 21).Considerable progress has been made in understanding the biochemical, structure-functional, and molecular aspects of hCTR1-mediated copper transport, although many questions remain unanswered (22). It is also important to determine whether or not hCTR1 has a regulatory role preventing the accumulation of toxic levels of copper and maintaining cellular copper homeostasis. Previous reports on whether or not hCTR1 is involved in an acute response to elevated copper have been somewhat controversial. It has been reported that elevated extracellular copper (1–100 μm) stimulates rapid endocytosis and degradation of hCTR1-Myc-tagged protein in HEK293 cells (23), but also high copper levels had no effect on endogenous hCTR1 localization in both HeLa and Caco-2 cells (14). In a study of overexpressed hCTR1 in insect cells, no evidence was seen of internalization in response to elevated copper (24). Imaging studies have shown that the cellular location of hCTR1 varies among cell lines, CTR1 in MDCK and HEK293 cells resides mainly at the plasma membrane (13, 15, 23, 24). Endogenous hCTR1 is located in cytoplasmic vesicular compartments in HeLa, Caco-2, and HepG2 cell lines with some plasma membrane staining in Caco-2 (14). In intestinal sections, basolateral and subapical staining is seen (15).Previous studies (see above) have utilized internalization of prebound antibody (23) or imaging methods (14) to characterize the response of hCTR1 to elevated copper. In the present work we employed HEK cells overexpressing hCTR1 and used cell surface biotinylation, a sensitive and quantitative measure of CTR1 at the cell surface (15, 17). We have combined this with measurements of hCTR1-mediated ⁶⁴Cu uptake as a functional measure of plasma membrane hCTR1 levels. We find that a fraction (∼40%) of hCTR1 is rapidly internalized in the presence of elevated copper and that there is a concomitant reduction in the hCTR1-mediated copper uptake rate. The internalized transporter is not degraded and can be detected in the cytosol. On removal of extracellular copper, the transporter is recycled promptly to the plasma membrane. Internalization of endogenous CTR1 is also observed in MDCK and HepG2 cells, and no reduction is seen in T47D cells. This is, to our knowledge, the first such report of copper-dependent recycling of hCTR1 in response to copper and represents an acute regulatory mechanism that reversibly modulates cellular copper entry.     

ARF Induces Autophagy by Virtue of Interaction with Bcl-xl

The ARF tumor suppressor controls a well-described p53/Mdm2-dependent oncogenic stress checkpoint. In addition, ARF has recently been shown to localize to mitochondria, and to induce autophagy; however, this has never before been demonstrated for endogenous ARF, and the molecular basis for this activity of ARF has not been elucidated. Using an unbiased mass spectrometry-based approach, we show that mitochondrial ARF interacts with the Bcl2 family member Bcl-xl, which normally protects cells from autophagy by inhibiting the Beclin-1/Vps34 complex, which is essential for autophagy. We find that increased expression of ARF decreases Beclin-1/Bcl-xl complexes in cells, thereby providing a basis for ARF-induced autophagy. Our data also indicate that silencing p53 leads to high levels of ARF and increased autophagy, thereby providing a possible basis for the finding by others that p53 inhibits autophagy. The combined data support the premise that ARF induces autophagy in a p53-independent manner in part by virtue of its interaction with Bcl-xl.The ARF tumor suppressor, p14^ARF in humans and p19^ARF in mouse, is a critical growth suppressor that is up-regulated by chronic mitogenic signals and localizes predominantly to the nucleolus. At the nucleolus and in the nucleoplasm, ARF can exert both p53-dependent and -independent growth suppressive function, by virtue of interaction with and inhibition of MDM2, nucleophosmin, E2F-1, CtBP, c-Myc, as well as others (see Ref. 1 for review). Recently, a small molecular weight variant of ARF, generated by translation from an internal methionine, has been discovered to localize primarily to mitochondria and to induce autophagy (2). More recently, another group has shown that full-length ARF, in addition to the small molecular weight variant, can likewise induce autophagy (3). However, neither of these studies revealed a mechanism whereby ARF induces autophagy.Autophagy is an evolutionarily conserved homeostatic process whereby cytosolic components are targeted for removal or turnover in membrane-bound compartments (autophagosomes) that fuse with the lysosome (for review see Ref. 4). This process regulates the turnover of damaged organelles and long-lived proteins that are too large to be delivered to the proteasome. Autophagy occurs constitutively at low levels and is greatly induced during period of metabolic stress, where lysosome-mediated digestion of sequestered molecules serves to release free amino acids and ATP to fuel the continued survival of the cell.Several genes are implicated in the control of autophagy. Perhaps most notable of these is Beclin-1, which is an evolutionarily-conserved mediator of autophagy, with structural similarity to the yeast autophagy gene Apg6/Vps30. Beclin-1 is a component of the class III PI3 kinase complex that includes Vps34; this complex regulates the formation and nucleation of autophagosomes, and the regulation of the activity of this complex is tightly regulated. For example, Beclin-1 possesses a BH3 domain that interacts with the BH3 binding groove of certain members of the Bcl-2 family, including Bcl-2, Bcl-xl, Bcl-w, and to a lesser extent, Mcl-1 (5–9). Binding of Bcl-2 family members to Beclin-1 inhibits autophagy, possibly by decreasing the kinase activity of the Beclin/Bcl-2/Vps34 complex (5) or by negatively regulating Beclin-1 oligomerization (10). The interaction between Beclin-1 and Bcl-2 family members is also regulated; for example, BH3-only proteins can bind directly to Bcl-2 family members and disrupt complex formation with Beclin-1 (11). Additionally, phosphorylation of Bcl-2 by Jun-N-terminal kinase (JNK) can interfere with its ability to bind to Beclin-1 (12). In all cases, dissociation of the Beclin-1/Bcl-2 complex is associated with induction of autophagy.In this report we confirm the findings of others that a fraction of ARF protein localizes to mitochondria and can induce autophagy. We show for the first time that endogenous ARF, up-regulated in non-transformed cells by oncogenes, is capable of inducing autophagy, and further that silencing of p53 is sufficient to de-repress ARF and induce autophagy. We report the identification of Bcl-xl as a mitochondrial ARF-binding protein, and show that ARF-mediated autophagy is enhanced in cells with Bcl-xl silenced. Finally, we show that ARF can reduce complex formation between Bcl-xl and Beclin-1. These data offer the first mechanistic insights into ARF-mediated autophagy. They also point to ARF as a novel regulator of Beclin/Bcl-xl complex formation.     

Modification of isoflavones in soybean seeds via expression of multiple phenolic biosynthetic genes

To modify the level and composition of isoflavones, the important bioactive constituents of soybean seeds, soybean was transformed via co-bombardment of embryogenic cultures with three DNA cassettes containing the CHS6-chalcone synthase and IFS2-isoflavone synthase genes, and a fragment of PAL5-phenylalanine ammonia-lyase gene, all in sense orientation under the lectin promoter mixed with the selectable marker gene, HPT (hygromycin phosphotransferase) under the 35S promoter. Four of six fertile lines produced integrated all four genes.Isoflavone levels were lower in T1 mature seeds of 5 of the 6 lines compared to the control. Transgene segregation was found in one selected line, with formation of additional sublines with different transgene composition found also in the homozygous plants. Decreased isoflavone concentrations (by about 70%) were found in T4 homozygous seeds of the two lines studied in detail here. The embryo axes accumulated most of the glycitein and contained a higher isoflavone concentration than the cotyledons. Expression of transgenes driven by the lectin promoter reduced the isoflavone concentration only in the cotyledons and not in embryo axes, indicating that this promoter is preferably active in cotyledons.     

Haplotype inference in crossbred populations without pedigree information

Background

Current methods for haplotype inference without pedigree information assume random mating populations. In animal and plant breeding, however, mating is often not random. A particular form of nonrandom mating occurs when parental individuals of opposite sex originate from distinct populations. In animal breeding this is called crossbreeding and hybridization in plant breeding. In these situations, association between marker and putative gene alleles might differ between the founding populations and origin of alleles should be accounted for in studies which estimate breeding values with marker data. The sequence of alleles from one parent constitutes one haplotype of an individual. Haplotypes thus reveal allele origin in data of crossbred individuals.

Results

We introduce a new method for haplotype inference without pedigree that allows nonrandom mating and that can use genotype data of the parental populations and of a crossbred population. The aim of the method is to estimate line origin of alleles. The method has a Bayesian set up with a Dirichlet Process as prior for the haplotypes in the two parental populations. The basic idea is that only a subset of the complete set of possible haplotypes is present in the population.

Conclusion

Line origin of approximately 95% of the alleles at heterozygous sites was assessed correctly in both simulated and real data. Comparing accuracy of haplotype frequencies inferred with the new algorithm to the accuracy of haplotype frequencies inferred with PHASE, an existing algorithm for haplotype inference, showed that the DP algorithm outperformed PHASE in situations of crossbreeding and that PHASE performed better in situations of random mating.     

Calibration of nitric oxide flux generation from diazeniumdiolate NO donors

The 1-(secondary amino) diazen-1-ium-1,2-diolates (NONOates) are the most commonly utilized nitric oxide (NO, nitrogen monoxide) donor because of the ability of different NONOates to spontaneously break down liberating NO at different rates, which can be utilized to control NO fluxes. However, the parameters that determine these fluxes of NO generation, half-lives and stoichiometry of NO per donor, can vary significantly with specific experimental conditions in addition to the donor chosen. Here we report straightforward methods that can be used to determine these parameters. For donors of intermediate half-life (10–80 min) a real-time oxymyoglobin (oxyMb) assay can be analyzed to simultaneously determine both the half-life and the total amount of NO liberated, from which the NO flux can be obtained for any given donor concentration. The half-lives obtained by oxyMb assay are very similar to those obtained by following NONOate decomposition kinetics spectrophotometrically, and a survey of several NONOates from different commercial sources show consistent results. These data provide validation for the methodologies employed. In addition, procedures are described for calibration of donors with shorter (<10 min) and longer (>80 min) half-lives. These procedures can be used to reproducibly and routinely calibrate NO fluxes for a variety of donors under any specific condition.