A Comparative Study of the Involvement of 17 Arabidopsis Myosin Family Members on the Motility of Golgi and Other Organelles

Gene families with multiple members are predicted to have individuals with overlapping functions. We examined all of the Arabidopsis (Arabidopsis thaliana) myosin family members for their involvement in Golgi and other organelle motility. Truncated fragments of all 17 annotated Arabidopsis myosins containing either the IQ tail or tail domains only were fused to fluorescent markers and coexpressed with a Golgi marker in two different plants. We tracked and calculated Golgi body displacement rate in the presence of all myosin truncations and found that tail fragments of myosins MYA1, MYA2, XI-C, XI-E, XI-I, and XI-K were the best inhibitors of Golgi body movement in the two plants. Tail fragments of myosins XI-B, XI-F, XI-H, and ATM1 had an inhibitory effect on Golgi bodies only in Nicotiana tabacum, while tail fragments of myosins XI-G and ATM2 had a slight effect on Golgi body motility only in Nicotiana benthamiana. The best myosin inhibitors of Golgi body motility were able to arrest mitochondrial movement too. No exclusive colocalization was found between these myosins and Golgi bodies in our system, although the excess of cytosolic signal observed could mask myosin molecules bound to the surface of the organelle. From the preserved actin filaments found in the presence of enhanced green fluorescent protein fusions of truncated myosins and the motility of myosin punctae, we conclude that global arrest of actomyosin-derived cytoplasmic streaming had not occurred. Taken together, our data suggest that the above myosins are involved, directly or indirectly, in the movement of Golgi and mitochondria in plant cells.The Arabidopsis (Arabidopsis thaliana) myosin gene family contains 17 members: myosin group XI, which includes 13 members (myosins XI-A, -B, -C, -D, -E, -F, -G, -H, -I, -J, and -K, MYA1, and MYA2), and myosin group VIII, which includes four members (ATM1, ATM2, myosin VIIIA, and myosin VIIIB). Both groups are related to unconventional myosin V (Berg et al., 2001; Foth et al., 2006). The Arabidopsis myosins contain a conserved motor domain with ATPase and actin-binding activities, a number of IQ domains that bind myosin light chains, a coiled-coil domain for dimerization, and a specific tail that binds different cargo (Kinkema and Schiefelbein, 1994; Tominaga et al., 2003). Using these functional domains, myosins convert chemical energy from ATP hydrolysis into physical movement along actin fibers, carrying with their tails membrane-bound organelles or RNA/protein complexes (Li and Nebenführ, 2008b).Plant myosins have been implicated in various cellular activities, such as cytoplasmic streaming (Shimmen and Yokota, 2004; Esseling-Ozdoba et al., 2008), plasmodesmata function (Baluska et al., 2001; Volkmann et al., 2003), organelle movement (Nebenführ et al., 1999; Jedd and Chua, 2002), cytokinesis (Molchan et al., 2002; Collings et al., 2003; Volkmann et al., 2003), endocytosis (Volkmann et al., 2003; Baluska et al., 2004; Samaj et al., 2005), and targeted RNA transport (Hamada et al., 2003). Actomyosin mediated cytoplasmic streaming found in various algae cells reach velocities of up to 100 μm s⁻¹, which is the fastest known myosin-mediated movement (Shimmen and Yokota, 1994).The information that exists regarding specific roles of each plant myosin is rather limited. Immunolocalization studies indicated that myosin XIs are associated with various particles in lily (Lilium longiflorum) and tobacco (Nicotiana tabacum) pollen tubes (Yokota et al., 1995), with mitochondria, plastids, and low-density membranes in maize (Zea mays) root cells (Liu et al., 2001; Wang and Pesacreta, 2004), and with endoplasmic reticulum (ER) in tobacco BY2 cells (Yokota et al., 2008). Specific antibodies against MYA2 showed that it is associated with peroxisomes in epidermal and guard cells of Arabidopsis leaves (Hashimoto et al., 2005). More recent studies using recombinant DNA fusions to fluorescent proteins showed localization of the tails of MYA2, MYA1, XI-K, and XI-I to peroxisomes (Li and Nebenführ, 2007; Reisen and Hanson, 2007) and MYA1 partially localized to Golgi (Li and Nebenführ, 2007). Furthermore, it was shown that peroxisomes, Golgi, and mitochondrial motility were arrested by dominant negative mutants of myosin XI-K and myosin XI-E (Avisar et al., 2008b; Sparkes et al., 2008). Arrest of organelle motility was also found in Arabidopsis knockout plants xi-k and mya2 (Peremyslov et al., 2008) and double mutants xi-k/mya1, xi-k/mya2, and mya2/xi-b (Prokhnevsky et al., 2008). In contrast, the association of the single globular tail domain of MYA1 or MYA2 with peroxisomes did not arrest their motility (Li and Nebenführ, 2007). Knockout plants for myosin xi-k and mya2 had root hair phenotypes (Ojangu et al., 2007; Peremyslov et al., 2008); however, all other 11 myosin XI single knockouts looked normal under regular growth conditions (Peremyslov et al., 2008). Reciprocal stimulation between dimerization via the coiled-coil domains of MYA1 and organelle binding was suggested (Li and Nebenführ, 2008a). As for myosin VIII, immunostaining studies showed that it localized to the cell periphery at plant-specific structures such as plasmodesmata and cytokinetic cell plates (Reichelt et al., 1999; Baluska et al., 2001). Recent data from our laboratory and from others confirmed the presence of myosin VIII in plasmodesmata (Golomb et al., 2008) and the cell plate (Van Damme et al., 2004) and further provided evidence for its involvement with endocytosis (Golomb et al., 2008; Sattarzadeh et al., 2008) and its colocalization with the ER (Golomb et al., 2008). In addition, it was shown that myosin VIII is involved in the plasmodesmata targeting of the beet yellows virus protein Hsp70h (Avisar et al., 2008a).We have determined the role of all 17 genes through transient overexpression of dominant negative forms in leaf epidermal cells. Fluorescent dominant negative fusions not only provide data on the subcellular location but also provide a relatively easy way of determining expression. Additionally, overexpression of dominant negative forms can expose a role of an individual member, which might be masked by redundant activity, if it was silenced. In order to undertake such a large-scale study, we needed to choose an efficient, fast, and reproducible expression system. Therefore, Agrobacterium tumefaciens-mediated transient expression in Nicotiana leaves was suitable.     

Change your diet or die: predator-induced shifts in insectivorous lizard feeding ecology

Animal feeding ecology and diet are influenced by the fear of predation. While the mechanistic bases for such changes are well understood, technical difficulties often prevent testing how these mechanisms interact to affect a mesopredator’s diet in natural environments. Here, we compared the insectivorous lizard Acanthodactylus beershebensis’ feeding ecology and diet between high- and low-risk environments, using focal observations, intensive trapping effort and fecal pellet analysis. To create spatial variation in predation risk, we planted “artificial trees” in a scrubland habitat that lacks natural perches, allowing avian predators to hunt for lizards in patches that were previously unavailable to them. Lizards in elevated-risk environments became less mobile but did not change their microhabitat use or temporal activity. These lizards changed their diet, consuming smaller prey and less plant material. We suggest that diet shifts were mainly because lizards from risky environments consumed prey items that required shorter handling time.     

Comparison of Effects of Compost Amendment and of Single-Strain Inoculation on Root Bacterial Communities of Young Cucumber Seedlings

Compost amendment and inoculations with specific microorganisms are fundamentally different soil treatment methods, commonly used in agriculture for the improvement of plant growth and health. Although distinct, both methods affect the rhizosphere and the plant roots. In the present study we used a 16S rRNA gene approach to achieve an overview of early consequences of these treatments on the assemblage of plant root bacterial communities. For this purpose, cucumber seedlings were grown, under controlled conditions, in perlite potting mix amended with biosolid compost or straw compost, or inoculated with Streptomyces spp. A uniform trend of response of root bacterial communities for all treatments was observed. Root bacterial density, measured as bacterial targets per plant tef gene by real-time PCR, was reduced in 31 to 67%. In addition, increased taxonomic diversity accompanied shifts in composition (α-diversity). The magnitude of change in these parameters relative to the perlite control varied between the different treatments but not in relation to the treatment method (compost amendments versus inoculations). Similarity between the compositions of root and of potting mix bacterial communities (β-diversity) was relatively unchanged. The abundance of Oxalobacteraceae was >50% of the total root bacterial community in the untreated perlite. Root domination by this group subsided >10-fold (straw compost) to >600-fold (Streptomyces sp. strain S1) after treatment. Thus, loss of dominance appears to be the major phenomenon underlining the response trend of the root bacterial communities.Environmental concern over conventional agricultural fertilization and disease control measures has led to increased interest in finding environmentally friendly alternatives. The most explored ones include compost amendments (18, 36) and the application of different microbial preparations (11, 19, 37). These are widely distinct applications. The first approach adds to the amended medium not only a rich and diverse consortium of biological agents but also organic matter and nutrients. It was confirmed that the efficacy of such treatments involves the response of the soil, the plant, and the rhizosphere microbial communities (19, 56). The activities of rhizosphere microorganisms alter the rhizosphere and thus affect plant health and root growth and development (24). Therefore, one of the main objectives of compost amendment or of inoculation with specific microbial strains is manipulation of the plant rhizosphere conditions, particularly via manipulation of the microbial community composition (32).The response of rhizosphere bacterial communities to different anthropogenic and other disturbances has been discussed in terms of resilience (3, 32). Generally, the introduction of new microorganisms produces only restricted spatial and temporal effects on the soil, rhizosphere, and root microbial communities (4, 29, 35). Thus, the plant growth-promoting effect of such treatments may be related to microbial events occurring during the early stages of plant development. Such early effects were pointed out for inoculants of different bacterial species (14, 42) and for compost amendment (15, 21, 50).Consequences of compost amendment or of single species inoculation often include shifts in the plant roots hormonal balance or a plant systemic response, namely, induced systemic resistance (8, 38, 52). Thus, direct or indirect activities of the introduced microorganisms may result in similar modifications of the root habitat. If so, bacterial assemblages of treated roots may share qualitative and quantitative characteristics different from those exhibited by untreated roots.The objective of the present study was therefore to describe and compare responses of bacterial communities of young plant roots to the application of compost or bacterial inoculants. This was performed in a simple model comprised of cucumber seedlings grown in potting mixes amended with compost or inoculated with Streptomyces spp. isolated from the two different composts.     

Blood Levels of Carbonic Anhydrase 9 Correlate with Clear Cell Renal Cell Carcinoma Activity

Introduction  Biomarkers for early detection of renal cell carcinoma (RCC) may help diagnose minimal residual disease in patients at risk for RCC, can guide anti-angiogenic therapy, or may help identify candidates for adjuvant treatment. In this study, we investigated whether blood levels of carbonic anhydrase 9 (CA9) correlate with RCC tumor burden and therefore disease activity. Methods  CA9 is a von Hippel–Lindau–hypoxia inducible factor target upregulated in clear cell RCC. We used an anti-CA9 antibody (M75)-based enzyme-linked immunosorbent assay test to measure CA9 levels in blood obtained before and after nephrectomy for clinically localized disease in patients with: (1) clear cell RCC, (2) papillary and chromophobe RCC or oncocytoma, or (3) benign kidney lesions, and we compared these samples to blood drawn from normal control individuals. Results  We observed a significant (p < 0.006) decrease in the blood levels of CA9, after nephrectomy for localized disease, in the majority of patients with clear cell RCC (57%). In contrast, patients with nonclear cell RCC, benign disease, or those having undergone debulking nephrectomy for metastatic disease did not have a decrease in CA9 blood levels after nephrectomy. Preliminary longitudinal follow up measurements of CA9 levels in a small group of patients indicated that rising CA9 levels may correlate with disease progression. Conclusions  Plasma CA9 levels correlate with disease activity in a subset of clear cell RCC patients and should be considered in future multiplex RCC biomarker development algorithms.     

An ancient autosomal haplotype bearing a rare achromatopsia-causing founder mutation is shared among Arab Muslims and Oriental Jews

Numerous cultural aspects, mainly based on historical records, suggest a common origin of the Middle-Eastern Arab Muslim and Jewish populations. This is supported, to some extent, by Y-chromosome haplogroup analysis of Middle-Eastern and European samples. Up to date, no genomic regions that are shared among Arab Muslim and Jewish chromosomes and are unique to these populations have been reported. Here, we report of a rare achromatopsia-causing CNGA3 mutation (c.1585G>A) presents in both Arab Muslim and Oriental Jewish patients. A haplotype analysis of c.1585G>A-bearing chromosomes from Middle Eastern and European origins revealed a shared Muslim–Jewish haplotype, which is different from those detected in European patients, indicating a recurrent mutation stratified by a Jewish–Muslim founder effect. Comprehensive whole-genome haplotype analysis using 250 K single nucleotide polymorphism arrays revealed a large homozygous region of ~11 Mbp shared by both Arab Muslim and Oriental Jewish chromosomes. A subsequent microsatellite analysis of a 21.5 cM interval including CNGA3 and the adjacent chromosome 2 centromere revealed a unique and extremely rare haplotype associated with the c.1585G>A mutation. The age of the shared c.1585G>A mutation was calculated using the microsatellite genotyping data to be about 200 generations ago. A similar analysis of mutation age based on the Arab Muslim data alone showed that the mutation was unlikely to be the product of a recent gene flow event. The data present here demonstrate a large (11 Mbp) genomic region that is likely to originate from an ancient common ancestor of Middle-Eastern Arab Muslims and Jews who lived approximately 5,000 years ago.     

Designing coarse grained-and atom based-potentials for protein-protein docking

Background  

Protein-protein docking is a challenging computational problem in functional genomics, particularly when one or both proteins undergo conformational change(s) upon binding. The major challenge is to define a scoring function soft enough to tolerate these changes and specific enough to distinguish between near-native and "misdocked" conformations.     

Dominating clasp of the financial sector revealed by partial correlation analysis of the stock market

What are the dominant stocks which drive the correlations present among stocks traded in a stock market? Can a correlation analysis provide an answer to this question? In the past, correlation based networks have been proposed as a tool to uncover the underlying backbone of the market. Correlation based networks represent the stocks and their relationships, which are then investigated using different network theory methodologies. Here we introduce a new concept to tackle the above question—the partial correlation network. Partial correlation is a measure of how the correlation between two variables, e.g., stock returns, is affected by a third variable. By using it we define a proxy of stock influence, which is then used to construct partial correlation networks. The empirical part of this study is performed on a specific financial system, namely the set of 300 highly capitalized stocks traded at the New York Stock Exchange, in the time period 2001–2003. By constructing the partial correlation network, unlike the case of standard correlation based networks, we find that stocks belonging to the financial sector and, in particular, to the investment services sub-sector, are the most influential stocks affecting the correlation profile of the system. Using a moving window analysis, we find that the strong influence of the financial stocks is conserved across time for the investigated trading period. Our findings shed a new light on the underlying mechanisms and driving forces controlling the correlation profile observed in a financial market.     

Sex differences in the perceived intensity of breathlessness during exercise with advancing age.

The prevalence of activity-related breathlessness increases with age, particularly in women, but the specific underlying mechanisms have not been studied. This novel cross-sectional study was undertaken to examine the effects of age and sex, and their interaction, on the perceptual and ventilatory responses to incremental treadmill exercise in 73 healthy participants (age range 40-80 yr old) with normal pulmonary function. Age-related changes at a standardized oxygen uptake (Vo(2)) during exercise included significant increases in breathlessness ratings (Borg scale), ventilation (Ve), ventilatory equivalent for carbon dioxide, and the ratio of tidal volume (Vt) to dynamic inspiratory capacity (IC) (all P < 0.05). These changes were quantitatively similar in women (n = 39) and in men (n = 34). For the group as a whole, exertional breathlessness ratings increased as resting static inspiratory muscle strength diminished (P = 0.05), as exercise ventilation increased relative to capacity (P = 0.013) and as the Vt/IC ratio increased (P = 0.003) during exercise. Older women (60-80 yr old, n = 23) reported greater (P < 0.05) intensity of exertional breathlessness at a standardized Vo(2) and Ve than age-matched men (n = 16), despite similar age-related changes in ventilatory demand and dynamic ventilatory mechanics. These increases in breathlessness ratings in older women disappeared when sex differences in baseline maximal ventilatory capacity were accounted for. In conclusion, although increased exertional breathlessness with advancing age is multifactorial, contributory factors included higher ventilatory requirements during exercise, progressive inspiratory muscle weakness, and restrictive mechanical constraints on Vt expansion related to reduced IC. The sensory consequences of this age-related respiratory impairment were more pronounced in women, who, by nature, have relatively reduced maximal ventilatory reserve.     

The role of Bacillus thuringiensis Cry1C and Cry1E separate structural domains in the interaction with Spodoptera littoralis gut epithelial cells

The Bacillus thuringiensis delta-endotoxins Cry1C and Cry1E share toxicity against several important lepidopteran species. Their combined use to delay development of resistance in target insects depends on their differential interaction with the gut epithelial cells. The three structural domains and combinations of two consecutive domains of Cry1C and Cry1E were separately expressed in Escherichia coli, and their interactions with the brush border membrane vesicles (BBMV) of Cry1E-tolerant and -susceptible Spodoptera littoralis larvae were studied. About 80% reduction in binding of Cry1E and each of its separate domains to BBMV of Cry1E-tolerant larvae was observed, whereas Cry1C was toxic to all larvae and bound equally to BBMV derived from both Cry1E-tolerant and -susceptible larvae. These results suggest differential interactions of the two toxins with BBMV encompassing all three domains. Comparable binding assays performed with fluorescent Cry1C and Cry1C domain II showed that Cry1C has higher Bmax and lower Kd than Cry1C domain II and further supported the existence of toxin multisite interactions. Competitive binding assays were used to estimate the sequence of interaction events. Cry1C domain II could compete with domain III binding, whereas domain III did not interfere with domain II binding, indicating sequential interactions of domain III and then domain II with the same membrane site. No competition between domain II of Cry1C and Cry1E was observed, confirming the existence of different domain II binding sites for the two toxins. Taken together, all three domains specifically interact with the epithelial cell membrane. The folding of the three-domain toxin probably dictates the sequence of interaction events.