Gender-Related developmental instability and herbivory ofPistacia atlantica across a steep environmental gradient

To examine gender-related developmental instability and herbivory of a plant across a steep climatic gradient, we studiedPistacia atlantica DESF., a dioecious tree of the Irano-Turanian zone in the Middle East. Leaves were sampled from five populations along a climatic gradient in Israel from mesic Mediterranean to xeric (and geographically peripheral) sites. Leaves of the xeric populations were ca. 25% smaller in size (length) than leaves of other populations. Leaf developmental instability (an indicator of stress) was examined using the measurement of leaf asymmetry (LA), estimated by the deviation from the origin of paired lateral leaflets and by the presence vs. absence of the terminal leaflet. LA was not correlated with the climatic (site) gradient and had the highest, though not significantly, levels in the intermediate ecotonal zone between the Mediterranean and the arid ecosystems. Male trees were 13% higher in LA than females. Density of two specialist gall-forming aphids varied with site but was not affected by plant gender. Gender-related developmental instability is discussed in relation to resource allocation in early spring. Because the study was limited to five populations further research is clearly needed.     

Host Location by Apterous Aphids After Escape Dropping from the Plant

In response to approaching enemies aphids may drop from their host plant to the ground. The risk of predation on the ground, desiccation and host loss, create the need for efficient host location by the dropping aphids. Most studies have focused on the factors that influence dropping behavior; only a few have addressed host location after dropping from the plant. We assessed post-dropping behavior in apterous Macrosiphoniella artemisiae (Boyer de Fonscolombe) (Aphididae), which feed on Artemisia arborescens L. Vibration of the apical bud induced dropping in 36% of the colony members. Dropping rates were highest in mature aphids (63%). In the experimental arena (without ground predators), nearly all mature aphids that were dropped 13 cm from the plant, found their way back in ca. 40 s. The location process may be based on visual cues, as M. artemisiae is capable of visually discriminating between host and non-host targets and apparently does not react to volatiles emitted from the plant.     

Inhibiting protein-amyloid interactions with small molecules: a surface chemistry approach

This paper presents a surface-based approach to inhibit the binding of proteins to Alzheimer's-related beta-amyloid (Abeta) fibrils with small molecules. It reports the idea of using an intracellular, disease-related fibril as a material whose surface can be coated with small molecules. Using an ELISA-based assay, molecular surface coatings with thioflavin T are shown to inhibit 65+/-10% of the binding of two different anti-Abeta IgGs to Abeta fibrils. A molecular surface coating with 3,6-diamino acridine was able to inhibit 76+/-10% of the binding of an anti-Abeta IgG to Abeta fibrils. Maximal inhibition of these protein-amyloid interactions appears in the low to mid-micromolar range of small molecule. This demonstration that molecular surface coatings can be used to attenuate the interaction of proteins with these fibrils suggests a potentially new strategy for therapeutics in neurodegenerative amyloid diseases.     

Cytosolic activity of SPINDLY implies the existence of a DELLA-independent gibberellin-response pathway

Specific plant developmental processes are modulated by cross-talk between gibberellin (GA)- and cytokinin-response pathways. Coordination of the two pathways involves the O-linked N -acetylglucosamine transferase SPINDLY (SPY) that suppresses GA signaling and promotes cytokinin responses in Arabidopsis. Although SPY is a nucleocytoplasmic protein, its site of action and targets are unknown. Several studies have suggested that SPY acts in the nucleus, where it modifies nuclear components such as the DELLA proteins to regulate signaling networks. Using chimeric GFP–SPY fused to a nuclear-export signal or to a glucocorticoid receptor, we show that cytosolic SPY promotes cytokinin responses and suppresses GA signaling. In contrast, nuclear-localized GFP–SPY failed to complement the spy mutation. To examine whether modulation of cytokinin activity by GA and spy is mediated by the nuclear DELLA proteins, cytokinin responses were studied in double and quadruple della mutants lacking the activities of REPRESSOR OF GA1-3 (RGA) and GA-INSENSITIVE (GAI) or RGA, GAI, RGA Like1 (RGL1) and RGL2. Unlike spy , the della mutants were cytokinin-sensitive. Moreover, when GA was applied to a cytokinin-treated quadruple della mutant it was able to suppress various cytokinin responses. These results suggest that cytosolic SPY and GA regulate cytokinin responses via a DELLA-independent pathway(s).     

Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions

Background  

Accurate evaluation and modelling of residue-residue interactions within and between proteins is a key aspect of computational structure prediction including homology modelling, protein-protein docking, refinement of low-resolution structures, and computational protein design.     

Deconvolution and Database Search of Complex Tandem Mass Spectra of Intact Proteins: A COMBINATORIAL APPROACH*

Top-down proteomics studies intact proteins, enabling new opportunities for analyzing post-translational modifications. Because tandem mass spectra of intact proteins are very complex, spectral deconvolution (grouping peaks into isotopomer envelopes) is a key initial stage for their interpretation. In such spectra, isotopomer envelopes of different protein fragments span overlapping regions on the m/z axis and even share spectral peaks. This raises both pattern recognition and combinatorial challenges for spectral deconvolution. We present MS-Deconv, a combinatorial algorithm for spectral deconvolution. The algorithm first generates a large set of candidate isotopomer envelopes for a spectrum, then represents the spectrum as a graph, and finally selects its highest scoring subset of envelopes as a heaviest path in the graph. In contrast with other approaches, the algorithm scores sets of envelopes rather than individual envelopes. We demonstrate that MS-Deconv improves on Thrash and Xtract in the number of correctly recovered monoisotopic masses and speed. We applied MS-Deconv to a large set of top-down spectra from Yersinia rohdei (with a still unsequenced genome) and further matched them against the protein database of related and sequenced bacterium Yersinia enterocolitica. MS-Deconv is available at http://proteomics.ucsd.edu/Software.html.Top-down proteomics is a mass spectrometry-based approach for identification of proteins and their post-translational modifications (PTMs)1 (1–14). Unlike the “bottom-up” approach where proteins are first digested into peptides and then a peptide mixture is analyzed by mass spectrometry, the top-down approach analyzes intact proteins. Thus, it has advantages in detecting and localizing PTMs as well as identifying multiple protein species (e.g. proteolytically processed protein species). Despite its advantages, top-down proteomics presents many challenges. These include requirement of high sample quantity, sophisticated instrumentation, protein separation, and robust computational analysis tools. For this reason, top-down proteomics has rarely been used for analyzing complex mixtures (12–18), and it is typically used to study single purified proteins. However, this situation is quickly changing with recent top-down studies of complex protein mixtures (14, 19).Because of the existence of natural isotopes, fragment ions of the same chemical formula and charge state are usually represented by a collection of spectral peaks in tandem mass spectra called an isotopomer envelope. The monoisotopic mass of a chemical formula is the sum of the masses of the atoms using the principal (most abundant) isotope for each element. Spectral deconvolution focuses on grouping spectral peaks into isotopomer envelopes. By doing so, the charge state and monoisotopic mass of each envelope are effectively determined. A complex multi-isotopic peak list in the m/z space is translated into a simple monoisotopic mass list that is easier to analyze.Given the monoisotopic mass and charge state of a fragment ion, its theoretical isotopic distribution can be predicted by assuming the fragment ion has an average elemental composition with respect to its mass (20) or using its precise elemental composition if the protein is known. Exploiting this, many deconvolution methods use theoretical isotopic distributions to detect and evaluate candidate isotopomer envelopes, which is the envelope detection problem (Fig. 1). To evaluate the fit of a candidate envelope to its theoretical isotopic distribution, many metrics have been proposed (20–32).Open in a separate windowFig. 1.Envelope detection. a, a theoretical isotopic distribution is predicted with the monoisotopic mass and charge state of a fragment ion. b, an observed envelope is detected by mapping peaks in the theoretical distribution to the spectrum. c, match between the theoretical isotopic distribution and the observed envelope. d, the theoretical isotopic distribution is scaled (the intensities of the peaks are multiplied by a constant) to have the best fit with the intensities of peaks in the observed envelope. Finally, a score for the observed envelope can be computed by comparing it with the intensity-scaled theoretical isotopic distribution.The candidate envelopes often overlap and share peaks, leading to a combinatorial problem of selecting the list of envelopes that best explains the spectrum (Fig. 2). In contrast to the well studied envelope detection problem, the envelope selection problem remains poorly explored. Most deconvolution algorithms follow a simple greedy approach to selecting the set of envelopes where the highest scoring envelopes are iteratively selected and removed from the spectrum. Although this approach often generates reasonable sets of envelopes for simple spectra, its performance deteriorates in cases of complex spectra.Open in a separate windowFig. 2.Envelope selection problem. Overlapping envelopes lead to a difficult combinatorial problem of selecting an optimal set of envelopes. We illustrate two cases where a deconvolution method that follows a greedy envelope selection outputs the envelope E₂, whereas the optimal solution consists of the envelopes E₁ and E₃. Example a illustrates the case where envelopes do not share peaks, and example b illustrates the case where envelopes share a spectral peak (E₁ and E₃).In particular, the greedy approach performs well when the envelopes are distributed sparsely along the m/z axis. Large proteins have many fragments that appear in multiple charge states. The high number of envelopes/peaks and the small m/z spread of the fragments with high charge states result in narrow m/z regions with high peak density. In these peak-dense regions, envelopes may overlap and share peaks, and the greedy approach and even manual interpretation often fail to find the optimal combination of envelopes (supplemental Fig. 1).Several methods have been proposed to explore the envelope selection problem. McIlwain et al. (33) presented a dynamic programming algorithm for selecting a set of envelopes such that the m/z ranges of the envelopes do not overlap. This non-overlapping condition becomes too restrictive for complex spectra of intact proteins. Samuelsson et al. (34) proposed a method that follows a non-negative sparse regression scheme. Du and Angeletti (35) and Renard et al. (36) addressed the envelope selection problem as a statistical problem of variable selection and used LASSO to solve it.Here, we present MS-Deconv, a combinatorial algorithm for spectral deconvolution. MS-Deconv (i) generates a large set of candidate envelopes, (ii) constructs an envelope graph encoding all envelopes and relationships between them, and (iii) finds a heaviest path in the envelope graph. Although the envelope graph of a complex spectrum is large (exceeding a million nodes in some cases), the heaviest path algorithm can efficiently find an optimal set of envelopes. MS-Deconv explicitly scores combinations of candidate envelopes rather than individual envelopes as in previous approaches.We tested MS-Deconv on a data set of top-down spectra from known proteins and evaluated the monoisotopic masses recovered by MS-Deconv. A mass was classified as a true positive if it was matched to the monoisotopic mass of a theoretical fragment ion of the protein within a specific parts per million (ppm) tolerance. We compared the performance of MS-Deconv with the widely used Thrash (20) and Xtract (37) and demonstrated that, with a few exceptions, MS-Deconv recovers more true positive masses. For example, for the collisionally activated dissociation (CAD) spectrum of bacteriorhodopsin (BR) with charge 10, the percentage of true positive masses among the top 150 masses is above 70% for MS-Deconv and less than 50% for Thrash. Additionally, MS-Deconv is ∼33 times faster than Thrash and 4 times faster than Xtract. Furthermore, MS-Deconv implements some user-friendly features: (i) outputs the set of peptide sequence tags, (ii) provides protein and spectral annotations, and (iii) allows one to inspect the recovered envelopes. We also tested MS-Deconv on a large LC-MS/MS data set from Yersinia rohdei (with a still unsequenced genome) (19). Y. rohdei is a non-pathogenic bacterium that is often used as a simulant for the potential bioterrorism agent Yersinia pestis, the causative agent of plague. We applied MS-Deconv to extract monoisotopic mass lists from top-down spectra and compared the mass lists with those reported by Thrash. We used ProSightPC (38) and the spectral alignment algorithm (39) to identify related proteins from a protein database of Yersinia enterocolitica (with a closely related and sequenced genome). The results demonstrated that MS-Deconv reported more matched fragments than Thrash for most proteins. Additionally, using spectral alignment, we identified eight proteins in Y. rohdei that were not reported in the ProSightPC-based searches (19) of the Y. enterocolitica protein database.     

Why do many galls have conspicuous colors? A new hypothesis

Galls are abnormal plant growth induced by various parasitic organisms, mainly insects. They serve as “incubators” for the developing insects in which they gain nutrition and protection from both abiotic factors and natural enemies. Galls are typically armed with high levels of defensive secondary metabolites. Conspicuousness by color, size and shape is a common gall trait. Many galls are colorful (red, yellow etc.) and therefore can be clearly distinguished from the surrounding host plant organs. Here we outlined a new hypothesis, suggesting that chemically protected galls which are also conspicuous are aposematic. We discuss predictions, alternative hypotheses and experimental tests of this hypothesis.     

Decision-making tools for Frankliniella occidentalis management in strawberry: consideration of target markets

The western flower thrips (WFT), Frankliniella occidentalis Pergande (Thysanoptera: Thripidae), a cosmopolitan pest of many crops, is considered a major pest of low tunnel and greenhouse strawberries. The extent of damage to strawberry is unclear because different studies have produced contradictory results. Also, economic thresholds published for WFT in strawberry vary greatly, and most fail to incorporate economic factors. This study was aimed at developing a decision‐making tool for WFT management in strawberries in Israel. Toward this end, economic injury levels (EIL) and economic thresholds were calculated, based on target markets (export vs. domestic). Results indicate that serious infestation of ripe berries may cause a dull, rough appearance, and the fruit may be soft and have a reduced shelf life, rendering it unsuitable for export. Most fruit damage occurred at green and turning‐red stages of development. Two decision‐making tools were developed, one for winter, when WFT populations increase slowly but crop value is high (export market); and the second for spring, when the pest increases rapidly but crop value is low (local markets). Economic thresholds of 10 and 24 WFT/flower were calculated for winter and spring strawberries, respectively, based on direct thrips damage to fruit. This calculation does not take into account the recorded WFT damage to flowers, or its role in facilitating Botrytis cinerea fruit infection. Western flower thrips has proved only an occasional economic pest in Israeli strawberries, and no routine control measures are warranted. Furthermore, augmentative releases of Orius laevigatus or Neoseilus cucumeris against WFT are not justified in this system, because Orius colonizes strawberry fields spontaneously in high numbers when no broad spectrum insecticides are used.     

A phase II study of combined administration of dacarbazine and carboplatin with home therapy of recombinant interleukin-2 and interferon-α2a in patients with advanced malignant melanoma

Chemotherapy and interleukin-2 (IL-2) and/or interferon (IFN) produce objective responses in a proportion of patients with advanced malignant melanoma. The duration of response to chemotherapy is usually less than 4 months, and immunotherapy has resulted in longlasting remissions in a small number of patients with metastatic melanoma. The current study was conducted to improve the antitumor efficacy and the interactions between recombinant (r) IL-2, rIFN2a and chemotherapy. A total of 16 evaluable patients with metastatic malignant melanoma were entered into a phase-II study designed to assess the response rate and therapeutic efficacy of dacarbazine and carboplatin followed by rIL-2 and rIFN2a. Patients received 750 mg/m² dacarbazine with 400 mg/m² carboplatin each by intravenous bolus on days 1 and 22. Recombinant IL-2 and IFN2a were administered on an outpatient basis (home therapy) subcutaneously for 6 consecutive weeks: 4.8×10⁶ IU/m² rIL-2 daily, 5 days a week; 6.0×10⁶ IU/m² rIFN2a thrice weekly. There were responses in 6 of the 16 enrolled patients with an overall response rate of 37.5% (95% confidence interval: 14%–61%). All responding patients had partial responses. The median survival time of the responding patients was significantly better than that of patients with progressive and stable disease (P=0.03). The median duration of response was 11 months (range 2–24 months). Responses in lung, liver, soft tissue and lymph-node sites were noted.