Affordable biocomputing for everyone: using the Internet,freeware and open-source software

How to build your own complete working biocomputing platform with nothing more than a desktop computer and an Internet connection.     

Biofumigation and Enhanced Biodegradation: Opportunity and Challenge in Soilborne Pest and Disease Management

Management of soilborne pests and diseases in cropping systems is often highly challenging—in implementation of acceptable methodologies and in dealing with secondary problems. The phase-out of methyl bromide brings this into particularly sharp focus. There is a need for diversified options and alternatives to fill different roles across the soilborne pest and disease management spectrum, but flexibility is limited, as practicalities demand that they fit into a prophylactic methodology. It is against such a backdrop that expectations and promotion of alternatives must be set. There is also a need to recognize potentially serious problems that may have been masked under historical management regimes, but for which the nature of the system offers little scope to avoid or manage.

Biofumigation is the beneficial use of Brassica green manures that release isothiocyanates chemically similar to methyl isothiocyanate, the active agent from the synthetic fumigant metam sodium, which is used as a substitute for methyl bromide in some systems. A systematic approach to research into biofumigation, specifically aimed at overcoming a long history of empiricism, has seen significant recent advances in both basic and applied knowledge. A key development has been achievement of maximal biofumigation potential through greatly enhanced release of appropriate isothiocyanates into soil. These advances have led to commercial adoption, demonstrating that biofumigation, when applied to appropriate production systems, can have efficacy and offer cost savings. Crucially, these systematically derived research and development findings and their adoption now provide the impetus for self-sustaining further development and market penetration of the concept. Despite this success, biofumigation is not seen as being sufficiently powerful or practical in implementation to be an alternative to methyl bromide on a broad scale and misdirection in that regard could be counterproductive to more appropriately targeted further development.

Enhanced microbial biodegradation is a cryptic phenomenon that can diminish the efficacy of soil-applied pesticides, including isothiocyanates and most other currently available methyl bromide substitutes. Because methyl bromide is not susceptible, the phenomenon has potentially serious implications in intensive production systems switching from methyl bromide to reliance on other compounds that are. It is an intractable problem once induced. Avoidance of its onset is the only feasible management strategy. This has been aided for some particularly vulnerable environments by recent clarification of key risk factors associated with soil type, soil pH, and calcium content.     

Selective acylation enhances membrane charge sensitivity of the antimicrobial peptide mastoparan-x

The partitioning of the wasp venom peptide mastoparan-X (MPX) into neutral and negatively charged lipid membranes has been compared with two new synthetic analogs of MPX where the N^α-terminal of MPX was acylated with propanoic acid (PA) and octanoic acid (OA). The acylation caused a considerable change in the membrane partitioning properties of MPX and it was found that the shorter acylation with PA gave improved affinity and selectivity toward negatively charged membranes, whereas OA decreased the selectivity. Based on these findings, we hypothesize that minor differences in the embedding and positioning of the peptide in the membrane caused by either PA or OA acylation play a critical role in the fine-tuning of the effective charge of the peptide and thereby the fine-tuning of the peptide's selectivity between neutral and negatively charged lipid membranes. This finding is unique compared to previous reports where peptide acylation enhanced membrane affinity but also resulted in impaired selectivity. Our result may provide a method of enhancing selectivity of antimicrobial peptides toward bacterial membranes due to their high negative charge—a finding that should be investigated for other, more potent antimicrobial peptides in future studies.     

Spring migration dynamics and sex-specific patterns in stopover strategy in the Wood Sandpiper Tringa glareola

Due to being a virtually monomorphic wader species, migration dynamics and sex-related migration patterns in the Wood Sandpiper (Tringa glareola) have rarely been investigated. We captured spring migrants at an important stopover site in northeastern Austria. Birds were individually color-marked, and sex was determined by an analysis of DNA from tail feather material. Among temporary residents (birds seen again after day of capture), males migrated on average 3 days earlier than females. However, since sexes did not differ in fat score, the length of stay and the proportion of transients (birds not seen again after day of capture) and temporary residents, we suggest that males and females adopt similar migration strategies in the spring. The large number of transients captured as well as shorter stopover durations in later temporary residents indicate that Wood Sandpipers minimize time at this stage of their northbound migration. Temporary residents earlier in the season exhibited lower fat stores than later ones. Nevertheless, since the fat stores of transients and temporary residents were similar even after the progress of the season had been accounted for, we assume that Wood Sandpipers may afford to exhibit individual flexibility in migration strategy and the use of stopover sites, especially early in the season. This variability may be a necessary adaptation to cope with possible varying environmental conditions at dynamic and unpredictable inland stopover sites. After having reached North Mediterranean regions, mean body mass of spring migrants gradually increases during successive stopovers, indicating that Wood Sandpipers follow a ‘hopping’ migration strategy. This emphasizes the high conservation value of even small artificial mudflat pools as important stepping stones in order to maintain a continuous network of wetland habitats for this continental migrant.     

The multivesicular body-localized GTPase ARFA1b/1c is important for callose deposition and ROR2 syntaxin-dependent preinvasive basal defense in barley

Host cell vesicle traffic is essential for the interplay between plants and microbes. ADP-ribosylation factor (ARF) GTPases are required for vesicle budding, and we studied the role of these enzymes to identify important vesicle transport pathways in the plant-powdery mildew interaction. A combination of transient-induced gene silencing and transient expression of inactive forms of ARF GTPases provided evidence that barley (Hordeum vulgare) ARFA1b/1c function is important for preinvasive penetration resistance against powdery mildew, manifested by formation of a cell wall apposition, named a papilla. Mutant studies indicated that the plasma membrane-localized REQUIRED FOR MLO-SPECIFIED RESISTANCE2 (ROR2) syntaxin, also important for penetration resistance, and ARFA1b/1c function in the same vesicle transport pathway. This was substantiated by a requirement of ARFA1b/1c for ROR2 accumulation in the papilla. ARFA1b/1c is localized to multivesicular bodies, providing a functional link between ROR2 and these organelles in penetration resistance. During Blumeria graminis f sp hordei penetration attempts, ARFA1b/1c-positive multivesicular bodies assemble near the penetration site hours prior to the earliest detection of callose in papillae. Moreover, we showed that ARFA1b/1c is required for callose deposition in papillae and that the papilla structure is established independently of ARFA1b/1c. This raises the possibility that callose is loaded into papillae via multivesicular bodies, rather than being synthesized directly into this cell wall apposition.     

Identification of thermostable β-xylosidase activities produced by <Emphasis Type="Italic">Aspergillus brasiliensis</Emphasis> and <Emphasis Type="Italic">Aspergillus niger</Emphasis>

Twenty Aspergillus strains were evaluated for production of extracellular cellulolytic and xylanolytic activities. Aspergillus brasiliensis, A. niger and A. japonicus produced the highest xylanase activities with the A. brasiliensis and A. niger strains producing thermostable β-xylosidases. The β-xylosidase activities of the A. brasiliensis and A. niger strains had similar temperature and pH optima at 75°C and pH 5 and retained 62% and 99%, respectively, of these activities over 1 h at 60°C. At 75°C, these values were 38 and 44%, respectively. Whereas A. niger is a well known enzyme producer, this is the first report of xylanase and thermostable β-xylosidase production from the newly identified, non-ochratoxin-producing species A. brasiliensis.