Selecting appropriate methods of knowledge synthesis to inform biodiversity policy

Responding to different questions generated by biodiversity and ecosystem services policy or management requires different forms of knowledge (e.g. scientific, experiential) and knowledge synthesis. Additionally, synthesis methods need to be appropriate to policy context (e.g. question types, budget, timeframe, output type, required scientific rigour). In this paper we present a range of different methods that could potentially be used to conduct a knowledge synthesis in response to questions arising from knowledge needs of decision makers on biodiversity and ecosystem services policy and management. Through a series of workshops attended by natural and social scientists and decision makers we compiled a range of question types, different policy contexts and potential methodological approaches to knowledge synthesis. Methods are derived from both natural and social sciences fields and reflect the range of question and study types that may be relevant for syntheses. Knowledge can be available either in qualitative or quantitative form and in some cases also mixed. All methods have their strengths and weaknesses and we discuss a sample of these to illustrate the need for diversity and importance of appropriate selection. To summarize this collection, we present a table that identifies potential methods matched to different combinations of question types and policy contexts, aimed at assisting teams undertaking knowledge syntheses to select appropriate methods.     

Instability of Pressure-Treated Reconstituted Skim Milk to Acidification

When high-pressure (HP)-treated reconstituted skim milks (200–600 MPa/5–30 min) were acidified with glucono-δ-lactone, the elastic modulus (G′) displayed atypical behaviour with pH, increasing as the pH decreased between 6.0 and 5.3, indicating that a weak gel had formed as soon as the pH of the milk decreased. The formation of a weak gel at pH 6.0 to 5.3 indicates that HP milks are more unstable to acidification than untreated or heated milks; this effect has not been previously reported. Untreated and heated (90 °C/30 min) milks did not show an increase in G′ until the pH was below 4.9 and 5.3, respectively. Frequency sweeps confirmed that the HP-treated milks formed weak gels at pH much higher than where typical acid gelation of milk occurs. Microstructural and particle size analyses indicated that the HP-treated milks started aggregating as soon as the pH declined whereas the heated milks did not aggregate until the pH was below 5.5. Heat treatment of milk either before or after HP treatment completely eliminated the weak gelation as these samples did not form gels until the pH decreased below pH 5.3. It is apparent that the restructured colloidal particles formed when milk is HP treated are unstable to acidification, and it is proposed that the redistributed κ-casein cannot stabilize these particles when the milk is acidified. The role of denatured whey proteins in the weak gelation phenomenon is unclear.     

A comparison study reveals important features of agreement and disagreement between summarized DNA and RNA data obtained from renal cell carcinoma

Cytogenetic abnormalities, such as DNA amplifications and deletions, often lead to significant changes in gene expression levels within a chromosomal region. Instead of generating additional DNA copy number data, one method to identify DNA copy number abnormalities has been to search existing gene expression data for regional perturbations in gene expression. However, it is not clear how well this surrogate method performs in the examination of individual tumors and how we can use both DNA and RNA data to identify candidate genes that may be mutated. Here we report a comparison study using summarized DNA and RNA data to identify chromosomal abnormalities in human samples. Forty-four tissue samples from patients diagnosed as having renal cell carcinoma (RCC) were collected, together with 15 normal kidney samples as controls, and for each sample the genome-wide DNA and RNA data were obtained for comparison using Affymetrix 100K SNP and HGU133plus2 gene expression chips, respectively. The DNA and RNA data was summarized by both chromosome arm and cytogenetic banding patterns and compared. The result of this analysis revealed that the two summarized data sets used to identify cytogenetic changes agreed well. However, some differences between the two were also identified. These differences of large-scale gene expression deregulation without evidence of the comparable DNA copy number alterations may be the result of known mechanisms, such as large-scale methylation or chromosome inactivation, or may be the result of some new mechanism of DNA-RNA translation. The usefulness of the combined data set for identifying regions of mutated genes is also discussed.     

Effect of pH on the Heat Resistance of Clostridium sporogenes Spores in Minced Meat

S ummary : The effect of the pH value of minced meat on the heat resistance of Clostridium sporogenes spores inoculated in it was examined. A drop in pH from 6·0 to 4·8 decreased the decimal reduction time by 40%, irrespective of the heating temperature. In other words, the z value is independent of pH.     

A lactational study of the composition and integrity of casein micelles from the milk of the tammar wallaby (Macropus eugenii)

The amount of casein found in the milk of the tammar wallaby increases as lactation progresses. The increase is due to increasing amounts of β-casein; the α-casein remains largely constant. The α-casein is the more highly phosphorylated; the most abundant form is the 10-P, throughout lactation. The level of phosphorylation of β-casein shifts to lower average values in late lactation, possibly indicating the enzymatic reaction is overloaded by the increasing amounts of β-casein. Unlike bovine casein micelles, the wallaby micelles are not completely disrupted at pH 7.0 by sequestration of their calcium content with ethylene diamine tetraacetic acid (EDTA). Complete disruption only follows the addition of sodium dodecyl sulphate, indicating considerably greater importance for hydrophobic bonds in maintaining their integrity. This micellar behaviour indicates that, despite the evolutionary divergence of marsupials millennia ago, the caseins of wallaby milk assemble into micelles in much the same fashion as in bovine milk.     

Cloning and functional characterization of the Rvi15 (Vr2) gene for apple scab resistance

Apple scab, caused by Venturia inaequalis, is a serious disease of apple. Previously, the scab resistance Rvi15 (Vr2) from the accession GMAL 2473 was genetically mapped, and three candidate resistance genes were identified. Here, we report the cloning and functional characterization of these three genes, named Vr2-A, Vr2-B, and Vr2-C. Each gene was cloned with its native promoter, terminator and introns, and inserted into the susceptible apple cultivar ‘Gala’. Inoculation of the plants containing Vr2-A and Vr2-B induced no resistance symptoms, but abundant sporulation. However, inoculation of the plants harboring Vr2-C showed a hypersensitive response with clear pinpoint pits, and no or very little sporulation. We conclude that Vr2-C is the Rvi15 (Vr2) gene. This gene belongs to the Toll and mammalian interleukin-1 receptor protein nucleotide-binding site leucine-rich repeat structure resistance gene family. The proteins of this gene family reside in the cytoplasm, whereas V. inaequalis develops in the apoplast, between the epidermis and cuticle, without making haustoria. The spatial separation of the recognizing resistance protein and the pathogen is discussed. This is the second cloned gene for apple scab resistance, and out of these two the only one leading to a symplastic protein.     

SOBIR1 requires the GxxxG dimerization motif in its transmembrane domain to form constitutive complexes with receptor‐like proteins

Receptor‐like proteins (RLPs), forming an important group of transmembrane receptors in plants, play roles in development and immunity. RLPs contain extracellular leucine‐rich repeats (LRRs) and, in contrast with receptor‐like kinases (RLKs), lack a cytoplasmic kinase required for the initiation of downstream signalling. Recent studies have revealed that the RLK SOBIR1/EVR (SUPPRESSOR OF BIR1‐1/EVERSHED) specifically interacts with RLPs. SOBIR1 stabilizes RLPs and is required for their function. However, the mechanism by which SOBIR1 associates with RLPs and regulates RLP function remains unknown. The Cf immune receptors of tomato (Solanum lycopersicum), mediating resistance to the fungus Cladosporium fulvum, are RLPs that also interact with SOBIR1. Here, we show that both the LRR and kinase domain of SOBIR1 are dispensable for association with the RLP Cf‐4, whereas the highly conserved GxxxGxxxG motif present in the transmembrane domain of SOBIR1 is essential for its interaction with Cf‐4 and additional RLPs. Complementation assays in Nicotiana benthamiana, in which endogenous SOBIR1 levels were knocked down by virus‐induced gene silencing, showed that the LRR domain as well as the kinase activity of SOBIR1 are required for the Cf‐4/Avr4‐triggered hypersensitive response (HR). In contrast, the LRRs and kinase activity of SOBIR1 are not required for facilitation of Cf‐4 accumulation. Together, these results suggest that, in addition to being a stabilizing scaffold for RLPs, SOBIR1 is also required for the initiation of downstream signalling through its kinase domain.     

Fingers Crossed! An Investigation of Somatotopic Representations Using Spatial Directional Judgements

Processing of tactile stimuli requires both localising the stimuli on the body surface and combining this information with a representation of the current posture. When tactile stimuli are applied to crossed hands, the system first assumes a prototypical (e.g. uncrossed) positioning of the limbs. Remapping to include the crossed posture occurs within about 300 ms. Since fingers have been suggested to be represented in a mainly somatotopic reference frame we were interested in how the processing of tactile stimuli applied to the fingers would be affected by an unusual posture of the fingers. We asked participants to report the direction of movement of two tactile stimuli, applied successively to the crossed or uncrossed index and middle fingers of one hand at different inter-stimulus intervals (15 to 700 ms). Participants almost consistently reported perceiving the stimulus direction as opposite to what it was in the fingers crossed condition, even with SOAs of 700 ms, suggesting that on average they did not incorporate the unusual relative finger positions. Therefore our results are in agreement with the idea that, by default, the processing of tactile stimuli assumes a prototypical positioning of body parts. However, in contrast to what is generally found with tactile perception with crossed hands, performance did not improve with SOAs as long as 700 ms. This suggests that the localization of stimuli in a somatotopic reference and the integration of this representation with postural information are two separate processes that apply differently to the hands and fingers.     

Importance of host feeding for parasitoids that attack honeydew-producing hosts

Insect parasitoids lay their eggs in arthropods. Some parasitoid species not only use their arthropod host for oviposition but also for feeding. Host feeding provides nutrients to the adult female parasitoid. However, in many species, host feeding destroys an opportunity to oviposit. For parasitoids that attack Homoptera, honeydew is a nutrient‐rich alternative that can be directly imbibed from the host anus without injuring the host. A recent study showed that feeding on host‐derived honeydew can be an advantageous alternative in terms of egg quantity and longevity. Here we explore the conditions under which destructive host feeding can provide an advantage over feeding on honeydew. For 5 days, Encarsia formosa Gahan (Hymenoptera: Aphelinidae) parasitoids were allowed daily up to 3 h to oviposit until host feeding was attempted. Host feedings were either prevented or allowed and parasitoids had ad libitum access to honeydew between foraging bouts. Even in the presence of honeydew, parasitoids allowed to host feed laid more eggs per hour of foraging per host‐feeding attempt than parasitoids that were prevented from host feeding. The higher egg‐laying rate was not compromised by survival or by change in egg volume over time. In conclusion, host feeding can provide an advantage over feeding on honeydew. This applies most likely under conditions of high host density or low extrinsic mortality of adult parasitoids, when alternative food sources cannot supply enough nutrients to prevent egg limitation. We discuss how to integrate ecological and physiological studies on host‐feeding behavior