Evidence for template-specific sites in DNA polymerases

Using rabbit hemoglobin messenger RNA as template, $\text{E. coli}$ polymerase I produces poly (dT), poly (dA)·(dT) and antimessenger DNA products. Mild heating of the enzyme causes a differential loss in activity as indicated by three rates of inactivation for the three types of synthesis. Heat inactivation studies have also been carried out with DNA polymerases from oncogenic RNA viruses and mammalian sources using various homopolymer-oligomer pairs as primertemplates. In general, for any given enzyme these synthetic primer-templates reveal different extents of inactivation of the polymerase. These findings may be interpreted to suggest a) that the binding of DNA polymerase to various primer-templates produces conformational changes in the enzyme which are dependent on the type of template bound, or b) that many, if not all, DNA polymerases have different subsites for different templates.     

Nitric oxide regulates ganoderic acid biosynthesis by the S-nitrosylation of aconitase under heat stress in Ganoderma lucidum

Nitric oxide (NO) is an important signalling molecule in stress response of organisms. We previously reported that NO decreases heat stress (HS)-induced ganoderic acid (GA) accumulation in Ganoderma lucidum. To explore the mechanisms by which NO modulates GA biosynthesis under HS, the effect of NO on the reactive oxygen species (ROS) content was examined. The results showed that NO decreased the production of mitochondrial ROS (mitROS) by 60% under HS. Further research revealed that NO reduced the mitROS content by inhibiting aconitase (Acon) activity. The GA content in Acon-silenced (Aconi) strains treated with NO donor did not differ significantly from that in untreated Aconi strains. To study the mechanism by which Acon activity is inhibited, the S-nitrosylation level of Acon was determined. Biotin-switch technology and mass spectrometry analysis were used to show that Acon is S-nitrosylated at the Cys-594 amino acid residue. Substitution of Cys-594 with a Ser, which cannot be S-nitrosylated, abolished the responsiveness of Acon to the NO-induced reduction in its enzymatic activity. These findings demonstrate that NO inhibits Acon activity through S-nitrosylation at Cys-594. In summary, these findings describe mechanism by which NO regulates GA biosynthesis via S-nitrosylation of Acon under HS condition in G. lucidum.     

Accelerating Neuroimage Registration through Parallel Computation of Similarity Metric

Neuroimage registration is crucial for brain morphometric analysis and treatment efficacy evaluation. However, existing advanced registration algorithms such as FLIRT and ANTs are not efficient enough for clinical use. In this paper, a GPU implementation of FLIRT with the correlation ratio (CR) as the similarity metric and a GPU accelerated correlation coefficient (CC) calculation for the symmetric diffeomorphic registration of ANTs have been developed. The comparison with their corresponding original tools shows that our accelerated algorithms can greatly outperform the original algorithm in terms of computational efficiency. This paper demonstrates the great potential of applying these registration tools in clinical applications.     

Assessing the Status of Wild Felids in a Highly-Disturbed Commercial Forest Reserve in Borneo and the Implications for Camera Trap Survey Design

The proliferation of camera-trapping studies has led to a spate of extensions in the known distributions of many wild cat species, not least in Borneo. However, we still do not have a clear picture of the spatial patterns of felid abundance in Southeast Asia, particularly with respect to the large areas of highly-disturbed habitat. An important obstacle to increasing the usefulness of camera trap data is the widespread practice of setting cameras at non-random locations. Non-random deployment interacts with non-random space-use by animals, causing biases in our inferences about relative abundance from detection frequencies alone. This may be a particular problem if surveys do not adequately sample the full range of habitat features present in a study region. Using camera-trapping records and incidental sightings from the Kalabakan Forest Reserve, Sabah, Malaysian Borneo, we aimed to assess the relative abundance of felid species in highly-disturbed forest, as well as investigate felid space-use and the potential for biases resulting from non-random sampling. Although the area has been intensively logged over three decades, it was found to still retain the full complement of Bornean felids, including the bay cat Pardofelis badia, a poorly known Bornean endemic. Camera-trapping using strictly random locations detected four of the five Bornean felid species and revealed inter- and intra-specific differences in space-use. We compare our results with an extensive dataset of >1,200 felid records from previous camera-trapping studies and show that the relative abundance of the bay cat, in particular, may have previously been underestimated due to the use of non-random survey locations. Further surveys for this species using random locations will be crucial in determining its conservation status. We advocate the more wide-spread use of random survey locations in future camera-trapping surveys in order to increase the robustness and generality of inferences that can be made.     

Acceleration of high gravity yeast fermentations by acetaldehyde addition

In high gravity Saccharomyces cerevisiae fermentations containing 300 g glucose l^–1, daily addition of acetaldehyde to a total of 93 mM shortened the time required to ferment the first 250 g glucose l^–1 from 790 h to 585 h. Acetaldehyde feeding had no effect on the ethanol yield but increased by 135%, 78% and 77% the final concentrations of 2,3-butanediol, 2-methylpropanol and acetate, while decreasing that of glycerol by 14%. Controlled acetaldehyde feeding has potential as a technique for accelerating high gravity fuel or industrial ethanol fermentations and may be useful in preventing incomplete fermentations.     

Compositional Characterization and Pyrolysis of Loblolly Pine and Douglas-fir Bark

Two potential biofuel resources, Douglas-fir and Loblolly pine bark, were subjected to extensive chemical and compositional analysis. The barks were initially extracted with dichloromethane, and the resulting extracted compounds were characterized by gas chromatography coupled with mass spectrometric analysis. Characterization of the major bark biocomponents indicated that Douglas-fir and Loblolly pine bark contained 22.5 and 13.2 % tannins, 44.2 and 43.5 % lignin, 16.5 and 23.1 % cellulose, and 7.6 and 14.1 % hemicellulose, respectively. Of particular interest is the high content of tannins and lignin, which make these barks excellent potential precursors for bio-oils and/or other value-added chemicals. ¹³C nuclear magnetic resonance (NMR) was used to characterize the chemical structure of the lignin and tannins. These samples were also analyzed by ³¹P NMR after phosphitylation of the hydroxyl groups in lignin and tannins. The NMR spectral data indicated that the lignin in both barks contained p-hydroxyphenyl (h) and guaiacyl (g) of lignin monomers with an h/g ratio of 10:90 and 22:78 for Douglas-fir and Loblolly pine bark, respectively. Gel permeation chromatography was used to analyze the molecular weight distributions of extracted tannins, isolated cellulose, and ball-milled lignin. The pyrolysis of Douglas-fir and pine bark at 500°C in a tubular reactor generated 48.2 and 45.2 % of total oil, of which the light oil contents are 14.1 and 20.7 % and heavy oil are 34.1 and 24.4 %. Similarly, fast pyrolysis at 375°C yielded 56.1 and 49.8 % of total oil for Douglas-fir and pine bark, respectively.     

Gender Differentiated Preferences for a Community-Based Conservation Initiative

Community-based conservation (CBC) aims to benefit local people as well as to achieve conservation goals, but has been criticised for taking a simplistic view of “community” and failing to recognise differences in the preferences and motivations of community members. We explore this heterogeneity in the context of Kenya’s conservancies, focussing on the livelihood preferences of men and women living adjacent to the Maasai Mara National Reserve. Using a discrete choice experiment we quantify the preferences of local community members for key components of their livelihoods and conservancy design, differentiating between men and women and existing conservancy members and non-members. While Maasai preference for pastoralism remains strong, non-livestock-based livelihood activities are also highly valued and there was substantial differentiation in preferences between individuals. Involvement with conservancies was generally perceived to be positive, but only if households were able to retain some land for other purposes. Women placed greater value on conservancy membership, but substantially less value on wage income, while existing conservancy members valued both conservancy membership and livestock more highly than did non-members. Our findings suggest that conservancies can make a positive contribution to livelihoods, but care must be taken to ensure that they do not unintentionally disadvantage any groups. We argue that conservation should pay greater attention to individual-level differences in preferences when designing interventions in order to achieve fairer and more sustainable outcomes for members of local communities.