Paul T. Scott

Pongamia pinnata : An Untapped Resource for the Biofuels Industry of the Future

Pongamia pinnata (L.) Pierre is a fast-growing leguminous tree with the potential for high oil seed production and the added benefit of the ability to grow on marginal land. These properties support the suitability of this plant for large-scale vegetable oil production required by a sustainable biodiesel industry. The future success of P. pinnata as a sustainable source of feedstock for the biofuels industry is dependent on an extensive knowledge of the genetics, physiology and propagation of this legume. In particular, research should be targeted to maximizing plant growth as it relates to oil biosynthesis. This review assesses and integrates the biological, chemical and genetic attributes of the plant, providing the basis for future research into Pongamia’s role in an emerging industry.

Legume nodulation: successful symbiosis through short- and long-distance signalling

Nodulation in legumes provides a major conduit of available nitrogen into the biosphere. The development of nitrogen-fixing nodules results from a symbiotic interaction between soil bacteria, commonly called rhizobia, and legume plants. Molecular genetic analysis in both model and agriculturally important legume species has resulted in the identification of a variety of genes that are essential for the establishment, maintenance and regulation of this symbiosis. Autoregulation of nodulation (AON) is a major internal process by which nodule numbers are controlled through prior nodulation events. Characterisation of AON-deficient mutants has revealed a novel systemic signal transduction pathway controlled by a receptor-like kinase. This review reports our present level of understanding on the short- and long-distance signalling networks controlling early nodulation events and AON.

Reference ranges for the clinical laboratory derived from a rural population in Kericho, Kenya.

The conduct of Phase I/II HIV vaccine trials internationally necessitates the development of region-specific clinical reference ranges for trial enrolment and participant monitoring. A population based cohort of adults in Kericho, Kenya, a potential vaccine trial site, allowed development of clinical laboratory reference ranges. Lymphocyte immunophenotyping was performed on 1293 HIV seronegative study participants. Hematology and clinical chemistry were performed on up to 1541 cohort enrollees. The ratio of males to females was 1.9∶1. Means, medians and 95% reference ranges were calculated and compared with those from other nations. The median CD4+ T cell count for the group was 810 cells/µl. There were significant gender differences for both red and white blood cell parameters. Kenyan subjects had lower median hemoglobin concentrations (9.5 g/dL; range 6.7–11.1) and neutrophil counts (1850 cells/µl; range 914–4715) compared to North Americans. Kenyan clinical chemistry reference ranges were comparable to those from the USA, with the exception of the upper limits for bilirubin and blood urea nitrogen, which were 2.3-fold higher and 1.5-fold lower, respectively. This study is the first to assess clinical reference ranges for a highland community in Kenya and highlights the need to define clinical laboratory ranges from the national community not only for clinical research but also care and treatment.

Capturing the biofuel wellhead and powerhouse: the chloroplast and mitochondrial genomes of the leguminous feedstock tree Pongamia pinnata.

Pongamia pinnata (syn. Millettia pinnata) is a novel, fast-growing arboreal legume that bears prolific quantities of oil-rich seeds suitable for the production of biodiesel and aviation biofuel. Here, we have used Illumina® ‘Second Generation DNA Sequencing (2GS)’ and a new short-read de novo assembler, SaSSY, to assemble and annotate the Pongamia chloroplast (152,968 bp; cpDNA) and mitochondrial (425,718 bp; mtDNA) genomes. We also show that SaSSY can be used to accurately assemble 2GS data, by re-assembling the Lotus japonicus cpDNA and in the process assemble its mtDNA (380,861 bp). The Pongamia cpDNA contains 77 unique protein-coding genes and is almost 60% gene-dense. It contains a 50 kb inversion common to other legumes, as well as a novel 6.5 kb inversion that is responsible for the non-disruptive, re-orientation of five protein-coding genes. Additionally, two copies of an inverted repeat firmly place the species outside the subclade of the Fabaceae lacking the inverted repeat. The Pongamia and L. japonicus mtDNA contain just 33 and 31 unique protein-coding genes, respectively, and like other angiosperm mtDNA, have expanded intergenic and multiple repeat regions. Through comparative analysis with Vigna radiata we measured the average synonymous and non-synonymous divergence of all three legume mitochondrial (1.59% and 2.40%, respectively) and chloroplast (8.37% and 8.99%, respectively) protein-coding genes. Finally, we explored the relatedness of Pongamia within the Fabaceae and showed the utility of the organellar genome sequences by mapping transcriptomic data to identify up- and down-regulated stress-responsive gene candidates and confirm in silico predicted RNA editing sites.

Prevalence of HIV, hepatitis B and hepatitis C and associated risk behaviours amongst injecting drug users in three Afghan cities

BACKGROUND HIV amongst injecting drug users (IDUs) has been described in Kabul but little data exists for other Afghan cities. We assessed HIV, hepatitis B virus (HBV), and C virus (HCV) prevalence and associated risk behaviours amongst IDUs in Hirat, Jalalabad, and Mazar-i-Sharif, Afghanistan. METHODS Consented participants reporting injecting drugs within the previous 6 months completed interviewer-administered questionnaires and testing for HIV, hepatitis C antibody (HCV Ab), and hepatitis B surface antigen (HBsAg). Logistic regression was used to determine characteristics associated with each infection. RESULTS Of 623 participants, most (98.7%) were male. Prevalence of HIV, HCV, and HBV was 1.8% (95% CI: 0.88-3.2), 36.0% (95% CI: 33-41), and 5.8% (95% CI: 3.9-7.6), respectively. All HIV cases and highest HCV prevalence were detected in Hirat; HBV prevalence was highest in Jalalabad. Amongst male IDUs, 62.9% had been imprisoned, of whom 17.2% (n=66) injected in prison. High risk behaviours were common; 30.2% reported needle sharing in the last 6 months, 23.1% reported sex with another male, and 50.4% reported paying females for sex. Behaviours varied significantly by site; generally, Hirat participants reported fewer sexual risk behaviours. Sex with other males was negatively associated with both HBV and HCV in multivariate logistic regression analysis; no injecting behaviours were associated with both HBV and HCV. CONCLUSIONS Whilst HIV prevalence is low, HCV prevalence and high risk behaviours were common in these populations. Regional variations should be considered in programming to prevent transmission of HIV and viral hepatitis amongst IDUs in Afghanistan.

The value of biodiversity in legume symbiotic nitrogen fixation and nodulation for biofuel and food production.

Much of modern agriculture is based on immense populations of genetically identical or near-identical varieties, called cultivars. However, advancement of knowledge, and thus experimental utility, is found through biodiversity, whether naturally-found or induced by the experimenter. Globally we are confronted by ever-growing food and energy challenges. Here we demonstrate how such biodiversity from the food legume crop soybean (Glycine max L. Merr) and the bioenergy legume tree Pongamia (Millettia) pinnata is a great value. Legume plants are diverse and are represented by over 18,000 species on this planet. Some, such as soybean, pea and medics are used as food and animal feed crops. Others serve as ornamental (e.g., wisteria), timber (e.g., acacia/wattle) or biofuel (e.g., Pongamia pinnata) resources. Most legumes develop root organs (nodules) after microsymbiont induction that serve as their habitat for biological nitrogen fixation. Through this, nitrogen fertiliser demand is reduced by the efficient symbiosis between soil Rhizobium-type bacteria and the appropriate legume partner. Mechanistic research into the genetics, biochemistry and physiology of legumes is thus strategically essential for future global agriculture. Here we demonstrate how molecular plant science analysis of the genetics of an established food crop (soybean) and an emerging biofuel P. pinnata feedstock contributes to their utility by sustainable production aided by symbiotic nitrogen fixation.

Transfusion‐transmissible viral infections among US military recipients of whole blood and platelets during Operation Enduring Freedom and Operation Iraqi Freedom

BACKGROUND: Current US military clinical practice guidelines permit emergency transfusions of non–Food and Drug Administration (FDA)‐compliant freshly collected blood products in theaters of war. This investigation aimed to characterize the risks of transfusion‐transmitted infections (TTIs) associated with battlefield transfusions of non–FDA‐compliant blood products.

A common view of the opportunities, challenges, and research actions for Pongamia in Australia.

Interest in biofuels is increasing in Australia due to volatile and rising oil prices, the need to reduce GHG emissions, and the recent introduction of a price on carbon. The seeds of Pongamia (Millettia pinnata) contain oils rich in C18:1 fatty acid, making it useful for the manufacture of biodiesel and other liquid fuels. Preliminary assessments of growth and seed yield in Australia have been promising. However, there is a pressing need to synthesise practical experience and existing fragmented research and to use this to underpin a well-founded and co-ordinated research strategy to support industry development, including better management of the risks associated with investment. This comprehensive review identifies opportunities for Pongamia in Australia and provides a snapshot of what is already known and the risks, uncertainties, and challenges based on published research, expert knowledge, and industry experience. We conclude that whilst there are major gaps in fundamental understanding of the limitations to growth of Pongamia in Australia, there is sufficient evidence indicating the potential of Pongamia as a feedstock for production of biofuel to warrant investment into a structured research and development program over the next decade. We identify ten critical research elements and propose a comprehensive research approach that links molecular level genetic research, paddock scale agronomic studies, landscape scale investigations, and new production systems and value chains into a range of aspects of sustainability.

Application of nox-restriction fragment length polymorphism for the differentiation of Brachyspira intestinal spirochetes isolated from pigs and poultry in Australia.

Sixty-nine intestinal spirochetes isolated from pigs and poultry in eastern Australia were selected to evaluate the effectiveness of a species-specific PCR-based restriction fragment length polymorphism (RFLP) analysis of the Brachyspira nox gene. For comparative purposes, all isolates were subjected to species-specific PCRs for the pathogenic species Brachyspira hyodysenteriae and Brachyspira pilosicoli, and selected isolates were examined further by sequence analysis of the nox and 16S ribosomal RNA genes. Modifications to the original nox-RFLP method included direct inoculation of bacterial cells into the amplification mixture and purification of the PCR product, which further optimized the nox-RFLP for use in a veterinary diagnostic laboratory, producing sufficient product for both species identification and future comparisons. Although some novel profiles that prevented definitive identification were observed, the nox-RFLP method successfully classified 45 of 51 (88%) porcine and 15 of 18 (83%) avian isolates into 5 of the 6 recognized species of Brachyspira. This protocol represents a significant improvement over conventional methods currently used in veterinary diagnostic laboratories for rapid specific identification of Brachyspira spp. isolated from both pigs and poultry.

Characterization of Streptococcus bovis from the rumen of the dromedary camel and Rusa deer

Aims:  Isolation and characterization of Streptococcus bovis from the dromedary camel and Rusa deer.