A collaborative tool for mobilizing knowledge in agrobiodiversity and the interface with climate change: the Platform for Agrobiodiversity Research

Poster presented at 2nd ANAFE International Symposium. Lilongwe (Malawi), Jul 200

Highly syntenic and yet divergent: a tale of two Theilerias

The published genomic sequences of the two major host-transforming Theileria species of cattle represent a rich resource of information that has allowed novel bioinformatic and experimental studies into these important apicomplexan parasites. Since their publication in 2005, the genomes of T. annulata and T. parva have been utilised for a diverse range of applications, ranging from candidate antigen discovery to the identification of genetic markers for population analysis. This has led to advancements in the quest for a sub-unit vaccine, while providing a greater understanding of variation among parasite populations in the field. The unique ability of these Theileria species to induce host cell transformation is the subject of considerable scientific interest and the availability of full genomic sequences has provided new insights into this area of research. This article reviews the data underlying published comparative analyses, focussing on the general features of gene expression, the major Tpr/Tar multi-copy gene family and a re-examination of the predicted macroschizont secretome. Codon usage between the Theileria species is reviewed in detail, as this underpins ongoing comparative studies investigating selection at the intra- and inter-species level. The TashAT/TpshAT family of genes, conserved between T. annulata and T. parva, encodes products targeted to the host nucleus and has been implicated in contributing to the transformed bovine phenotype. Species-specific expansion and diversification at this critical locus is discussed with reference to the availability, in the near future, of genomic datasets which are based on non-transforming Theileria species

Aortic intima media thickness in children and adolescents with type 1 diabetes : A systematic review

Aims Greater aortic intima media thickness (aIMT), a marker of subclinical atherosclerosis, can identify individuals at risk of CVD. This systematic review with meta-analysis compared aIMT in youth with type 1 diabetes and healthy controls. Methods A systematic search of published literature (to July 2021) was undertaken using electronic databases MEDLINE, EMBASE, Scopus, CINAHL and AMED. Eligible studies reported aIMT in participants aged <20 years with type 1 diabetes and healthy controls. Meta-analysis was used to combine outcome data, presented as forest plots. Moderator analysis and metaregression were conducted to identify study and participant characteristics associated with aIMT. Publication bias was assessed by funnel plot inspection. Results Meta-analysis of nine studies (n = 1030 with type 1 diabetes and n = 498 healthy control participants) indicated, with high heterogeneity (I2 98%), that youth with type 1 diabetes have higher aIMT compared with healthy controls (mean difference [95% CIs]: 0.11 [0.04, 0.18] mm, P = 0.003). Factors associated with greater aIMT in type 1 diabetes compared to controls included: use of a phased array probe versus linear array probe; longer diabetes duration; higher insulin dose; higher BMI z score and waist circumference; higher LDL cholesterol; higher triglycerides; and higher diastolic blood pressure. Conclusions Type 1 diabetes in youth is associated with higher aIMT compared with healthy control individuals. Longer duration of diabetes and major CVD risk factors were also associated with higher aIMT. Together, these findings provide a strong rationale for targeting modifiable risk factors in CVD prevention. Registered in PROSPERO on 8 August 2019 (CRD42019137559)

Reproducibility of aortic intima-media thickness in infants using edge-detection software and manual caliper measurements

Background: Aortic intima-media thickness measured by transabdominal ultrasound (aIMT) is an intermediate phenotype of cardiovascular risk. We aimed to (1) investigate the reproducibility of aIMT in a population-derived cohort of infants; (2) establish the distribution of aIMT in early infancy; (3) compare measurement by edge-detection software to that by manual sonographic calipers; and (4) assess the effect of individual and environmental variables on image quality. Methods. Participants were term infants recruited to a population-derived birth cohort study. Transabdominal ultrasound was performed at six weeks of age by one of two trained operators. Thirty participants had ultrasounds performed by both operators on the same day. Data were collected on environmental (infant sleeping, presence of a sibling, use of sucrose, timing during study visit) and individual (post-conception age, weight, gender) variables. Two readers assessed image quality and measured aIMT by edge-detection software and a subset by manual sonographic calipers. Measurements were repeated by the same reader and between readers to obtain intra-observer and inter-observer reliability. Results: Aortic IMT was measured successfully using edge-detection in 814 infants, and 290 of these infants also had aIMT measured using manual sonographic calipers. The intra-reader intra-class correlation (ICC) (n = 20) was 0.90 (95% CI 0.76, 0.96), mean difference 1.5 &mu;m (95% LOA -39, 59). The between reader ICC using edge-detection (n = 20) was 0.92 (95% CI 0.82, 0.97) mean difference 2 &mu;m (95% LOA -45.0, 49.0) and with manual caliper measurement (n = 290) the ICC was 0.84 (95% CI 0.80, 0.87) mean difference 5 &mu;m (95% LOA -51.8, 61.8). Edge-detection measurements were greater than those from manual sonographic calipers (mean aIMT 618 &mu;m (50) versus mean aIMT 563 &mu;m (49) respectively; p &lt; 0.001, mean difference 44 &mu;m, 95% LOA -54, 142). With the exception of infant crying (p = 0.001), no associations were observed between individual and environmental variables and image quality. Conclusion: In a population-derived cohort of term infants, aIMT measurement has a high level of intra and inter-reader reproducibility. Measurement of aIMT using edge-detection software gives higher inter-reader ICC than manual sonographic calipers. Image quality is not substantially affected by individual and environmental factors. &copy; 2014 McCloskey et al.; licensee BioMed Central Ltd

DNA species surveillance: Monitoring bushmeat poaching and trading in Kenya using partial cytochrome b gene

DNA species identification has applications in such areas as forensic science, systematics, conservation genetics and agriculture. One key anthropogenic activity threatening large wildlife fauna is illegal exploitation. In Kenya, species identification of raw and processed meat products remains a constraint to effective enforcement of illegal trade in game meat (bushmeat) and products. We tested the reliability of a 321 bp mitochondrial cytochrome b (cyt b) region as a species identification tool for application in wildlife forensics. Query sequences were generated from known specimens of 14 Eastern African wildlife species, 13 representing commonly poached ungulates, and three domesticated species. These were compared, using Basic Local Alignment Search Tool (BLAST) algorithm, with NCBI GenBank reference sequences for species identity. These query sequences were subsequently deposited on Genbank. They represent a contribution to a diagnostic internal East African Wildlife reference cyt b database. The test species comprised: Cape buffalo, bushbuck, Guenther’s dik-dik, common duiker, common eland, Grant’s gazelle, hartebeest, impala, lesser kudu, plains zebra, Thomson’s gazelle, common warthog, wildebeest, Maasai ostrich, cattle, goat and sheep. Additionally, cooked beef and pork samples were analyzed. The results show that, when conspecific sequences were available in the database, species discrimination was 100%. Phylogeny clustering of the species by maximum likelihood supported the species determination by BLAST. The second part of the study carried out a preliminary survey of the prevalence of illegal game meat sold in the dispersal area of Tsavo National Park, Kenya. Sixty two raw meat samples were randomly collected from small roadside retail outlets along the Nairobi-Mombasa highway (A109), a major transnational highway that transverses Tsavo National Park. The results indicate a 9.7% (n = 6) illegal game meat sale, comprising five Guenther’s dik-diks and a Beisa oryx. A 2 km radius hotspot, with 83% (n = 5) of the bushmeat sales was identified just south of Tsavo East National Park.Key words: East Africa, Kenya, bushmeat, poaching, wildlife conservation, species identification, mitochondrial cytochrome b gene

Book Reviews

Book reviews of: In the Wake of War: Military Occupation, Emancipation, and Civil War America. By Andrew F. Lang. (Baton Rouge: Louisiana State University Press, 2017. Acknowledgements, notes, bibliography, index. Pp. xi, 317. $47.50 cloth. ISBN: 978-0-8071-6706-9.) Keep the Days: Reading the Civil War Diaries of Southern Women. By Steven M. Stowe (Chapel Hill: The University of North Carolina Press, 2018. Acknowledgements, bibliographical references, and index. Pp. xxv, 199.$29.95 paper. ISBN: 9781469640969.) The Guerrilla Hunters: Irregular Conflicts during the Civil War. Edited by Brian D. McKnight and Marton A. Myers. (Baton Rouge: Louisiana State University Press, 2017. Acknowledgments, illustrations, maps, notes, index. Pp. ix, 399. $49.95, cloth. ISBN: 0807164976.) Strategic Sisterhood: The National Council of Negro Women in the Black Freedom Struggle. By Rebecca Tuuri. (Chapel Hill: University of North Carolina Press, 2018. Acknowledgements, illustrations, notes, index. Pp. xi, 313.$90 cloth, $29.95 paperback. ISBN: 9781469638898.) Environmental Disaster in the Gulf South: Two Centuries of Catastrophe, Risk, and Resilience. Edited by Cindy Ermus. (Baton Rouge: Louisiana State University Press, 2018. Pp. 1-206.$45 hardcover. ISBN-978-0-8071-6710-6.) In Remembrance of Emmett Till: Regional Stories and Media Responses to the Black Freedom Struggle. By Darryl Mace. (Lexington: University Press of Kentucky, 2014. Preface, introduction, illustrations, acknowledgements, notes, bibliography, index. Pp. xi, 212. $40 cloth. ISBN: 978-0-8131-4536-5.) The Annotated Pickett’s History of Alabama And Incidentally of Georgia and Mississippi, from the Earliest Period. Edited by James P. Pate. (Montgomery: New South Books, 2018. Notes, acknowledgements, illustrations, index. Pp. 600.$60.00. ISBN: 978- 1-58838-032-6.

Framework for transforming best practices for landrace conservation to policies

Traditional farming systems and conservation of local cultivars and associated indigenous knowledge are under threat and growing pressure resulting in genetic erosion of crop diversity. These systems are an essential component of sustainable crop production, household income and human nutrition for many of the poor farmers found in fragile semiarid ecosystems of Sub-Saharan Africa (SSA). With the signing of the Convention on Biological Diversity (CBD) in 1992, in situ conservation for crops and their related genetic resources has been given prominent mention in global and national policies for biodiversity conservation. In situ strategies are an important and complementary component of the overall agrobiodiversity conservation efforts that aim to conserve not only crop genetic resources but also crop evolutionary processes. However, policy support of the science and practice of in situ conservation, lag behind CBD commitment in much of SSA. The need for activities on in situ conservation of plant genetic resources is emphasized in the CBD and in Agenda 21. Article 2 of the Convention specifically includes reference to domesticated or cultivated species. This is also anticipated in Article 8, which requires signatory nations to “preserve and maintain knowledge, innovations and practices of indigenous and local communities embodying traditional lifestyles relevant for the conservation and sustainable use of biological diversity …” Agenda 21 reflects this commitment to in situ conservation as an essential component of sustainable agriculture, and in Chapter 14, notes the need for establishing programmes and policies to strengthen in situ conservation. In its second meeting, the Conference of the Parties to the CBD (COP 2) identified implementation of Article 8 of the CBD as a high priority and reaffirmed the importance of regional and international cooperationfor the implementation of this Article. It also stressed the importance of the exchange of relevant information and experience among all stakeholders on measures taken for its implementation (Decision II/7 of COP 2). Many national PGR programmes in SSA are unable to meet their obligations towards in situ (more specifically on-farm) conservation as stated in the CBD and the GPA because of ineffective enabling of national policy environments that do not support traditional farming systems and in situ conservation on-farm. The countries involved in the project were Benin, Burkina Faso, Ghana, Kenya, Malawi, Mali, Uganda and Zimbabwe. Through case studies, the project analysed farming systems in semi-arid ecosystems in these countries, focussing on how these systems supported the conservation of landraces of local and global significance. The methodology described in the present publication was designed within this project to draw out ‘best’ practices on how landraces have been incorporated into farming systems and/or national agricultural policies and biodiversity conservation strategies. On one hand, the farmer or resource user determines what makes the practice the ‘best one’, and they base their choices on a survival strategy or utilitarian point of view. On the other hand, the scientists on the project primarily judged how effective the practices are in conserving agrobiodiversity at different levels. The project attempted to reconcile the two views in developing frameworks for the determination of ‘best practice’

Managing biological and genetic diversity in tropical agroforestry

Abstract The issues of biological and genetic diversity management in agroforestry are extremely complex. This paper focuses on genetic diversity management and its implications for sustainable agroforestry systems in the tropics, and presents an analysis of the role and importance of inter-and intra-specific diversity in agroforestry. Diversity within and between tree species in traditional agroforestry systems and modern agroforestry technologies in the tropics is assessed, with a view to understanding the functional elements within them and assessing the role and place of diversity. The assessment shows that although the practice of agroforestry has been a diversity management and conservation system, research in agroforestry over time has de-emphasized the diversity element; nevertheless farmers do value diversity and do manage agroforestry from that perspective. Based on a profiling of various traditional agroforestry systems and research-developed technologies, a strong case is made for increased speciesand genetic diversity, at both inter-and intra-specific levels. The review and analysis point to the need for increased awareness, training/education, partnerships and collaborative efforts in support of genetic diversity in agroforestry systems; of special importance is increased cross-disciplinary research. All the flowers of all the tomorrows are in the seeds of today -A Chinese prover

The Chlamydia muridarum plasmid revisited : new insights into growth kinetics.

Background: Research in chlamydial genetics is challenging because of its obligate intracellular developmental cycle. In vivo systems exist that allow studies of different aspects of basic biology of chlamydiae, the murine Chlamydia muridarum model is one of great importance and thus an essential research tool. C. muridarum carries a plasmid that has a role in virulence.  Our aim was to compare and contrast the C. muridarum plasmid-free phenotype with that of a chromosomally isogenic plasmid-bearing strain, through the inclusion phase of the developmental cycle. Methods: We measured infectivity for plasmid bearing and plasmid-cured C. muridarum by inclusion forming assays in McCoy cells and in parallel bacterial chromosome replication by quantitative PCR, throughout the developmental cycle. In addition to these studies, we have carefully monitored chlamydial inclusion formation by confocal microscopy and transmission electron microscopy. A new E.coli/chlamydial shuttle vector (pNigg::GFP) was constructed using standard cloning technology and used to transform C. muridarum for further phenotypic studies. Results: We have advanced the definition of the chlamydial phenotype away from the simple static observation of mature inclusions and redefined the C. muridarum plasmid-based phenotype on growth profile and inclusion morphology. Our observations on the growth properties of plasmid-cured C. muridarum challenge the established interpretations, especially with regard to inclusion growth kinetics. Introduction of the shuttle plasmid pNigg::GFP into plasmid-cured C. muridarum restored the wild-type plasmid-bearing phenotype and confirmed that loss of the plasmid was the sole cause for the changes in growth and chromosomal replication. Conclusions: Accurate growth curves and sampling at multiple time points throughout the developmental cycle is necessary to define plasmid phenotypes.  There are subtle but important (previously unnoticed) differences in the overall growth profile of plasmid-bearing and plasmid-free C. muridarum.  We have proven that the differences described are solely due to the plasmid pNigg