Biodiversity conservation in cocoa production landscapes: an overview

Cocoa agroforests that retain a floristically diverse and structurally complex shade canopy have the potential to harbour significant levels of biodiversity, yet few studies have documented the plant and animal species occurring within these systems or within landscapes dominated by cocoa production. In this special issue, we bring together nine studies from Latin America, Africa and Asia that document the contribution of cocoa agroforestry systems to biodiversity conservation, and explore how the design, management and location of these systems within the broader landscape influence their value as habitats, resources and biological corridors. Tree diversity within the cocoa production systems is variable, depending on management, cultural differences, location and farm history, among other factors. Animal diversity is typically highest in those cocoa agroforests that have high plant diversity, structurally complex canopies, and abundant surrounding forest cover. In general, both plant and animal diversity within cocoa agroforests is greater than those of other agricultural land uses, but lower than in the original forest habitat. There are several emerging threats to biodiversity conservation within cocoa production landscapes, including the loss of remaining forest cover, the simplification of cocoa shade canopies and the conversion of cocoa agroforestry systems to other agricultural land uses with lower biodiversity value. To counter these threats and conserve biodiversity over the long-term, land management should focus on conserving native forest habitat within cocoa production landscapes, maintaining or restoring floristically diverse and structurally complex shade canopies within cocoa agroforests, and retaining other types of on-farm tree cover to enhance landscape connectivity and habitat availability.     

Stress and immune responses in abalone: limitations in current knowledge and investigative methods based on other models

Increasing mariculture of abalone focuses attention on their immune and stress responses. For abalone, as well as many invertebrates, the function and relationship of these systems and how in vitro tests relate to them are not fully understood. This review focuses on research into the immune system and stress response conducted on abalone and on aspects that can be monitored in vitro. To fill the considerable knowledge gaps, we discuss work on other invertebrate taxa, concentrating on those closest to abalone, and making explicit the phylogenetic relations involved. The stress response appears to be very similar to that in vertebrates, but interpreting most immune responses remains problematic. Phylogeny must be considered: immune function tests derived from research into vertebrates or distantly related invertebrates should not be used in abalone until they have been validated in abalone by studies of susceptibility to pathogens. We suggest phagocytic activity of haemocytes and their efficiency in clearing bacteria are reliable parameters to measure, because they have been directly related to immune competency and are consistently depressed by stress. Carefully designed assays of antimicrobial activity may also be useful. Important aims of future research will be to investigate the relationship between growth, stress and robust immunity, and to develop tests that can be run on production animals, which accurately depict immune status.     

In vitro response to Candida albicans in cultures of whole human blood from young and aged donors

Invasive infections with opportunistic fungi, such as Candida albicans, have become an increasing problem in aged adults in recent years. This work investigates the influence of human ageing on C. albicans recognition by toll-like receptors (TLRs), essential components of the innate immune system, using a cohort of 96 young (15-42 years) and aged (>70 years) human volunteers. No significant differences between aged and young donors were observed on (1) cell surface TLR2, TLR6 and TLR4 expression on lymphocytes, monocytes and granulocytes, (2) production of cytokines [IL-8, IL-1beta, IL-6, IL-10, tumour necrosis factor (TNF)-alpha and IL-12p70] and prostaglandin E(2) (PGE(2)) by whole human blood in response to C. albicans and (3) fungicidal activity of whole blood. A statistically significant higher titre of natural anti-C. albicans antibodies was found in plasma of volunteers between 80 and 95 years old when compared with other age groups, probably as a consequence of the increased levels of serum Ig that has been described in elderly subjects. Therefore, the results indicate that the increased susceptibility to C. albicans infections in the elderly is not a consequence of defects in TLRs expression or signalling, nor of an impaired fungicidal activity of blood.     

Mutations in Either TUBB or MAPRE2 Cause Circumferential Skin Creases Kunze Type

Circumferential skin creases Kunze type (CSC-KT) is a specific congenital entity with an unknown genetic cause. The disease phenotype comprises characteristic circumferential skin creases accompanied by intellectual disability, a cleft palate, short stature, and dysmorphic features. Here, we report that mutations in either MAPRE2 or TUBB underlie the genetic origin of this syndrome. MAPRE2 encodes a member of the microtubule end-binding family of proteins that bind to the guanosine triphosphate cap at growing microtubule plus ends, and TUBB encodes a β-tubulin isotype that is expressed abundantly in the developing brain. Functional analyses of the TUBB mutants show multiple defects in the chaperone-dependent tubulin heterodimer folding and assembly pathway that leads to a compromised yield of native heterodimers. The TUBB mutations also have an impact on microtubule dynamics. For MAPRE2, we show that the mutations result in enhanced MAPRE2 binding to microtubules, implying an increased dwell time at microtubule plus ends. Further, in vivo analysis of MAPRE2 mutations in a zebrafish model of craniofacial development shows that the variants most likely perturb the patterning of branchial arches, either through excessive activity (under a recessive paradigm) or through haploinsufficiency (dominant de novo paradigm). Taken together, our data add CSC-KT to the growing list of tubulinopathies and highlight how multiple inheritance paradigms can affect dosage-sensitive biological systems so as to result in the same clinical defect.     

A pathogenicity determinant maps to the N‐terminal coat protein region of the Pepino mosaic virus genome

Pepino mosaic virus (PepMV) poses a worldwide threat to the tomato industry. Considerable differences at the genetic level allow for the distinction of four main genotypic clusters; however, the basis of the phenotypic outcome is difficult to elucidate. This work reports the generation of wild‐type PepMV infectious clones of both EU (mild) and CH2 (aggressive) genotypes, from which chimeric infectious clones were created. Phenotypic analysis in three solanaceous hosts, Nicotiana benthamiana, Datura stramonium and Solanum lycopersicum, indicated that a PepMV pathogenicity determinant mapped to the 3′‐terminal region of the genome. Increased aggression was only observed in N. benthamiana, showing that this factor is host specific. The determinant was localized to amino acids 11–26 of the N‐terminal coat protein (CP) region; this is the first report of this region functioning as a virulence factor in PepMV.     

Identification and characterization of expressed retrotransposons in the genome of the Paracoccidioides species complex

Background

Species from the Paracoccidioides complex are thermally dimorphic fungi and the causative agents of paracoccidioidomycosis, a deep fungal infection that is the most prevalent systemic mycosis in Latin America and represents the most important cause of death in immunocompetent individuals with systemic mycosis in Brazil. We previously described the identification of eight new families of DNA transposons in Paracoccidioides genomes. In this work, we aimed to identify potentially active retrotransposons in Paracoccidioides genomes.

Results

We identified five different retrotransposon families (four LTR-like and one LINE-like element) in the genomes of three Paracoccidioides isolates. Retrotransposons were present in all of the genomes analyzed. P. brasiliensis and P. lutzii species harbored the same retrotransposon lineages but differed in their copy numbers. In the Pb01, Pb03 and Pb18 genomes, the number of LTR retrotransposons was higher than the number of LINE-like elements, and the LINE-like element RtPc5 was transcribed in Paracoccidioides lutzii (Pb01) but could not be detected in P. brasiliensis (Pb03 and Pb18) by semi-quantitative RT-PCR.

Conclusion

Five new potentially active retrotransposons have been identified in the genomic assemblies of the Paracoccidioides species complex using a combined computational and experimental approach. The distribution across the two known species, P. brasiliensis and P. lutzii, and phylogenetics analysis indicate that these elements could have been acquired before speciation occurred. The presence of active retrotransposons in the genome may have implications regarding the evolution and genetic diversification of the Paracoccidioides genus.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1564-7) contains supplementary material, which is available to authorized users.     

Carotenoid‐based plumage coloration in golden‐crowned kinglets Regulus satrapa: pigment characterization and relationships with migratory timing and condition

Carotenoid‐based ornamental coloration has long been proposed to honestly signal quality due to its dependence on individual condition. Because migration can be one of the most stressful periods of an animal's annual cycle, developing colourful plumage may be particularly challenging for species in which migration and moult periods overlap or occur sequentially. The purpose of this study was to investigate pigmentary and condition‐dependent bases of carotenoid colour variation in a small migratory passerine, the golden‐crowned kinglet Regulus satrapa (Family Regulidae). We captured 186 male and female kinglets of various ages during fall migration in southwestern Ontario, Canada and recorded arrival date, body condition index, fat and pectoral muscle scores, wing mite infestation, and feather growth rate as measures of condition. We quantified crown coloration using reflectance spectrometry and analyzed feather carotenoids using high‐performance liquid chromatography. Yellow crown feathers of female kinglets contained only yellow hydroxycarotenoids, whereas orange feathers of males harboured a suite of eight carotenoid pigments. Males with longer wavelength orange crown hues deposited greater concentrations of ketocarotenoids, especially canthaxanthin. Female kinglets with longer wavelength crown hues and males with longer wavelength crown hues and more saturated crown coloration left for migration earlier in the year. Females with longer wavelength crown hues had fewer feather mites and tended to be in better condition. However, male kinglets with more saturated coloration possessed smaller pectoral muscles. This is the first study to identify plumage carotenoids in this North American bird family and to determine the pigmentary basis for both inter‐ and intrasexual colour variation. Our results provide further support for the condition‐dependence of carotenoid coloration and suggest that ornamental elaboration in both sexes may encode information about fall condition and migratory performance.