Relative contribution of neutral and deterministic processes in shaping fruit‐feeding butterfly assemblages in Afrotropical forests

The unified neutral theory of biodiversity and biogeography has gained the status of a quantitative null model for explaining patterns in ecological (meta)communities. The theory assumes that individuals of trophically similar species are functionally equivalent. We empirically evaluate the relative contribution of neutral and deterministic processes in shaping fruit‐feeding butterfly assemblages in three tropical forests in Africa, using both direct (confronting the neutral model with species abundance data) and indirect approaches (testing the predictions of neutral theory using data other than species abundance distributions). Abundance data were obtained by sampling butterflies using banana baited traps set at the forest canopy and understorey strata. Our results indicate a clear consistency in the kind of species or species groups observed at either the canopy or understorey in the three studied communities. Furthermore, we found significant correlation between some flight‐related morphological traits and species abundance at the forest canopy, but not at the understorey. Neutral theory's contribution to explaining our data lies largely in identifying dispersal limitation as a key process regulating fruit‐feeding butterfly community structure. Our study illustrates that using species abundance data alone in evaluating neutral theory can be informative, but is insufficient. Species‐level information such as habitat preference, host plants, geographical distribution, and phylogeny is essential in elucidating the processes that regulate biodiversity community structures and patterns.     

Comparative life cycle analysis of producing charcoal from bamboo,teak, and acacia species in Ghana

Background, aim, and scope

The rise in wood fuel consumption, particularly of charcoal, has been associated with increased deforestation in Ghana. Plantation developments from teak (Tectona grandis), bamboo (Bambusa balcooa), and Acacia auriculiformis are now being promoted to produce sustainable biomass for charcoal production. While all species have comparable charcoal quality, there is limited available data to elucidate the environmental impacts associated with their plantation development and use as biomass sources for producing charcoal. Therefore, this study quantified and compared the cradle-to-gate environmental impacts of producing charcoal from T. grandis, A. auriculiformis, and B. balcooa.

Methods

The study was conducted in accordance with ISO 14040/14044, an international procedural framework for performing life cycle analysis (LCA). For this study, the functional unit of charcoal used was 1 MJ energy produced from three species: T. grandis, A. auriculiformis, and B. balcooa. Data on B. balcooa plantations was collected from a B. balcooa-based intercropping system set up by the International Network for Bamboo and Rattan in Sekyere Central District, Ghana. Input data for A. auriculiformis and T. grandis came from the Forestry Commission of Ghana plantations established within the forest agroecological zone of Ghana. All input data came from primary local sources. Pollutant emissions were also calculated in order to analyze the contribution of all the flow processes to the emissions. The analysis used Simapro version 8, as well as life cycle inventory (LCI) databases of Ecoinvent V3 and Idemat 2015 (a database developed by Delft University of Technology, the Netherlands). The emissions were expressed as eco-costs and used as indicators in an impact assessment.

Results and discussion

The results showed that relative to B. balcooa, the total eco-cost (comprising of human health, ecosystem, resource depletion, and global warming eco-costs) of a cradle-to-gate production of 1 MJ of charcoal will be 140% higher with T. grandis and 113% higher with A. auriculiformis. The increased environmental impacts associated with T. grandis and A. auriculiformis occurred at their biomass production stage. As these species use comparatively large quantities of pesticides, weedicides, and fertilizers with high acidification, ozone depletion, and global warming potentials, their biomass production stage accounted for approximately 85% of their total eco-cost.

Conclusions

The study results suggest that B. balcooa plantations are the most environmentally viable option. In cases where T. grandis or A. auriculiformis plantations are widespread, improvement options at the biomass production stage are required in order to reduce their environmental costs.

     

A glimpse into the active site of a group II intron and maybe the spliceosome, too

The X-ray crystal structure of an excised group II self-splicing intron was recently solved by the Pyle group. Here we review some of the notable features of this structure and what they may tell us about the catalytic active site of the group II ribozyme and potentially the spliceosome. The new structure validates the central role of domain V in both the structure and catalytic function of the ribozyme and resolves several outstanding puzzles raised by previous biochemical, genetic and structural studies. While lacking both exons as well as the cleavage sites and nucleophiles, the structure reveals how a network of tertiary interactions can position two divalent metal ions in a configuration that is ideal for catalysis.     

RNAs synthesized using photocleavable biotinylated nucleotides have dramatically improved catalytic efficiency

Obtaining homogeneous population of natively folded RNAs is a crippling problem encountered when preparing RNAs for structural or enzymatic studies. Most of the traditional methods that are employed to prepare large quantities of RNAs involve procedures that partially denature the RNA. Here, we present a simple strategy using 'click' chemistry to couple biotin to a 'caged' photocleavable (PC) guanosine monophosphate (GMP) in high yield. This biotin-PC GMP, accepted by T7 RNA polymerase, has been used to transcribe RNAs ranging in size from 27 to 527 nt. Furthermore we show, using an in-gel fluorescence assay, that natively prepared 160 and 175 kDa minimal group II intron ribozymes have enhanced catalytic activity over the same RNAs, purified via denaturing conditions and refolded. We conclude that large complex RNAs prepared by non-denaturing means form a homogeneous population and are catalytically more active than those prepared by denaturing methods and subsequent refolding; this facile approach for native RNA preparation should benefit synthesis of RNAs for biophysical and therapeutic applications.     

Spatial and temporal variation in butterfly biodiversity in a West African forest: lessons for establishing efficient rapid monitoring programmes

Because tropical forests face serious threats and are usually situated in developing countries, cheap and easy Rapid Biodiversity Assessment (RBA) seems an ideal strategy for documenting changes in habitat quality and setting conservation priorities. Fruit‐feeding butterflies are often used as focal taxa to document biodiversity trends in tropical forests. However, the choice of inappropriate sampling strategies may nullify its value. More extensive data sets that sample multiple months and seasons and incorporate the vertical dimension are needed as a baseline for designing reliable sampling regimes. Therefore, we performed a butterfly trapping study in Ghana, using both understorey and canopy traps, and sampling seven periods covering dry and wet seasons. Both individual numbers and species richness were on average three to four times higher in the understorey than in the canopy traps with strikingly different species composition (only 11% overlap in species). The number of species and individual abundance recorded in a month varied extensively. This study underlined the importance of taking into account temporal variation and vertical stratification when designing RBAs of fruit‐feeding butterflies in West African forests. We recommend the use of both understorey and canopy traps and inclusion of both ‘wet’ and ‘dry’ seasons into RBA sampling regimes.     

Experiences with the Mass Distribution of LPG Stoves in Rural Communities of Ghana

Household air pollution (HAP) is a leading cause of morbidity and mortality worldwide. To limit HAP exposure and environmental degradation from biomass fuel use, the Government of Ghana promotes liquefied petroleum gas (LPG) use in rural Ghana via the Rural LPG program (RLP). We assessed the experiences of the RLP in 2015, 2 years after its launch. A mixed methods approach was used involving Focus Group Discussions (19) and in-depth interviews (25). In addition, a survey questionnaire was administered to elicit socio-demographic characteristics, household cooking practices and stove use patterns of 200 randomly selected respondents. At about 9 months after LPG acquisition,?<?5% of LPG beneficiaries used their stoves. Some of the reasons ascribed to the low usage of the LPG cookstoves were financial constraints, distance to LPG filling point and fear of burns. Community members appreciate the convenience of using LPG. Our results underscore a need for innovative funding mechanisms contextualized within an overall economic empowerment of rural folks to encourage sustained LPG use. It emphasizes the need for innovative accessibility interventions. This could include establishing new LPG filling stations in RLP beneficiary districts to overcome the barriers to sustained LPG use.     

Extracellular Synthesis and Characterization of Gold Nanoparticles Using <Emphasis Type="Italic">Mycobacterium</Emphasis> sp. BRS2A-AR2 Isolated from the Aerial Roots of the Ghanaian Mangrove Plant, <Emphasis Type="Italic">Rhizophora racemosa</Emphasis>

Through the use of genomes that have undergone millions of years of evolution, marine Actinobacteria are known to have adapted to rapidly changing environmental pressures. The result is a huge chemical and biological diversity among marine Actinobacteria. It is gradually becoming a known fact that, marine Actinobacteria have the capability to produce nanoparticles which have reasonable sizes and structures with possible applications in biotechnology and pharmacology. Mycobacterium sp. BRS2A-AR2 was isolated from the aerial roots of the mangrove plant Rhizophora racemosa. The Mycobacterium was demonstrated for the first time ever to produce AuNPs with sizes that range between 5 and 55 nm. The highest level absorbance of the biosynthesized AuNPs was typical for actinobacterial strains (2.881 at 545 nm). The polydispersity index was measured as 0.207 in DLS and the zeta potential was negatively charged (? 28.3 mV). Significant vibration stretches were seen at 3314, 2358, 1635 and 667 cm^?1 in FT-IR spectra. This demonstrated the possible use of small aliphatic compounds containing –COOH, –OH, –Cl and –NH₂ functional groups in the stabilization of the AuNPs. The effect of the biosynthesized AuNPs on HUVEC and HeLA cell lines was measured at 48 h. IC₅₀ values were determined at 3500 µg/ml concentration for HUVEC and HeLA cell lines at 45.25 and 53.41% respectively.     

Site-specific labeling of nucleotides for making RNA for high resolution NMR studies using an <Emphasis Type="Italic">E. coli</Emphasis> strain disabled in the oxidative pentose phosphate pathway

Escherichia coli (E. coli) is a versatile organism for making nucleotides labeled with stable isotopes (¹³C, ¹⁵N, and/or ²H) for structural and molecular dynamics characterizations. Growth of a mutant E. coli strain deficient in the pentose phosphate pathway enzyme glucose-6-phosphate dehydrogenase (K10-1516) on 2-¹³C-glycerol and ¹⁵N-ammonium sulfate in Studier minimal medium enables labeling at sites useful for NMR spectroscopy. However, ¹³C-sodium formate combined with ¹³C-2-glycerol in the growth media adds labels to new positions. In the absence of labeled formate, both C5 and C6 positions of the pyrimidine rings are labeled with minimal multiplet splitting due to ¹J_C5C6 scalar coupling. However, the C2/C8 sites within purine rings and the C1′/C3′/C5′ positions within the ribose rings have reduced labeling. Addition of ¹³C-labeled formate leads to increased labeling at the base C2/C8 and the ribose C1′/C3′/C5′ positions; these new specific labels result in two- to three-fold increase in the number of resolved resonances. This use of formate and ¹⁵N-ammonium sulfate promises to extend further the utility of these alternate site specific labels to make labeled RNA for downstream biophysical applications such as structural, dynamics and functional studies of interesting biologically relevant RNAs.