α/β Barrel evolution and the modular assembly of enzymes: Emerging trends in the flavin oxidase/dehydrogenase family

α/β barrels have an ill-defined origin. Evidence exists which favours their divergent evolution from a common ancestral barrel and convergent evolution to a stable fold. However, recent sequence and structural information for the flavin oxidase/dehydrogenase family of barrel enzymes indicate that sub-families of α/β barrels have evolved divergently. The modular fusion of barrel domains with core structures from other gene families has also contributed to the evolution of related but catalytically distinct enzyme molecules within each sub-family of the flavin oxidases/dehydrogenases. An analysis of the structures and sequences of the flavin oxidases/dehydrogenases has now enabled studies focusing on the evolutionary origins and modular assembly of this important family of proteins to be initiated.     

Metaheuristic approaches in biopharmaceutical process development data analysis

Bioprocess and Biosystems Engineering - There is a growing interest in mining and handling of big data, which has been rapidly accumulating in the repositories of bioprocess industries....     

The relationship between pheromone trap catch and local population density of the oak processionary moth Thaumetopoea processionea (Lepidoptera: Thaumetopoeidae)

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Lianas as a food resource for herbivorous insects: a comparison with trees

Woody climbers or, ‘lianas’, are one of the features that characterise rainforests. They contribute substantially to plant diversity and leaf biomass which makes them a potentially important food source for herbivores. Here, we focus on insect herbivores, folivores in particular, to show how disparities in the quantitative and qualitative availability of leaves between lianas and trees may differentially influence insect folivory and the herbivore communities themselves. We develop a conceptual model and show that lianas in general have lower structural and chemical defences, a greater nutritional profile and a preferable phenology in comparison with trees, which, contrary to our expectations, has led to assemblages of more‐specialised insects. The impacts this has on higher trophic levels and broader ecological networks, however, are poorly known. We show through a study of four tropical floras from different biogeographic realms that lianas are likely to be a target for a wide range of insect herbivore taxa as they are a phylogenetically diverse group and increase diversity of higher taxa at local scales. This, in combination with their highly palatable leaves, may also make them a suitable temporary food source for insects during times when preferred host plants are scarce. This phenomenon has been observed in mammalian herbivores but awaits investigation in insects as does the effects this may have on survival and fitness. Apparent recent increases in liana abundances in some forests, likely due to climate change, makes understanding their role in supporting and maintaining biodiversity an increasingly important and necessary challenge. Since trees or saplings have usually been the subject of studies on insect herbivory, major knowledge gaps remain about the ways in which lianas contribute to, support and maintain the ecosystems in which they exist. We use our conceptual model to guide future research directions and express the necessity for caution when extrapolating explanations of herbivory derived from data on trees to growth forms with fundamentally different ecologies.     

Female reproduction bears no survival cost in captivity for gray mouse lemurs

The survival cost of reproduction has been revealed in many free‐ranging vertebrates. However, recent studies on captive populations failed to detect this cost. Theoretically, this lack of survival/reproduction trade‐off is expected when resources are not limiting, but these studies may have failed to detect the cost, as they may not have fully accounted for potential confounding effects, in particular interindividual heterogeneity. Here, we investigated the effects of current and past reproductive effort on later survival in captive females of a small primate, the gray mouse lemur. Survival analyses showed no cost of reproduction in females; and the pattern was even in the opposite direction: the higher the reproductive effort, the higher the chances of survival until the next reproductive event. These conclusions hold even while accounting for interindividual heterogeneity. In agreement with aforementioned studies on captive vertebrates, these results remind us that reproduction is expected to be traded against body maintenance and the survival prospect only when resources are so limiting that they induce an allocation trade‐off. Thus, the cost of reproduction has a major extrinsic component driven by environmental conditions.     

A new perspective on the function of Tissue Non-Specific Alkaline Phosphatase: from bone mineralization to intra-cellular lipid accumulation

Molecular and Cellular Biochemistry - Tissue-nonspecific alkaline phosphatase (TNAP) is one of four isozymes, which include germ cell, placental and intestinal alkaline phosphatases. The TNAP...     

Direct electrical stimulation enhances osteogenesis by inducing Bmp2 and Spp1 expressions from macrophages and preosteoblasts

The capability of electrical stimulation (ES) in promoting bone regeneration has already been addressed in clinical studies. However, its mechanism is still being investigated and discussed. This study aims to investigate the responses of macrophages (J774A.1) and preosteoblasts (MC3T3-E1) to ES and the faradic by-products from ES. It is found that pH of the culture media was not significantly changed, whereas the average hydrogen peroxide concentration was increased by 3.6 and 5.4 µM after 1 and 2 hr of ES, respectively. The upregulation of Bmp2 and Spp1 messenger RNAs was observed after 3 days of stimulation, which is consistent among two cell types. It is also found that Spp1 expression of macrophages was partially enhanced by faradic by-products. Osteogenic differentiation of preosteoblasts was not observed during the early stage of ES as the level of Runx2 expression remains unchanged. However, cell proliferation was impaired by the excessive current density from the electrodes, and also faradic by-products in the case of macrophages. This study shows that macrophages could respond to ES and potentially contribute to the bone formation alongside preosteoblasts. The upregulation of Bmp2 and Spp1 expressions induced by ES could be one of the mechanisms behind the electrically stimulated osteogenesis.     

Rapid prototyping of proteins: Mail order gene fragments to assayable proteins within 24 hours

In this study, we present a minimal template design and accompanying methods to produce assayable quantities of custom sequence proteins within 24 hr from receipt of inexpensive gene fragments from a DNA synthesis vendor. This is done without the conventional steps of plasmid cloning or cell-based amplification and expression. Instead the linear template is PCR amplified, circularized, and isothermally amplified using a rolling circle polymerase. The resulting template can be used directly with cost-optimized, scalably-manufactured Escherichia coli extract and minimal supplement reagents to perform cell-free protein synthesis (CFPS) of the template protein. We demonstrate the utility of this template design and 24 hr process with seven fluorescent proteins (sfGFP, mVenus, mCherry, and four GFP variants), three enzymes (chloramphenicol acetyltransferase, a chitinase catalytic domain, and native subtilisin), a capture protein (anti-GFP nanobody), and 2 antimicrobial peptides (BP100 and CA(1–7)M(2–9)). We detected each of these directly from the CFPS reaction using colorimetric, fluorogenic, and growth assays. Of especial note, the GFP variant sequences were found from genomic screening data and had not been expressed or characterized before, thus demonstrating the utility of this approach for phenotype characterization of sequenced libraries. We also demonstrate that the rolling circle amplified version of the linear template exhibits expression similar to that of a complete plasmid when expressing sfGFP in the CFPS reaction. We evaluate the cost of this approach to be $61/mg sfGFP for a 4 hr reaction. We also detail limitations of this approach and strategies to overcome these, namely proteins with posttranslational modifications.