Giant clams discriminate threats along a risk gradient and display varying habituation rates to different stimuli

It is often beneficial for animals to discriminate between different threats and to habituate to repeated exposures of benign stimuli. While much is known about risk perception in vertebrates and some invertebrates, risk perception in marine invertebrates is less extensively studied. One method to study risk perception is to habituate animals to a series of exposures to one stimulus, and then present a novel stimulus to test if it transfers habituation. Transfer of habituation is seen as a continued decrease in response while lack of transfer is seen either by having a similar or greater magnitude response. We asked whether giant clams (Tridacna maxima) discriminate between biologically relevant types of threats along a risk gradient. Giant clams retract their mantle and close their shell upon detecting a threat. While closed, they neither feed nor photosynthesize, and prior work has shown that the cost of being closed increases as the duration of their response increases. We recorded a clam's latency to emerge after simulated threats chosen to represent a risk gradient: exposure to a small shading event, a medium shading event, a large shading event (chosen to simulate fish swimming above them), tapping on their shell and touching their mantle (chosen to simulate different degrees of direct attack). Although these stimuli are initially perceived as threatening, we expected clams to habituate to them because they are ultimately non‐damaging and it would be costly for clams to remain closed for extended periods of time when there is no threat present. Clams had different initial latencies to emerge and different habituation rates to these treatments, and they did not transfer habituation to higher risk stimuli and to some lower risk stimuli. These results suggest that clams discriminated between these stimuli along a risk gradient and the lack of habituation transfer shows that the new stimulus was perceived as a potential threat. This study demonstrates that sessile bivalves can discern between levels of predatory threat. These photosynthetic clams may benefit from being able to categorize predator cues for efficient energy allocation.     

Synthetic biology and metabolic engineering of actinomycetes for natural product discovery

Actinomycetes are one of the most valuable sources of natural products with industrial and medicinal importance. After more than half a century of exploitation, it has become increasingly challenging to find novel natural products with useful properties as the same known compounds are often repeatedly re-discovered when using traditional approaches. Modern genome mining approaches have led to the discovery of new biosynthetic gene clusters, thus indicating that actinomycetes still harbor a huge unexploited potential to produce novel natural products. In recent years, innovative synthetic biology and metabolic engineering tools have greatly accelerated the discovery of new natural products and the engineering of actinomycetes. In the first part of this review, we outline the successful application of metabolic engineering to optimize natural product production, focusing on the use of multi-omics data, genome-scale metabolic models, rational approaches to balance precursor pools, and the engineering of regulatory genes and regulatory elements. In the second part, we summarize the recent advances of synthetic biology for actinomycetal metabolic engineering including cluster assembly, cloning and expression, CRISPR/Cas9 technologies, and chassis strain development for natural product overproduction and discovery. Finally, we describe new advances in reprogramming biosynthetic pathways through polyketide synthase and non-ribosomal peptide synthetase engineering. These new developments are expected to revitalize discovery and development of new natural products with medicinal and other industrial applications.     

Human p38α mitogen-activated protein kinase in the Asp168-Phe169-Gly170-in (DFG-in) state can bind allosteric inhibitor Doramapimod

Doramapimod (BIRB-796) is widely recognized as one of the most potent and selective type II inhibitors of human p38α mitogen-activated protein kinase (MAPK); however, the understanding of its binding mechanism remains incomplete. Previous studies indicated high affinity of the ligand to a so-called allosteric pocket revealed only in the ‘out’ state of the DFG motif (i.e. Asp168-Phe169-Gly170) when Phe169 becomes fully exposed to the solvent. The possibility of alternative binding in the DFG-in state was hypothesized, but the molecular mechanism was not known. Methods of bioinformatics, docking and long-time scale classical and accelerated molecular dynamics have been applied to study the interaction of Doramapimod with the human p38α MAPK. It was shown that Doramapimod can bind to the protein even when the Phe169 is fully buried inside the allosteric pocket and the kinase activation loop is in the DFG-in state. Orientation of the inhibitor in such a complex is significantly different from that in the known crystallographic complex formed by the kinase in the DFG-out state; however, the Doramapimod’s binding is followed by the ligand-induced conformational changes, which finally improve accommodation of the inhibitor. Molecular modelling has confirmed that Doramapimod combines the features of type I and II inhibitors of p38α MAPK, i.e. can directly and indirectly compete with the ATP binding. It can be concluded that optimization of the initial binding in the DFG-in state and the final accommodation in the DFG-out state should be both considered at designing novel efficient type II inhibitors of MAPK and homologous proteins.

Communicated by Ramaswamy H. Sarma     

Alternative Ways to Become a Juvenile or a Definitive Phenotype (and on Some Persisting Linguistic Offenses)

Lack of knowledge of early and juvenile development often makes it difficult to decide when a fish becomes a juvenile or, for that matter, a definitive phenotype. According to the established life-history model, a fish develops naturally in a saltatory manner, its entire life consisting of a sequence of stabilized self-organizing steps, separated by distinct less stabilized thresholds. Changes are usually introduced during thresholds. In principle, there are two ways to reach the juvenile period: by indirect or by direct development. Indirectly developing fishes have a distinct larva period that ends in a cataclysmic or mild remodeling process, called metamorphosis, from which the fishes emerge as juveniles. During metamorphosis, most temporary organs and structures of the embryos and larvae are replaced by definitive organs and structures that are also possessed by the adults. In contrast, directly developing fishes have no larvae. Their embryos develop directly into juveniles and do not need major remodeling. Consequently, the beginning of their juvenile period is morphologically and functionally less distinct than in indirect development. The life-history model helps to find criteria that identify the natural boundaries between the different periods in the life of a fish, among them, the beginning of the juvenile period. Looking at it from a different angle, when ontogeny progresses from small eggs with little yolk, larvae are required as the necessary providers of additional nutrients (feeding entities similar to amphibian tadpoles or butterfly caterpillars) in order to accumulate materials for the metamorphosis into the definitive phenotypes. Directly developing fishes start with large demersal eggs provided with an adequate volume of high density yolk and so require no or little external nutrients to develop into the definitive phenotype. These large eggs are released and develop in concentrated clutches. It therefore becomes possible and highly effective to guard them in nests or bear them in external pouches, gill chambers or the buccal cavity. Viviparity is the next natural step. Now the maternal investment into large yolks can be supplemented or replaced by direct food supply to the developing embryos like, for example, the secretion of uterine histotrophe or nutrient transfer via placental analogues. When the young of guarders and bearers start exogenous feeding, they are much larger or better developed than larvae of nonguarders and the larva period in the former is reduced to a vestige or eliminated entirely. In the latter case, the juvenile period begins with the first exogenous feeding. Such precocial fishes are more specialized and able to survive better in competitive environments. In contrast, altricial forms retain or revert to a life-history style with indirect development and high fecundity when dispersal is advantageous or essential. Fishes become juveniles when the definitive phenotype is formed in most structures, either indirectly from a larva via metamorphosis or directly from the embryo.     

Spherical composite particles of rice starch and microcrystalline cellulose: A new coprocessed excipient for direct compression

Composite particles of rice starch (RS) and microcrystalline cellulose were fabricated by spray-drying technique to be used as a directly compressible excipient. Two size fractions of microcry stalline cellulose, sieved (MCS) and jet milled (MCJ), having volumetric mean diameter (D₅₀) of 13.61 and 40.51 μm, respectively, were used to form composite particles with RS in various mixing ratios. The composite particles produced were evaluated for their powder and compression properties. Although an increase in the microcrystalline cellulose proportion imparted greater compressibility of the composite particles, the shape of the particles was typically less spherical with rougher surface resulting in a decrease in the degree of flowability. Compressibility of composite particles made from different size fractions of microcrystalline cellulose was not different; however, using MCJ, which had a particle size range close to the size of RS (D₅₀=13.57 μm), provided more spherical particles than using MCS. Spherical composite particles between RS and MCJ in the ratio of 7∶3 (RS-MCJ-73) were then evaluated for powder properties and compressibility in comparison with some marketed directly compressible diluents. Compressibility of RS-MCJ-73 was greater than commercial spray-dried RS (Eratab), coprocessed lactose and microcrystalline cellulose (Cellactose), and agglomerated lactose (Tablettose), but, as expected, lower than microcrystalline cellulose (Vivapur 101). Flowability index of RS-MCJ-73 appeared to be slightly lower than Eratab but higher than Vivapur 101, Cellactose, and Tablettose. Tablets of RS-MCJ-73 exhibited low friability and good self-disintegrating property. It was concluded that these developed composite particles could be introduced as a new coprocessed direct compression excipient.     

Growth and architecture of small honey mesquites under jackrabbit browsing: overcoming the disadvantage of being eaten

Browsing is an important mortality factor in seedlings and small plants. However, the induced changes in the architecture of plant survivors may influence subsequent browsing, opening the possibility of compensating for the damage done. How jackrabbit (Lepus californicus) browsing affects the growth and architecture of small individuals of honey mesquite, Prosopis glandulosa var. torreyana, a tree/shrub that produces spines at every node, was explored. Naturally established mesquites of unknown age were selected in one site, and 2-year-old mesquites were transplanted in another site. In both cases, half of them were exposed to jackrabbits and the other half were excluded as controls. After 4 years, shoot production (height, length and number of derived shoots) and plant growth (height and cover) increased 1.4-2.5-fold in naturally established controls relative to exposed plants, depending on the measured variable. In the transplant experiment, the increases were 2.8-7.1-fold in controls relative to exposed plants 2 years after initiation of the experiment. The net loss of biomass in treatment vs. control plants in these experiments suggests a negative response to browsing which has been defined as under-compensation. Alternative architectures in honey mesquites were evident at the end of the exclusion experiments: controls had long branches and an extended crown cover, while exposed plants had short branches and a compact crown cover. Results indicated that mesquites were able to grow under browser pressure by packing many stems in a compact matrix armed with spines and producing one or more shoots tall and wide enough to escape from jackrabbits.     

In vitro propagation of loblolly pine via direct somatic organogenesis from mature cotyledons and hypocotyls

A high-efficiency two-step culture procedure for direct somaticorganogenesis in loblolly pine (Pinus taeda L.) resulting inthe formation of multiple shoot structures induced on cotyledons andhypocotyls of mature zygotic embryos is described. Mature zygoticembryos of eight genotypes of loblolly pine were used as explants toinduce direct somatic organogenesis with this two-step culture method,involving the induction and the differentiation of direct adventitiousshoots. After mature zygotic embryos of eight genotypes of loblolly pinewere cultured on induction medium containing 2,4-dichlorophenoxyaceticacid (2,4-D) or -naphthaleneacetic acid (NAA), 6-benzyladenine(BA), and kinetin for 2–3 weeks, embryos were transferred todifferentiation medium. Adventitious shoot regeneration via directsomatic organogenesis with the frequency of 8.7–27.8% wasobtained from mature zygotic embryo cultures of the genotypes tested.The highest mean number of 32.6 adventitious shoots per mature zygoticembryo was produced from genotype La. The tissue culture protocol of invitro shoot regeneration via direct somatic embryogenesis was optimizedafter examining the periods of the induction culture, chillingtreatment, glutamine concentration, and basic medium levels. Rooting wasachieved on TE medium supplemented with 0.5 mg/l indole-3-butyric acid(IBA), 0.5 mg/l gibberellic acid (GA₃), and 1 mg/l6-benzyladenine (BA), and regenerated plantlets were established insoil. These results suggested that adventitious shoot regeneration viadirect somatic organogenesis could be useful for clonal micropropagationof some genotypes of loblolly pine and for establishing a transformationsystem of this coniferous species.     

Role of antioxidant defences in the species-specific response of isolated atria to menadione

In previous works we demonstrated that 2-methyl-1,4-naphthoquinone (menadione) causes a marked increase in the force of contraction of guinea pig and rat isolated atria. This inotropic effect was significantly higher in the guinea pig than in the rat and was strictly related to the amount of superoxide anion (O(2)(*-)), generated as a consequence of cardiac menadione metabolism through mitochondrial NADH-ubiquinone oxidoreductase. The present study was designed to further elucidate the basis of these quantitatively different positive inotropic responses. To this purpose, we measured O(2)(*-) and hydrogen peroxide (H(2)O(2)) produced by mitochondria isolated from guinea pig and rat hearts in the presence of 20 microM menadione. Moreover, we evaluated the menadione detoxification activity (DT-diaphorase) and the antioxidant defences of guinea pig and rat hearts, namely their GSH/GSSG content, Cu/Zn- and Mn-dependent superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (Gpx) activities. Our results indicate that DT-diaphorase activity and glutathione levels were similar in both animal species. By contrast, guinea pig mitochondria produced greater amounts of O(2)(*-) and H(2)O(2) than those of rat heart. This is probably due to both the higher Mn-SOD activity (2.93 +/- 0.02 vs. 1.95 +/- 0.06 units/mg protein; P < 0.05) and to the lower Gpx activity (10.09 +/- 0.30 vs. 32.67 +/- 1.02 units/mg protein; P < 0.001) of guinea pig mitochondria. A lower CAT activity was also observed in guinea pig mitochondria (2.40 +/- 0.80 vs. 6.13 +/- 0.20 units/mg protein; P < 0.01). Taken together, these data provide a rational explanation for the greater susceptibility of guinea pig heart to the toxic effect of menadione: because of the greater amount of O(2)(*-) generated by the quinone and the higher mitochondrial Mn-SOD activity, guinea pig heart is exposed to more elevated concentrations of H(2)O(2) that is less efficiently detoxified, because of lower Gpx and CAT levels of mitochondria.     

DNA-based methods for the detection and the identification of phytoplasmas in insect vector extracts

DNA extraction and storage methods have been evaluated with laboratory-reared leafhoppers and/or field-collected leafhoppers and psyllids. Detection of four different phytopathogenic phytoplasmas, belonging to three taxonomic groups, has been achieved by several direct or nested polymerase chain reaction (PCR) methods with such DNA extracts. Reactions differed in both the 16/23S ribosomal primer pairs used and the specific assay and cycling conditions. Merits and possible hindrances of the various primer pairs, in relation to insect DNA extracts, are discussed. However, identification of the phytoplasma(s) necessarily relied on comparison of the polymorphism in length of the amplified DNA fragments obtained by restriction with appropriate endonucleases. Endonuclease digestion is crucial for determining the identity (subgroup affiliation) of phytoplasmas of the same groups that can be carried by an individual vector.     

Evaluation of the influence of anisotropic indirect nuclear spin-spin coupling tensors on effective residual dipolar couplings for model peptides

Residual dipolar couplings (RDCs) observed between nuclear spins in molecules in partially oriented media have become a valuable source of information for NMR spectroscopists seeking to structurally characterize biological macromolecules. Examination of the form of the direct (D) and indirect (J) nuclear spin-spin coupling Hamiltonians indicates that all observed RDCs contain an unknown contribution from the anisotropic part of J (J) in addition to the direct dipolar contribution, D _PQ. Here, we evaluate the influence of J on RDCs through a series of DFT calculations on model peptides. Very small corrections to one-bond RDCs measured between heavy atoms in peptides and proteins are recommended: +0.51% for N-C spin pairs, and +0.45% for C-C spin pairs. The corrections to RDCs involving at least one proton are negligible. This latter point is likely to be equally applicable to nucleic acids and oligosaccharides in addition to peptides and proteins. Finally, the orientations of the J(N, C) and J(C, C) tensors in the molecular framework are reported for glycylglycine.