Testing the quick meal hypothesis: The effect of pulp on hoarding and seed predation of Hymenaea courbaril by red‐rumped agoutis (Dasyprocta leporina)

Abstract: Red‐rumped agoutis (Dasyprocta leporina) are important seed dispersers/predators of Neotropical large‐seeded plants. Several species of seeds cached by agoutis have an edible reward, in contrast to temperate rodent‐dispersed diaspores. The quick meal hypothesis states that the presence of a reward such as edible pulp will enhance the efficiency of rodents as seed disperses by satiating the animal and, consequently, reducing seed predation and enhancing hoarding. In this study, this hypothesis was tested using as the reference system the pulp and seeds of Hymenaea courbaril. Seeds with and without pulp were offered to agoutis and the behaviour of each individual was recorded. Since the probability of predation and hoarding were complementary, we used the probability of predation. The proportion of agoutis that preyed on at least one seed was similar for seeds with (42.8% of individuals) and without (40.0% of individuals) pulp. In agoutis that preyed upon at least one seed, the probability that they killed a seed did not differ between seeds with (0.17 ± 0.03) and without (0.20 ± 0.08) pulp. Hence, these results do not support the ‘quick meal hypothesis’.     

Extrafloral nectaries as a deterrent mechanism against seed predators in the chemically protected weed Crotalaria pallida (Leguminosae)

Abstract In several plants, extrafloral nectaries (EFN) are located close to the reproductive structures, suggesting that ants may act as a defence against specialized seed predators that overcome chemical defences. Alternatively, ants may also deter herbivores in a generalized manner, thereby protecting the whole plant. In this work, we examined the relationship between the chemically protected weed Crotalaria pallida Ait. (Leguminosae) that bears EFN, its specialized seed predator, the larvae of the arctiid moth Utetheisa ornatrix L. (Arctiidae) and ants. We tested two hypotheses related to the type of deterrence caused by ants. The Seed Predator Deterrence Hypothesis predicts that ant deterrence is directed primarily towards herbivores that destroy seeds and other reproductive structures, without attacking herbivores on vegetative structures. The General Deterrence Hypothesis states that ants are general in their effects, equally deterring herbivores in vegetative and reproductive structures. Our results supported the predictions of the Seed Predator Deterrence Hypothesis, namely, that (i) ant activity on EFN was related to the vulnerability of reproductive structures to attack by U. ornatrix; (ii) ant patrolling was restricted almost entirely to racemes; (iii) ants removed termites used as baits more frequently on racemes than on leaves; and (iv) U. ornatrix larvae were often expulsed from the racemes. These results indicate that EFN can act as another deterrent mechanism in chemically protected plants by promoting the expulsion of specialist seed predators.     

Prediction of indirect interactions in proteins

Background  

Both direct and indirect interactions determine molecular recognition of ligands by proteins. Indirect interactions can be defined as effects on recognition controlled from distant sites in the proteins, e.g. by changes in protein conformation and mobility, whereas direct interactions occur in close proximity of the protein's amino acids and the ligand. Molecular recognition is traditionally studied using three-dimensional methods, but with such techniques it is difficult to predict the effects caused by mutational changes of amino acids located far away from the ligand-binding site. We recently developed an approach, proteochemometrics, to the study of molecular recognition that models the chemical effects involved in the recognition of ligands by proteins using statistical sampling and mathematical modelling.     

Quantification of Uncultured Ruminococcus obeum-Like Bacteria in Human Fecal Samples by Fluorescent In Situ Hybridization and Flow Cytometry Using 16S rRNA-Targeted Probes

A 16S rRNA-targeted probe was designed and validated in order to quantify the number of uncultured Ruminococcus obeum-like bacteria by fluorescent in situ hybridization (FISH). These bacteria have frequently been found in 16S ribosomal DNA clone libraries prepared from bacterial communities in the human intestine. Thirty-two reference strains from the human intestine, including a phylogenetically related strain and strains of some other Ruminococcus species, were used as negative controls and did not hybridize with the new probe. Microscopic and flow cytometric analyses revealed that a group of morphologically similar bacteria in feces did hybridize with this probe. Moreover, it was found that all hybridizing cells also hybridized with a probe specific for the Clostridium coccoides-Eubacterium rectale group, a group that includes the uncultured R. obeum-like bacteria. Quantification of the uncultured R. obeum-like bacteria and the C. coccoides-E. rectale group by flow cytometry and microscopy revealed that these groups comprised approximately 2.5 and 16% of the total community in fecal samples, respectively. The uncultured R. obeum-like bacteria comprise about 16% of the C. coccoides-E. rectale group. These results indicate that the uncultured R. obeum-like bacteria are numerically important in human feces. Statistical analysis revealed no significant difference between the microscopic and flow cytometric counts and the different feces sampling times, while a significant host-specific effect on the counts was observed. Our data demonstrate that the combination of FISH and flow cytometry is a useful approach for studying the ecology of uncultured bacteria in the human gastrointestinal tract.     

Rapid identification of lettuce seed germination mutants by bulked segregant analysis and whole genome sequencing

Lettuce (Lactuca sativa) seeds exhibit thermoinhibition, or failure to complete germination when imbibed at warm temperatures. Chemical mutagenesis was employed to develop lettuce lines that exhibit germination thermotolerance. Two independent thermotolerant lettuce seed mutant lines, TG01 and TG10, were generated through ethyl methanesulfonate mutagenesis. Genetic and physiological analyses indicated that these two mutations were allelic and recessive. To identify the causal gene(s), we applied bulked segregant analysis by whole genome sequencing. For each mutant, bulked DNA samples of segregating thermotolerant (mutant) seeds were sequenced and analyzed for homozygous single‐nucleotide polymorphisms. Two independent candidate mutations were identified at different physical positions in the zeaxanthin epoxidase gene (ABSCISIC ACID DEFICIENT 1/ZEAXANTHIN EPOXIDASE, or ABA1/ZEP) in TG01 and TG10. The mutation in TG01 caused an amino acid replacement, whereas the mutation in TG10 resulted in alternative mRNA splicing. Endogenous abscisic acid contents were reduced in both mutants, and expression of the ABA1 gene from wild‐type lettuce under its own promoter fully complemented the TG01 mutant. Conventional genetic mapping confirmed that the causal mutations were located near the ZEP/ABA1 gene, but the bulked segregant whole genome sequencing approach more efficiently identified the specific gene responsible for the phenotype.     

REINTERPRETATION OF A CONULARIID-LIKE FOSSIL FROM THE VENDIAN OF RUSSIA

Abstract:  Vendoconularia triradiata Ivantsov and Fedonkin, recently described from Vendian (latest Proterozoic) strata of Russia, has been interpreted as a six-sided conulariid cnidarian. However, comparison of published illustrations of V .  triradiata with Palaeozoic conulariids suggests that certain key features of the anatomy of V .  triradiata should be reinterpreted. Specifically, features previously homologized with the corners of conulariid thecae may actually be homologous to the conulariid midlines. Under this new interpretation, the corners of the Vendoconularia theca were sulcate, and the midline of each face was non-sulcate and flanked by a pair of low internal carinae. This alternative set of hypotheses of homology makes the argument for a conulariid affinity for Vendoconularia stronger.     

CLADISTIC ANALYSIS OF THE SUBORDER CONULARIINA MILLER AND GURLEY, 1896 (CNIDARIA, SCYPHOZOA; VENDIAN–TRIASSIC)

Abstract: Results of a cladistic analysis of the suborder Conulariina Miller and Gurley, 1896, a major extinct (Vendian–Triassic) group of scyphozoan cnidarians, are presented. The analysis sought to test whether the three conulariid subfamilies (Conulariinae Walcott, 1886 , Paraconulariinae Sinclair, 1952 and Ctenoconulariinae Sinclair, 1952 ) recognized in the Treatise on Invertebrate Paleontology (TIP) are monophyletic. A total of 17 morphological characters were scored for 16 ingroup taxa, namely the genera Archaeoconularia, Baccaconularia, Climacoconus, Conularia, Conulariella, Conularina, Ctenoconularia, Eoconularia, Glyptoconularia, Metaconularia, Notoconularia, Paraconularia, Pseudoconularia, Reticulaconularia, Teresconularia and Vendoconularia. The extant medusozoan taxa Cubozoa, Stauromedusae, Coronatae and Semaeostomeae served as outgroups. Unweighted analysisof the data matrix yielded 1057 trees, and successive weighting analysis resulted in one of the 1057 original trees. The ingroup is monophyletic with two autapomorphies: (1) the quadrate geometry of the oral region; and (2) the presence of a mineralized (phosphatic) periderm. Within the ingroup, the clade (Vendoconularia, Teresconularia, Conularina, Eoconularia) is supported by the sinusoidal longitudinal geometry of the transverse ridges, and the much larger clade (Baccaconularia, Glyptoconularia, Metaconularia, Pseudoconularia, Conularia, Ctenoconularia, Archaeoconularia, Notoconularia, Climacoconus, Paraconularia, Reticulaconularia) is supported by the presence of external tubercles, which, however, were lost in the clade (Notoconularia, Climacoconus, Paraconularia, Reticulaconularia). As proposed by Van Iten et al. (2000) , the clade (Notoconularia, Climacoconus, Paraconularia, Reticulaconularia) is supported by the termination and alternation of the transverse ribs in the corner sulcus. The previously recognized subfamilies Conulariinae, Paraconulariinae and Ctenoconulariinae were not recovered from this analysis. The diagnostic features of Conulariinae (continuation of the transverse ornament across the corner sulcus and lack of carinae) and Ctenoconulariinae (presence of carinae) are symplesiomorphic or homoplastic, and Paraconulariinae is polyphyletic. The families Conulariellidae Kiderlen, 1937 and Conulariopsidae Sugiyama, 1942 , also recognized in the TIP, are monogeneric, and since they provide no additional phylogenetic information, should be abandoned.     

The Iron-Hydrogenase of Thermotoga maritima Utilizes Ferredoxin and NADH Synergistically: a New Perspective on Anaerobic Hydrogen Production

The hyperthermophilic and anaerobic bacterium Thermotoga maritima ferments a wide variety of carbohydrates, producing acetate, CO₂, and H₂. Glucose is degraded through a classical Embden-Meyerhof pathway, and both NADH and reduced ferredoxin are generated. The oxidation of these electron carriers must be coupled to H₂ production, but the mechanism by which this occurs is unknown. The trimeric [FeFe]-type hydrogenase that was previously purified from T. maritima does not use either reduced ferredoxin or NADH as a sole electron donor. This problem has now been resolved by the demonstration that this hydrogenase requires the presence of both electron carriers for catalysis of H₂ production. The enzyme oxidizes NADH and ferredoxin simultaneously in an approximately 1:1 ratio and in a synergistic fashion to produce H₂. It is proposed that the enzyme represents a new class of bifurcating [FeFe] hydrogenase in which the exergonic oxidation of ferredoxin (midpoint potential, −453 mV) is used to drive the unfavorable oxidation of NADH (E₀′ = −320 mV) to produce H₂ (E₀′ = −420 mV). From genome sequence analysis, it is now clear that there are two major types of [FeFe] hydrogenases: the trimeric bifurcating enzyme and the more well-studied monomeric ferredoxin-dependent [FeFe] hydrogenase. Almost one-third of the known H₂-producing anaerobes appear to contain homologs of the trimeric bifurcating enzyme, although many of them also harbor one or more homologs of the simpler ferredoxin-dependent hydrogenase. The discovery of the bifurcating hydrogenase gives a new perspective on our understanding of the bioenergetics and mechanism of H₂ production and of anaerobic metabolism in general.The order Thermotogales is characterized by the ability of its members to utilize a wide variety of carbohydrates (8). All of these organisms ferment sugars predominantly to acetate, CO₂, and H₂ (23). They thrive mainly at elevated temperatures, although a new subclass of mesophilic “mesotoga” has also been proposed (19). These properties also make the Thermotoga species excellent candidates for biohydrogen production from plant-based biomass. The genome of the type strain, T. maritima, was one of the first to be sequenced, and this revealed a high degree of lateral gene transfer between archaea and bacteria (17, 18). In addition, T. maritima is part of a structural genomics effort, and the structures of over 100 of its proteins have been determined (20, 21). The organism degrades a wide variety of both simple and complex carbohydrates (4, 5), and the glucose that is produced is oxidized by both classical Embden-Meyerhof (85%) and Entner-Douderhoff (15%) pathways (23). The generation of H₂ is accomplished by the enzyme hydrogenase. However, little is known about the bioenergetics of the reaction and the pathways of electron flow from carbohydrate oxidation to H₂ formation.Although hydrogenases catalyze the simplest of chemical reactions, the reversible interconversion of protons, electrons, and H₂, they are surprisingly complex proteins, some more so than others (33). They can be divided into two major groups, the [NiFe]- and [FeFe]-type hydrogenases, based on the presence of nickel and iron or only iron in their active sites. In general, the physiological roles of the [FeFe] hydrogenases are to evolve H₂, while the roles of the [NiFe] enzymes are to oxidize it (33). For example, several Clostridium spp. evolve H₂ via a cytoplasmic, monomeric [FeFe] hydrogenase that uses the low-potential redox protein ferredoxin (Fd) (midpoint potential [E_m], <−400 mV) as the electron donor (15). In contrast, H₂ production using NAD(P)H (E₀′ = −320 mV) as the electron donor is thermodynamically unfavorable under physiological conditions because of the more positive redox potential of the pyridine nucleotides (30). Nevertheless, cytoplasmic NAD(P)H-dependent [FeFe] hydrogenases have been reported, although how the endergonic reaction of NAD(P)H-dependent H₂ production is accomplished under physiological conditions is not clear (13, 28).During the oxidation of glucose by T. maritima, both Fd and NAD function as physiological electron acceptors (1, 26, 34). NADH is generated via the glyceraldehyde-3-phosphate dehydrogenase reaction of glycolysis, while the pyruvate that is generated by this pathway is oxidized by pyruvate Fd oxidoreductase (POR) to acetyl coenzyme A (acetyl-CoA), producing reduced Fd. Acetyl-CoA is converted to acetate by phosphotransacetylase and acetate kinase with the concomitant production of ATP. This pathway leads to the production of four moles of H₂ per mole of glucose, with reductant provided by two moles of NADH and four moles of reduced Fd, together with two moles of acetate and two moles of CO₂ (23). The oxidation of reduced Fd and NADH must be directly or indirectly coupled to the reduction of protons to H₂ by hydrogenase, but the trimeric cytoplasmic [FeFe] hydrogenase characterized from T. maritima more than a decade ago does not use either T. maritima Fd or NADH as the sole electron donor (10, 31). Consequently, the mechanism by which the oxidation of Fd and NADH is coupled in vivo to H₂ production is not known. In this study, we have resolved this long-standing problem by showing that this cytoplasmic enzyme represents a novel type of hydrogenase that requires both physiological electron carriers to be present for the efficient catalysis of H₂ production in which both serve as electron donors.     

Prevalence of tick-borne encephalitis virus antibodies in dogs from Denmark

Background  

Large regions of central and eastern Europe are recognized as areas where tick-borne encephalitis virus (TBEV) is endemic, including countries neighbouring Denmark. It is therefore timely and relevant to determine if TBEV infections occur in Denmark. This study investigates the presence of antibodies against TBEV in a cross-section of the Danish canine population to assess the level of exposure to TBEV and possibly identify TBEV microfoci in Denmark.