A Conserved Motif in the 5.8S Ribosomal RNA (rRNA) Gene is a Useful Diagnostic Marker for Plant Internal Transcribed Spacer (ITS) Sequences

The nuclear ribosomal DNA (rDNA) internal transcribed spacer (ITS) region has become an important nuclear locus for molecular systematic investigations of angiosperms at the intergenic and interspecific levels. Universal PCR primers are positioned on the conserved rRNA genes (18S, 5.8S, 26S) to amplify the entire ITS spacer region. Recent reports of fungal and algal contaminants, first described as plant ITS sequences, stress the need for diagnostic markers specific for the angiosperm ITS region. This report describes a conserved 14 base pair (bp) motif in the 5.8S rRNA gene that can be used to differentiate between flowering plants, bryophytes, and several orders of algae and fungi, including common plant pathogenic and non-pathogenic fungi. A variant of the motif (found in fungi and algae) contains a convenient EcoRI restriction site that has several applications for eliminating problematic contaminants from plant ITS preparations.     

Floral development and floral phyllotaxis in Anaxagorea (Annonaceae)

Background and Aims Anaxagorea is the phylogenetically basalmost genus in the large tropical Annonaceae (custard apple family) of Magnoliales, but its floral structure is unknown in many respects. The aim of this study is to analyse evolutionarily interesting floral features in comparison with other genera of the Annonaceae and the sister family Eupomatiaceae. Methods Live flowers of Anaxagorea crassipetala were examined in the field with vital staining, liquid-fixed material was studied with scanning electron microscopy, and microtome section series were studied with light microscopy. In addition, herbarium material of two other Anaxagorea species was cursorily studied with the dissecting microscope. Key Results Floral phyllotaxis in Anaxagorea is regularly whorled (with complex whorls) as in all other Annonaceae with a low or medium number of floral organs studied so far (in those with numerous stamens and carpels, phyllotaxis becoming irregular in the androecium and gynoecium). The carpels are completely plicate as in almost all other Annonaceae. In these features Anaxagorea differs sharply from the sister family Eupomatiaceae, which has spiral floral phyllotaxis and ascidiate carpels. Flat stamens and the presence of inner staminodes differ from most other Annonaceae and may be plesiomorphic in Anaxagorea. However, the inner staminodes appear to be non-secretory in most Anaxagorea species, which differs from inner staminodes in other families of Magnoliales (Eupomatiaceae, Degeneriacae, Himantandraceae), which are secretory. Conclusions Floral phyllotaxis in Anaxagorea shows that there is no signature of a basal spiral pattern in Annonaceae and that complex whorls are an apomorphy not just for a part of the family but for the family in its entirety, and irregular phyllotaxis is derived. This and the presence of completely plicate carpels in Anaxagorea makes the family homogeneous and distinguishes it from the closest relatives in Magnoliales.     

Morphology and distribution of trichomes in Italian species of the Stachys germanica group (Labiatae): a taxonomic evaluation

The micromorphology and distribution of secreting and non-secreting trichomes in different parts of plants of the species belonging to Stachys, S. germanica group, of the Italian Flora, were studied. A peculiar capitate hair with multicellular head was found in all the species examined, with the exception of S. germanica ssp. germanica. This type of trichome is typically 4-celled in S. tymphaea. The distribution of trichomes on the calyces is particularly interesting and some peculiar features better characterize S. germanica ssp. germanica, S. germanica ssp. dasyanthes, S. cretica ssp. salviifolia, S. alpina and S. heraclea.     

Repetitive sequences in phylogeographic inference: a reply to Saltonstall and Lambertini (2012)

In 2011, Vachon and Freeland presented the results of a study that illustrated the importance of considering mutation patterns, including the potential for homoplasy, when deciding whether to include or exclude repetitive sequences from phylogeographic inferences. Saltonstall and Lambertini (2012) criticized this study by suggesting that some of the analyses and interpretations were flawed. In this reply, we explain why we disagree with most of their criticisms and identify some inconsistencies in their analyses. Most importantly, we reiterate the need to examine underlying assumptions, particularly with respect to mutation patterns, when using molecular genetic data to untangle evolutionary relationships.     

Population decline despite high genetic diversity in the new allopolyploid species Senecio cambrensis (Asteraceae)

Senecio cambrensis (Welsh groundsel) is a new allohexaploid species, which originated in Wales, UK, in the early part of the 20th century following hybridization between the native tetraploid groundsel (Senecio vulgaris) and the introduced diploid Oxford ragwort (Senecio squalidus). A survey of the number of populations and flowering individuals per population of S. cambrensis in Wales was conducted at peak flowering time in June 2002, 2003 and 2004. The results show a dramatic decrease in both population number and population size of the species since the 1980s when the last population census was conducted. A survey of amplified fragment length polymorphism (AFLP) variation showed that this decline has occurred despite the fact that S. cambrensis contains a high level of genetic diversity with each individual screened possessing a unique multilocus phenotype. The level of variance within the species was similar to that found in one parent (S. vulgaris) and slightly greater than that among samples of the other parent (S. squalidus). Only a small proportion (5%) of AFLP diversity was partitioned among populations indicating a lack of population structure and possibly high levels of gene flow via seed dispersal in what is predominantly a selfing species. Senecio cambrensis showed closer similarity in AFLP phenotype to S. vulgaris than to S. squalidus. Possible causes of this and also the high level of AFLP diversity found in S. cambrensis are discussed. It is suggested that intergenomic recombination following occasional multivalent formation during meiosis in S. cambrensis is likely to be an important cause of both phenomena, although other causes are not ruled out.     

Hexanuclear copper(II) complex of a novel poly(pyridine) ligand exhibiting unique long distance ferromagnetic interactions through a nitrato-O,O bridge

A novel hexanuclear copper complex [Cu₆(NO₃)₁₂(opytrizediam)₂(H₂O)][(CH₃)₂CO]_0.5(CH₃CH₂CH₂OH)_0.5 (1) with a NO₃ bridge has been synthesized by reaction of Cu(NO₃)₂ · 3H₂O with the new potentially octadentate ligand opytrizediam in n-propanol/acetone solution (opytrizediam=N,N^′-{2,4-di[(di-pyridin-2-yl)amine]-1,3,5-triazine} ethylenediamine). A single-crystal X-ray diffraction analysis showed the presence of six structurally different copper centres. The coordination spheres of four copper(II) ions are best described as square-pyramidal CuN₂O₃ chromophores while the two other copper(II) ions are in a trigonal-bipyramidal CuN₄O environment. Variable-temperature studies on 1 revealed a unique ferromagnetic coupling of two copper(II) ions bridged by a didentate nitrate anion and separated by a distance of 6.391(6) Å, with J=8.6(1) cm⁻¹.     

PREM-1, a putative maize retroelement has LTR (long terminal repeat) sequences that are preferentially transcribed in pollen

A family of highly dispersed repetitive elements, designated PREM-1, which are transcribed primarily during pollen development, has been identified in maize. Sequence data from six PREM-1-containing genomic clones suggest that the PREM-1 sequences are the LTRs of a family of putative retroelements. PREM-1 LTRs are estimated to be present in about 10 000 to 40 000 copies in the maize genome. Although related sequences have been detected in sorghum and crab grass, highly homologous sequences appear to be specific to the genus Zea (maize and teosinte). A diverse group of RNAs that contain portions of the PREM-1 sequence at their 3 ends are transcribed in pollen; highest levels appear in early uninucleate microspores. The PREM-1-containing cDNAs do not appear to code for protein products since stop codons are present in all three reading frames. The possible significance of expression of retroelements in the male gametophyte, in terms of transposition of DNA, is discussed.     

The pollination of Trimenia moorei (Trimeniaceae): floral volatiles,insect/wind pollen vectors and stigmatic self-incompatibility in a basal angiosperm

Trimenia moorei (Oliv.) Philipson is an andromonoecious liane with >0.40 of the total flower buds maturing as bisexual flowers. Male and bisexual flowers are strongly scented with pollen, anther sacs and receptacle scars testing positively for volatile emissions. Scent analyses detect over 20 components. The major fatty acid derivative is 8-heptadecene, and 2-phenylethanol dominates the benzenoids. While hover-flies in the genera Melangyna and Triglyphus contact the stigma with their probosces, the stigma secretes no free-flowing, edible fluids. Copious pollen is the only edible reward consumed by hover-flies (Syprhidae), sawflies (Pergidae) and bees in the families Apidae, Colletidae and Halictidae. All these insects carried pollen of T. moorei on their heads, legs and thoraces and female bees in the genera Apis, Exoneura, Leioproctus and Lasioglossum stored pollen on their hind legs. Pollen traps also indicate that pollen is shed directly into the air, permitting wind pollination. When bisexual flower buds are bagged (isolated from insect foragers) on the liane then subjected to a series of hand-pollination experiments after perianth segments open, the structural analyses of pollen-carpel interactions indicate that T. moorei has a trichome-rich dry-type stigma with an early-acting self-incompatibility (SI) system. Bicellular pollen grains deposited on stigmas belonging to the same plant germinate but fail to penetrate intercellular spaces, while grains deposited following cross-pollination reach the ovule within 24 h. Fluorescence analyses of 76 carpels collected at random from unbagged (open-pollinated) flowers on five plants indicates that at least 64% of carpels are cross-pollinated in situ. Trimenia moorei is the first species within the ANITA group, and second within reilictual-basal angiosperm lineages, to exhibit stigmatic SI in combination with dry-type stigma and bicellular pollen, a condition once considered to be atypical for angiosperms as a whole but now known to be present in numerous taxa.     

Irreversibility of chilling injury in zucchini squash (Cucurbita pepo L) could be a programmed event long before the visible symptoms are evident

Zucchini fruits were subjected to 2.5 or 10 degrees C for 16d, followed by transfer to 20 degrees C for 24h in order to evaluate the relationship between ripening pattern, measured as CO(2) evolution and ethylene (C(2)H(4)) production, and metabolic heat production (q). Chilling injury (CI) visible symptoms were evident after 8d at 2.5 degrees C, but none were recorded on fruits kept at 10 degrees C. In fruits held at 10 degrees C, q, C(2)H(4) production, and CO(2) evolution diminished in the course of 16d, whereas in those at 2.5 degrees C CO(2) evolution showed an early burst peaking at 8d. Both C(2)H(4) production and q also showed a burst at 2.5 degrees C but they started at 4 and 8d, respectively, and peaked at 12d. The results showed that irreversibility of chilling injury in zucchini could occur long before the appearance of visible symptoms, although the metabolic activity accompanying the irreversibility process was not noticeable by isothermal calorimetry.     

Persistent size variation in the anthophorine bee Centris pallida (Apidae) despite a large male mating advantage

Abstract.

• 1 Despite apparent directional sexual selection in favour of large body size, males of the anthophorine bee Centris pallida remain highly variable in body size.
• 2 One possible cause of persistent size variation among males is geographic variation in the extent of the large male mating advantage. However, a study of a population in an area not previously investigated revealed that the large male mating advantage was as strong here as it has been elsewhere in other years.
• 3 Although the reproductive benefits of being large were consistent in populations separated spatially and temporally, the intensity of bird predation on mate-searching males varied greatly between locations.
• 4 The bee-killing birds focused exclusively on bees which were digging down to meet emerging females or fighting on the ground, never on flying males. Males which were collected on the ground by hand (to simulate avian predation) were significantly larger on average than flying males collected by sweep netting.
• 5 Therefore, in some location in some years, sexual selection in favour of large body size may be opposed by natural selection exerted by predators, perhaps contributing to the maintenance of size variation in this bee.

     

Pigs aerogenously immunized with genetically inactivated (ghosts) or irradiated Actinobacillus pleuropneumoniae are protected against a homologous aerosol challenge despite differing in pulmonary cellular and antibody responses.

Aerosol immunization is a safe way to induce complete protection against pleuropneumonia in pigs caused by the lung pathogenic bacterium Actinobacillus pleuropneumoniae. In order to determine the local immune responses of vaccinees in concomitant with protection, lung lining fluid before and 3 weeks after immunization from pigs immunized three times with aerosols of either genetically inactivated ghosts which represent whole cell envelope preparations, or irradiated bacteria were examined following an homologous aerosol challenge. Specific antibody isotypes in the bronchoalveolar lavage were assayed by whole cell ELISAs. Total and relative numbers of cells including lymphocyte subsets were determined. In both vaccinated groups a net influx of plasma cells and lymphocytes, as well as a significant increase of specific IgG occurred. Concurrently, the CD4+/CD8+ ratio was found to increase after aerosol immunization. The lymphocyte subsets of IgG+ and IgA+ cells were found significantly higher in the group immunized with irradiated bacteria when compared to pigs immunized with bacterial ghosts. The latter group showed a significant increase of IgA, IgM, and a net influx of lymphoid blasts and granulocytes in the bronchoalveolar lining fluid. Although differences between the local immune responses of both immunized groups occurred, a significant increase of specific IgG and a net influx of plasma cells and lymphocytes were found to be associated with complete protection against a homologous aerosol challenge infection.     

Charge-charge interactions are key determinants of the pK values of ionizable groups in ribonuclease Sa (pI=3.5) and a basic variant (pI=10.2)

The pK values of the titratable groups in ribonuclease Sa (RNase Sa) (pI=3.5), and a charge-reversed variant with five carboxyl to lysine substitutions, 5K RNase Sa (pI=10.2), have been determined by NMR at 20 degrees C in 0.1M NaCl. In RNase Sa, 18 pK values and in 5K, 11 pK values were measured. The carboxyl group of Asp33, which is buried and forms three intramolecular hydrogen bonds in RNase Sa, has the lowest pK (2.4), whereas Asp79, which is also buried but does not form hydrogen bonds, has the most elevated pK (7.4). These results highlight the importance of desolvation and charge-dipole interactions in perturbing pK values of buried groups. Alkaline titration revealed that the terminal amine of RNase Sa and all eight tyrosine residues have significantly increased pK values relative to model compounds.A primary objective in this study was to investigate the influence of charge-charge interactions on the pK values by comparing results from RNase Sa with those from the 5K variant. The solution structures of the two proteins are very similar as revealed by NMR and other spectroscopic data, with only small changes at the N terminus and in the alpha-helix. Consequently, the ionizable groups will have similar environments in the two variants and desolvation and charge-dipole interactions will have comparable effects on the pK values of both. Their pK differences, therefore, are expected to be chiefly due to the different charge-charge interactions. As anticipated from its higher net charge, all measured pK values in 5K RNase are lowered relative to wild-type RNase Sa, with the largest decrease being 2.2 pH units for Glu14. The pK differences (pK(Sa)-pK(5K)) calculated using a simple model based on Coulomb's Law and a dielectric constant of 45 agree well with the experimental values. This demonstrates that the pK differences between wild-type and 5K RNase Sa are mainly due to changes in the electrostatic interactions between the ionizable groups. pK values calculated using Coulomb's Law also showed a good correlation (R=0.83) with experimental values. The more complex model based on a finite-difference solution to the Poisson-Boltzmann equation, which considers desolvation and charge-dipole interactions in addition to charge-charge interactions, was also used to calculate pK values. Surprisingly, these values are more poorly correlated (R=0.65) with the values from experiment. Taken together, the results are evidence that charge-charge interactions are the chief perturbant of the pK values of ionizable groups on the protein surface, which is where the majority of the ionizable groups are positioned in proteins.     

Learning in a sedentary insect predator: Antlions (Neuroptera: Myrmeleontidae) anticipate a long wait

Pit-building antlions, the larvae of a winged adult insect, capture food by digging funnel-shaped pits in sand and then lying in wait, buried at the vertex, for prey to fall inside. The sedentary nature of this sit-and-wait predatory behaviour and, especially, antlions’ innate ability to detect prey arrival, do not fit the typical profile of insects that possess learning capabilities. However, we show, for the first time, that learning can play an important role in this unique form of predation. In three separate experiments, individual antlions received, once per training day, either a vibrational cue presented immediately before the arrival of food or that same cue presented independently of food arrival. Signalling of food not only produced a learned anticipatory behavioural response (Experiment 1), but also conferred a fitness advantage: Associative learning enabled antlions to dig better pits (Experiments 2 and 3), extract food more efficiently (Experiments 2 and 3), and, in turn, moult sooner (Experiment 3) than antlions not receiving the associative learning treatment.     

Invertebrate communities associated with a native (Vallisneria americana) and an alien (Trapa natans) macrophyte in a large river

1. We used a corer and a Downing box sampler to sample macroinvertebrates living on and beneath the introduced Trapa natans and the native Vallisneria americana in the freshwater tidal Hudson River, New York. 2. Densities of macroinvertebrates were higher in Trapa than in Vallisneria, and higher in the interior of plant beds than at their edges. These effects were largely a result of high plant biomass in Trapa beds and in bed interiors (the plants have similar surface area per unit mass). 3. The composition of both epiphytic and benthic macroinvertebrates differed distinctly between Trapa and Vallisneria, and also seasonally. 4. These compositional differences were not easily interpretable as rising from possible differences in oxygen concentrations, fish predation, or water circulation in the two macrophytes. 5. Sida crystallina (Cladocera) collected from Trapa contained more haemoglobin than those collected from Vallisneria. 6. The replacement of Vallisneria by Trapa in the Hudson probably increased system‐wide biodiversity and food for fish, although macroinvertebrates in Trapa beds may not be readily available to fish because of low oxygen concentration there.     

Mouse fatty acid transport protein 4 (FATP4): characterization of the gene and functional assessment as a very long chain acyl-CoA synthetase

FATP4 (SLC27A4) is a member of the fatty acid transport protein (FATP) family, a group of evolutionarily conserved proteins that are involved in cellular uptake and metabolism of long and very long chain fatty acids. We cloned and characterized the murine FATP4 gene and its cDNA. From database analysis we identified the human FATP4 genomic sequence. The FATP4 gene was assigned to mouse chromosome 2 band B, syntenic to the region 9q34 encompassing the human gene. The open reading frame was determined to be 1929 bp in length, encoding a polypeptide of 643 amino acids. Within the coding region, the exon-intron structures of the murine FATP4 gene and its human counterpart are identical, revealing a high similarity to the FATP1 gene. The overall amino acid identity between the deduced murine and human FATP4 polypeptides is 92.2%, and between the murine FATP1 and FATP4 polypeptides is 60.3%. Northern analysis showed that FATP4 mRNA was expressed most abundantly in small intestine, brain, kidney, liver, skin and heart. Transfection of FATP4 cDNA into COS1 cells resulted in a 2-fold increase in palmitoyl-CoA synthetase (C16:0) and a 5-fold increase in lignoceroyl-CoA synthetase (C24:0) activity from membrane extracts, indicating that the FATP4 gene encodes an acyl-CoA synthetase with substrate specificity biased towards very long chain fatty acids.     

Strong population structure despite evidence of recent migration in a selfing hermaphroditic vertebrate, the mangrove killifish (Kryptolebias marmoratus)

We employ a battery of 33 polymorphic microsatellite loci to describe geographical population structure of the mangrove killifish (Kryptolebias marmoratus), the only vertebrate species known to have a mixed-mating system of selfing and outcrossing. Significant population genetic structure was detected at spatial scales ranging from tens to hundreds of kilometres in Florida, Belize, and the Bahamas. The wealth of genotypic information, coupled with the highly inbred nature of most killifish lineages due to predominant selfing, also permitted treatments of individual fish as units of analysis. Genetic clustering algorithms, neighbour-joining trees, factorial correspondence, and related methods all earmarked particular killifish specimens as products of recent outcross events that could often be provisionally linked to specific migration events. Although mutation is the ultimate source of genetic diversity in K. marmoratus, our data indicate that interlocality dispersal and outcross-mediated genetic recombination (and probably genetic drift also) play key proximate roles in the local 'clonal' dynamics of this species.     

Stability in the historical pattern of genetic structure of Newfoundland cod (Gadus morhua) despite the catastrophic decline in population size from 1964 to 1994

We report on evidence of long term stability inthe geographic pattern of geneticdifferentiation among cod (Gadus morhua)collected from 5 spawning banks offNewfoundland and Labrador over a periodspanning three decades (1964–1994) and 2orders of magnitude of population sizevariation. Six microsatellite DNA lociamplified from archived otoliths (1964 and1978) and contemporary (1990s) tissue samplesrevealed fidelity to natal spawning banks overthis period. A two level (spawning bank anddecade) hierarchical and multilocus AMOVAindicated that 1.55% of the total variation inallele frequencies could be attributed(P = 0.036) to spatial structure while novariance component could be attributed totemporal changes. A finer scale analysis amongcod from just 3 of these spawning banksreveals, however, evidence consistent with somepost-collapse mixing between cod from twobanks. In the context of fisheries managementand conservation, the survival of the spatialpattern of genetic differentiation during thepopulation collapse suggests that if recoveryeventually occurs it will likely be throughpopulation re-growth in situ rather thanby migratory influx.     

Molecular evidence that phoronids are a subtaxon of brachiopods (Brachiopoda: Phoronata) and that genetic divergence of metazoan phyla began long before the early Cambrian

Concatenated SSU (18S) and partial LSU (28S) sequences (2 kb) from 12 ingroup taxa, comprising 2 phoronids, 2 members of each of the craniid, discinid, and lingulid inarticulate brachiopod lineages, and 4 rhynchonellate, articulate brachiopods (2 rhynchonellides, 1 terebratulide and 1 terebratellide) were aligned with homologous sequences from 6 protostome, deuterostome and sponge outgroups (3964 sites). Regions of potentially ambiguous alignment were removed, and the resulting data (3275 sites, of which 377 were parsimony-informative and 635 variable) were analysed by parsimony, and by maximum and Bayesian likelihood using objectively selected models. There was no base composition heterogeneity. Relative rate tests led to the exclusion (from most analyses) of the more distant outgroups, with retention of the closer pectinid and polyplacophoran (chiton). Parsimony and likelihood bootstrap and Bayesian clade support values were generally high, but only likelihood analyses recovered all brachiopod indicator clades designated a priori. All analyses confirmed the monophyly of (brachiopods+phoronids) and identified phoronids as the sister-group of the three inarticulate brachiopod lineages. Consequently, a revised Linnean classification is proposed in which the subphylum Linguliformea comprises three classes: Lingulata, ‘Phoronata’ (the phoronids), and ‘Craniata’ (the current subphylum Craniiformea). Divergence times of all nodes were estimated by regression from node depths in non-parametrically rate-smoothed and other chronograms, calibrated against palaeontological data, with probable errors not less than 50 My. Only three predicted brachiopod divergence times disagree with palaeontological ages by more than the probable error, and a reasonable explanation exists for at least two. Pruning long-branched ingroups made scant difference to predicted divergence time estimates. The palaeontological age calibration and the existence of Lower Cambrian fossils of both main brachiopod clades together indicate that initial genetic divergence between brachiopod and molluscan (chiton) lineages occurred well before the Lower Cambrian, suggesting that much divergence between metazoan phyla took place in the Proterozoic.

See also Electronic Supplement at: http://www.senckenberg.de/odes/05-11.htm     

Genetic Structure in a Heterocyanic Population of Trillium sessile (Liliaceae)

Abstract Species of Trillium in the subgenus Phyllantherum are either polymorphic for flower color, or monomorphic for flower color and related to a polymorphic species. This leads to the suggestion that polymorphic species may be the progenitors for monomorphic ones. For this to be true, it must be demonstrated that genetic divergence among flower morphs can occur within polymorphic populations. Genetic structure was assessed in a population of T. sessile that contains a polymorphism for flower color. A survey of 11 enzyme systems using starch gel electrophoresis revealed three polymorphic loci: 6PGD-1, AAT-1 and AAT-2. Analysis of large and small scale spatial structure, stage classes, and flower color classes revealed significant genetic divergence in all instances. Spatial structure in the population is likely a result of genetic neighborhoods which can maintain populational variation via random genetic drift. Genetic divergence of the yellow flower color morph was probably initiated through genetic drift since the morph occurs in low frequencies. The results imply that the initial genetic divergence of species in the subgenus can arise within polymorphic populations.