Lactobacillus plantarum 24, Isolated From the Marula Fruit (Sclerocarya birrea), has Probiotic Properties and Harbors Genes Encoding the Production of Three Bacteriocins

Lactobacillus plantarum 24, isolated from marula fruit grows at pH 4.0 and tolerates acid levels and bile concentrations normally present in the human gastro-intestinal tract. Wistar rats that have been administered L. plantarum 24 showed no signs of discomfort or abnormal behavior. Tissue samples from the liver, spleen and intestine appeared normal. Furthermore, strain 24 harbors the genes encoding plantaricins A, F, and NC8α, a gene encoding immunity to plantaricin, and an ABC transporter similar in sequence to that reported for plantaricin G. At least one antimicrobial peptide within the size range of plantaricins A, F, and NC8α has been detected on a tricine-SDS–PAGE gel. Little is known about the microbial population in marula. This is the first report of a L. plantarum strain from marula fruit with bacteriocin genes and probiotic properties.     

CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences

Codon models of evolution have facilitated the interpretation of selective forces operating on genomes. These models, however, assume a single rate of non-synonymous substitution irrespective of the nature of amino acids being exchanged. Recent developments have shown that models which allow for amino acid pairs to have independent rates of substitution offer improved fit over single rate models. However, these approaches have been limited by the necessity for large alignments in their estimation. An alternative approach is to assume that substitution rates between amino acid pairs can be subdivided into rate classes, dependent on the information content of the alignment. However, given the combinatorially large number of such models, an efficient model search strategy is needed. Here we develop a Genetic Algorithm (GA) method for the estimation of such models. A GA is used to assign amino acid substitution pairs to a series of rate classes, where is estimated from the alignment. Other parameters of the phylogenetic Markov model, including substitution rates, character frequencies and branch lengths are estimated using standard maximum likelihood optimization procedures. We apply the GA to empirical alignments and show improved model fit over existing models of codon evolution. Our results suggest that current models are poor approximations of protein evolution and thus gene and organism specific multi-rate models that incorporate amino acid substitution biases are preferred. We further anticipate that the clustering of amino acid substitution rates into classes will be biologically informative, such that genes with similar functions exhibit similar clustering, and hence this clustering will be useful for the evolutionary fingerprinting of genes.     

Use of molecular markers as indicators for winter zooplankton grazing on toxic benthic cyanobacteria colonies in an urban Colorado lake

Laboratory experiments provide no general answer to the question of whether zooplankton affects cyanobacteria or are affected by prokaryotes. A cyanobacterium may be grazed upon as small colonies, and the same species, as larger colonies, may inhibit zooplankton feeding. Within zooplankton, different species or groups may be affected differently. With this background we set out to detect winter zooplankton grazing and toxicity of overwintering populations of Microcystis aeruginosa. A polymerase chain reaction (PCR) method with oligonucleotide primers for the mcy gene cluster that encodes microcystin synthetase was employed for detection of M. aeruginosa reminiscent products in grazing cladocera. In our field studies, we detected the mcy gene cluster in strains of overwintering colonies of benthic Microcystis and also confirmed the expression of toxicity by quantitative PCR, phosphatase inhibition and enzyme-linked immunosorbent assays (ELISA). We further confirmed the presence of the mcy gene cluster in DNA and RNA isolated from sampled Daphnia magna specimens, indicating that zooplankton in the natural environment may ingest toxic Microcystis cells as part of their diet during winter months.     

Effect of octanoic acid on ethylene-mediated flower induction in Dutch iris

Treatment of Dutch iris (Iris × hollandica Hoog. cv. Sapphire Beauty) bulbs with ethylene prior to precooling stimulated flowering in bulbs of various sizes. In large sized bulbs exposure to ethylene followed by precooling resulted in 100% flowering over a five months period after planting. Flowering in control bulbs which were not treated with ethylene prior to precooling was limited to 67% during the same five months period. In medium sized bulbs flowering in the ethylene treatment was 90% compared to 75% in the control. However, the biggest stimulation of flowering by ethylene was found in small sized bulbs (from 16 to 56%). Application of octanoic acid for a short time period prior to exposure to ethylene stimulated flowering in all bulb sizes. After five months the final percentage flowering in large and medium sized bulbs of the octanoic acid plus ethylene treatment did not differ from that of the ethylene only treatment. However, the initial rate of flowering was higher in the former treatment. In small bulbs the percentage flowering was much higher in the octanoic acid plus ethylene treatment than in the ethylene only treatment. The results of this study indicate that, just as in certain flowers, fruit and seeds, treatment with octanoic acid stimulates ethylene sensitivity in Dutch iris bulbs. The sensitivity of untreated bulbs to ethylene was highest in large bulbs and lowest in small bulbs. This correlated well with the endogenous octanoic acid content of the bulbs. Octanoic acid levels were highest in large bulbs and lowest in small Bulbs. It appears that the endogenous levels of octanoic acid in the bulbs is determined prior to the onset of dormancy.     

Induction of Pyrophosphate-Dependent Phosphofructokinase in Watermelon (Citrullus lanatus) Cotyledons Coincides with Insufficient Cytosolic D-Fructose-1,6-Bisphosphate 1-Phosphohydrolase to Sustain Gluconeogenesis

During germination of Citrullus lanatus, pyrophosphate-dependent phosphofructokinase (PFP) activity is induced. The peak of PFP activity coincides with the maximum gluconeogenic flux and high fructose-2,6-bisphosphate (Fru-2,6-P2) concentrations. Determination of cytosolic fructose-1,6 bisphosphatase (FBPase) activity in crude extracts is unreliable because of the high PFP activity. The FBPase activity, after correction for the contaminating PFP, is only one-third of the PFP activity. Purified cytosolic FBPase is inhibited by Fru-2,6-P2. The low cytosolic FBPase activity and high Fru-2,6-P2 most probably result in inadequate in vivo activity to catalyze the observed gluconeogenic flux. The total PFP activity is sufficient to catalyze the required carbon flux.     

Stimulation of seed germination in South African species of Restionaceae by plant-derived smoke

The Restionaceae is one of the three major families defining fynbos, the characteristic vegetation type of the Cape Floristic Region. Periodic fires with a frequency of 5 to 40 years are a natural phenomenon in fynbos vegetation. Fire-stimulated seed germination has been reported for a variety of fynbos species, and species in the Asteraceae, Ericaceae, Proteaceae and Restionaceae have shown a germination response to smoke and/or aqueous smoke extracts. In the present study seed of 32 species was screened to obtain an indication of how important the smoke cue is for germination in the South African Restionaceae. The results of the present study represents the first occasion that comparative germination data for South African species in this family have ever been obtained. Twenty-five of the 32 species tested showed a statistically significant improvement in germination following smoke treatment. Untreated seeds of 18 of the species responding, showed a high degree of dormancy with only 0.1% to 2.0% germination. These results suggest that under natural conditions smoke from fynbos fires may provide an important cue for triggering seed germination in this family. The degree of improvement in germination following smoke treatment ranged from 147% in the case of Restio festuciformis to 25300% in the case of Rhodocoma capensis. It is suggested that the 16 species which showed a 1000% or more increase in germination following smoke treatment form a group in which smoke is likely to be the major cue for germination. In those species in which there is a lesser response, smoke may be one of a number of germination cues which include heat, and possibly alternating high and low incubation temperatures. The four species that did not germinate were all myrmecochorus, nut-fruited species. More information is needed concerning the fire survival strategy of South African Restionaceae species and many more will have to be investigated in the nursery and in the field, before the full pattern of response within the family and its significance can be elucidated.     

Species delimitation of the liquorice tribe (Leguminosae: Glycyrrhizeae) based on phylogenomic and machine learning analyses

The liquorice tribe Glycyrrhizeae is a leguminous herbaceous group of plants comprised of the genera Glycyrrhiza and Glycyrrhizopsis. Some Glycyrrhiza taxa contain glycyrrhizin, a pharmacologically significant sweet substance that also has applications in crafting industrial materials. Here, we utilized an expanded taxon sampling of Glycyrrhizeae to reconstruct the phylogenetic relationships in the tribe based on genome skimming data, including whole chloroplast genomes, nuclear ribosomal DNA, and low-copy nuclear DNA. We also launched machine learning analysis (MLA) for one species pair with controversial taxonomic boundary. The integrated results indicated Glycyrrhizopsis should be split from Glycyrrhiza, while the former genus Meristotropis should be treated as part of Glycyrrhiza. Glycyrrhizopsis includes two species, Glycyrrhizopsis asymmetrica and Glycyrrhizopsis flavescens, and we recognize 13 species in Glycyrrhiza: Glycyrrhiza acanthocarpa, Glycyrrhiza astragalina, Glycyrrhiza bucharica, Glycyrrhiza echinata, Glycyrrhiza foetida, Glycyrrhiza glabra, Glycyrrhiza gontscharovii, Glycyrrhiza lepidota, Glycyrrhiza macedonica, Glycyrrhiza pallidiflora, Glycyrrhiza squamulosa, Glycyrrhiza triphylla, and Glycyrrhiza yunnanensis. We propose a broader G. glabra that includes former Glycyrrhiza aspera, G. glabra s.s., Glycyrrhiza inflata, and Glycyrrhiza uralensis, and represents the glycyrrhizin-contained medicinal group. Our ancestral state inferences show the ancestor of Glycyrrhiza lacked glycyrrhizin, and the presence of glycyrrhizin evolved twice within Glycyrrhiza during the last one million years. Our integrative phylogenomics-MLA study not only provides new insights into long-standing taxonomic controversies of Glycyrrhizeae, but also represents a useful approach for future taxonomic studies on other plant taxa.     

Rearrangements of integral membrane components during in vitro aging of sheep erythrocyte membranes

In vitro aged sheep erythrocytes and sheep erythrocyte ghosts spontaneously release vesicles that consist of long protrusions affixed to flattened headlike structures. The intramembranous particles seen on the protoplasmic face of freeze fracture electron micrographs of vesicle protrusions are arranged in paired particle rows. On the equivalent fracture face of headlike structures, the particle density is low; if particles are present, they are clustered along the rim of the flattened headlike structure and at the junction with the protrusion. The released vesicles are depleted of the intramembranous particles seen on the exoplasmic face of ghost but retain almost exclusively particles of the protoplasmic face. Correspondingly, the exoplasmic face of ghosts that have released vesicles reveals a 28 percent higher density of intramembranous particles than that of fresh ghosts. Purified vesicles are depleted of spectrin but retain integral membrane proteins, with one of an apparent mol wt of 160,000 accounting for nearly 50 percent of the total protein (Lutz, H.U.,R. Barber, and R.F. McGuire. 1976. J. Biol. Chem. 251:3500-3510). When vesicles are modified with the cleavable cross-linking reagent [(35)S]dithiobis (succinimidyl propionate)at 0 degrees C, the 160,000 mol wt protein is rapidly converted to disulfide-linked dimers and higher oligomers. Exposure of intact ghosts to the reagent in the same way fails to yield equivalent polymers. A comparison of the morphological and biochemical aspects of ghosts and vesicles suggest that a marked rearrangement of membrane proteins accompanies the supramolecular redistribution of intramembranous particles during spontaneous vesiculation. The results also suggest that the paired particles of the protoplasmic face of vesicle protrusions are arranged in paired helices and contain the 160,000 mol wt protein as dimers.     

Ultrastructure of buffalo,Syncerus caffer,platelets: Comparison with bovine and human platelets

Platelets are found in the blood of all mammals and serve the same basic hemostatic functions in all. Species differences in the morphology and activities of platelets in human and domesticated animals have been observed, but there is little published information regarding the blood pictures of wild animals. In this study, the ultrastructure of buffalo platelets was compared with that of bovine and human platelets. Buffalo platelets were found to be smaller than human platelets and intracellularly had larger α-granules, possessed distinctive dense granules and a more distinct microtubuli system, but they lacked the open canalicular system observed in the human type. This morphology is similar to that of cattle platelets. © 1996 Wiley-Liss, Inc.