Characterization of pentocin TV35b, a bacteriocin-like peptide isolated from Lactobacillus pentosus with a fungistatic effect on Candida albicans

Lactobacillus pentosus TV35b, isolated from the posterior fornix secretions of the vagina of a prenatal patient, produced a bacteriocin-like peptide (pentocin TV35b), which is inhibitory to Clostridium sporogenes, Cl. tyrobutyricum, Lact. curvatus, Lact. fermentum, Lact. sake, Listeria innocua, Propionibacterium acidipropionici, Propionibacterium sp. and Candida albicans. The mechanism of activity of pentocin TV35b is bactericidal, as shown by a decrease in the viable cell numbers of Lact. sake from approximately 4 x 108 to less than 10 cfu ml - 1 over a period of 4 h. Pentocin TV35b added to the growth medium of C. albicans stimulated the formation of pseudohyphae during the first 36 h, followed by a slight repression in cell growth. Production of pentocin TV35b was at its maximum towards the end of the logarithmic growth phase of strain TV35b. The peptide was purified by ammonium sulphate precipitation, followed by SP-Sepharose cation exchange chromatography. The molecular size of pentocin TV35b was estimated to be between 2.35 and 3.4 kDa, according to tricine-SDS PAGE. However, results obtained by electrospray ionization mass spectroscopy indicated that the peptide is 3930.2 Da in size. Amino acid analysis performed by using the Pico-Tag(R) method and a Nova-Pak C18 HPLC column indicated that pentocin TV35b consists of 33 amino acids with a total mass of 3929.63 Da. Pentocin TV35b is inactivated when treated with papain and Proteinase K, but remains active after incubation at pH 1-10 for 2 h at 25 degrees C, and when heat-treated for 30 min at 100 degrees C.     

High Spatial Resolution Infrared Micro-Spectroscopy Reveals the Mechanism of Leaf Lignin Decomposition by Aquatic Fungi

Organic carbon is a critical component of aquatic systems, providing energy storage and transfer between organisms. Fungi are a major decomposer group in the aquatic carbon cycle, and are one of few groups thought to be capable of breaking down woody (lignified) tissue. In this work we have used high spatial resolution (synchrotron light source) infrared micro-spectroscopy to study the interaction between aquatic fungi and lignified leaf vein material (xylem) from River Redgum trees (E. camaldulensis) endemic to the lowland rivers of South-Eastern Australia. The work provides spatially explicit evidence that fungal colonisation of leaf litter involves the oxidative breakdown of lignin immediately adjacent to the fungal tissue and depletion of the lignin-bound cellulose. Cellulose depletion occurs over relatively short length scales (5–15 µm) and highlights the likely importance of mechanical breakdown in accessing the carbohydrate content of this resource. Low bioavailability compounds (oxidized lignin and polyphenols of plant origin) remain in colonised leaves, even after fungal activity diminishes, and suggests a possible pathway for the sequestration of carbon in wetlands. The work shows that fungi likely have a critical role in the partitioning of lignified material into a biodegradable fraction that can re-enter the aquatic carbon cycle, and a recalcitrant fraction that enters long-term storage in sediments or contribute to the formation of dissolved organic carbon in the water column.     

DNA origami signposts for identifying proteins on cell membranes by electron cryotomography

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The Emergence of Predators in Early Life: There was No Garden of Eden

Background

Eukaryote cells are suggested to arise somewhere between 0.85∼2.7 billion years ago. However, in the present world of unicellular organisms, cells that derive their food and metabolic energy from larger cells engulfing smaller cells (phagocytosis) are almost exclusively eukaryotic. Combining these propositions, that eukaryotes were the first phagocytotic predators and that they arose only 0.85∼2.7 billion years ago, leads to an unexpected prediction of a long period (∼1–3 billion years) with no phagocytotes – a veritable Garden of Eden.

Methodology

We test whether such a long period is reasonable by simulating a population of very simple unicellular organisms - given only basic physical, biological and ecological principles. Under a wide range of initial conditions, cellular specialization occurs early in evolution; we find a range of cell types from small specialized primary producers to larger opportunistic or specialized predators.

Conclusions

Both strategies, specialized smaller cells and phagocytotic larger cells are apparently fundamental biological strategies that are expected to arise early in cellular evolution. Such early predators could have been ‘prokaryotes’, but if the earliest cells on the eukaryote lineage were predators then this explains most of their characteristic features.     

Amplification of 16S rRNA genes from Frankia strains in root nodules of Ceanothus griseus, Coriaria arborea, Coriaria plumosa, Discaria toumatou, and Purshia tridentata.

To study the global diversity of plant-symbiotic nitrogen-fixing Frankia strains, a rapid method was used to isolate DNA from these actinomycetes in root nodules. The procedure used involved dissecting the symbiont from nodule lobes; ascorbic acid was used to maintain plant phenolic compounds in the reduced state. Genes for the small-subunit rRNA (16S ribosomal DNA) were amplified by the PCR, and the amplicons were cycle sequenced. Less than 1 mg (fresh weight) of nodule tissue and fewer than 10 vesicle clusters could serve as the starting material for template preparation. Partial sequences were obtained from symbionts residing in nodules from Ceanothus griseus, Coriaria arborea, Coriaria plumosa, Discaria toumatou, and Purshia tridentata. The sequences obtained from Ceonothus griseus and P. tridentata nodules were identical to the sequence previously reported for the endophyte of Dryas drummondii. The sequences from Frankia strains in Coriaria arborea and Coriaria plumosa nodules were identical to one another and indicate a separate lineage for these strains. The Frankia strains in Discaria toumatou nodules yielded a unique sequence that places them in a lineage close to bacteria that infect members of the Elaeagnaceae.     

Three genetically divergent lineages of the Oryx in eastern Africa: Evidence for an ancient introgressive hybridization

Phylogeographic and population genetic studies using sequence information are frequently used to infer species boundaries and history; and to assess hybridization and population level processes. In this study, partial mitochondrial DNA (mtDNA) control region (423 bp) and cytochrome b sequences (666 bp) of Oryx beisa sampled from five isolated localities in its entire current range in Africa were analyzed to investigate the extent of genetic variation and differentiation between populations. We observed high nucleotide diversity at the control region in the total sample (6.3%) but within populations, it varied considerably ranging from 1.6% to 8.1%. Population pairwise genetic differentiation was generally significantly high (ranging from F _ST = 0.15, P<0.01 to F _ST = 0.54, P<0.001). In the total sample, 29 and 12 haplotypes were observed in the control region and the cytochrome b data sets respectively. For both data sets, the haplotypes cluster into three distinct clades (sequence divergence ranged from 6.0%–12.9% to 0.8%–1.0% for the control region and cytochrome b sequences, respectively) that do not correspond to sampling locations. Two of these clades are found in the same localities (Samburu and Marsabit), which represent the O.beisa beisa subspecies, whereas the last clade represents the fringe-eared oryx (O. beisa callotis). We interpret these findings in terms of an ancient hybridization and introgression between two formerly isolated taxa of Oryx beisa.