Zoogeography of the southern African ascidian fauna

Aim To describe the biogeography of the ascidian fauna of southern Africa, to compare the results obtained with those reported for other fauna and flora of the same region, and to speculate about the origin of ascidians in the region. Location Southern Africa extending over 4000 km from Mossâmedes (15° S–12° E) to Inhaca Island (26°30′ S–33° E), including Vema Seamount (31°40′ S–8 °20′ E), Amsterdam‐Saint Paul Islands (38° S–77°30′ E) and the Tristan‐Gough Islands (38° S–12°20′ W). Methods We constructed a presence/absence matrix of 168 species for 26 biogeographical divisions, 21 classical biogeographical regions described by Briggs (Marine zoogeography, McGraw‐Hill, New York, 1974) and five provinces within the southern African region. We considered the following limits and divisions into provinces for the southern African region: Namibia, Namaqua, Agulhas and Natal as proposed by Branch et al. (Two oceans. A guide to the marine life of southern Africa, David Philip Publishers, 1994), and the West Wind Drift Islands province (WWD) according to Briggs (Global biogeography, Elsevier Health Sciences, Amsterdam, 1995). To examine the biogeographical structure, species and divisions were classified using cluster analysis (based on UPGMA as the aggregation algorithm) with the Bray–Curtis index of similarity. This classification was combined with MDS ordination. Main conclusions Four main groups were obtained from the analysis of affinities among species: (1) species present in the WWD, separated by a high percentage of endemisms and a low number of species with a southern African distribution. Moreover, in the light of the species distribution and the results of further analysis, which revealed that they are completely separated and not at all related to the southern African region, it appears that there are no close relationships among the different islands and seamounts of the West Wind Drift Island province. This province was therefore removed from the remaining analyses; (2) species with a wide distribution; (3) species of colder waters present in Namaqua and Agulhas provinces, a transitional temperate area in which gradual mixing and replacement of species negate previous hypotheses on the existence of a marked distributional break at Cape of Good Hope; (4) species of warmer waters related to Natal province. The classification into biogeographical components was dominated by the endemic (47%), Indo‐Pacific (25%) and cosmopolitan (13%) components. The analysis of affinities among biogeographical areas separated Namibia from the rest of the southern African provinces and showed that it was related to some extent to the Antarctic region because of the cold‐temperate character of the province and the low sampling effort; Namaqua, Agulhas and Natal were grouped together and found to be closely related to the Indo‐West Pacific region. In general, our results were consistent with those obtained for other southern African marine invertebrates. The frequency distribution of solitary/colonial strategies among provinces confirmed the domination of colonial organisms in tropical regions and solitary organisms in colder regions. Finally, we speculate that the southern African ascidian fauna mainly comprises Indo‐Pacific, Antarctic and eastern Atlantic ascidians.     

The complete methylome of Helicobacter pylori UM032

Background

The genome of the human gastric pathogen Helicobacter pylori encodes a large number of DNA methyltransferases (MTases), some of which are shared among many strains, and others of which are unique to a given strain. The MTases have potential roles in the survival of the bacterium. In this study, we sequenced a Malaysian H. pylori clinical strain, designated UM032, by using a combination of PacBio Single Molecule, Real-Time (SMRT) and Illumina MiSeq next generation sequencing platforms, and used the SMRT data to characterize the set of methylated bases (the methylome).

Results

The N4-methylcytosine and N6-methyladenine modifications detected at single-base resolution using SMRT technology revealed 17 methylated sequence motifs corresponding to one Type I and 16 Type II restriction-modification (R-M) systems. Previously unassigned methylation motifs were now assigned to their respective MTases-coding genes. Furthermore, one gene that appears to be inactive in the H. pylori UM032 genome during normal growth was characterized by cloning.

Conclusion

Consistent with previously-studied H. pylori strains, we show that strain UM032 contains a relatively large number of R-M systems, including some MTase activities with novel specificities. Additional studies are underway to further elucidating the biological significance of the R-M systems in the physiology and pathogenesis of H. pylori.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1585-2) contains supplementary material, which is available to authorized users.     

Colostrum of Healthy Slovenian Mothers: Microbiota Composition and Bacteriocin Gene Prevalence

Microbial communities inhabiting the breast milk microenvironment are essential in supporting mammary gland health in lactating women and in providing gut-colonizing bacterial ''inoculum'' for their infants’ gastro-intestinal development. Bacterial DNA was extracted from colostrum samples of 45 healthy Slovenian mothers. Characteristics of the communities in the samples were assessed by polymerase chain reaction (PCR) coupled with denaturing gradient gel electrophoresis (DGGE) and by quantitative real-time PCR (qPCR). PCR screening for the prevalence of bacteriocin genes was performed on DNA of culturable and total colostrum bacteria. DGGE profiling revealed the presence of Staphylococcus and Gemella in most of the samples and exposed 4 clusters based on the abundance of 3 bands: Staphylococcus epidermidis/Gemella, Streptococcus oralis/pneumonia and Streptococcus salivarius. Bacilli represented the largest proportion of the communities. High prevalence in samples at relatively low quantities was confirmed by qPCR for enterobacteria (100%), Clostridia (95.6%), Bacteroides-Prevotella group (62.2%) and bifidobacteria (53.3%). Bacterial quantities (genome equivalents ml^-1) varied greatly among the samples; Staphylococcus epidermidis and staphylococci varied in the range of 4 logs, streptococci and all bacteria varied in the range of 2 logs, and other researched groups varied in the range of 1 log. The quantity of most bacterial groups was correlated with the amount of all bacteria. The majority of the genus Staphylococcus was represented by the species Staphylococcus epidermidis (on average 61%), and their abundances were linearly correlated. Determinants of salivaricin A, salivaricin B, streptin and cytolysin were found in single samples. This work provides knowledge on the colostrum microbial community composition of healthy lactating Slovenian mothers and reports bacteriocin gene prevalence.     

Podosomes and invadopodia: tools to breach vascular basement membrane

The vascular basement membrane (BM) is a thin and dense cross-linked extracellular matrix layer that covers and protects blood vessels. Understanding how cells cross the physical barrier of the vascular BM will provide greater insight into the potentially critical role of vascular BM breaching in cancer extravasation, leukocyte trafficking and angiogenic sprouting. In the last year, new evidence has mechanistically linked the breaching of vascular BM with the formation of specific cellular micro-domains known as podosomes and invadopodia. These structures are specialized cell-matrix contacts with an inherent ability to degrade the extracellular matrix. Specifically, the formation of podosomes or invadopodia was shown as an important step in vascular sprouting and tumor cell extravasation, respectively. Here, we review and comment on these recent findings and explore the functions of podosomes and invadopodia within the context of pathological processes such as tumor dissemination and tumor angiogenesis.     

Shiny wing scales cause spec(tac)ular camouflage of the angled sunbeam butterfly,Curetis acuta

The angled sunbeam butterfly, Curetis acuta (Lycaenidae), is a distinctly sexually dimorphic lycaenid butterfly from Asia. The dorsal wings of female and male butterflies have a similar pattern, with a large white area in the female and an orange area in the male, framed within brown–black margins. The ventral wings of both sexes are silvery white, which is caused by stacks of overlapping, non‐pigmented, and specular‐reflecting scales. With oblique illumination, the reflected light of the ventral wings is strongly polarized. We show that the silvery reflection facilitates camouflage in a shaded, foliaceous environment. The ecological function of the silvery reflection is presumably two‐fold: for intraspecific signalling in flight, and for reducing predation risk at rest and during hibernation. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 279–289.     

Self‐pollination and parthenocarpic ability in developing ovaries of self‐incompatible Clementine mandarins (Citrus clementina)

This study aimed to determine if self‐pollination is needed to trigger facultative parthenocarpy in self‐incompatible Clementine mandarins (Citrus clementina Hort. ex Tan.). ‘Marisol’ and ‘Clemenules’ mandarins were selected, and self‐pollinated and un‐pollinated flowers from both cultivars were used for comparison. These mandarins are always seedless after self‐pollination and show high and low ability to develop substantial parthenocarpic fruits, respectively. The time‐course for pollen grain germination, tube growth and ovule abortion was analyzed as well as that for carbohydrates, active gibberellins (GA₁ and GA₄), auxin (IAA) and abscisic acid (ABA) content in the ovary. ‘Clemenules’ showed higher pollen grain germination, but pollen tube development was arrested in the upper style 9 days after pollination in both cultivars. Self‐pollination did not stimulate parthenocarpy, whereas both un‐pollinated and self‐pollinated ovaries set fruit regardless of the cultivar. On the other hand, ‘Marisol’ un‐pollinated flowers showed greater parthenocarpic ovary growth than ‘Clemenules’ un‐pollinated flowers, i.e. higher ovule abortion rate (+21%), higher fruit set (+44%) and higher fruit weight (+50%). Further, the greater parthenocarpic ability of ‘Marisol’ paralleled higher levels of GA₁ in the ovary (+34% at anthesis). ‘Marisol’ ovary also showed higher hexoses and starch mobilization, but lower ABA levels (?64% at anthesis). Self‐pollination did not modify carbohydrates or GA content in the ovary compared to un‐pollination. Results indicate that parthenocarpy in the Clementine mandarin is pollination‐independent with its ability to set depending on the ovary hormone levels. These findings suggest that parthenocarpy in fertile self‐incompatible mandarins is constitutively regulated.     

ELF exposure system for live cell imaging

A programmable system has been developed for the study of both transient and persistent effects of extremely low frequency (ELF) magnetic field exposure of cell cultures. This high‐precision exposure system enables experimental blinding and fully characterized exposure while simultaneously allowing live cell imaging. It is based on a live imaging cell around which two asymmetrical coils are wound in good thermal contact to a temperature‐controlled water jacket, and is mounted on a microscope stage insert. The applied B‐field uniformity of the active volume is better than 1.2% with an overall exposure uncertainty of less than 4.3% with very low transient field levels. The computer‐controlled apparatus allows signal waveforms that are sinusoidal or composed of several harmonics, blind protocols, and monitoring of exposure and environmental conditions. B‐fields up to 4 mT root mean square amplitude are possible with minimal temperature variation and no recognizable temperature differences between exposure and sham states. Sources of artifacts have been identified and quantified. There are no visible vibrations observable even at the highest magnifications and exposure levels. Bioelectromagnetics 34:231–239, 2013. © 2012 Wiley Periodicals, Inc.     

MICROSPECTROPHOTOMETRY AS A METHOD TO IDENTIFY KLEPTOPLASTIDS IN THE NAKED FRESHWATER DINOFLAGELLATE GYMNODINIUM ACIDOTUM1

A relatively small number of freshwater dinoflagellates are involved in symbiotic association with cryptophytes. The chloroplasts of the cryptophytes are retained by the dinoflagellate and give it the characteristic phycobilin pigmentation, either phycoerythrin or phycocyanin. The pigment characterization of the retained chloroplasts can give precise and accurate information about the type of cryptophyte preyed upon by the dinoflagellate. For this purpose, we performed microspectrophotometric evaluation of the pigments of Gymnodinium acidotum Nygaard and three different cryptophytes present in samples collected from a tributary of the river Arno, in Tuscany (Italy). The comparison of the different spectroscopic data allowed us to discriminate effectively among the cryptophytes preyed upon by the dinoflagellate.     

Cytochrome P-450 4F18 is the leukotriene B4 omega-1/omega-2 hydroxylase in mouse polymorphonuclear leukocytes: identification as the functional orthologue of human polymorphonuclear leukocyte CYP4F3A in the down-regulation of responses to LTB4

Leukotriene B(4) (LTB(4)) is a potent chemoattractant for polymorphonuclear leukocytes (PMN) and other cells. Human PMN inactivate LTB(4) by omega-oxidation catalyzed by cytochrome P-450 (CYP) 4F3A. The contribution of the enzymatic inactivation of LTB(4) by CYP4Fs to down-regulating functional responses of cells to LTB(4) is unknown. To elucidate the role of CYP4F-mediated inactivation of LTB(4) in terminating the responses of PMN to LTB(4) and to identify a target for future genetic studies in mice, we have identified the enzyme that catalyzes the omega-1 and omega-2 oxidation of LTB(4) in mouse myeloid cells as CYP4F18. As determined by mass spectrometry, this enzyme catalyzes the conversion of LTB(4) to 19-OH LTB(4) and to a lesser extent 18-OH LTB(4). Inhibition of CYP4F18 resulted in a marked increase in calcium flux and a 220% increase in the chemotactic response of mouse PMN to LTB(4). CYP4F18 expression was induced in bone marrow-derived dendritic cells by bacterial lipopolysaccharide, a ligand for TLR4, and by poly(I.C), a ligand for TLR3. However, when bone marrow-derived myeloid dendritic cells trafficked to popliteal lymph nodes from paw pads, the expression of CYP4F18 was down-regulated. The results identify CYP4F18 as a critical protein in the regulation of LTB(4) metabolism and functional responses in mouse PMN and identify it as the functional orthologue of human PMN CYP4F3A.