Organization and behavior of the synaptonemal complex during achiasmatic meiosis of four buthid scorpions

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

High similarity of U2 snDNA sequence between A and B chromosomes in the grasshopper Abracris flavolineata

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Xylella fastidiosa comparative genomic database is an information resource to explore the annotation, genomic features, and biology of different strains

The Xylella fastidiosa comparative genomic database is a scientific resource with the aim to provide a user-friendly interface for accessing high-quality manually curated genomic annotation and comparative sequence analysis, as well as for identifying and mapping prophage-like elements, a marked feature of Xylella genomes. Here we describe a database and tools for exploring the biology of this important plant pathogen. The hallmarks of this database are the high quality genomic annotation, the functional and comparative genomic analysis and the identification and mapping of prophage-like elements. It is available from web site http://www.xylella.lncc.br.

Molecular epidemiology and genetic linkage of macrolide and aminoglycoside resistance in Staphylococcus intermedius of canine origin

A collection of 77 Staphylococcus intermedius isolates from dogs and cats in Switzerland was examined for resistance to erythromycin. Resistance profiles for 14 additional antibiotics were compared between erythromycin-resistant and susceptible isolates. A resistance prevalence of 27% for erythromycin was observed in the population under study. Complete correlation between resistance to erythromycin, and to spiramycin, streptomycin, and neomycin was observed. The erythromycin-resistant isolates all had a reduced susceptibility to clindamycin when compared to the erythromycin-susceptible isolates. Both constitutive and inducible resistance phenotypes were observed for clindamycin. Ribotyping showed that macrolide-aminoglycoside resistance was randomly distributed among unrelated strains. This suggests that this particular resistance profile is not related to a single bacterial clone but to the horizontal transfer of resistance gene clusters in S. intermedius populations. The erythromycin-resistant isolates were all carrying erm(B), but not erm(A), erm(C), or msr(A). The erm(B) gene was physically linked to Tn5405-like elements known as resistance determinants for streptomycin, streptothricin, neomycin and kanamycin. Analysis of the region flanking erm(B) showed the presence of two different groups of erm(B)-Tn5405-like elements in the S. intermedius population examined and of elements found in Gram-positive species other than staphylococci. This strongly suggests that erm(B) or the whole erm(B)-Tn5405-like elements in S. intermedius originate from other bacterial species, possibly from enterococci.

Sedimentological and palynological study of sediment cores from the northern Mekong River Delta

A sedimentological and palynological study of three sediment cores from the northern Mekong River Delta shows the regional sedimentary and environmental development since the mid-Holocene sea level highstand. A sub- to intertidal flat deposit of mid-Holocene age is recorded in the northernmost core. Shoreline deposits in all three cores show descending ages from N to S documenting 1) the early stages of the late Holocene regression and 2) the subsequent delta progradation. The delta plain successions vary from floodplain deposits with swamp-like elements to natural levee sediments. The uppermost sediments in all cores show human disturbance to varying degrees. The most intense alteration is recorded in the northernmost core where the palynological signal together with a charcoal peak indicates the profound change of the environment during the modern land reclamation. The sediments from at least one of the three presented cores do not show a "true" delta facies succession, but rather estuary-like features, as also observed in records from southern Cambodia. This absence is probably due to lack of accommodation space during the initial phase of rapid delta progradation which impeded the development of "true" delta successions as shown in cores from the southern Mekong River Delta.

Geometric diagnostics of complex patterns: Spiral defect chaos

Motivated by the observation of spiral patterns in a wide range of physical, chemical, and biological systems, we present an automated approach that aims at characterizing quantitatively spiral-like elements in complex stripelike patterns. The approach provides the location of the spiral tip and the size of the spiral arms in terms of their arc length and their winding number. In addition, it yields the number of pattern components (Betti number of order 1), as well as their size and certain aspects of their shape. We apply the method to spiral defect chaos in thermally driven Rayleigh- Bénard convection and find that the arc length of spirals decreases monotonically with decreasing Prandtl number of the fluid and increasing heating. By contrast, the winding number of the spirals is nonmonotonic in the heating. The distribution function for the number of spirals is significantly narrower than a Poisson distribution. The distribution function for the winding number shows approximately an exponential decay. It depends only weakly on the heating, but strongly on the Prandtl number. Large spirals arise only for larger Prandtl numbers. In this regime the joint distribution for the spiral length and the winding number exhibits a three-peak structure, indicating the dominance of Archimedean spirals of opposite sign and relatively straight sections. For small Prandtl numbers the distribution function reveals a large number of small compact pattern components.

Evolutionary relationships among diverse bacteriophages and prophages: All the world’s a phage

We report DNA and predicted protein sequence similarities, implying homology, among genes of double-stranded DNA (dsDNA) bacteriophages and prophages spanning a broad phylogenetic range of host bacteria. The sequence matches reported here establish genetic connections, not always direct, among the lambdoid phages of Escherichia coli, phage φC31 of Streptomyces, phages of Mycobacterium, a previously unrecognized cryptic prophage, φflu, in the Haemophilus influenzae genome, and two small prophage-like elements, φRv1 and φRv2, in the genome of Mycobacterium tuberculosis. The results imply that these phage genes, and very possibly all of the dsDNA tailed phages, share common ancestry. We propose a model for the genetic structure and dynamics of the global phage population in which all dsDNA phage genomes are mosaics with access, by horizontal exchange, to a large common genetic pool but in which access to the gene pool is not uniform for all phage.

Arrayed transposase-binding sequences on the ends of transposon Tn5090/Tn402

The transposon Tn5090/Tn402 encodes a 559 amino acid transposase, TniA, with a DDE motif. Gel mobility shifting and cleavage protection analysis with DNase I and hydroxyl radical probes revealed that TniA binds to multiple repeat sequences on either terminus of Tn5090/Tn402. Four of these TniA-binding 19mers occurred on the left-hand (t) end and two on the right-hand (i) end. Hydroxyl radical cleavage protection demonstrated the presence of 3–6 bp contact sequences on one face of the DNA helix. The binding pattern and organisation of repeats suggested parallels between Tn5090/Tn402 and Mu, which controls its transpositional activity in the assembly step of a higher order transpososome complex. The complex terminal structure and genes of transposase and nucleotide-binding proteins in tandem are hallmarks of the handful of Mu-like elements that are known to date.

Dynamics of mobile element activity in chalcone synthase loci in the common morning glory (Ipomoea purpurea)

Mobile element dynamics in seven alleles of the chalcone synthase D locus (CHS-D) of the common morning glory (Ipomoea purpurea) are analyzed in the context of synonymous nucleotide sequence distances for CHS-D exons. By using a nucleotide sequence of CHS-D from the sister species Ipomoea nil (Japanese morning glory [Johzuka-Hisatomi, Y., Hoshino, A., Mori, T., Habu, Y. & Iida, S. (1999) Genes Genet. Syst. 74, 141–147], it is also possible to determine the relative frequency of insertion and loss of elements within the CHS-D locus between these two species. At least four different types of transposable elements exist upstream of the coding region, or within the single intron of the CHS-D locus in I. purpurea. There are three distinct families of miniature inverted-repeat transposable elements (MITES), and some recent transpositions of Activator/Dissociation (Ac/Ds)-like elements (Tip100), of some short interspersed repetitive elements (SINEs), and of an insertion sequence (InsIpCHSD) found in the neighborhood of this locus. The data provide no compelling evidence of the transposition of the mites since the separation of I. nil and I. purpurea roughly 8 million years ago. Finally, it is shown that the number and frequency of mobile elements are highly heterogeneous among different duplicate CHS loci, suggesting that the dynamics observed at CHS-D are locus-specific.

The SEF14 fimbrial antigen of Salmonella enterica serovar Enteritidis is encoded within a pathogenicity islet

The DNA sequence of the chromosomal gene cluster encoding the SEF14 fimbriae of Salmonella enterica serovar Enteritidis was determined. Five contiguous open reading frames, sefABCDE, were identified. The sefE gene shared significant homology with araC-like positive regulators. Serovar-associated virulence plasmid (SAP) genes orf7,8,9 and pefI were identified immediately adjacent to the sef operon. The pefI gene encoded a putative regulator of the Plasmid-encoded fimbrial antigen (PEF) expression. The entire sef--pef region, flanked by two IS-like elements, was inserted adjacent to leuX that encoded a transfer RNA molecule. The organisation of this region was suggestive of a classic pathogenicity islet. Southern hybridisation confirmed two copies of the SAP derived orf7,8,9 and pefI region in S. Enteritidis, one in the chromosome and one on the SAP. Of other group D Salmonella, only S. Blegdam and S. Moscow harboured both chromosomal and plasmid copies of pefI--orf9 region although polymorphism was evident.

Genomic diversity of Lactobacillus salivarius

Lactobacillus salivarius is unusual among the lactobacilli due to its multireplicon genome architecture. The circular megaplasmids harboured by L. salivarius strains encode strain-specific traits for intestinal survival and probiotic activity. L. salivarius strains are increasingly being exploited for their probiotic properties in humans and animals. In terms of probiotic strain selection, it is important to have an understanding of the level of genomic diversity present in this species. Comparative genomic hybridization (CGH) and multilocus sequence typing (MLST) were employed to assess the level of genomic diversity in L. salivarius. The wellcharacterised probiotic strains L. salivarius UCC118 was employed as a genetic reference strain. The group of test strains were chosen to reflect the range of habitats from which L. salivarius strains are frequently recovered, including human, animal, and environmental sources. Strains of L. salivarius were found to be genetically diverse when compared to the UCC118 genome. The most conserved strains were human GIT isolates, while the greatest level of divergence were identified in animal associated isolates. MLST produced a better separation of the test strains according to their isolation origins, than that produced by CGHbased strain clustering. The exopolysaccharide (EPS) associated genes of L. salivarius strains were found to be highly divergent. The EPS-producing phenotype was found to be carbonsource dependent and inversely related to a strain's ability to produce a biofilm. The genome of the porcine isolate L. salivarius JCM1046 was shown by sequencing to harbour four extrachromosomal replicons, a circular megaplasmid (pMP1046A), a putative chromid (pMP1046B), a linear megaplasmid (pLMP1046) and a smaller circular plasmid (pCTN1046) which contains an integrated Tn916-like element (Tn6224), which carries the tetracycline resistance gene tetM. pLMP1046 represents the first sequence of a linear plasmid in a Lactobacillus species. Dissemination of antibiotic resistance genes among species with food or probiotic-association is undesirable, and the identification of Tn6224-like elements in this species has implications for strain selection for probiotic applications. In summary, this thesis used a comparative genomics approach to examine the level of genotypic diversity in L. salivarius, a species which contains probiotic strains. The genome sequence of strain JCM1046 provides additional insight into the spectrum of extrachromosomal replicons present in this species.

Posidonia oceanica (L.) Delile in its westernmost biogeographical limit (northwestern Alboran Sea): Meadows characterisation, phenology and flowering events

Posidonia oceanica is a Mediterranean endemic seagrass species that forms meadows covering ca. 2.5–4.5 millions of hectares, representing ca.25 % of the infralittoral and shallow circalittoral (down to 50m) bottoms of the Mediterranean. This seagrass is considered a habitat-engineer species and provides an elevated number of ecosystem services. In addition the Marine Strategy Framework Directive (MSFD, 2008/56/EC) includes seagrass like elements to evaluate the “Good Environmental Status” of the European coasts. Information about their phenological characteristic and structure of the meadows is needed for indicator estimations in order to establish their conservation status. The studied meadows are located in the westernmost limit of the P. oceanica distribution (North-western Alboran Sea) in the vecinity of the Strait of Gibraltar, an Atlantic-Mediterranean water transition area. Four sites were selected from East to West: Paraje Natural de Acantilados de Maro-Cerro Gordo (hereafter Maro), Special Area of Conservation “Calahonda” (hereafter Calahonda), Site of Community Importance Estepona (hereafter Estepona) and Punta Chullera (hereafter Chullera) where P. oceanica present their westernmost meadows. Phenological data were recorded from mid November to mid December in P. oceanica patches located at 2 – 3 m depth. At each site three types of patches (patch area <1m2, small patches; 1-2 m2, medium patches and >2 m2, large patches) were sampled. At each patch and site, 3 quadrants of 45 x 45 cm were sampled for shoot and inflorescences density measurements. In each quadrant, 10 random shoots were sampled for shoot morphology (shoot height and number of leaves). Shoot and inflorescences densities were standardized to squared meters. All the studied P. oceanica meadows develop on rocks and they present a fragmented structure with a coverage ranging between ca. 45% in Calahonda and Estepona and ca. 31% in Maro. The meadows of Chullera are reduced to a few small - medium patches with areas ranging between 0.5-1.5 m2 (Fig. 1). The meadows of Chullera and Estepona presented similar values of shoot density (ca. 752 – 662 shoots m-2, respectively) and leaf height (ca. 25 cm). Similarly, the Calahonda and Maro meadows also showed similar values of shoot density (ca. 510 – 550 shoots m-2, respectively) but displaying lower values than those of sites located closer to the Strait of Gibraltar. Regarding patch sizes and leaf height, the longest leaves (ca. 25 cm) were found in medium and large patches, but the number of leaves per shoot were higher in the small and the medium size patches (ca. 6.3 leaves per shoot). Flowering was only detected at the Calahonda meadows with maximum values of ca. 330 inflorescences m-2 (115.2 ± 98.2 inflorescences m-2, n= 9; mean ± SD) (Fig.1). Inflorescence density was not significant different among patches of different sizes. In the Alboran Sea and unlike the studied meadows, extensive beds of P. oceanica occur at the National Park of Cabo de Gata (northeastern Alboran Sea), but from east to west (Strait of Gibraltar), meadows are gradually fragmenting and their depth range decrease from 30m to 2m depth between Cabo de Gata and Chullera, respectively. Probably, the Atlantic influence and the characteristic oceanographic conditions of the Alboran Sea (i.e., higher turbidity, higher water turbulence) represent a developmental limiting factor for P. oceanica at higher depths. Similarities between the meadows located closer to Strait of Gibraltar (Chullera and Estepona) were detected as well as between those more distant (Calahonda and Maro). The first ones showed higher values of shoot densities and leaf heights than the formers, which could be relating to the higher hydrodynamic exposure found at Chullera and Estepona meadows. Regarding flowering events, sexual reproduction in P. oceanica is not common in different locations of the Mediterranean Sea. The available information seems to indicate that flowering represent an irregular event and it is related to high seawater temperature. In fact, the flowering episodes that occurred in Calahonda in November 2015, match with the warmest year ever recorded. This is the third flowering event registered in these meadows located close to the westernmost distributional limit of P. oceanica (Málaga, Alboran Sea), which could indicates that these meadows presents a healthy status. Furthermore, the absence of significant differences in relation to inflorescence density between patches of different sizes may be indicating that the fragmentation does not necessarily influence on the flowering of this seagrass species.

Enterococcus faecalis prophage dynamics and contributions to pathogenic traits

Polylysogeny is frequently considered to be the result of an adaptive evolutionary process in which prophages confer fitness and/or virulence factors, thus making them important for evolution of both bacterial populations and infectious diseases. The Enterococcus faecalis V583 isolate belongs to the high-risk clonal complex 2 that is particularly well adapted to the hospital environment. Its genome carries 7 prophage-like elements (V583-pp1 to -pp7), one of which is ubiquitous in the species. In this study, we investigated the activity of the V583 prophages and their contribution to E. faecalis biological traits. We systematically analyzed the ability of each prophage to excise from the bacterial chromosome, to replicate and to package its DNA. We also created a set of E. faecalis isogenic strains that lack from one to all six non-ubiquitous prophages by mimicking natural excision. Our work reveals that prophages of E. faecalis V583 excise from the bacterial chromosome in the presence of a fluoroquinolone, and are able to produce active phage progeny. Intricate interactions between V583 prophages were also unveiled: i) pp7, coined EfCIV583 for E. faecalis chromosomal island of V583, hijacks capsids from helper phage 1, leading to the formation of distinct virions, and ii) pp1, pp3 and pp5 inhibit excision of pp4 and pp6. The hijacking exerted by EfCIV583 on helper phage 1 capsids is the first example of molecular piracy in Gram positive bacteria other than staphylococci. Furthermore, prophages encoding platelet-binding-like proteins were found to be involved in adhesion to human platelets, considered as a first step towards the development of infective endocarditis. Our findings reveal not only a role of E. faecalis V583 prophages in pathogenicity, but also provide an explanation for the correlation between antibiotic usage and E. faecalis success as a nosocomial pathogen, as fluoriquinolone may provoke release of prophages and promote gene dissemination among isolates.