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1.  Arthritis Induces Early Bone High Turnover, Structural Degradation and Mechanical Weakness 
PLoS ONE  2015;10(1):e0117100.
Background
We have previously found in the chronic SKG mouse model of arthritis that long standing (5 and 8 months) inflammation directly leads to high collagen bone turnover, disorganization of the collagen network, disturbed bone microstructure and degradation of bone biomechanical properties. The main goal of the present work was to study the effects of the first days of the inflammatory process on the microarchitecture and mechanical properties of bone.
Methods
Twenty eight Wistar adjuvant-induced arthritis (AIA) rats were monitored during 22 days after disease induction for the inflammatory score, ankle perimeter and body weight. Healthy non-arthritic rats were used as controls for compar-ison. After 22 days of disease progression rats were sacrificed and bone samples were collected for histomorphometrical, energy dispersive X-ray spectroscopical analysis and 3-point bending. Blood samples were also collected for bone turnover markers.
Results
AIA rats had an increased bone turnover (as inferred from increased P1NP and CTX1, p = 0.0010 and p = 0.0002, respectively) and this was paralleled by a decreased mineral content (calcium p = 0.0046 and phos-phorus p = 0.0046). Histomorphometry showed a lower trabecular thickness (p = 0.0002) and bone volume (p = 0.0003) and higher trabecular sepa-ration (p = 0.0009) in the arthritic group as compared with controls. In addition, bone mechanical tests showed evidence of fragility as depicted by diminished values of yield stress and ultimate fracture point (p = 0.0061 and p = 0.0279, re-spectively) in the arthritic group.
Conclusions
We have shown in an AIA rat model that arthritis induc-es early bone high turnover, structural degradation, mineral loss and mechanical weak-ness.
doi:10.1371/journal.pone.0117100
PMCID: PMC4305284  PMID: 25617902
2.  Noise rich in low frequency components, a new comorbidity for periodontal disease? An experimental study 
Introduction:
Exposure to noise rich in low frequency components induces abnormal proliferation of extracellular matrix and collagens. The previous studies have shown alterations in the periodontium of both humans and animals. Our objective was the evaluation of collagens I, IV and V of the periodontium of Wistar rats exposed to noise rich in low frequency components.
Materials and Methods:
5 groups (each with 10 animals) were exposed to continuous low frequency noise (LFN). The LFN, from previously recorded white noise, frequency filtered and amplified, was applied in growing periods of 1, 3, 5, 9 and 13 weeks, in order to characterize the alterations with exposure time. A control group of ten animals was kept in silence. These animals were used in groups of 2 as aged-matched controls. After exposure, sections were obtained including teeth, alveolar bone and periodontium and observed after immunollabeling for collagens I, IV and V.
Results:
A significant increase in collagen I was observed in exposed groups (P < 0.001) (Kruskal-Wallis test). Post-hoc comparisons (Mann-Whitney test with Bonferroni correction) showed an increase in collagen I in animals exposed for 3 weeks or more (P < 0.001). The same test was applied to collagen V where significant differences were found when comparing control and exposed groups (P ≤ 0.004). The t-test for independent samples was applied to collagen type IV where no significant differences were found (P = 0.410), when comparing to the control group.
Discussion:
As in other organs, we can observe fibrosis and the newly formed collagen is likely to be “nonfunctional”, which could have clinical impact.
Conclusion:
Noise may constitute a new comorbidity for periodontal disease.
doi:10.4103/0972-124X.138729
PMCID: PMC4158595  PMID: 25210268
Fibrosis; low frequency noise; periodontal disease; periodontium
3.  Should I Stay or Should I Go? Dispersal and Population Structure in Small, Isolated Desert Populations of West African Crocodiles 
PLoS ONE  2014;9(4):e94626.
The maintenance of both spatial and genetic connectivity is paramount to the long-term persistence of small, isolated populations living in environments with extreme climates. We aim to identify the distribution of genetic diversity and assess population sub-structuring and dispersal across dwarfed desert populations of Crocodylus suchus, which occur in isolated groups, usually less than five individuals, along the mountains of Mauritania (West Africa). We used both invasive and non-invasive sampling methods and a combination of mitochondrial DNA (12 S and ND4) and microsatellite markers (32 loci and a subset of 12 loci). Our results showed high genetic differentiation and geographic structure in Mauritanian populations of C. suchus. We identified a metapopulation system acting within four river sub-basins (high gene flow and absence of genetic structure) and considerable genetic differentiation between sub-basins (FST range: 0.12–0.24) with rare dispersal events. Effective population sizes tend to be low within sub-basins while genetic diversity is maintained. Our study suggests that hydrographic networks (temporal connections along seasonal rivers during rainy periods) allow C. suchus to disperse and maintain metapopulation dynamics within sub-basins, which attenuate the loss of genetic diversity and the risk of extinction. We highlight the need of hydrographic conservation to protect vulnerable crocodiles isolated in small water bodies. We propose C. suchus as an umbrella species in Mauritania based on ecological affinities shared with other water-dependent species in desert environments.
doi:10.1371/journal.pone.0094626
PMCID: PMC3989217  PMID: 24740183
4.  Large Spatial Scale of the Phenotype-Environment Color Matching in Two Cryptic Species of African Desert Jerboas (Dipodidae: Jaculus) 
PLoS ONE  2014;9(4):e94342.
We tested the camouflage hypothesis, or the linkage between animal (Saharan rodent) and habitat coloration, on the largest geographical scale yet conducted. We aimed to determine whether phenotypic variation is explained by micro-habitat variation and/or genetic polymorphism to determine 1) the strength of linkage between fur color and local substrate color, and 2) the divergence in fur coloration between two genetic clades, representing cryptic species, throughout the complete range of the African desert jerboas (Jaculus jaculus). We used a combination of museum and field-collected specimens, remote sensing tools, satellite and digital photography and molecular genetic and phylogenetic methods to investigate the above hypotheses. Along with showing that the two divergent genetic clades of jerboas occur sympatrically throughout their African distribution, we showed significant covariation between dorsal fur coloration of the animals and the color of their habitat. We also described significant phenotypic divergence in fur color, consistent with genetic divergence between the sympatric clades. The linkage between environment and phenotype supports the idea that the selection promoting cryptic coloration is persistent in contemporary populations of jerboas, however the phenotypic divergence indicates that it has different strengths (or optima) in the two clades. The mosaic distribution of micro-habitats occupied by geographically sympatric clades suggests that it may influence both ecological and evolutionary dynamics between these two cryptic species.
doi:10.1371/journal.pone.0094342
PMCID: PMC3979769  PMID: 24714509
5.  Population Structure of the Endangered Franciscana Dolphin (Pontoporia blainvillei): Reassessing Management Units 
PLoS ONE  2014;9(1):e85633.
Franciscanas are the most endangered dolphins in the Southwestern Atlantic. Due to their coastal and estuarine habits, franciscanas suffer from extensive fisheries bycatch, as well as from habitat loss and degradation. Four Franciscana Management Areas (FMA), proposed based on biology, demography, morphology and genetic data, were incorporated into management planning and in the delineation of research efforts. We re-evaluated that proposal through the analysis of control region sequences from franciscanas throughout their distribution range (N = 162), including novel sequences from the northern limit of the species and two other previously unsampled localities in Brazil. A deep evolutionary break was observed between franciscanas from the northern and southern portions of the species distribution, indicating that they must be managed as two Evolutionarily Significant Units (ESU). Furthermore, additional FMAs should be recognised to accommodate the genetic differentiation found in each ESU. These results have immediate consequences for the conservation and management of this endangered species.
doi:10.1371/journal.pone.0085633
PMCID: PMC3908959  PMID: 24497928
6.  Trophic Relationships and Habitat Preferences of Delphinids from the Southeastern Brazilian Coast Determined by Carbon and Nitrogen Stable Isotope Composition 
PLoS ONE  2013;8(12):e82205.
To investigate the foraging habitats of delphinids in southeastern Brazil, we analyzed stable carbon (δ13C) and nitrogen (δ15N) isotopes in muscle samples of the following 10 delphinid species: Sotalia guianensis, Stenella frontalis, Tursiops truncatus, Steno bredanensis, Pseudorca crassidens, Delphinus sp., Lagenodelphis hosei, Stenella attenuata, Stenella longirostris and Grampus griseus. We also compared the δ13C and δ15N values among four populations of S. guianensis. Variation in carbon isotope results from coast to ocean indicated that there was a significant decrease in δ13C values from estuarine dolphins to oceanic species. S. guianensis from Guanabara Bay had the highest mean δ13C value, while oceanic species showed significantly lower δ13C values. The highest δ15N values were observed for P. crassidens and T. truncatus, suggesting that these species occupy the highest trophic position among the delphinids studied here. The oceanic species S. attenuata, G. griseus and L. hosei had the lowest δ15N values. Stable isotope analysis showed that the three populations of S. guianensis in coastal bays had different δ13C values, but similar δ15N results. Guiana dolphins from Sepetiba and Ilha Grande bays had different foraging habitat, with specimens from Ilha Grande showing more negative δ13C values. This study provides further information on the feeding ecology of delphinids occurring in southeastern Brazil, with evidence of distinctive foraging habitats and the occupation of different ecological niches by these species in the study area.
doi:10.1371/journal.pone.0082205
PMCID: PMC3864921  PMID: 24358155
7.  Stereotactic radiosurgery for the treatment of Glomus Jugulare Tumors 
Surgical Neurology International  2013;4(Suppl 6):S429-S435.
Background:
The glomus jugulare tumor is a slowly growing benign neoplasm originating from neural crest. There is a high morbidity associated with surgical resection of glomus jugulare. Radiosurgery play a relevant role as a therapeutic option in these tumors and its use has grown in popularity. The authors describe a retrospective series of 15 patients and reviewed the literature about the glomus jugulare tumors.
Methods:
We reviewed retrospectively the data of 15 patients treated with stereotactic linear accelerator stereotactic radiosurgery (LINAC) radiosurgery between 2006 and 2011.
Results:
The average tumor volume was 18.5 cm3. The radiation dose to the tumor margin ranged between 12 and 20 Gy. The neurological status improved in three patients and remained unchanged in 12 patients. One patient developed a transient 7th nerve palsy that improved after clinical treatment. All tumors remained stable in size on follow-up with resonance magnetic images.
Conclusions:
The radiosurgery is a safe and effective therapy for patients with glomus jugulare tumor. Despite the short follow-up period and the limited number of patients analyzed, we can infer that radiosurgery produce a tumor growth control with low morbidity, and may be used as a good option to surgical resection in selected cases.
doi:10.4103/2152-7806.121629
PMCID: PMC3858802  PMID: 24349866
Chemodectoma; glomus jugulare tumor; radiosurgery
9.  The Transcriptomics of Secondary Growth and Wood Formation in Conifers 
In the last years, forestry scientists have adapted genomics and next-generation sequencing (NGS) technologies to the search for candidate genes related to the transcriptomics of secondary growth and wood formation in several tree species. Gymnosperms, in particular, the conifers, are ecologically and economically important, namely, for the production of wood and other forestry end products. Until very recently, no whole genome sequencing of a conifer genome was available. Due to the gradual improvement of the NGS technologies and inherent bioinformatics tools, two draft assemblies of the whole genomes sequence of Picea abies and Picea glauca arose in the current year. These draft genome assemblies will bring new insights about the structure, content, and evolution of the conifer genomes. Furthermore, new directions in the forestry, breeding and research of conifers will be discussed in the following. The identification of genes associated with the xylem transcriptome and the knowledge of their regulatory mechanisms will provide less time-consuming breeding cycles and a high accuracy for the selection of traits related to wood production and quality.
doi:10.1155/2013/974324
PMCID: PMC3830773  PMID: 24288610
10.  Effects of low-frequency noise on cardiac collagen and cardiomyocyte ultrastructure: an immunohistochemical and electron microscopy study 
Introduction: Low-frequency noise (LFN) leads to the development of tissue fibrosis. We previously reported the development of myocardial and perivascular fibrosis and a reduction of cardiac connexin43 in rats, but data is lacking concerning the affected type of collagen as well as the ultrastructural myocardial modifications. Objectives: The aim of this study was to quantify cardiac collagens I and III and to evaluate myocardial ultrastructural changes in Wistar rats exposed to LFN. Methods: Two groups of rats were considered: A LFN-exposed group with 8 rats continuously submitted to LFN during 3 months and a control group with 8 rats. The hearts were sectioned and the mid-ventricular fragment was selected. After immunohistochemical evaluation, quantification of the collagens and muscle were performed using the image J software in the left ventricle, interventricular septum and right ventricle and the collagen I/muscle and collagen III/muscle ratios were calculated. Transmission electron microscopy (TEM) was used to analyze mid-ventricular samples taken from each group. Results: The collagen I/muscle and collagen III/muscle ratios increased in totum respectively 80% (p<0.001) and 57.4% (p<0.05) in LFN-exposed rats. TEM showed interstitial collagen deposits and changes in mitochondria and intercalated discs of the cardiomyocytes in LFN-exposed animals. Conclusions: LFN increases collagen I and III in the extracellular matrix and induces ultrastructural alterations in the cardiomyocytes. These new morphological data open new and promising paths for further experimental and clinical research regarding the cardiac effects of low-frequency noise.
PMCID: PMC3816801  PMID: 24228094
Low-frequency noise; collagen I and III; myocardial ultrastructure; immunohistochemistry; transmission electron microscopy
11.  An Efficient Strategy for Small-Scale Screening and Production of Archaeal Membrane Transport Proteins in Escherichia coli 
PLoS ONE  2013;8(10):e76913.
Background
Membrane proteins play a key role in many fundamental cellular processes such as transport of nutrients, sensing of environmental signals and energy transduction, and account for over 50% of all known drug targets. Despite their importance, structural and functional characterisation of membrane proteins still remains a challenge, partially due to the difficulties in recombinant expression and purification. Therefore the need for development of efficient methods for heterologous production is essential.
Methodology/Principal Findings
Fifteen integral membrane transport proteins from Archaea were selected as test targets, chosen to represent two superfamilies widespread in all organisms known as the Major Facilitator Superfamily (MFS) and the 5-Helix Inverted Repeat Transporter superfamily (5HIRT). These proteins typically have eleven to twelve predicted transmembrane helices and are putative transporters for sugar, metabolite, nucleobase, vitamin or neurotransmitter. They include a wide range of examples from the following families: Metabolite-H+-symporter; Sugar Porter; Nucleobase-Cation-Symporter-1; Nucleobase-Cation-Symporter-2; and neurotransmitter-sodium-symporter. Overproduction of transporters was evaluated with three vectors (pTTQ18, pET52b, pWarf) and two Escherichia coli strains (BL21 Star and C43 (DE3)). Thirteen transporter genes were successfully expressed; only two did not express in any of the tested vector-strain combinations. Initial trials showed that seven transporters could be purified and six of these yielded quantities of ≥ 0.4 mg per litre suitable for functional and structural studies. Size-exclusion chromatography confirmed that two purified transporters were almost homogeneous while four others were shown to be non-aggregating, indicating that they are ready for up-scale production and crystallisation trials.
Conclusions/Significance
Here, we describe an efficient strategy for heterologous production of membrane transport proteins in E. coli. Small-volume cultures (10 mL) produced sufficient amount of proteins to assess their purity and aggregation state. The methods described in this work are simple to implement and can be easily applied to many more membrane proteins.
doi:10.1371/journal.pone.0076913
PMCID: PMC3838208  PMID: 24282478
12.  Immunohistochemical evaluation of cardiac connexin43 in rats exposed to low-frequency noise 
Introduction: Low-frequency noise (LFN) leads to an abnormal proliferation of collagen and development of tissue fibrosis. It has been shown that myocardial fibrosis in association with gap junction remodeling occurs in several cardiac diseases and can be implicated in the development of ventricular tachyarrhythmias. We previously reported a strong development of myocardial fibrosis induced by LFN in rats but it is not known whether LFN induces any modification on cardiac connexin43 (Cx43). Objectives: The aim of this study was to evaluate modifications on cardiac Cx43 induced by LFN in Wistar rats. Methods: Two groups of rats were considered: A LFN-exposed group with 10 rats submitted continuously to LFN during 3 months and a control group with 8 rats. The hearts were sectioned from the ventricular apex to the atria and the mid-ventricular fragment was selected. The immunohistochemical evaluation of Cx43 was performed using the polyclonal antibody connexin-43m diluted 1:1000 overnight at 4°C. Quantifications of Cx43 and muscle were performed with the image J software and the ratio Cx43/muscle was analyzed in the left ventricle, interventricular septum and right ventricle. Results: The ratio Cx43/muscle was significantly reduced in LFN-exposed rats (p=0.001). The mean value decreased 46.2%, 22.2% and 55.6% respectively in the left ventricle (p=0.008), interventricular septum (p=0.301) and right ventricle (p=0.004). Conclusions: LFN induces modifications on cardiac Cx43 in rats. The Cx43 reduction observed in our study suggests that LFN may induce an arrhythmogenic substrate and opens a new investigational area concerning the effects of LFN on the heart.
PMCID: PMC3759495  PMID: 24040453
Low-frequency noise; connexin43; gap junction; intercalated disks; ventricular myocardium
13.  Conquering the Sahara and Arabian deserts: systematics and biogeography of Stenodactylus geckos (Reptilia: Gekkonidae) 
Background
The evolutionary history of the biota of North Africa and Arabia is inextricably tied to the complex geological and climatic evolution that gave rise to the prevalent deserts of these areas. Reptiles constitute an exemplary group in the study of the arid environments with numerous well-adapted members, while recent studies using reptiles as models have unveiled interesting biogeographical and diversification patterns. In this study, we include 207 specimens belonging to all 12 recognized species of the genus Stenodactylus. Molecular phylogenies inferred using two mitochondrial (12S rRNA and 16S rRNA) and two nuclear (c-mos and RAG-2) markers are employed to obtain a robust time-calibrated phylogeny, as the base to investigate the inter- and intraspecific relationships and to elucidate the biogeographical history of Stenodactylus, a genus with a large distribution range including the arid and hyper-arid areas of North Africa and Arabia.
Results
The phylogenetic analyses of molecular data reveal the existence of three major clades within the genus Stenodactylus, which is supported by previous studies based on morphology. Estimated divergence times between clades and sub-clades are shown to correlate with major geological events of the region, the most important of which is the opening of the Red Sea, while climatic instability in the Miocene is hypothesized to have triggered diversification. High genetic variability is observed in some species, suggesting the existence of some undescribed species. The S. petrii - S. stenurus species complex is in need of a thorough taxonomic revision. New data is presented on the distribution of the sister species S. sthenodactylus and S. mauritanicus.
Conclusions
The phylogenetic hypothesis for the genus Stenodactylus presented in this work permits the reconstruction of the biogeographical history of these common desert dwellers and confirms the importance of the opening of the Red Sea and the climatic oscillations of the Miocene as major factors in the diversification of the biota of North Africa and Arabia. Moreover, this study traces the evolution of this widely distributed and highly specialized group, investigates the patterns of its high intraspecific diversity and elucidates its systematics.
doi:10.1186/1471-2148-12-258
PMCID: PMC3582542  PMID: 23273581
Stenodactylus; Gekkonidae; Arabia; North Africa; Phylogeny; Biogeography; Desert; Red Sea
14.  Production, crystallization and preliminary X-ray analysis of CTP:inositol-1-phosphate cytidylyltransferase from Archaeoglobus fulgidus  
The expression, purification, crystallization and preliminary X-ray diffraction analysis of CTP:inositol-1-phosphate cytidylyltransferase from A. fulgidus is described.
Archaeoglobus fulgidus, a hyperthermophilic archaeon, accumulates di-myo-inositol phosphate (DIP) in response to heat stress. Recently, the pathway for biosynthesis of DIP has been elucidated in this organism and involves a bifunctional enzyme that contains two domains: CTP:inositol-1-phosphate cytidylyltransferase (IPCT) as a soluble domain and di-myo-inositol-1,3′-phosphate-1-phosphate synthase (DIPPS) as a membrane domain. Here, the expression, purification, crystallization and preliminary X-ray diffraction analysis of the IPCT domain from A. fulgidus in the apo form are reported. The crystals diffracted to 2.4 Å resolution using a synchrotron source and belonged to the orthorhombic space group P21212, with unit-cell parameters a = 154.7, b = 83.9, c = 127.7 Å.
doi:10.1107/S1744309110032677
PMCID: PMC3001648  PMID: 21045295
CTP:inositol-1-phosphate cytidylyltransferase; Archaeoglobus fulgidus; compatible solutes; CDP-inositol; di-myo-inositol phosphate
15.  Correction: Phylogenetic Status and Timescale for the Diversification of Steno and Sotalia Dolphins 
PLoS ONE  2012;7(8):10.1371/annotation/e624380d-1b9c-4134-a68d-83629fbf26e1.
doi:10.1371/annotation/e624380d-1b9c-4134-a68d-83629fbf26e1
PMCID: PMC3425628
16.  Mercury-Selenium Relationships in Liver of Guiana Dolphin: The Possible Role of Kupffer Cells in the Detoxification Process by Tiemannite Formation 
PLoS ONE  2012;7(7):e42162.
Top marine predators present high mercury concentrations in their tissues as consequence of biomagnification of the most toxic form of this metal, methylmercury (MeHg). The present study concerns mercury accumulation by Guiana dolphins (Sotalia guianensis), highlighting the selenium-mediated methylmercury detoxification process. Liver samples from 19 dolphins incidentally captured within Guanabara Bay (Rio de Janeiro State, Brazil) from 1994 to 2006 were analyzed for total mercury (THg), methylmercury (MeHg), total organic mercury (TOrgHg) and selenium (Se). X-ray microanalyses were also performed. The specimens, including from fetuses to 30-year-old dolphins, comprising 8 females and 11 males, presented high THg (0.53–132 µg/g wet wt.) and Se concentrations (0.17–74.8 µg/g wet wt.). Correlations between THg, MeHg, TOrgHg and Se were verified with age (p<0.05), as well as a high and positive correlation was observed between molar concentrations of Hg and Se (p<0.05). Negative correlations were observed between THg and the percentage of MeHg contribution to THg (p<0.05), which represents a consequence of the selenium-mediated methylmercury detoxification process. Accumulation of Se-Hg amorphous crystals in Kupffer Cells was demonstrated through ultra-structural analysis, which shows that Guiana dolphin is capable of carrying out the demethylation process via mercury selenide formation.
doi:10.1371/journal.pone.0042162
PMCID: PMC3409158  PMID: 22860072
17.  Physiological and Morphological Aspects of Aedes aegypti Developing Larvae: Effects of the Chitin Synthesis Inhibitor Novaluron 
PLoS ONE  2012;7(1):e30363.
Population control of the dengue vector mosquito, Aedes aegypti, is difficult due to many reasons, one being the development of resistance to neurotoxic insecticides employed. The biosynthesis of chitin, a major constituent of insect cuticle, is a novel target for population control. Novaluron is a benzoylphenylurea (BPU) that acts as a chitin synthesis inhibitor, already used against mosquitoes. However, information regarding BPU effects on immature mosquito stages and physiological parameters related with mosquito larval development are scarce. A set of physiological parameters were recorded in control developing larvae and novaluron was administered continuously to Ae. aegypti larvae, since early third instar. Larval instar period duration was recorded from third instar until pupation. Chitin content was measured during third and fourth instars. Fourth instars were processed histochemically at the mesothorax region, stained with hematoxylin and eosin (HE) for assessment of internal tissues, and labeled with WGA-FITC to reveal chitinized structures. In control larvae: i) there is a chitin content increase during both third and fourth instars where late third instars contain more chitin than early fourth instars; ii) thoracic organs and a continuous cuticle, closely associated with the underlying epidermis were observed; iii) chitin was continuously present throughout integument cuticle. Novaluron treatment inhibited adult emergence, induced immature mortality, altered adult sex ratio and caused delay in larval development. Moreover, novaluron: i) significantly affected chitin content during larval development; ii) induced a discontinuous and altered cuticle in some regions while epidermis was often thinner or missing; iii) rendered chitin cuticle presence discontinuous and less evident. In both control and novaluron larvae, chitin was present in the peritrophic matrix. This study showed quantitatively and qualitatively evidences of novaluron effects on Ae. aegypti larval development. To our knowledge, this is the first report describing histological alterations produced by a BPU in immature vector mosquitoes.
doi:10.1371/journal.pone.0030363
PMCID: PMC3265478  PMID: 22291942
18.  Phylogenetic Status and Timescale for the Diversification of Steno and Sotalia Dolphins 
PLoS ONE  2011;6(12):e28297.
Molecular data have provided many insights into cetacean evolution but some unsettled issues still remain. We estimated the topology and timing of cetacean evolutionary relationships using Bayesian and maximum likelihood analyses of complete mitochondrial genomes. In order to clarify the phylogenetic placement of Sotalia and Steno within the Delphinidae, we sequenced three new delphinid mitogenomes. Our analyses support three delphinid clades: one joining Steno and Sotalia (supporting the revised subfamily Stenoninae); another placing Sousa within the Delphininae; and a third, the Globicephalinae, which includes Globicephala, Feresa, Pseudorca, Peponocephala and Grampus. We also conclude that Orcinus does not belong in the Globicephalinae, but Orcaella may be part of that subfamily. Divergence dates were estimated using the relaxed molecular clock calibrated with fossil data. We hypothesise that the timing of separation of the marine and Amazonian Sotalia species (2.3 Ma) coincided with the establishment of the modern Amazon River basin.
doi:10.1371/journal.pone.0028297
PMCID: PMC3233566  PMID: 22163290
19.  Crystal Structure of Archaeoglobus fulgidus CTP:Inositol-1-Phosphate Cytidylyltransferase, a Key Enzyme for Di-myo-Inositol-Phosphate Synthesis in (Hyper)Thermophiles▿† 
Journal of Bacteriology  2011;193(9):2177-2185.
Many Archaea and Bacteria isolated from hot, marine environments accumulate di-myo-inositol-phosphate (DIP), primarily in response to heat stress. The biosynthesis of this compatible solute involves the activation of inositol to CDP-inositol via the action of a recently discovered CTP:inositol-1-phosphate cytidylyltransferase (IPCT) activity. In most cases, IPCT is part of a bifunctional enzyme comprising two domains: a cytoplasmic domain with IPCT activity and a membrane domain catalyzing the synthesis of di-myo-inositol-1,3′-phosphate-1′-phosphate from CDP-inositol and l-myo-inositol phosphate. Herein, we describe the first X-ray structure of the IPCT domain of the bifunctional enzyme from the hyperthermophilic archaeon Archaeoglobus fulgidus DSMZ 7324. The structure of the enzyme in the apo form was solved to a 1.9-Å resolution. The enzyme exhibited apparent Km values of 0.9 and 0.6 mM for inositol-1-phosphate and CTP, respectively. The optimal temperature for catalysis was in the range 90 to 95°C, and the Vmax determined at 90°C was 62.9 μmol · min−1 · mg of protein−1. The structure of IPCT is composed of a central seven-stranded mixed β-sheet, of which six β-strands are parallel, surrounded by six α-helices, a fold reminiscent of the dinucleotide-binding Rossmann fold. The enzyme shares structural homology with other pyrophosphorylases showing the canonical motif G-X-G-T-(R/S)-X4-P-K. CTP, l-myo-inositol-1-phosphate, and CDP-inositol were docked into the catalytic site, which provided insights into the binding mode and high specificity of the enzyme for CTP. This work is an important step toward the final goal of understanding the full catalytic route for DIP synthesis in the native, bifunctional enzyme.
doi:10.1128/JB.01543-10
PMCID: PMC3133074  PMID: 21378188
20.  Crocodiles in the Sahara Desert: An Update of Distribution, Habitats and Population Status for Conservation Planning in Mauritania 
PLoS ONE  2011;6(2):e14734.
Background
Relict populations of Crocodylus niloticus persist in Chad, Egypt and Mauritania. Although crocodiles were widespread throughout the Sahara until the early 20th century, increased aridity combined with human persecution led to local extinction. Knowledge on distribution, occupied habitats, population size and prey availability is scarce in most populations. This study evaluates the status of Saharan crocodiles and provides new data for Mauritania to assist conservation planning.
Methodology/Principal Findings
A series of surveys in Mauritania detected crocodile presence in 78 localities dispersed across 10 river basins and most tended to be isolated within river basins. Permanent gueltas and seasonal tâmoûrts were the most common occupied habitats. Crocodile encounters ranged from one to more than 20 individuals, but in most localities less than five crocodiles were observed. Larger numbers were observed after the rainy season and during night sampling. Crocodiles were found dead in between water points along dry river-beds suggesting the occurrence of dispersal.
Conclusion/Significance
Research priorities in Chad and Egypt should focus on quantifying population size and pressures exerted on habitats. The present study increased in by 35% the number of known crocodile localities in Mauritania. Gueltas are crucial for the persistence of mountain populations. Oscillations in water availability throughout the year and the small dimensions of gueltas affect biological traits, including activity and body size. Studies are needed to understand adaptation traits of desert populations. Molecular analyses are needed to quantify genetic variability, population sub-structuring and effective population size, and detect the occurrence of gene flow. Monitoring is needed to detect demographical and genetical trends in completely isolated populations. Crocodiles are apparently vulnerable during dispersal events. Awareness campaigns focusing on the vulnerability and relict value of crocodiles should be implemented. Classification of Mauritanian mountains as protected areas should be prioritised.
doi:10.1371/journal.pone.0014734
PMCID: PMC3045445  PMID: 21364897
21.  Homozygous Deletion Mapping in Myeloma Samples Identifies Genes and an Expression Signature Relevant to Pathogenesis and Outcome 
Purpose
Myeloma is a clonal malignancy of plasma cells. Poor prognosis risk is currently identified by clinical and cytogenetic features. However, these indicators do not capture all prognostic information. Gene expression analysis can be used to identify poor prognosis patients and this can be improved by combination with information about DNA level changes.
Experimental Design
Using SNP-based gene mapping in combination with global gene expression analysis we have identified homozygous deletions in genes and networks that are relevant to myeloma pathogenesis and outcome.
Results
We identified 170 genes with homozygous deletions and corresponding loss of expression. Deletion within the “Cell Death” network was over-represented and cases with these deletions have impaired overall survival. From further analysis of these events, we have generated an expression-based signature associated with shorter survival in 258 patients and confirmed this signature in data from 2 independent groups totalling 800 patients. We defined a gene expression signature of 97 cell death genes that reflects prognosis confirmed this in two independent data sets.
Conclusions
We developed a simple 6-gene expression signature from the 97-gene signature that can be used to identify poor prognosis myeloma in the clinical environment. The signature can form the basis of future trials aimed at improving the outcome of poor prognosis myeloma.
doi:10.1158/1078-0432.CCR-09-2831
PMCID: PMC2841345  PMID: 20215539
22.  Variation in Phenotype, Parasite Load and Male Competitive Ability across a Cryptic Hybrid Zone 
PLoS ONE  2009;4(5):e5677.
Background
Molecular genetic studies are revealing an increasing number of cryptic lineages or species, which are highly genetically divergent but apparently cannot be distinguished morphologically. This observation gives rise to three important questions: 1) have these cryptic lineages diverged in phenotypic traits that may not be obvious to humans; 2) when cryptic lineages come into secondary contact, what are the evolutionary consequences: stable co-existence, replacement, admixture or differentiation and 3) what processes influence the evolutionary dynamics of these secondary contact zones?
Methodology/Principal Findings
To address these questions, we first tested whether males of the Iberian lizard Lacerta schreiberi from two highly genetically divergent, yet morphologically cryptic lineages on either side of an east-west secondary contact could be differentiated based on detailed analysis of morphology, coloration and parasite load. Next, we tested whether these differences could be driven by pre-copulatory intra-sexual selection (male-male competition). Compared to eastern males, western males had fewer parasites, were in better body condition and were more intensely coloured. Although subtle environmental variation across the hybrid zone could explain the differences in parasite load and body condition, these were uncorrelated with colour expression, suggesting that the differences in coloration reflect heritable divergence. The lineages did not differ in their aggressive behaviour or competitive ability. However, body size, which predicted male aggressiveness, was positively correlated with the colour traits that differed between genetic backgrounds.
Conclusions/Significance
Our study confirms that these cryptic lineages differ in several aspects that are likely to influence fitness. Although there were no clear differences in male competitive ability, our results suggest a potential indirect role for intra-sexual selection. Specifically, if lizards use the colour traits that differ between genetic backgrounds to assess the size of potential rivals or mates, the resulting fitness differential favouring western males could result in net male-mediated gene flow from west to east across the current hybrid zone.
doi:10.1371/journal.pone.0005677
PMCID: PMC2682578  PMID: 19479073
23.  Water Buffaloes (Bubalus bubalis) Identified as an Important Reservoir of Shiga Toxin-Producing Escherichia coli in Brazil▿  
Applied and Environmental Microbiology  2007;73(18):5945-5948.
The presence of Shiga toxin-producing Escherichia coli (STEC) in water buffaloes is reported for the first time in South America. The prevalence of STEC ranged from 0 to 64% depending on the farm. STEC isolates exhibiting the genetic profiles stx1stx2ehxA iha saa and stx2ehxA iha saa predominated. Of the 20 distinct serotypes identified, more than 50% corresponded to serotypes associated with human diseases.
doi:10.1128/AEM.00929-07
PMCID: PMC2074925  PMID: 17644639

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