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Combinatorial DNA Rearrangement Facilitates the Origin of New Genes in Ciliates

Chen, Xiao; Jung, Seolkyoung; Beh, Leslie Y.; Eddy, Sean R.; Landweber, Laura F.
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Text
Publicado em 02/09/2015 Português
Programmed genome rearrangements in the unicellular eukaryote Oxytricha trifallax produce a transcriptionally active somatic nucleus from a copy of its germline nucleus during development. This process eliminates noncoding sequences that interrupt coding regions in the germline genome, and joins over 225,000 remaining DNA segments, some of which require inversion or complex permutation to build functional genes. This dynamic genomic organization permits some single DNA segments in the germline to contribute to multiple, distinct somatic genes via alternative processing. Like alternative mRNA splicing, the combinatorial assembly of DNA segments contributes to genetic variation and facilitates the evolution of new genes. In this study, we use comparative genomic analysis to demonstrate that the emergence of alternative DNA splicing is associated with the origin of new genes. Short duplications give rise to alternative gene segments that are spliced to the shared gene segments. Alternative gene segments evolve faster than shared, constitutive segments. Genes with shared segments frequently have different expression profiles, permitting functional divergence. This study reports alternative DNA splicing as a mechanism of new gene origination...

Evidence of Intense Chromosomal Shuffling during Conifer Evolution

de Miguel, Marina; Bartholomé, Jérôme; Ehrenmann, François; Murat, Florent; Moriguchi, Yoshinari; Uchiyama, Kentaro; Ueno, Saneyoshi; Tsumura, Yoshihiko; Lagraulet, Hélène; de Maria, Nuria; Cabezas, José-Antonio; Cervera, María-Teresa; Gion, Jean
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Text
Publicado em 23/09/2015 Português
Although recent advances have been gained on genome evolution in angiosperm lineages, virtually nothing is known about karyotype evolution in the other group of seed plants, the gymnosperms. Here, we used high-density gene-based linkage mapping to compare the karyotype structure of two families of conifers (the most abundant group of gymnosperms) separated around 290 Ma: Pinaceae and Cupressaceae. We propose for the first time a model based on the fusion of 20 ancestral chromosomal blocks that may have shaped the modern karyotpes of Pinaceae (with n = 12) and Cupressaceae (with n = 11). The considerable difference in modern genome organization between these two lineages contrasts strongly with the remarkable level of synteny already reported within the Pinaceae. It also suggests a convergent evolutionary mechanism of chromosomal block shuffling that has shaped the genomes of the spermatophytes.

The Dynamics of Genetic Interactions between Vibrio metoecus and Vibrio cholerae, Two Close Relatives Co-Occurring in the Environment

Orata, Fabini D.; Kirchberger, Paul C.; Méheust, Raphaël; Barlow, E. Jed; Tarr, Cheryl L.; Boucher, Yan
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Text
Publicado em 09/10/2015 Português
Vibrio metoecus is the closest relative of Vibrio cholerae, the causative agent of the potent diarrheal disease cholera. Although the pathogenic potential of this new species is yet to be studied in depth, it has been co-isolated with V. cholerae in coastal waters and found in clinical specimens in the United States. We used these two organisms to investigate the genetic interaction between closely related species in their natural environment. The genomes of 20 V. cholerae and 4 V. metoecus strains isolated from a brackish coastal pond on the US east coast, as well as 4 clinical V. metoecus strains were sequenced and compared with reference strains. Whole genome comparison shows 86–87% average nucleotide identity (ANI) in their core genes between the two species. On the other hand, the chromosomal integron, which occupies approximately 3% of their genomes, shows higher conservation in ANI between species than any other region of their genomes. The ANI of 93–94% observed in this region is not significantly greater within than between species, meaning that it does not follow species boundaries. Vibrio metoecus does not encode toxigenic V. cholerae major virulence factors, the cholera toxin and toxin-coregulated pilus. However, some of the pathogenicity islands found in pandemic V. cholerae were either present in the common ancestor it shares with V. metoecus...

Recombining without Hotspots: A Comprehensive Evolutionary Portrait of Recombination in Two Closely Related Species of Drosophila

Smukowski Heil, Caiti S.; Ellison, Chris; Dubin, Matthew; Noor, Mohamed A.F.
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Text
Publicado em 01/10/2015 Português
Meiotic recombination rate varies across the genome within and between individuals, populations, and species in virtually all taxa studied. In almost every species, this variation takes the form of discrete recombination hotspots, determined in some mammals by a protein called PRDM9. Hotspots and their determinants have a profound effect on the genomic landscape, and share certain features that extend across the tree of life. Drosophila, in contrast, are anomalous in their absence of hotspots, PRDM9, and other species-specific differences in the determination of recombination. To better understand the evolution of meiosis and general patterns of recombination across diverse taxa, we present a truly comprehensive portrait of recombination across time, combining recently published cross-based contemporary recombination estimates from each of two sister species with newly obtained linkage-disequilibrium-based historic estimates of recombination from both of these species. Using Drosophila pseudoobscura and Drosophila miranda as a model system, we compare recombination rate between species at multiple scales, and we suggest that Drosophila replicate the pattern seen in human–chimpanzee in which recombination rate is conserved at broad scales. We also find evidence of a species-wide recombination modifier(s)...

Different Ancestries of R Tailocins in Rhizospheric Pseudomonas Isolates

Ghequire, Maarten G.K.; Dillen, Yörg; Lambrichts, Ivo; Proost, Paul; Wattiez, Ruddy; De Mot, René
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Text
Publicado em 26/09/2015 Português
Bacterial genomes accommodate a variety of mobile genetic elements, including bacteriophage-related clusters that encode phage tail-like protein complexes playing a role in interactions with eukaryotic or prokaryotic cells. Such tailocins are unable to replicate inside target cells due to the lack of a phage head with associated DNA. A subset of tailocins mediate antagonistic activities with bacteriocin-like specificity. Functional characterization of bactericidal tailocins of two Pseudomonas putida rhizosphere isolates revealed not only extensive similarity with the tail assembly module of the Pseudomonas aeruginosa R-type pyocins but also differences in genomic integration site, regulatory genes, and lytic release modules. Conversely, these three features are quite similar between strains of the P. putida and Pseudomonas fluorescens clades, although phylogenetic analysis of tail genes suggests them to have evolved separately. Unlike P. aeruginosa R pyocin elements, the tailocin gene clusters of other pseudomonads frequently carry cargo genes, including bacteriocins. Compared with P. aeruginosa, the tailocin tail fiber sequences that act as specificity determinants have diverged much more extensively among the other pseudomonad species...

Introns Structure Patterns of Variation in Nucleotide Composition in Arabidopsis thaliana and Rice Protein-Coding Genes

Ressayre, Adrienne; Glémin, Sylvain; Montalent, Pierre; Serre-Giardi, Laurana; Dillmann, Christine; Joets, Johann
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Text
Publicado em 07/10/2015 Português
Plant genomes present a continuous range of variation in nucleotide composition (G + C content). In coding regions, G + C-poor species tend to have unimodal distributions of G + C content among genes within genomes and slight 5′–3′ gradients along genes. In contrast, G + C-rich species display bimodal distributions of G + C content among genes and steep 5′–3′ decreasing gradients along genes. The causes of these peculiar patterns are still poorly understood. Within two species (Arabidopsis thaliana and rice), each representative of one side of the continuum, we studied the consequences of intron presence on coding region and intron G + C content at different scales. By properly taking intron structure into account, we showed that, in both species, intron presence is associated with step changes in nucleotide, codon, and amino acid composition. This suggests that introns have a barrier effect structuring G + C content along genes and that previous continuous characterizations of the 5′–3′ gradients were artifactual. In external gene regions (located upstream first or downstream last introns), species-specific factors, such as GC-biased gene conversion, are shaping G + C content whereas in internal gene regions (surrounded by introns)...

Deciphering Genome Content and Evolutionary Relationships of Isolates from the Fungus Magnaporthe oryzae Attacking Different Host Plants

Chiapello, Hélène; Mallet, Ludovic; Guérin, Cyprien; Aguileta, Gabriela; Amselem, Joëlle; Kroj, Thomas; Ortega-Abboud, Enrique; Lebrun, Marc-Henri; Henrissat, Bernard; Gendrault, Annie; Rodolphe, François; Tharreau, Didier; Fournier, Elisabeth
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Text
Publicado em 09/10/2015 Português
Deciphering the genetic bases of pathogen adaptation to its host is a key question in ecology and evolution. To understand how the fungus Magnaporthe oryzae adapts to different plants, we sequenced eight M. oryzae isolates differing in host specificity (rice, foxtail millet, wheat, and goosegrass), and one Magnaporthe grisea isolate specific of crabgrass. Analysis of Magnaporthe genomes revealed small variation in genome sizes (39–43 Mb) and gene content (12,283–14,781 genes) between isolates. The whole set of Magnaporthe genes comprised 14,966 shared families, 63% of which included genes present in all the nine M. oryzae genomes. The evolutionary relationships among Magnaporthe isolates were inferred using 6,878 single-copy orthologs. The resulting genealogy was mostly bifurcating among the different host-specific lineages, but was reticulate inside the rice lineage. We detected traces of introgression from a nonrice genome in the rice reference 70-15 genome. Among M. oryzae isolates and host-specific lineages, the genome composition in terms of frequencies of genes putatively involved in pathogenicity (effectors, secondary metabolism, cazome) was conserved. However, 529 shared families were found only in nonrice lineages, whereas the rice lineage possessed 86 specific families absent from the nonrice genomes. Our results confirmed that the host specificity of M. oryzae isolates was associated with a divergence between lineages without major gene flow and that...

Somatotopic Representation of Location: Evidence from the Simon Effect

Medina, Jared; McCloskey, Michael; Coslett, H. Branch; Rapp, Brenda
Fonte: PubMed Publicador: PubMed
Tipo: Text
Português
Representing the locations of tactile stimulation can involve somatotopic reference frames in which locations are defined relative to a position on the skin surface, and also external reference frames which take into account stimulus position in external space. Locations in somatotopic and external reference frames can conflict in terms of left/right assignment when the hands are crossed or positioned outside of their typical hemispace. To investigate the spatial codes of the representation of both tactile stimuli and responses to touch, a Simon effect task, often used in the visual modality to examine issues of spatial reference frames, was deployed in the tactile modality. Participants performed the task with stimuli delivered to the hands with arms in crossed or uncrossed postures and responses were produced with foot pedals. Across all four experiments, participants were faster on somatotopically congruent trials (e.g., left hand stimulus, left foot response) than on somatotopically incongruent trials (left hand stimulus, right foot response) regardless of arm or leg position. However, some evidence of an externally-based Simon effect also appeared in one experiment in which arm (stimulus) and leg (response) position were both manipulated. Overall...

Insights into the structure and function of membrane-integrated processive glycosyltransferases

Bi, Yunchen; Hubbard, Caitlin; Purushotham, Pallinti; Zimmer, Jochen
Fonte: PubMed Publicador: PubMed
Tipo: Text
Português
Complex carbohydrates perform essential functions in life, including energy storage, cell signaling, protein targeting, quality control, as well as supporting cell structure and stability. Extracellular polysaccharides (EPS) represent mainly structural polymers and are found in essentially all kingdoms of life. For example, EPS are important biofilm and capsule components in bacteria, represent major constituents in cell walls of fungi, algae, arthropods and plants, and modulate the extracellular matrix in vertebrates. Different mechanisms evolved by which EPS are synthesized. Here, we review the structures and functions of membrane-integrated processive glycosyltransferases (GTs) implicated in the synthesis and secretion of chitin, alginate, hyaluronan and poly-N-acetylglucosamine (PNAG).

Bacterial genome mining of enzymatic tools for alkyne biosynthesis

Zhu, Xuejun; Su, Michael; Manickam, Kadhirvel; Zhang, Wenjun
Fonte: PubMed Publicador: PubMed
Tipo: Text
Português
The alkyne is an important functionality widely used in material science, pharmaceutical science, and chemical biology, but the importance of this functionality is contrasted by the very limited number of enzymes known to be involved in alkyne biosynthesis. We recently reported the first known carrier protein-dependent pathway for terminal alkyne formation, and in silico analysis suggested that this mechanism could be widespread in bacteria. In this paper, we screened additional homologous gene cassettes presumed to be involved in alkyne biosynthesis using both in vitro biochemical study and an E. coli-polyketide synthase (PKS) reporting system for in vivo analysis. We discovered and characterized a new terminal alkyne biosynthetic pathway comprised of TtuA, B, and C from Teredinibacter turnerae T7901. While the acyl-CoA ligase homolog (TtuA) demonstrated promiscuity in the activation and loading of medium-chain fatty acids onto the carrier protein (TtuC), the desaturase homolog (TtuB) showed stringent substrate specificity towards C10 fatty acyl moieties. In addition, TtuB was demonstrated to be a bifunctional desaturase/acetylenase that efficiently catalyzed two sequential O2-dependent dehydrogenation reactions. A novel terminal-alkyne bearing polyketide was further produced upon co-expression of ttuABC and a PKS gene in E. coli. The discovery and characterization of TtuA...

Structure and membrane remodeling activity of ESCRT-III helical polymers

McCullough, John; Clippinger, Amy K.; Talledge, Nathaniel; Skowyra, Michael L.; Saunders, Marissa G.; Naismith, Teresa V.; Colf, Leremy A.; Afonine, Pavel; Arthur, Christopher; Sundquist, Wesley I.; Hanson, Phyllis I.; Frost, Adam
Fonte: PubMed Publicador: PubMed
Tipo: Text
Português
The Endosomal Sorting Complexes Required for Transport (ESCRT) proteins mediate fundamental membrane remodeling events that require stabilizing negative membrane curvature. These include endosomal intralumenal vesicle formation, HIV budding, nuclear envelope closure and cytokinetic abscission. ESCRT-III subunits perform key roles in these processes by changing conformation and polymerizing into membrane-remodeling filaments. Here, we report the 4 Å resolution cryo-EM reconstruction of a one-start, double-stranded helical copolymer composed of two different human ESCRT-III subunits, CHMP1B and IST1. The inner strand comprises “open” CHMP1B subunits that interlock in an elaborate domain-swapped architecture, and is encircled by an outer strand of “closed” IST1 subunits. Unlike other ESCRT-III proteins, CHMP1B and IST1 polymers form external coats on positively-curved membranes in vitro and in vivo. Our analysis suggests how common ESCRT-III filament architectures could stabilize different degrees and directions of membrane curvature.

Maternal obesity during pregnancy and cardiovascular development and disease in the offspring

Gaillard, Romy
Fonte: Springer Netherlands Publicador: Springer Netherlands
Tipo: Text
Português
Maternal obesity during pregnancy is an important public health problem in Western countries. Currently, obesity prevalence rates in pregnant women are estimated to be as high as 30 %. In addition, approximately 40 % of women gain an excessive amount of weight during pregnancy in Western countries. An accumulating body of evidence suggests a long-term impact of maternal obesity and excessive weight gain during pregnancy on adiposity, cardiovascular and metabolic related health outcomes in the offspring in fetal life, childhood and adulthood. In this review, we discuss results from recent studies, potential underlying mechanisms and challenges for future epidemiological studies.

Body mass index, gestational weight gain and fatty acid concentrations during pregnancy: the Generation R Study

Vidakovic, Aleksandra Jelena; Jaddoe, Vincent W. V.; Gishti, Olta; Felix, Janine F.; Williams, Michelle A.; Hofman, Albert; Demmelmair, Hans; Koletzko, Berthold; Tiemeier, Henning; Gaillard, Romy
Fonte: Springer Netherlands Publicador: Springer Netherlands
Tipo: Text
Português
Obesity during pregnancy may be correlated with an adverse nutritional status affecting pregnancy and offspring outcomes. We examined the associations of prepregnancy body mass index and gestational weight gain with plasma fatty acid concentrations in mid-pregnancy. This study was embedded in a population-based prospective cohort study among 5636 women. We obtained prepregnancy body mass index and maximum weight gain during pregnancy by questionnaires. We measured concentrations of saturated fatty acid (SFA), monounsaturated fatty acid (MUFA), n-3 polyunsaturated fatty acid (n-3 PUFA) and n-6 polyunsaturated fatty acid (n-6 PUFA) at a median gestational age of 20.5 (95 % range 17.1–24.9) weeks. We used multivariate linear regression models. As compared to normal weight women, obese women had higher total SFA concentrations [difference: 0.10 standard deviation (SD) (95 % Confidence Interval (CI) 0, 0.19)] and lower total n-3 PUFA concentrations [difference: − 0.11 SD (95 % CI − 0.20, − 0.02)]. As compared to women with sufficient gestational weight gain, those with excessive gestational weight gain had higher SFA concentrations [difference: 0.16 SD (95 % CI 0.08, 0.25)], MUFA concentrations [difference: 0.16 SD (95 % CI 0.08...

Detection and investigation of temporal clusters of congenital anomaly in Europe: seven years of experience of the EUROCAT surveillance system

Dolk, Helen; Loane, Maria; Teljeur, Conor; Densem, James; Greenlees, Ruth; McCullough, Nichola; Morris, Joan; Nelen, Vera; Bianchi, Fabrizio; Kelly, Alan
Fonte: Springer Netherlands Publicador: Springer Netherlands
Tipo: Text
Português
Detection and investigation of congenital anomaly clusters is one part of surveillance to detect new or changing teratogenic exposures in the population. The EUROCAT (European Surveillance of Congenital Anomalies) cluster monitoring system and results are described here. Monitoring was conducted annually from 2007 to 2013 for 18 registries covering an annual birth population up to 0.5 million births. For each registry and 72 anomaly subgroups, the scan “moving window” technique was used to detect clusters in time occurring within the last 2 years based on estimated date of conception. Registries conducted preliminary investigations using a standardised protocol to determine whether there was cause for concern, and expert review was used at key points. 165 clusters were detected, a rate of 3.4 % of all 4823 cluster tests performed over 7 years, more than expected by chance. Preliminary investigations of 126 new clusters confirmed that 35 % were an unusual aggregation of cases, while 56 % were explained by data quality or diagnostic issues, and 9 % were not investigated. For confirmed clusters, the registries’ course of action was continuing monitoring. Three confirmed clusters continued to grow in size for a limited period in subsequent monitoring. This system is best suited to early detection of exposures which are sudden...

An overview of poultry industry in Pakistan

HUSSAIN, J.; RABBANI, I.; ASLAM, S.; AHMAD, H.A.
Fonte: PubMed Publicador: PubMed
Tipo: Text
Português
The poultry sector is an important and vibrant segment of agriculture in Pakistan with a significant contribution to the national GDP (1.3%). Commercial poultry production in Pakistan started in the 1960’s and has been providing a significant portion of daily proteins to the Pakistani population ever since. During its evolution the industry enjoyed promotional policies of the Government, but has faced several challenges such as disease outbreaks and retail price fluctuations. Despite its important role in the country’s economy, not a single scientific study is available on its evolutionary history. The data available in this regard are scattered and lack reliability. This review is an effort to encompass the history of the overall growth of the poultry industry in Pakistan, its present status (2012 statistics) and future directions and challenges. This article may serve as the basic source of information on Pakistan’s poultry industry achievements. It will also guide poultry experts and policy makers for developing strategic planning for further growth of the industry.

The histone demethylase KDM5 activates gene expression by recognizing chromatin context through its PHD reader motif

Liu, Xingyin; Secombe, Julie
Fonte: PubMed Publicador: PubMed
Tipo: Text
Português
KDM5 family proteins are critically important transcriptional regulators whose physiological functions in the context of a whole animal remain largely unknown. Using genome-wide gene expression and binding analyses in Drosophila adults, we demonstrate that KDM5 (Lid) is a direct regulator of genes required for mitochondrial structure and function. Significantly, this occurs independently of KDM5’s well-described JmjC domain-encoded histone demethylase activity. Instead, it requires the PHD motif of KDM5 that binds to histone H3 that is di- or trimethylated on lysine 4 (H3K4me2/3). Genome-wide, KDM5 binding overlaps with the active chromatin mark H3K4me3, and a fly strain specifically lacking H3K4me2/3 binding shows defective KDM5 promoter recruitment and gene activation. KDM5 therefore plays a central role in regulating mitochondrial function by utilizing its ability to recognize specific chromatin contexts. Importantly, KDM5-mediated regulation of mitochondrial activity is likely to play key roles in human diseases caused by dysfunction of this family of proteins.

Direct in vivo manipulation and imaging of calcium transients in neutrophils identifies a critical role for leading-edge calcium flux

Beerman, Rebecca W.; Matty, Molly A.; Au, Gina G.; Looger, Loren L.; Choudhury, Kingshuk Roy; Keller, Philipp J.; Tobin, David M.
Fonte: PubMed Publicador: PubMed
Tipo: Text
Português
Calcium signaling has long been associated with key events of immunity, including chemotaxis, phagocytosis, and activation. However, imaging and manipulation of calcium flux in motile immune cells in live animals remains challenging. Using light-sheet microscopy for in vivo calcium imaging in zebrafish, we observe characteristic patterns of calcium flux triggered by distinct events, including phagocytosis of pathogenic bacteria and migration of neutrophils toward inflammatory stimuli. In contrast to findings from ex vivo studies, we observe enriched calcium influx at the leading edge of migrating neutrophils. To directly manipulate calcium dynamics in vivo, we have developed transgenic lines with cell-specific expression of the mammalian TRPV1 channel, enabling ligand-gated, reversible and spatiotemporal control of calcium influx. We find that controlled calcium influx can function to help define the neutrophil’s leading edge. Cell-specific TRPV1 expression may have broad utility for precise control of calcium dynamics in other immune cell types and organisms.

Preventing the Androgen Receptor N/C Interaction Delays Disease Onset in a Mouse Model of SBMA

Zboray, Lori; Pluciennik, Anna; Curtis, Dana; Liu, Yuhong; Berman-Booty, Lisa D.; Orr, Christopher; Kesler, Cristina T.; Berger, Tamar; Gioeli, Daniel; Paschal, Bryce M.; Merry, Diane E.
Fonte: PubMed Publicador: PubMed
Tipo: Text
Português
Spinal and bulbar muscular atrophy (SBMA) is a neurodegenerative disease caused by a polyglutamine expansion in the androgen receptor (AR) and is associated with misfolding and aggregation of the mutant AR. We investigated the role of an interdomain interaction between the amino (N)-terminal FxxLF motif and carboxyl (C)-terminal AF-2 domain in a mouse model of SBMA. Male transgenic mice expressing polyQ-expanded AR with a mutation in the FxxLF motif (F23A) to prevent the N/C interaction displayed substantially improved motor function, compared to N/C-intact AR-expressing mice, and showed reduced pathological features of SBMA. Serine 16 phosphorylation was substantially enhanced by the F23A mutation; moreover, the protective effect of AR F23A was dependent on this phosphorylation. These results reveal an important role for the N/C interaction on disease onset in mice, and suggest that targeting AR conformation could be a therapeutic strategy for patients with SBMA.

Treatment with G-CSF reduces acute myeloid leukemia blast viability in the presence of bone marrow stroma

Nomdedeu, Meritxell; Lara-Castillo, María Carmen; Etxabe, Amaia; Cornet-Masana, Josep María; Pratcorona, Marta; Díaz-Beyá, Marina; Calvo, Xavier; Rozman, María; Costa, Dolors; Esteve, Jordi; Risueño, Ruth M.
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Text
Publicado em 21/12/2015 Português

Comparative morphology of the postpharyngeal gland in the Philanthinae (Hymenoptera, Crabronidae) and the evolution of an antimicrobial brood protection mechanism

Weiss, Katharina; Strohm, Erhard; Kaltenpoth, Martin; Herzner, Gudrun
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Text
Publicado em 21/12/2015 Português