With nearly 1,100 species, the fish family Characidae represents more than half of the species of Characiformes, and is a key component of Neotropical freshwater ecosystems. The composition, ...phylogeny, and classification of Characidae is currently uncertain, despite significant efforts based on analysis of morphological and molecular data. No consensus about the monophyly of this group or its position within the order Characiformes has been reached, challenged by the fact that many key studies to date have non-overlapping taxonomic representation and focus only on subsets of this diversity.
In the present study we propose a new definition of the family Characidae and a hypothesis of relationships for the Characiformes based on phylogenetic analysis of DNA sequences of two mitochondrial and three nuclear genes (4,680 base pairs). The sequences were obtained from 211 samples representing 166 genera distributed among all 18 recognized families in the order Characiformes, all 14 recognized subfamilies in the Characidae, plus 56 of the genera so far considered incertae sedis in the Characidae. The phylogeny obtained is robust, with most lineages significantly supported by posterior probabilities in Bayesian analysis, and high bootstrap values from maximum likelihood and parsimony analyses.
A monophyletic assemblage strongly supported in all our phylogenetic analysis is herein defined as the Characidae and includes the characiform species lacking a supraorbital bone and with a derived position of the emergence of the hyoid artery from the anterior ceratohyal. To recognize this and several other monophyletic groups within characiforms we propose changes in the limits of several families to facilitate future studies in the Characiformes and particularly the Characidae. This work presents a new phylogenetic framework for a speciose and morphologically diverse group of freshwater fishes of significant ecological and evolutionary importance across the Neotropics and portions of Africa.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Recent molecular hypotheses suggest that some traditional suprageneric taxa of Characiformes require revision, as they may not constitute monophyletic groups. This is the case for the Bryconidae. ...Various studies have proposed that this family (considered a subfamily by some authors) may be composed of different genera. However, until now, no phylogenetic study of all putative genera has been conducted.
In the present study, we analyzed 27 species (46 specimens) of all currently recognized genera of the Bryconidae (ingroup) and 208 species representing all other families and most genera of the Characiformes (outgroup). Five genes were sequenced: 16SrRNA, Cytochrome b, recombination activating gene 1 and 2 and myosin heavy chain 6 cardiac muscle. The final matrix contained 4699 bp and was analyzed by maximum likelihood, maximum parsimony and Bayesian analyses. The results show that the Bryconidae, composed of Brycon, Chilobrycon, Henochilus and Salminus, is monophyletic and is the sister group of Gasteropelecidae + Triportheidae. However, the genus Brycon is polyphyletic. Fossil studies suggest that the family originated approximately 47 million years ago (Ma) and that one of the two main lineages persisted only in trans-Andean rivers, including Central American rivers, suggesting a much older origin of Mesoamerican ichthyofauna than previously accepted.
Bryconidae is composed by five main clades, including the genera Brycon, Chilobrycon, Henochilus and Salminus, but a taxonomic review of these groups is needed. Our results point to a possible ancient invasion of Central America, dating about 20.3 ± 5.0 Ma (late Oligocene--early Miocene), to explain the occurrence of Brycon in Central America.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Moenkhausia is one of the most speciose genera in Characidae, currently composed of 75 nominal species of small fishes distributed across South American hydrographic basins, primarily the Amazon and ...Guyanas. Despite the large number of described species, studies involving a substantial number of its species designed to better understand their relationships and putative monophyly are still lacking. In this study, we analysed a large number of species of Moenkhausia to test the monophyly of the genus based on the phylogenetic analysis of DNA sequences of two mitochondrial and three nuclear genes. The in‐group included 29 species of Moenkhausia, and the out‐group was composed of representatives of Characidae and other members of Characiformes. All species of Moenkhausia belong to the same clade (Clade C); however, they appear distributed in five monophyletic groups along with other different genera, which means that Moenkhausia is polyphyletic and indicates the necessity of an extensive revision of the group.
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•Gasteropelecidae is the sister group of Bryconidae.•Absence of a supraorbital bone in most gasteropelecids is an independently acquired trait related to the small size of ...them.•Results corroborate the morphology-based monophyly of Gasteropelecidae and most of the relationships among its genera.•The genera Gasteropelecus and species Carnegiella strigata are polyphyletic.
The characiform family Gasteropelecidae, the so-called freshwater hatchetfishes, is comprised of three genera and nine species found in Panama and all South American countries except Chile. Our goal was to investigate the molecular characteristics, phylogenetic relationships among the species and genera of Gasteropelecidae and phylogenetic relationships between the Gasteropelecidae family with other Characiformes. DNA fragments from two mitochondrial (16S rRNA and Cytochrome B) and three nuclear genes (Rag1, Rag2 and Myh6) were sequenced. Our results corroborate the morphology-based hypothesized monophyly of the Gasteropelecidae family and most of the relationships among its genera. However, the genus Gasteropelecus is polyphyletic because G. maculatus is placed as the sister group to all other gasteropelecids, whereas G. sternicla is more closely related to species of Carnegiella. Similarly, the species Carnegiella strigata is not monophyletic, which suggests that the family needs a taxonomic review. Moreover, the species Thoracocharax stellatus was composed by four distinct lineages suggesting the this species may represents a species complex.
With nearly 1,100 species, the fish family Characidae represents more than half of the species of Characiformes, and is a key component of Neotropical freshwater ecosystems. The composition, ...phylogeny, and classification of Characidae is currently uncertain, despite significant efforts based on analysis of morphological and molecular data. No consensus about the monophyly of this group or its position within the order Characiformes has been reached, challenged by the fact that many key studies to date have non-overlapping taxonomic representation and focus only on subsets of this diversity. In the present study we propose a new definition of the family Characidae and a hypothesis of relationships for the Characiformes based on phylogenetic analysis of DNA sequences of two mitochondrial and three nuclear genes (4,680 base pairs). The sequences were obtained from 211 samples representing 166 genera distributed among all 18 recognized families in the order Characiformes, all 14 recognized subfamilies in the Characidae, plus 56 of the genera so far considered incertae sedis in the Characidae. The phylogeny obtained is robust, with most lineages significantly supported by posterior probabilities in Bayesian analysis, and high bootstrap values from maximum likelihood and parsimony analyses. A monophyletic assemblage strongly supported in all our phylogenetic analysis is herein defined as the Characidae and includes the characiform species lacking a supraorbital bone and with a derived position of the emergence of the hyoid artery from the anterior ceratohyal. To recognize this and several other monophyletic groups within characiforms we propose changes in the limits of several families to facilitate future studies in the Characiformes and particularly the Characidae. This work presents a new phylogenetic framework for a speciose and morphologically diverse group of freshwater fishes of significant ecological and evolutionary importance across the Neotropics and portions of Africa.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Multiple myeloma is a deadly malignancy characterized by plasma cell infiltration of bones. The resulting effect is painful "punched-out" lesions where bone is eroded and filled with myeloma cells ...that suppress and replace the normal marrow components. Recently it has been shown that myeloma cells produce matrix-metalloproteinase-9 (MMP-9) and MMP-2 and that accumulation of MMP-9 protein is suppressed upon expression of the heparan sulfate proteoglycan, syndecan-1. In this review, we briefly consider the potential roles for MMPs in the pathogenesis of multiple myeloma. MMPs likely have major roles in: 1) the infiltration of bone and other tissues by the myeloma cells; 2) the osteolytic bone destruction caused by overly active osteoclasts, 3) extracellular matrix remodeling by bone marrow stromal cells; 4) promoting the invasion of the endothelial cells that form neoangiogenic blood vessels necessary to sustain tumor foci; and 5) promoting the growth of myeloma cells. Effective and safe synthetic inhibitors of MMPs are available and these may prove useful in limiting the growth and spread of myeloma cells. In addition, recent insights into the suppression of MMP-9 by syndecan-1 may suggest new strategies for treatment of myeloma.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
DNA methylation, histone modifications, and nucleosomal occupancy collaborate to cause silencing of tumor-related genes in
cancer. The development of drugs that target these processes is therefore ...important for cancer therapy. Inhibitors of DNA
methylation and histone deacetylation have been approved by the Food and Drug Administration for treatment of hematologic
malignancies. However, drugs that target other mechanisms still need to be developed. Recently, 3-deazaneplanocin A (DZNep)
was reported to selectively inhibit trimethylation of lysine 27 on histone H3 (H3K27me3) and lysine 20 on histone H4 (H4K20me3)
as well as reactivate silenced genes in cancer cells. This finding opens the door to the pharmacologic inhibition of histone
methylation. We therefore wanted to further study the mechanism of action of DZNep in cancer cells. Western blot analysis
shows that DZNep globally inhibits histone methylation and is not selective. Two other drugs, sinefungin and adenosine dialdehyde,
have similar effects as DZNep on H3K27me3. Intriguingly, chromatin immunoprecipitation of various histone modifications and
microarray analysis show that DZNep acts through a different pathway than 5-aza-2′-deoxycytidine, a DNA methyltransferase
inhibitor. These observations give us interesting insight into how chromatin structure affects gene expression. We also determined
the kinetics of gene activation to understand if the induced changes were somatically heritable. We found that upon removal
of DZNep, gene expression is reduced to its original state. This suggests that there is a homeostatic mechanism that returns
the histone modifications to their “ground state” after DZNep treatment. Our data show the strong need for further development
of histone methylation inhibitors. Mol Cancer Ther 2009;8(6):1579–88
Galactose oxidase catalyzes a two-electron oxidation, mainly from the C6 hydroxyl group of
d
-galactose, with the concomitant reduction of water to hydrogen peroxide. This enzyme is secreted by
...Fusarium
species and has several biotechnological applications. In this study, a screening of galactose oxidase production among species of the
Fusarium fujikuroi
species complex demonstrated
Fusarium subglutinans
to be the main producer. The truncated
F. subglutinans gaoA
gene coding for the mature galactose oxidase was expressed from the prokaryotic vector pTrcHis2B in the
E. coli
Rosetta™ (DE3) strain. The purified recombinant enzyme presented temperature and pH optima of 30 °C and 7.0, respectively,
K
M
of 132.6 ± 18.18 mM,
V
max
of 3.2 ± 0.18 µmol of H
2
O
2
/min,
k
cat
of 12,243 s
−1
, and a catalytic efficiency (
k
cat
/
K
M
) of 9.2 × 10
4
M
−1
s
−1
. In the presence of 50% glycerol, the enzyme showed a
T
50
of 59.77 °C and was stable for several hours at pH 8.0 and 4 °C. Besides
d
-(+)-galactose, the purified enzyme also acted against
d
-(+)-raffinose, α-
d
-(+)-melibiose, and methyl-α-
d
-galactopyranoside, and was strongly inhibited by SDS. Although the
F. subglutinans gaoA
gene was successfully expressed in
E. coli
, its endogenous transcription was not confirmed by RT-PCR.
Lysosomal phospholipase A2 (LPLA2) and lecithin:cholesterol acyltransferase (LCAT) belong to a structurally uncharacterized family of key lipid-metabolizing enzymes responsible for lung surfactant ...catabolism and for reverse cholesterol transport, respectively. Whereas LPLA2 is predicted to underlie the development of drug-induced phospholipidosis, somatic mutations in LCAT cause fish eye disease and familial LCAT deficiency. Here we describe several high-resolution crystal structures of human LPLA2 and a low-resolution structure of LCAT that confirms its close structural relationship to LPLA2. Insertions in the α/β hydrolase core of LPLA2 form domains that are responsible for membrane interaction and binding the acyl chains and head groups of phospholipid substrates. The LCAT structure suggests the molecular basis underlying human disease for most of the known LCAT missense mutations, and paves the way for rational development of new therapeutics to treat LCAT deficiency, atherosclerosis and acute coronary syndrome.
A key aspect of neuroscience research is the development of powerful, general-purpose data analyses that process large datasets. Unfortunately, modern data analyses have a hidden dependence upon ...complex computing infrastructure (e.g., software and hardware), which acts as an unaddressed deterrent to analysis users. Although existing analyses are increasingly shared as open-source software, the infrastructure and knowledge needed to deploy these analyses efficiently still pose significant barriers to use. In this work, we develop Neuroscience Cloud Analysis As a Service (NeuroCAAS): a fully automated open-source analysis platform offering automatic infrastructure reproducibility for any data analysis. We show how NeuroCAAS supports the design of simpler, more powerful data analyses and that many popular data analysis tools offered through NeuroCAAS outperform counterparts on typical infrastructure. Pairing rigorous infrastructure management with cloud resources, NeuroCAAS dramatically accelerates the dissemination and use of new data analyses for neuroscientific discovery.
•The NeuroCAAS platform provides reproducible data analysis infrastructure at scale•Reproducible, cloud-based infrastructure enables novel analysis design•Popular data analyses adapted to NeuroCAAS are faster and cheaper than alternatives
Computing infrastructure is a fundamental part of neural data analysis. Abe et al. present an open-source, cloud-based platform called NeuroCAAS to automatically build reproducible computing infrastructure for neural data analysis. They show that NeuroCAAS supports novel analysis design and can improve the efficiency of popular existing methods.
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