Codon usage in twelve species of \u3ci\u3eDrosophila\u3c/i\u3e

Background: Codon usage bias (CUB), the uneven use of synonymous codons, is a ubiquitous observation in virtually all organisms examined. The pattern of codon usage is generally similar among closely related species, but differs significantly among distantly related organisms, e.g., bacteria, yeast, and Drosophila. Several explanations for CUB have been offered and some have been supported by observations and experiments, although a thorough understanding of the evolutionary forces (random drift, mutation bias, and selection) and their relative importance remains to be determined. The recently available complete genome DNA sequences of twelve phylogenetically defined species of Drosophila offer a hitherto unprecedented opportunity to examine these problems. We report here the patterns of codon usage in the twelve species and offer insights on possible evolutionary forces involved. Results: (1) Codon usage is quite stable across 11/12 of the species: G- and especially C-ending codons are used most frequently, thus defining the preferred codons. (2) The only amino acid that changes in preferred codon is Serine with six species of the melanogaster group favoring TCC while the other species, particularly subgenus Drosophila species, favor AGC. (3) D. willistoni is an exception to these generalizations in having a shifted codon usage for seven amino acids toward A/T in the wobble position. (4) Amino acids differ in their contribution to overall CUB, Leu having the greatest and Asp the least. (5) Among two-fold degenerate amino acids, A/G ending amino acids have more selection on codon usage than T/C ending amino acids. (6) Among the different chromosome arms or elements, genes on the non-recombining element F (dot chromosome) have the least CUB, while genes on the element A (X chromosome) have the most. (7) Introns indicate that mutation bias in all species is approximately 2:1, AT:GC, the opposite of codon usage bias. (8) There is also evidence for some overall regional bias in base composition that may influence codon usage. Conclusion: Overall, these results suggest that natural selection has acted on codon usage in the genus Drosophila, at least often enough to leave a footprint of selection in modern genomes. However, there is evidence in the data that random forces (drift and mutation) have also left patterns in the data, especially in genes under weak selection for codon usage for example genes in regions of low recombination. The documentation of codon usage patterns in each of these twelve genomes also aids in ongoing annotation efforts

Codon usage in twelve species of Drosophila

<p>Abstract</p> <p>Background</p> <p>Codon usage bias (CUB), the uneven use of synonymous codons, is a ubiquitous observation in virtually all organisms examined. The pattern of codon usage is generally similar among closely related species, but differs significantly among distantly related organisms, e.g., bacteria, yeast, and <it>Drosophila</it>. Several explanations for CUB have been offered and some have been supported by observations and experiments, although a thorough understanding of the evolutionary forces (random drift, mutation bias, and selection) and their relative importance remains to be determined. The recently available complete genome DNA sequences of twelve phylogenetically defined species of <it>Drosophila</it> offer a hitherto unprecedented opportunity to examine these problems. We report here the patterns of codon usage in the twelve species and offer insights on possible evolutionary forces involved.</p> <p>Results</p> <p>(1) Codon usage is quite stable across 11/12 of the species: G- and especially C-ending codons are used most frequently, thus defining the preferred codons. (2) The only amino acid that changes in preferred codon is Serine with six species of the <it>melanogaster </it>group favoring TCC while the other species, particularly subgenus <it>Drosophila</it> species, favor AGC. (3) <it>D. willistoni </it>is an exception to these generalizations in having a shifted codon usage for seven amino acids toward A/T in the wobble position. (4) Amino acids differ in their contribution to overall CUB, Leu having the greatest and Asp the least. (5) Among two-fold degenerate amino acids, A/G ending amino acids have more selection on codon usage than T/C ending amino acids. (6) Among the different chromosome arms or elements, genes on the non-recombining element F (dot chromosome) have the least CUB, while genes on the element A (X chromosome) have the most. (7) Introns indicate that mutation bias in all species is approximately 2:1, AT:GC, the opposite of codon usage bias. (8) There is also evidence for some overall regional bias in base composition that may influence codon usage.</p> <p>Conclusion</p> <p>Overall, these results suggest that natural selection has acted on codon usage in the genus <it>Drosophila</it>, at least often enough to leave a footprint of selection in modern genomes. However, there is evidence in the data that random forces (drift and mutation) have also left patterns in the data, especially in genes under weak selection for codon usage for example genes in regions of low recombination. The documentation of codon usage patterns in each of these twelve genomes also aids in ongoing annotation efforts.</p

Genetic identification of the central nucleus and other components of the central extended amygdala in chicken during development

In mammals, the central extended amygdala shows a highly complex organization, and is essential for animal survival due to its implication in fear responses. However, many aspects of its evolution are still unknown, and this structure is especially poorly understood in birds. The aim of this study was to define the central extended amygdala in chicken, by means of a battery of region-specific transcription factors (Pax6, Islet1, Nkx2.1) and phenotypic markers that characterized these different subdivisions in mammals. Our results allowed the identification of at least six distinct subdivisions in the lateral part of the avian central extended amygdala: 1) capsular central subdivision; 2) a group of intercalated-like cell patches; 3) oval central nucleus; 4) peri-intrapeduncular (peri-INP) island field; 5) perioval zone; and 6) a rostral part of the subpallial extended amygdala. In addition, we identified three subdivisions of the laterodorsal bed nucleus of the stria terminalis (BSTLd) belonging to the medial region of the chicken central extended amygdala complex. Based on their genetic profile, cellular composition and apparent embryonic origin of the cells, we discuss the similarity of these different subdivisions of chicken with different parts of the mouse central amygdala and surrounding cell masses, including the intercalated amygdalar masses and the sublenticular part of the central extended amygdala. Most of the subdivisions include various subpopulations of cells that apparently originate in the dorsal striatal, ventral striatal, pallidal and preoptic embryonic domains, reaching their final location by either radial or tangential migrations. Similarly to mammals, the central amygdala and BSTLd of chicken project to the hypothalamus, and include different neurons expressing proenkephalin, corticotropin-releasing factor, somatostatin or tyrosine hydroxylase, which may be involved in the control of different aspects of fear/anxiety-related behavior

Chronic \u3b1-synuclein accumulation in rat hippocampus induces lewy bodies formation and specific cognitive impairments

Occurrence of Lewy bodies (LBs)/Lewy neurites (LNs) containing misfolded fibrillar a-synuclein (a-syn) is one of the pathologic hallmarks of memory impairment-linked synucleinopathies, such as Parkinson\u2019s disease (PD) and dementia with LBs (DLB). While it has been shown that brainstem LBs may contribute to motor symptoms, the neuropatho-logical substrates for cognitive symptoms are still elusive. Here, recombinant mouse a-syn fibrils were bilaterally injected in the hippocampus of female Sprague Dawley rats, which underwent behavioral testing for sensorimotor and spatial learning and memory abilities. No sensorimotor deficits affecting Morris water maze task performance were observed, nor was any reference memory disturbances detectable in injected animals. By contrast, significant impairments in working memory performance became evident at 12 months postinjection. These deficits were associated to a time-dependent increase in the levels of phosphorylated a-syn at Ser129 and in the stereologically esti-mated numbers of proteinase K (PK)-resistant a-syn aggregates within the hippocampus. Interestingly, pathologic a-syn aggregates were found in the entorhinal cortex and, by 12 months postinjection, also in the vertical limb of the diagonal band and the piriform cortices. No pathologic a-syn deposits were found within the substantia nigra (SN), the ventral tegmental area (VTA), or the striatum, nor was any loss of dopaminergic, noradrenergic, or cholinergic neurons detected in a-syn-injected animals, compared with controls. This would suggest that the behavioral impairmentsseeninthea-syn-injected animals might be determined by the long-term a-syn neuropathology, rather than by neurodegeneration per se, thus leading to the onset of working memory deficits

Talking hands: tongue motor excitability during observation of hand gestures associated with words.

Perception of speech and gestures engage common brain areas. Neural regions involved in speech perception overlap with those involved in speech production in an articulator-specific manner. Yet, it is unclear whether motor cortex also has a role in processing communicative actions like gesture and sign language. We asked whether the mere observation of hand gestures, paired and not paired with words, may result in changes in the excitability of the hand and tongue areas of motor cortex. Using single-pulse transcranial magnetic stimulation (TMS), we measured the motor excitability in tongue and hand areas of left primary motor cortex, while participants viewed video sequences of bimanual hand movements associated or not-associated with nouns. We found higher motor excitability in the tongue area during the presentation of meaningful gestures (noun-associated) as opposed to meaningless ones, while the excitability of hand motor area was not differentially affected by gesture observation. Our results let us argue that the observation of gestures associated with a word results in activation of articulatory motor network accompanying speech production

Multiple myeloma-derived exosomes are enriched of amphiregulin (AREG) and activate the epidermal growth factor pathway in the bone microenvironment leading to osteoclastogenesis

Background: Multiple myeloma (MM) is a clonal plasma cell malignancy associated with osteolytic bone disease. Recently, the role of MM-derived exosomes in the osteoclastogenesis has been demonstrated although the underlying mechanism is still unknown. Since exosomes-derived epidermal growth factor receptor ligands (EGFR) are involved in tumor-associated osteolysis, we hypothesize that the EGFR ligand amphiregulin (AREG) can be delivered by MM-derived exosomes and participate in MM-induced osteoclastogenesis. Methods: Exosomes were isolated from the conditioned medium of MM1.S cell line and from bone marrow (BM) plasma samples of MM patients. The murine cell line RAW264.7 and primary human CD14 + cells were used as osteoclast (OC) sources. Results: We found that AREG was specifically enriched in exosomes from MM samples and that exosomes-derived AREG led to the activation of EGFR in pre-OC, as showed by the increase of mRNA expression of its downstream SNAIL in both RAW264.7 and CD14 + cells. The presence of neutralizing anti-AREG monoclonal antibody (mAb) reverted this effect. Consequently, we showed that the effect of MM-derived exosomes on osteoclast differentiation was inhibited by the pre-treatment of exosomes with anti-AREG mAb. In addition, we demonstrated the ability of MM-derived AREG-enriched exosomes to be internalized into human mesenchymal stromal cells (MSCs) blocking osteoblast (OB) differentiation, increasing MM cell adhesion and the release of the pro-osteoclastogenic cytokine interleukin-8 (IL8). Accordingly, anti-AREG mAb inhibited the release of IL8 by MSCs suggesting that both direct and indirect effects are responsible for AREG-enriched exosomes involvement on MM-induced osteoclastogenesis. Conclusions: In conclusion, our data indicate that AREG is packed into MM-derived exosomes and implicated in OC differentiation through an indirect mechanism mediated by OBs

Genetic background of semen parameters in Italian Simmental bulls

The aim of this study was to estimate genetic parameters and investigate the genomic background of scrotal circumference and semen parameters in the Italian Simmental bulls. Scrotal circumference, number of normal spermatozoa, ejaculate volume, spermatozoa motility, and total spermatozoa were measured on 622 bulls, of which 603 had genotypes for 42,141 SNP. Variance components of scrotal circumference were estimated with an animal model that included the fixed effects of birth year, animal age, and measurement method, and the random effects of day of measurement and animal. In the model for the other traits, the scrotal circumference was added as a covariate to account for its influence on the semen parameters. A genome-wide association study was carried out using the ssGBLUP-approach. Heritabilities ranged from 0.07 +/- 0.05 (spermatozoa motility) to 0.50 +/- 0.14 (scrotal circumference). A total of 13 SNP passed the Bonferroni correction threshold and the number of significantly associated markers ranged from 1 (ejaculate volume and spermatozoa motility) to 5 (total spermatozoa). Genes already associated with reproduction parameters were retrieved close to the significant SNP. Results of the present study gave preliminary insights about the genetic determinism of semen quality in Italian Simmental bulls

Do experts see it in slow motion? Altered timing of action simulation uncovers domain-specific perceptual processing in expert athletes

Accurate encoding of the spatio-temporal properties of others' actions is essential for the successful implementation of daily activities and, even more, for successful sportive performance, given its role in movement coordination and action anticipation. Here we investigated whether athletes are provided with special perceptual processing of spatio-temporal properties of familiar sportive actions. Basketball and volleyball players and novices were presented with short video-clips of free basketball throws that were partially occluded ahead of realization and were asked to judge whether a subsequently presented pose was either taken from the same throw depicted in the occluded video (action identification task) or temporally congruent with the expected course of the action during the occlusion period (explicit timing task). Results showed that basketball players outperformed the other groups in detecting action compatibility when the pose depicted earlier or synchronous, but not later phases of the movement as compared to the natural course of the action during occlusion. No difference was obtained for explicit estimations of timing compatibility. This leads us to argue that the timing of simulated actions in the experts might be slower than that of perceived actions ("slow-motion" bias), allowing for more detailed representation of ongoing actions and refined prediction abilities