Genome Evolution of a Tertiary Dinoflagellate Plastid

The dinoflagellates have repeatedly replaced their ancestral peridinin-plastid by plastids derived from a variety of algal lineages ranging from green algae to diatoms. Here, we have characterized the genome of a dinoflagellate plastid of tertiary origin in order to understand the evolutionary processes that have shaped the organelle since it was acquired as a symbiont cell. To address this, the genome of the haptophyte-derived plastid in Karlodinium veneficum was analyzed by Sanger sequencing of library clones and 454 pyrosequencing of plastid enriched DNA fractions. The sequences were assembled into a single contig of 143 kb, encoding 70 proteins, 3 rRNAs and a nearly full set of tRNAs. Comparative genomics revealed massive rearrangements and gene losses compared to the haptophyte plastid; only a small fraction of the gene clusters usually found in haptophytes as well as other types of plastids are present in K. veneficum. Despite the reduced number of genes, the K. veneficum plastid genome has retained a large size due to expanded intergenic regions. Some of the plastid genes are highly diverged and may be pseudogenes or subject to RNA editing. Gene losses and rearrangements are also features of the genomes of the peridinin-containing plastids, apicomplexa and Chromera, suggesting that the evolutionary processes that once shaped these plastids have occurred at multiple independent occasions over the history of the Alveolata

Genome Fragmentation Is Not Confined to the Peridinin Plastid in Dinoflagellates

When plastids are transferred between eukaryote lineages through series of endosymbiosis, their environment changes dramatically. Comparison of dinoflagellate plastids that originated from different algal groups has revealed convergent evolution, suggesting that the host environment mainly influences the evolution of the newly acquired organelle. Recently the genome from the anomalously pigmented dinoflagellate Karlodinium veneficum plastid was uncovered as a conventional chromosome. To determine if this haptophyte-derived plastid contains additional chromosomal fragments that resemble the mini-circles of the peridin-containing plastids, we have investigated its genome by in-depth sequencing using 454 pyrosequencing technology, PCR and clone library analysis. Sequence analyses show several genes with significantly higher copy numbers than present in the chromosome. These genes are most likely extrachromosomal fragments, and the ones with highest copy numbers include genes encoding the chaperone DnaK(Hsp70), the rubisco large subunit (rbcL), and two tRNAs (trnE and trnM). In addition, some photosystem genes such as psaB, psaA, psbB and psbD are overrepresented. Most of the dnaK and rbcL sequences are found as shortened or fragmented gene sequences, typically missing the 3′-terminal portion. Both dnaK and rbcL are associated with a common sequence element consisting of about 120 bp of highly conserved AT-rich sequence followed by a trnE gene, possibly serving as a control region. Decatenation assays and Southern blot analysis indicate that the extrachromosomal plastid sequences do not have the same organization or lengths as the minicircles of the peridinin dinoflagellates. The fragmentation of the haptophyte-derived plastid genome K. veneficum suggests that it is likely a sign of a host-driven process shaping the plastid genomes of dinoflagellates

Molecular evolution of cyclin proteins in animals and fungi

<p>Abstract</p> <p>Background</p> <p>The passage through the cell cycle is controlled by complexes of cyclins, the regulatory units, with cyclin-dependent kinases, the catalytic units. It is also known that cyclins form several families, which differ considerably in primary structure from one eukaryotic organism to another. Despite these lines of evidence, the relationship between the evolution of cyclins and their function is an open issue. Here we present the results of our study on the molecular evolution of A-, B-, D-, E-type cyclin proteins in animals and fungi.</p> <p>Results</p> <p>We constructed phylogenetic trees for these proteins, their ancestral sequences and analyzed patterns of amino acid replacements. The analysis of infrequently fixed atypical amino acid replacements in cyclins evidenced that accelerated evolution proceeded predominantly during paralog duplication or after it in animals and fungi and that it was related to aromorphic changes in animals. It was shown also that evolutionary flexibility of cyclin function may be provided by consequential reorganization of regions on protein surface remote from CDK binding sites in animal and fungal cyclins and by functional differentiation of paralogous cyclins formed in animal evolution.</p> <p>Conclusions</p> <p>The results suggested that changes in the number and/or nature of cyclin-binding proteins may underlie the evolutionary role of the alterations in the molecular structure of cyclins and their involvement in diverse molecular-genetic events.</p

Patterns and Consequences of Male–Infant Relationships in Wild Assamese Macaques (Macaca assamensis)

Male care for offspring is unexpected in polygynandrous mammals. Evidence from nonhuman primates, however, indicates not only the existence of stable male–immature associations in multimale–multifemale groups, but also male care in the form of protection from infanticidal attacks and conspecific harassment. Here, we investigate the relationship characteristics, dynamics, and consequences of male–immature associations in wild Assamese macaques, Macaca assamensis, at Phu Khieo Wildlife Sanctuary, Thailand, to inform hypotheses of their evolutionary origins. Female Assamese macaques reproduce seasonally and do not signal ovulation, resulting in low mating and paternity skew. However, male–immature associations are predicted by paternity, and male behavior potentially reflects paternal effort. We present focal animal data on 12 immatures followed from birth beyond weaning into their juvenile life (1188 focal hours). The distribution of composite sociality indices suggests that male–immature relationships were highly differentiated. Association patterns and the degree of differentiation remained stable from 6 mo well into the juvenile phase, suggesting that male protection extends beyond the phase of high infanticide risk. Based on Hinde indices, immatures were responsible for maintaining the relationships. The likelihood that an infant was associated with its preferred male increased if the mother was absent and if other males were present in proximity, suggesting that immatures sought protection. The presence of the preferred male did not decrease the rate of mild aggression immatures received from group members, but the stronger the relationship between an immature and a male, the more often it received agonistic support from him. Future studies will have to assess whether this agonistic support translates into improved fitness and represents true paternal care

GAS6-AS1 Overexpression Increases GIMAP6 Expression and Inhibits Lung Adenocarcinoma Progression by Sponging miR-24-3p

GAS6 antisense RNA 1 (GAS6-AS1) is a long non-coding RNA involved in hepatocellular carcinoma and gastric cancer. However, the functional role of GAS6-AS1 in lung adenocarcinoma (LUAD) remains unclear. In the present study, qRT-PCR was used to measure the levels of GAS6-AS1, GIMAP6 and miR-24-3p expression in LUAD samples and cell lines. CCK-8 and colony formation assays were used to determine cell proliferation. Cell migration and invasion were evaluated using wound healing and transwell assays, respectively. The potential interactions between molecules were assessed using RNA immunoprecipitation and luciferase reporter assays. Western blot analysis was used to quantify protein expression. The anti-tumor effect of over-expressed GAS6-AS1 on LUAD was also examined in vivo in xenograft tumor experiments. The expression of GAS6-AS1 was notably downregulated in LUAD samples and cell lines and associated with a poor prognosis. GAS6-AS1 overexpression inhibited the migration and invasion of A549 and H1650 cells. Down-expressed GAS6-AS1 acted as a sponge for miR-24-3p and down-regulated the expression of its target, GTPase IMAP Family Member 6. These findings suggested that GAS6-AS1 might represent a potential diagnostic biomarker for LUAD.</jats:p

Dynamic assessment of punctate white matter damage in premature infants based on conventional MRI and apparent diffusion coefficient value

Abstract Background The purpose of this study was to observe the distribution of punctate white matter damage (PWMD) in premature infants and the signal characteristics of conventional and diffusion weighted imaging MRI .To explore the application value of routine MRI and ADCvalue in evaluating white matter damage in premature infants. Methods A total of 218 premature infants were enrolled from the Affiliated Hospital of Qingdao University and divided into a case group (n=110) and a control group (n=108). ADC values of lesions in white matter, areas around lesions (within 5 mm) and contralateral areas of mirror images were measured. ADC values of the same areas were reexamined and measured after 5-7 weeks. ADC values were measured in normal appearing areas of the case group and control group. Results 1. A total of 390 white matter lesions were found in 110 children in the case group.324 lesions (83.1%) had a hyperintense signal in T1WI, 352 (90.3%) had a hyperintense signal in diffusion weighted imaging (DWI), 326 (83.5%) had a hyperintense signal in fluid-attenuated inversion recovery (FLAIR), and 118 (30.3%) had a low signal on T2WI. 2. The ADC value in the lesion was significantly lower than that in the surrounding area and the contralateral area, and the ADC value in the surrounding area was also lower than that in the contralateral area. At the time of reexamination, the ADC value of the lesions was still significantly lower than that of the surrounding and contralateral areas of the lesion. In the case group, the ADC values of the normal area in the bilateral centrum ovale and in the splenium of the corpus callosum were lower than those in the control group. Conclusion In the early stage, (within 7 days), DWI was the most sensitive to detecting lesions, and the detection rate of lesions on T1WI was the highest as time went on. By measuring the ADC value, we can find the damage in the surrounding area of the lesion and the damage in the normal area ，which can not be detected on a conventional MRI sequence.</jats:p