Extensive intron gain in the ancestor of placental mammals

<p>Abstract</p> <p>Background</p> <p>Genome-wide studies of intron dynamics in mammalian orthologous genes have found convincing evidence for loss of introns but very little for intron turnover. Similarly, large-scale analysis of intron dynamics in a few vertebrate genomes has identified only intron losses and no gains, indicating that intron gain is an extremely rare event in vertebrate evolution. These studies suggest that the intron-rich genomes of vertebrates do not allow intron gain. The aim of this study was to search for evidence of <it>de novo </it>intron gain in domesticated genes from an analysis of their exon/intron structures.</p> <p>Results</p> <p>A phylogenomic approach has been used to analyse all domesticated genes in mammals and chordates that originated from the coding parts of transposable elements. Gain of introns in domesticated genes has been reconstructed on well established mammalian, vertebrate and chordate phylogenies, and examined as to where and when the gain events occurred. The locations, sizes and amounts of <it>de novo </it>introns gained in the domesticated genes during the evolution of mammals and chordates has been analyzed. A significant amount of intron gain was found only in domesticated genes of placental mammals, where more than 70 cases were identified. <it>De novo </it>gained introns show clear positional bias, since they are distributed mainly in 5' UTR and coding regions, while 3' UTR introns are very rare. In the coding regions of some domesticated genes up to 8 <it>de novo </it>gained introns have been found. Intron densities in Eutheria-specific domesticated genes and in older domesticated genes that originated early in vertebrates are lower than those for normal mammalian and vertebrate genes. Surprisingly, the majority of intron gains have occurred in the ancestor of placentals.</p> <p>Conclusions</p> <p>This study provides the first evidence for numerous intron gains in the ancestor of placental mammals and demonstrates that adequate taxon sampling is crucial for reconstructing intron evolution. The findings of this comprehensive study slightly challenge the current view on the evolutionary stasis in intron dynamics during the last 100 - 200 My. Domesticated genes could constitute an excellent system on which to analyse the mechanisms of intron gain in placental mammals.</p> <p><b>Reviewers: </b>this article was reviewed by Dan Graur, Eugene V. Koonin and Jürgen Brosius.</p

Phylogenomic analysis of the cystatin superfamily in eukaryotes and prokaryotes

<p>Abstract</p> <p>Background</p> <p>The cystatin superfamily comprises cysteine protease inhibitors that play key regulatory roles in protein degradation processes. Although they have been the subject of many studies, little is known about their genesis, evolution and functional diversification. Our aim has been to obtain a comprehensive insight into their origin, distribution, diversity, evolution and classification in Eukaryota, Bacteria and Archaea.</p> <p>Results</p> <p>We have identified <it>in silico </it>the full complement of the cystatin superfamily in more than 2100 prokaryotic and eukaryotic genomes. The analysis of numerous eukaryotic genomes has provided strong evidence for the emergence of this superfamily in the ancestor of eukaryotes. The progenitor of this superfamily was most probably intracellular and lacked a signal peptide and disulfide bridges, much like the extant Giardia cystatin. A primordial gene duplication produced two ancestral eukaryotic lineages, cystatins and stefins. While stefins remain encoded by a single or a small number of genes throughout the eukaryotes, the cystatins have undergone a more complex and dynamic evolution through numerous gene and domain duplications. In the cystatin superfamily we discovered twenty vertebrate-specific and three angiosperm-specific orthologous families, indicating that functional diversification has occurred only in multicellular eukaryotes. In vertebrate orthologous families, the prevailing trends were loss of the ancestral inhibitory activity and acquisition of novel functions in innate immunity. Bacterial cystatins and stefins may be emergency inhibitors that enable survival of bacteria in the host, defending them from the host's proteolytic activity.</p> <p>Conclusion</p> <p>This study challenges the current view on the classification, origin and evolution of the cystatin superfamily and provides valuable insights into their functional diversification. The findings of this comprehensive study provide guides for future structural and evolutionary studies of the cystatin superfamily as well as of other protease inhibitors and proteases.</p

What Can Domesticated Genes Tell Us about the Intron Gain in Mammals?

Domesticated genes, originating from retroelements or from DNA-transposons, constitute an ideal system for testing the hypothesis on the absence of intron gain in mammals. Since single-copy domesticated genes originated from the intronless multicopy transposable elements, the ancestral intron state for domesticated genes is zero. A phylogenomic approach has been used to analyse all domesticated genes in mammals and chordates that originated from the coding parts of transposable elements. A significant amount of intron gain was found only in domesticated genes of placental mammals, where more than 70 cases were identified. De novo gained introns show clear positional bias, since they are distributed mainly in 5′ UTR and coding regions, while 3′ UTR introns are very rare. In the coding regions of some domesticated genes up to 8 de novo gained introns have been found. Surprisingly, the majority of intron gains have occurred in the ancestor of placental mammals. Domesticated genes could constitute an excellent system on which to analyse the mechanisms of intron gain. This paper summarizes the current understanding of intron gain in mammals

Social - emotional development of children in early childhood

Roditelji svojim postupcima utječu na socio - emotivni razvoj svoje djece. Svojim reakcijama na dječje emocije i ponašanje utječu na daljnje oblikovanje izražavanja njihovih emocija, te socijalno ponašanje. Roditeljski postupci predstavljaju određeno ponašanje koje oni koriste u usmjeravanju djece prema postizanju socijalizacijskih ciljeva.Parents with their actions affect the socio - emotional development of their children. Responding to the child's emotions and behavior they influence the further shaping of expressing their emotions, and social behavior. Parental procedures are specific behaviors that parents use in guiding children toward achieving the goals of socialization

Protection of vineyards on OPG Marinclin in Vetovo, 2015.

Kutjevačko vinogorje poznato je po cijenjena i traženim vinima visoke kvalitete. Za proizvodnju vrhunskih vina zaslužni su reljefni i klimatski čimbenici te se veliki broj ljudi upravo bavi proizvodnjom vina i vinogradarstvom. Vinograd koji je u vlasništvu obitelji Marinclin posađen je 2006. godine gdje prevladava sorta Graševina. Tijekom 2015. godine provedene su mjere zaštite vinove loze protiv bolesti i štetnika. U radu su opisani najvažniji štetnici i uzročnici bolesti vinove loze. Obiteljsko poljoprivredno gospodarstvo Marinclin provodilo je preventivnu zaštitu protiv uzročnika bolesti, a odnosila se na plamenjaču, pepelnicu, sivu plijesan. Od štetnika su se pojavile lozine grinje u slaboj populaciji i nije bilo potrebno provesti tretiranje, jer nisu ugrožavale prinos. Tijekom vegetacije vinograd je tretiran sedam puta. Od toga šest puta se tretiralo protiv plamenjače i pepelnice. Ostvaren je godišnji prinos od 12 000 t/ha.Kutjevačko vineyards a known for appreciated and sought wines of high quality. For the production of premium wines credited with relief and climatic factors and a great number people just engaged in the production of wine and viticulture. Vineyard which is owned by the family Marinclin planted in 2006, where the predominant variety is Graševina. Special measures to protect vines against fungal diseases and pests were carried out during 2015. This paper describes the most important pests and pathogens fungal diseases of the vineyard. Family farm Marinclin spent his preventive protection against fungal pathogens diseases related to the downy mildew, powdery mildew, gray mold. Pests that have appeared in vineyard were mites in poor population. During the growing season vineyard was treated seven times. Six times and vineyaed were treated against downy mildew and powdery mildew. Annual yield was 12 000 t / ha of grapes

Integration of children in firefighting

Gasilska organizacija je prostovoljna humanitarna organizacija, v katero se mladi zelo radi vključujejo in njihovo število vsako leto narašča. Vključevanje mladih v gasilsko organizacijo izboljša kvaliteto njihovega preživetega prostega časa. Mladi se najlažje učijo skozi igro, kar mentorji uspešno izkoristijo in jim pripravijo družabne igre, v katere vključijo praktična gasilska znanja. Pridobijo veliko praktičnih in uporabnih znanj, ki jih potrebujejo v vsakdanjem življenju – preventivno delo na področju varstva pred požarom in ukrepanje ob ostalih naravnih nesrečah. Tega se zavedajo tudi vrtci in številne osnovne šole, ki v svoje izobraževalno delo uspešno vključujejo dejavnosti s področja gasilstva. Mladi s prostovoljnim delovanjem v gasilskih društvih pridobijo veliko pozitivnih vzorcev. Delo v skupini izboljša njihovo vedenje, omogoči kvalitetno medsebojno sodelovanje in izboljša čut za pomoč drugemu. Pridobijo veliko novih dobrih prijateljev in to v njihovem najbolj občutljivem obdobju življenja, ko iščejo svoje mesto v družbi. K temu prispevajo tudi različna tekmovanja, kjer se mladi naučijo spoštovanja pravil in športnega obnašanja ter izboljšajo in ohranjajo gibalne sposobnosti in vzdržljivost. Poleg staršev imajo glavno vlogo pri vzgoji mladih mentorji v gasilskih društvih. Mentorji so mladim hkrati učitelji in prijatelji. Mentorji so tudi gasilci in tako so vzor mladim, ki v njih vidijo junake, ki pomagajo v najtežjih življenjskih situacijah.Firefighting organisation is a voluntary humanitarian organisation in which children love to participate, which can be seen by their growing numbers every year. Integration of youth in the firefighting organisation improves the quality of their free time. Children learn best through game, which is what mentors succesfully use by integrating practical firefighting skills into normal games. They learn many practical and useful skills, that are needed in everyday life – skills in fire prevention and course of action in case of a natural disaster. Many kindergartens and elementary schools are aware of this, which is why they also started to integrate some firefighting activities into their educational plans. Volunteering in a fire department also helps children to build their character. Having to work in a team improves their behaviour, teaches them cooperation and respect, and most important, they learn to care for others. They get to know a lot of new friends in their most sensitive period of life, when they are looking for their place in society. Different competitions teach them to respect the rules and sportsmanlike attitude. Practical exercises improve and maintain their physical abilities and endurance. In addition to parents, mentors in fire departments have the main role in upbringing the children. Mentors are not only teachers to children, but they are also their friends when they need one. Furthermore, because every mentor is also a certified firefighter, children see them as role models and heroes, who help people in their hour of need

Jugoslovanska naiva in popularna kultura

Naive art in Yugoslavia was not only an artistic phenomenon, but also a cultural and a social phenomenon that has grown into a form of popular culture. Using the example of the Trebnje Naive Artists’ Camp, it is argued that artistic creativity transcended the sphere of art and was shifted into popular culture through vigorous and large-scale production, reproduction, and commercialization of the artworks, and by a media and journalistic coverage of naive artists and the events related to naive art. However, without the support and Direction of the cultural policy of a socialist state, this would not have been possible. The term “naive art” was finally established in the 1950s and was applied to the art practiced by self-taught artists (mainly painters and less often sculptors), who often came from marginal backgrounds. Nonetheless, their talent was noticed by some art collectors, critics, and already established artists, as was the case in France or in Yugoslavia. Naive artists expressed themselves in a simplified form with figurative and narrative motifs related to their inner or outer world or local visual tradition. The masters of naive art were part of modern art and some avant-garde movements, exemplifying how no educated person from a marginal environment could attain a high aesthetic value and strong creative expression. Furthermore, after the Second World War naive art become quite popular among the general public in Europe and the rest of the world, yet this was also the time of its decline. Naive art in Yugoslavia and especially the Hlebine school may be considered the last phase in historic European naive art. After the Second World War, the Yugoslav socialist state also strove to equalize and democratize society through art by minimizing the differences between the producers and consumers of art. Such a policy led to the decentralization of culture by forming various cultural and artistic institutions and by holding cultural events and spectacles in the countryside and peripheral areas. Through these various informal ideological mechanisms, the state apparatus exercised its authority in socializing its people in the spirit of Yugoslav socialist self-management and the ideology of brotherhood and unity by joining together the producers and consumers of naive art from various ethnicities, cultures, and social classes. Unfortunately this transformed naive art at its peak of popularity into a decorative and souvenir artifact with a pastoral image and folklore motifs. The encouragement from the authorities on the one hand and the market on the other produced and reproduced simple art forms and narrative contents without a complex iconography, which were consumed uncritically and on a large scale. Consequently, this completely denied the core of naive art and resulted in its final devaluation

Evolutionary history of alpha satellite DNA repeats dispersed within human genome euchromatin

Major human alpha satellite DNA repeats are preferentially assembled within (peri)centromeric regions but are also dispersed within euchromatin in the form of clustered or short single repeat arrays. To study the evolutionary history of single euchromatic human alpha satellite repeats (ARs), we analyzed their orthologous loci across the primate genomes. The continuous insertion of euchromatic ARs throughout the evolutionary history of primates starting with the ancestors of Simiformes (45-60 Ma) and continuing up to the ancestors of Homo is revealed. Once inserted, the euchromatic ARs were stably transmitted to the descendant species, some exhibiting copy number variation, whereas their sequence divergence followed the species phylogeny. Many euchromatic ARs have sequence characteristics of (peri)centromeric alpha repeats suggesting heterochromatin as a source of dispersed euchromatic ARs. The majority of euchromatic ARs are inserted in the vicinity of other repetitive elements such as L1, Alu, and ERV or are embedded within them. Irrespective of the insertion context, each AR insertion seems to be unique and once inserted, ARs do not seem to be subsequently spread to new genomic locations. In spite of association with (retro)transposable elements, there is no indication that such elements play a role in ARs proliferation. The presence of short duplications at most of ARs insertion sites suggests site-directed recombination between homologous motifs in ARs and in the target genomic sequence, probably mediated by extrachromosomal circular DNA, as a mechanism of spreading within euchromatin

Estimating Genetic Variability in Non-Model Taxa: A General Procedure for Discriminating Sequence Errors from Actual Variation

Genetic variation is the driving force of evolution and as such is of central interest for biologists. However, inadequate discrimination of errors from true genetic variation could lead to incorrect estimates of gene copy number, population genetic parameters, phylogenetic relationships and the deposition of gene and protein sequences in databases that are not actually present in any organism. Misincorporation errors in multi-template PCR cloning methods, still commonly used for obtaining novel gene sequences in non-model species, are difficult to detect, as no previous information may be available about the number of expected copies of genes belonging to multi-gene families. However, studies employing these techniques rarely describe in any great detail how errors arising in the amplification process were detected and accounted for. Here, we estimated the rate of base misincorporation of a widely-used PCR-cloning method, using a single copy mitochondrial gene from a single individual to minimise variation in the template DNA, as 1.62×10−3 errors per site, or 9.26×10−5 per site per duplication. The distribution of errors among sequences closely matched that predicted by a binomial distribution function. The empirically estimated error rate was applied to data, obtained using the same methods, from the Phospholipase A2 toxin family from the pitviper Ovophis monticola. The distribution of differences detected closely matched the expected distribution of errors and we conclude that, when undertaking gene discovery or assessment of genetic diversity using this error-prone method, it will be informative to empirically determine the rate of base misincorporation