Origin of life

Predmet istraživanja porijekla života jest rasvjetljivanje puta koji je od jednostavnih kemijskih spojeva doveo do nastanka LUCA (last universal common ancestor) - zajedničkog pretka svih organizama. Zemlja je nastala prije oko 4.6 milijardi godina, a prvi dokazi života sežu 3.86 godina u prošlost, kada su na Zemlji još uvijek vladali reducirajući uvjeti uz obilje amonijaka, metana, dušika, ugljikova dioksida, vodika i vodene pare. Budući nije bilo kisika, nedostajao je i ozonski sloj, te je UV-zračenje u cijelom svom intenzitetu dolazilo do površine zemlje. Postoje mnoge teorije gdje je u uvjetima koje je pružala mlada Zemlja život mogao nastati: od ideja da je život došao iz svemira, preko vrućih izvora na površini zemlje do dubokomorskih hidrotermalnih izvora. Svaka od teorija ima svoj odgovor na pitanje je li prvo evoluirao metabolizam, u kojem se kasnije razvila molekula koja je mogla prenositi gensku informaciju, ili je prvo nastala molekula prenositelj genske informacije uz koju je kasnije evoluirao metabolizam. No, većina se slaže da je primarnu uloga prijenosa genske informacije vjerojatno imala RNA koja, za razliku od stabilnije DNA koja danas posjeduje tu ulogu, osim mogućnosti pohrane informacije u obliku slijeda nukleotida posjeduje i katalitičku aktivnost. Također, većina se i slaže da su za nastanak života bili izrazito bitni metalosumporni spojevi koji su imali katalitičku aktivnost, a očuvani su i danas kao dio, biokemijski vrlo bitnih, metaloproteina. Još uvijek ne znamo konačan odgovor na pitanje: „Kako je nastao život?“, ali svako novo otkriće je komadić slagalice koja daje odgovor na to pitanje.The object of origin of life research is to elucitade the pathway leading from simple chemical compounds rise to the LUCA (last universal common ancestor) - the common ancestor of all organisms. Earth was formed about 4.6 billion years ago, and the first evidence of life dates 3.86 years in the past, when the Earth was still characterized by reducing conditions with an abundance of ammonia, methane, nitrogen, carbon dioxide, hydrogen and water vapor. Since there was no oxygen, the ozone layer was also missing, and UV-radiation reached the surface of Earth in whole of its intensity. There are many theories where, in the conditions that early Earth offered, life might have originated: from the idea that life came from outer space, via the hot springs on the Earth's surface to the deep-sea hydrothermal vents. Each theory has its own answer to the question whether the metabolism is the one that evolved first and later developed a molecule that was able to carry and store genetic information, or the the molecule that carried genetic information first evolved around which later evolved metabolism. However, most agree that RNA had the primary role of storing replicable genetic information which, in contrast to the more stable DNA which now plays this role, in addition to capacity to store genetic information in the form of a sequence of nucleotides also possesses catalytic activity. As well, most agree that metallosulfuric compounds, that showed a catalytic activity and are preserved today as part of biochemically important metalloproteins were extremely important for the emergence of life. We are still not able to doubtlessly answer the question "How did life originate?", but each new discovery is part of the puzzle that gives us the answer

Origin of life

Predmet istraživanja porijekla života jest rasvjetljivanje puta koji je od jednostavnih kemijskih spojeva doveo do nastanka LUCA (last universal common ancestor) - zajedničkog pretka svih organizama. Zemlja je nastala prije oko 4.6 milijardi godina, a prvi dokazi života sežu 3.86 godina u prošlost, kada su na Zemlji još uvijek vladali reducirajući uvjeti uz obilje amonijaka, metana, dušika, ugljikova dioksida, vodika i vodene pare. Budući nije bilo kisika, nedostajao je i ozonski sloj, te je UV-zračenje u cijelom svom intenzitetu dolazilo do površine zemlje. Postoje mnoge teorije gdje je u uvjetima koje je pružala mlada Zemlja život mogao nastati: od ideja da je život došao iz svemira, preko vrućih izvora na površini zemlje do dubokomorskih hidrotermalnih izvora. Svaka od teorija ima svoj odgovor na pitanje je li prvo evoluirao metabolizam, u kojem se kasnije razvila molekula koja je mogla prenositi gensku informaciju, ili je prvo nastala molekula prenositelj genske informacije uz koju je kasnije evoluirao metabolizam. No, većina se slaže da je primarnu uloga prijenosa genske informacije vjerojatno imala RNA koja, za razliku od stabilnije DNA koja danas posjeduje tu ulogu, osim mogućnosti pohrane informacije u obliku slijeda nukleotida posjeduje i katalitičku aktivnost. Također, većina se i slaže da su za nastanak života bili izrazito bitni metalosumporni spojevi koji su imali katalitičku aktivnost, a očuvani su i danas kao dio, biokemijski vrlo bitnih, metaloproteina. Još uvijek ne znamo konačan odgovor na pitanje: „Kako je nastao život?“, ali svako novo otkriće je komadić slagalice koja daje odgovor na to pitanje.The object of origin of life research is to elucitade the pathway leading from simple chemical compounds rise to the LUCA (last universal common ancestor) - the common ancestor of all organisms. Earth was formed about 4.6 billion years ago, and the first evidence of life dates 3.86 years in the past, when the Earth was still characterized by reducing conditions with an abundance of ammonia, methane, nitrogen, carbon dioxide, hydrogen and water vapor. Since there was no oxygen, the ozone layer was also missing, and UV-radiation reached the surface of Earth in whole of its intensity. There are many theories where, in the conditions that early Earth offered, life might have originated: from the idea that life came from outer space, via the hot springs on the Earth's surface to the deep-sea hydrothermal vents. Each theory has its own answer to the question whether the metabolism is the one that evolved first and later developed a molecule that was able to carry and store genetic information, or the the molecule that carried genetic information first evolved around which later evolved metabolism. However, most agree that RNA had the primary role of storing replicable genetic information which, in contrast to the more stable DNA which now plays this role, in addition to capacity to store genetic information in the form of a sequence of nucleotides also possesses catalytic activity. As well, most agree that metallosulfuric compounds, that showed a catalytic activity and are preserved today as part of biochemically important metalloproteins were extremely important for the emergence of life. We are still not able to doubtlessly answer the question "How did life originate?", but each new discovery is part of the puzzle that gives us the answer

Origin of life

Predmet istraživanja porijekla života jest rasvjetljivanje puta koji je od jednostavnih kemijskih spojeva doveo do nastanka LUCA (last universal common ancestor) - zajedničkog pretka svih organizama. Zemlja je nastala prije oko 4.6 milijardi godina, a prvi dokazi života sežu 3.86 godina u prošlost, kada su na Zemlji još uvijek vladali reducirajući uvjeti uz obilje amonijaka, metana, dušika, ugljikova dioksida, vodika i vodene pare. Budući nije bilo kisika, nedostajao je i ozonski sloj, te je UV-zračenje u cijelom svom intenzitetu dolazilo do površine zemlje. Postoje mnoge teorije gdje je u uvjetima koje je pružala mlada Zemlja život mogao nastati: od ideja da je život došao iz svemira, preko vrućih izvora na površini zemlje do dubokomorskih hidrotermalnih izvora. Svaka od teorija ima svoj odgovor na pitanje je li prvo evoluirao metabolizam, u kojem se kasnije razvila molekula koja je mogla prenositi gensku informaciju, ili je prvo nastala molekula prenositelj genske informacije uz koju je kasnije evoluirao metabolizam. No, većina se slaže da je primarnu uloga prijenosa genske informacije vjerojatno imala RNA koja, za razliku od stabilnije DNA koja danas posjeduje tu ulogu, osim mogućnosti pohrane informacije u obliku slijeda nukleotida posjeduje i katalitičku aktivnost. Također, većina se i slaže da su za nastanak života bili izrazito bitni metalosumporni spojevi koji su imali katalitičku aktivnost, a očuvani su i danas kao dio, biokemijski vrlo bitnih, metaloproteina. Još uvijek ne znamo konačan odgovor na pitanje: „Kako je nastao život?“, ali svako novo otkriće je komadić slagalice koja daje odgovor na to pitanje.The object of origin of life research is to elucitade the pathway leading from simple chemical compounds rise to the LUCA (last universal common ancestor) - the common ancestor of all organisms. Earth was formed about 4.6 billion years ago, and the first evidence of life dates 3.86 years in the past, when the Earth was still characterized by reducing conditions with an abundance of ammonia, methane, nitrogen, carbon dioxide, hydrogen and water vapor. Since there was no oxygen, the ozone layer was also missing, and UV-radiation reached the surface of Earth in whole of its intensity. There are many theories where, in the conditions that early Earth offered, life might have originated: from the idea that life came from outer space, via the hot springs on the Earth's surface to the deep-sea hydrothermal vents. Each theory has its own answer to the question whether the metabolism is the one that evolved first and later developed a molecule that was able to carry and store genetic information, or the the molecule that carried genetic information first evolved around which later evolved metabolism. However, most agree that RNA had the primary role of storing replicable genetic information which, in contrast to the more stable DNA which now plays this role, in addition to capacity to store genetic information in the form of a sequence of nucleotides also possesses catalytic activity. As well, most agree that metallosulfuric compounds, that showed a catalytic activity and are preserved today as part of biochemically important metalloproteins were extremely important for the emergence of life. We are still not able to doubtlessly answer the question "How did life originate?", but each new discovery is part of the puzzle that gives us the answer

ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.

Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species A. sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species A. sp. Kazakhstan and several asexual lineages of A. parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality

Large-scale inference of gene gain and loss dynamics following gene duplication

Genomi eukariota kao i prokariota kontinuirano prolaze kroz procese dobivanja i gubljenja gena. Procesi dobivanja gena mogu biti: duplikacija postojećeg gena u genomu, de novo evolucija iz nekodirajućih dijelova genoma ili horizontalni transfer gena iz jednog genoma u drugi. Uobičajen pristup razotkrivanju događaja dobitka ili gubitka gena u povijestima genoma je usporedba stabla gena i stabla vrsta (tree reconciliation). Problem s postojećim algoritmima za tu svrhu je što su im rezultati uvelike ovisni o ulaznim parametrima koji su neprecizni. U ovom radu izrađen je jednostavan neparametarski algoritam za određivanje duplikacija gena, mapiranje duplikacije na odgovarajuću granu u stablu vrsta, te određivanje broja gubitaka kopija koji su uslijedili nakon te duplikacije. Prednost našeg algoritma je što su mu jedini ulazni parametri ukorijenjena stabla gena i stablo vrsta. Koristeći algoritam analizirana je dinamika dobivanja i gubljenja gena u evoluciji genoma prokariota i eukariota. Rezultati upućuju na veliku razliku frekvencije horizontalnog transfera gena u evoluciji prokariotskih i eukariotskih genoma te sveukupnu rasprostranjenost događaja duplikacije i gubljenja gena u evoluciji.Gene turnover (gene gain and loss) is ever occurring process in genomes of both eukaryotes and prokaryotes. Forms of gene gain are: duplication of an existing gene in a genome, de novo evolution from noncoding regions of a genome or horizontal gene transfer from one genome to another. Uncovering gene gain and loss events in genomes’ histories is usually done by comparing gene trees with species trees, that is, tree reconciliation. A caveat in the existing reconciliation algorithms is that their resulting inference largely depends on the input parameters set by the user which can by themselves be very error-prone. Therefore, in this thesis, we developed a simple parameter-free algorithm for inferring duplication events, mapping them on the branches a rooted species tree and inferring losses that followed the inferred duplication event. Our algorithm only assumes a rooted species tree and rooted gene trees. Developed algorithm was used to analyze genome evolution in prokaryotes and eukaryotes. Obtained results suggest differences in horizontal gene transfer rates between prokaryotic genomes evolution and eukaryotic genomes evolution and overall prevalence of duplication and loss processes

Large-scale inference of gene gain and loss dynamics following gene duplication

Genomi eukariota kao i prokariota kontinuirano prolaze kroz procese dobivanja i gubljenja gena. Procesi dobivanja gena mogu biti: duplikacija postojećeg gena u genomu, de novo evolucija iz nekodirajućih dijelova genoma ili horizontalni transfer gena iz jednog genoma u drugi. Uobičajen pristup razotkrivanju događaja dobitka ili gubitka gena u povijestima genoma je usporedba stabla gena i stabla vrsta (tree reconciliation). Problem s postojećim algoritmima za tu svrhu je što su im rezultati uvelike ovisni o ulaznim parametrima koji su neprecizni. U ovom radu izrađen je jednostavan neparametarski algoritam za određivanje duplikacija gena, mapiranje duplikacije na odgovarajuću granu u stablu vrsta, te određivanje broja gubitaka kopija koji su uslijedili nakon te duplikacije. Prednost našeg algoritma je što su mu jedini ulazni parametri ukorijenjena stabla gena i stablo vrsta. Koristeći algoritam analizirana je dinamika dobivanja i gubljenja gena u evoluciji genoma prokariota i eukariota. Rezultati upućuju na veliku razliku frekvencije horizontalnog transfera gena u evoluciji prokariotskih i eukariotskih genoma te sveukupnu rasprostranjenost događaja duplikacije i gubljenja gena u evoluciji.Gene turnover (gene gain and loss) is ever occurring process in genomes of both eukaryotes and prokaryotes. Forms of gene gain are: duplication of an existing gene in a genome, de novo evolution from noncoding regions of a genome or horizontal gene transfer from one genome to another. Uncovering gene gain and loss events in genomes’ histories is usually done by comparing gene trees with species trees, that is, tree reconciliation. A caveat in the existing reconciliation algorithms is that their resulting inference largely depends on the input parameters set by the user which can by themselves be very error-prone. Therefore, in this thesis, we developed a simple parameter-free algorithm for inferring duplication events, mapping them on the branches a rooted species tree and inferring losses that followed the inferred duplication event. Our algorithm only assumes a rooted species tree and rooted gene trees. Developed algorithm was used to analyze genome evolution in prokaryotes and eukaryotes. Obtained results suggest differences in horizontal gene transfer rates between prokaryotic genomes evolution and eukaryotic genomes evolution and overall prevalence of duplication and loss processes

Large-scale inference of gene gain and loss dynamics following gene duplication

Genomi eukariota kao i prokariota kontinuirano prolaze kroz procese dobivanja i gubljenja gena. Procesi dobivanja gena mogu biti: duplikacija postojećeg gena u genomu, de novo evolucija iz nekodirajućih dijelova genoma ili horizontalni transfer gena iz jednog genoma u drugi. Uobičajen pristup razotkrivanju događaja dobitka ili gubitka gena u povijestima genoma je usporedba stabla gena i stabla vrsta (tree reconciliation). Problem s postojećim algoritmima za tu svrhu je što su im rezultati uvelike ovisni o ulaznim parametrima koji su neprecizni. U ovom radu izrađen je jednostavan neparametarski algoritam za određivanje duplikacija gena, mapiranje duplikacije na odgovarajuću granu u stablu vrsta, te određivanje broja gubitaka kopija koji su uslijedili nakon te duplikacije. Prednost našeg algoritma je što su mu jedini ulazni parametri ukorijenjena stabla gena i stablo vrsta. Koristeći algoritam analizirana je dinamika dobivanja i gubljenja gena u evoluciji genoma prokariota i eukariota. Rezultati upućuju na veliku razliku frekvencije horizontalnog transfera gena u evoluciji prokariotskih i eukariotskih genoma te sveukupnu rasprostranjenost događaja duplikacije i gubljenja gena u evoluciji.Gene turnover (gene gain and loss) is ever occurring process in genomes of both eukaryotes and prokaryotes. Forms of gene gain are: duplication of an existing gene in a genome, de novo evolution from noncoding regions of a genome or horizontal gene transfer from one genome to another. Uncovering gene gain and loss events in genomes’ histories is usually done by comparing gene trees with species trees, that is, tree reconciliation. A caveat in the existing reconciliation algorithms is that their resulting inference largely depends on the input parameters set by the user which can by themselves be very error-prone. Therefore, in this thesis, we developed a simple parameter-free algorithm for inferring duplication events, mapping them on the branches a rooted species tree and inferring losses that followed the inferred duplication event. Our algorithm only assumes a rooted species tree and rooted gene trees. Developed algorithm was used to analyze genome evolution in prokaryotes and eukaryotes. Obtained results suggest differences in horizontal gene transfer rates between prokaryotic genomes evolution and eukaryotic genomes evolution and overall prevalence of duplication and loss processes

Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution

Differentiated X chromosomes are expected to have higher rates of adaptive divergence than autosomes, if new beneficial mutations are recessive (the “faster-X effect”), largely because these mutations are immediately exposed to selection in males. The evolution of X chromosomes after they stop recombining in males, but before they become hemizygous, has not been well explored theoretically. We use the diffusion approximation to infer substitution rates of beneficial and deleterious mutations under such a scenario. Our results show that selection is less efficient on diploid X loci than on autosomal and hemizygous X loci under a wide range of parameters. This “slower-X” effect is stronger for genes affecting primarily (or only) male fitness, and for sexually antagonistic genes. These unusual dynamics suggest that some of the peculiar features of X chromosomes, such as the differential accumulation of genes with sex-specific functions, may start arising earlier than previously appreciated

Multiplicity dependence of light (anti-)nuclei production in p–Pb collisions at sNN=5.02 TeV

The measurement of the deuteron and anti-deuteron production in the rapidity range −1 < y < 0 as a function of transverse momentum and event multiplicity in p–Pb collisions at √sNN = 5.02 TeV is presented. (Anti-)deuterons are identified via their specific energy loss dE/dx and via their time-of- flight. Their production in p–Pb collisions is compared to pp and Pb–Pb collisions and is discussed within the context of thermal and coalescence models. The ratio of integrated yields of deuterons to protons (d/p) shows a significant increase as a function of the charged-particle multiplicity of the event starting from values similar to those observed in pp collisions at low multiplicities and approaching those observed in Pb–Pb collisions at high multiplicities. The mean transverse particle momenta are extracted from the deuteron spectra and the values are similar to those obtained for p and particles. Thus, deuteron spectra do not follow mass ordering. This behaviour is in contrast to the trend observed for non-composite particles in p–Pb collisions. In addition, the production of the rare 3He and 3He nuclei has been studied. The spectrum corresponding to all non-single diffractive p-Pb collisions is obtained in the rapidity window −1 < y < 0 and the pT-integrated yield dN/dy is extracted. It is found that the yields of protons, deuterons, and 3He, normalised by the spin degeneracy factor, follow an exponential decrease with mass number

Observation of medium-induced yield enhancement and acoplanarity broadening of low-pTp_\mathrm{T} jets from measurements in pp and central Pb−-Pb collisions at sNN=5.02\sqrt{s_{\rm NN}}=5.02 TeV

International audienceThe ALICE Collaboration reports the measurement of semi-inclusive distributions of charged-particle jets recoiling from a high transverse momentum (high $p_{\rm T}$) hadron trigger in proton$-$proton and central Pb$-$Pb collisions at $\sqrt{s_{\rm NN}} = 5.02$ TeV. A data-driven statistical method is used to mitigate the large uncorrelated background in central Pb$-$Pb collisions. Recoil jet distributions are reported for jet resolution parameter $R=0.2$, 0.4, and 0.5 in the range $7 < p_{\rm T,jet} < 140$ GeV$/c$ and trigger$-$recoil jet azimuthal separation $\pi/2 < \Delta\varphi < \pi$. The measurements exhibit a marked medium-induced jet yield enhancement at low $p_{\rm T}$ and at large azimuthal deviation from $\Delta\varphi\sim\pi$. The enhancement is characterized by its dependence on $\Delta\varphi$, which has a slope that differs from zero by 4.7$\sigma$. Comparisons to model calculations incorporating different formulations of jet quenching are reported. These comparisons indicate that the observed yield enhancement arises from the response of the QGP medium to jet propagation