DNA-polymerase: mechanisms of replication fidelity

DNA-polimeraze su kompleksni, multikomponentni enzimi koji kataliziraju reakciju sinteze DNA. One postižu brzine sinteze koje su sukladne fiziološkoj brzini rasta, a uz to postižu relativno visoke stope vjernosti replikacije. Cilj ovog seminara je bio objasniti kako DNA-polimeraze to postižu. Pokazalo se da ovi enzimi to postižu korištenjem različitih domena za polimerizaciju i korekciju, s antagonističkim katalitičkim funkcijama. Možemo izvući općeniti zaključak da su za visoku vjernost sinteze DNA odgovorni komplementarnost baza, inducirano pristajanje i 3’-5’ egzonukleazna aktivnost. Prvo, imamo početnu selekciju pravilnih parova baza na temelju geometrije. Zatim, vezanjem odgovarajućeg nukleotida nastaje konformacijska promjena koja pruža steričku provjeru geometrije para baza, nakon čega slijedi brza ugradnja nukleotida u rastući polimer. Ugradnjom krive baze dolazi do inhibicije ove konformacijske promjene kao i inhibicije polimerizacije, čime se omogućuje prebacivanje novosintetiziranog lanca u mjesto za popravljanje gdje se 3’-5’ egzonukleaznom aktivnošću odstranjuje krivo ugrađena baza. Sveukupna vjernost replikacije dolazi i do vrijednosti od jedne greške na 1010 ugrađenih nukleotida, što je kombinacija selektivnosti u polimerizaciji (105-106) i korektivnoj aktivnosti (103-106). Također, uz polimeraze koje postižu visoku vjernost replikacije imamo i one koje nisu toliko vjerne, ali ni specifične, te su stoga pogodne za replikaciju oštećenih molekula DNA, koju ne mogu provoditi obične DNA-polimeraze. Potrebno je napomenuti da nijedna DNA-polimeraza ne djeluje sama. Replikacija DNA uključuje ogromne komplekse DNA-polimeraza sa mnoštvom pomoćnih proteina koji na razne načine utječu na njenu procesivnost i efikasnost. Budući da kompleksnost polimerizacijskih reakcija in vitro nije ni približna onima u stanici, preostaju nam mnoga istraživanja koja će nam dati jasniju i detaljniju sliku kako zapravo stanice repliciraju svoj genom.DNA-polymerases are complex, multidomain enzymes that catalyze reactions of DNA replication. They achieve rates of synthesis that support physiological growth rates and yet preserve relatively high fidelity. The goal of this seminar was to explain how do they manage to do that. It has been shown that they achieve that by using distinct domains for polymerization and for proofreading, with antagonistic catalytic functions. We can draw general conclusion that high fidelity synthesis of DNA are driven by several factors: complementary base pairing, induced fit and 3’-5’ exonuclease activity. Firsty, initial selection of correct base pair is achieved on the basis of geometry. Then, binding of the correct nucleotide induces conformational change, which provides steric check for the proper base pair geometry, followed by a rapid incorporation of nucleotide into the growing polymer. Mismatch inhibits this conformational change as well as polymerization, allowing the transfer of newly synthesized chain into editing site, where the incorrect base is removed by 3’-5’ exonuclease. The overall fidelity approaches one error in 1010 by a combination of selectivity in polymerization (105-106) and in proofreading (103-104). Also, beside the high fidelity polymerases there are low fidelity ones, which are not so specific, and are therefore suitable for the replication of damaged DNA molecules, which can not be carried out by normal DNA-polymerases. It is necessary to note that no DNA-polymerase works alone. DNA replication involves huge complexes of DNA-polymerases with multitude accessory proteins, which in many ways affect its processivity and efficiency. Since the complexity of polymerization reactions in vitro does not even approximate those in the cell, many research remains to be done that will give us a clearer and more detailed picture of how do cells replicate their own genome

Scholarly reference trees

In this paper, we propose, explain and implement bibliometric data analysis and visualization model in a web environment. We use NLP syntactic grammars for pattern recognition of references used in scholarly publications. The extracted information is used for visualizing author egocentric data via tree like structure. The ultimate goal of this work is to use the egocentric trees for comparisons of two authors and to build networks or forests of different trees depending on the forest’s attributes. We have stumbled upon many different problems ranging from exceptions in citation style structures to optimization of visualization model in order to achieve an optimal user experience. We will give a summary of our grammars’ restrictions and will provide some ideas for possible future work that could improve the overall user experience. The proposed trees can function by themselves, or they can be implemented in digital repositories of libraries and different types of citation databases

Building Scholarly Data Forest

In this paper, we will demonstrate syntactic analysis and visualization of scientific data, namely references from scientific papers. Our main goal is to build a parser which could extract references from scientific papers, convert them to XML format, send to custom visualization algorithm and present in a web interface as a ReferenceTree for a single author. For this process, we use several different technologies such as NLP software NooJ, programming languages PHP and JavaScript in combination with HTML5. Our main problem was dissimilarity in reference styles between articles. Thus, our parser was designed to recognize different reference source (book, paper, web page) in APA, MLA and Chicago reference styles. As for the visualization idea, we have chosen the concept of presenting an author as a tree, the publication years as the main branches, the articles/books as twigs and references used in each article/book as the leaves. The books are grouped on the left side of the tree while the articles are grouped on the right side. With final output, every processed author should have a unique tree (preferences of references) and could be compared with the rest of the scientific forest

DNA-polymerase: mechanisms of replication fidelity

DNA-polimeraze su kompleksni, multikomponentni enzimi koji kataliziraju reakciju sinteze DNA. One postižu brzine sinteze koje su sukladne fiziološkoj brzini rasta, a uz to postižu relativno visoke stope vjernosti replikacije. Cilj ovog seminara je bio objasniti kako DNA-polimeraze to postižu. Pokazalo se da ovi enzimi to postižu korištenjem različitih domena za polimerizaciju i korekciju, s antagonističkim katalitičkim funkcijama. Možemo izvući općeniti zaključak da su za visoku vjernost sinteze DNA odgovorni komplementarnost baza, inducirano pristajanje i 3’-5’ egzonukleazna aktivnost. Prvo, imamo početnu selekciju pravilnih parova baza na temelju geometrije. Zatim, vezanjem odgovarajućeg nukleotida nastaje konformacijska promjena koja pruža steričku provjeru geometrije para baza, nakon čega slijedi brza ugradnja nukleotida u rastući polimer. Ugradnjom krive baze dolazi do inhibicije ove konformacijske promjene kao i inhibicije polimerizacije, čime se omogućuje prebacivanje novosintetiziranog lanca u mjesto za popravljanje gdje se 3’-5’ egzonukleaznom aktivnošću odstranjuje krivo ugrađena baza. Sveukupna vjernost replikacije dolazi i do vrijednosti od jedne greške na 1010 ugrađenih nukleotida, što je kombinacija selektivnosti u polimerizaciji (105-106) i korektivnoj aktivnosti (103-106). Također, uz polimeraze koje postižu visoku vjernost replikacije imamo i one koje nisu toliko vjerne, ali ni specifične, te su stoga pogodne za replikaciju oštećenih molekula DNA, koju ne mogu provoditi obične DNA-polimeraze. Potrebno je napomenuti da nijedna DNA-polimeraza ne djeluje sama. Replikacija DNA uključuje ogromne komplekse DNA-polimeraza sa mnoštvom pomoćnih proteina koji na razne načine utječu na njenu procesivnost i efikasnost. Budući da kompleksnost polimerizacijskih reakcija in vitro nije ni približna onima u stanici, preostaju nam mnoga istraživanja koja će nam dati jasniju i detaljniju sliku kako zapravo stanice repliciraju svoj genom.DNA-polymerases are complex, multidomain enzymes that catalyze reactions of DNA replication. They achieve rates of synthesis that support physiological growth rates and yet preserve relatively high fidelity. The goal of this seminar was to explain how do they manage to do that. It has been shown that they achieve that by using distinct domains for polymerization and for proofreading, with antagonistic catalytic functions. We can draw general conclusion that high fidelity synthesis of DNA are driven by several factors: complementary base pairing, induced fit and 3’-5’ exonuclease activity. Firsty, initial selection of correct base pair is achieved on the basis of geometry. Then, binding of the correct nucleotide induces conformational change, which provides steric check for the proper base pair geometry, followed by a rapid incorporation of nucleotide into the growing polymer. Mismatch inhibits this conformational change as well as polymerization, allowing the transfer of newly synthesized chain into editing site, where the incorrect base is removed by 3’-5’ exonuclease. The overall fidelity approaches one error in 1010 by a combination of selectivity in polymerization (105-106) and in proofreading (103-104). Also, beside the high fidelity polymerases there are low fidelity ones, which are not so specific, and are therefore suitable for the replication of damaged DNA molecules, which can not be carried out by normal DNA-polymerases. It is necessary to note that no DNA-polymerase works alone. DNA replication involves huge complexes of DNA-polymerases with multitude accessory proteins, which in many ways affect its processivity and efficiency. Since the complexity of polymerization reactions in vitro does not even approximate those in the cell, many research remains to be done that will give us a clearer and more detailed picture of how do cells replicate their own genome

DNA-polymerase: mechanisms of replication fidelity

DNA-polimeraze su kompleksni, multikomponentni enzimi koji kataliziraju reakciju sinteze DNA. One postižu brzine sinteze koje su sukladne fiziološkoj brzini rasta, a uz to postižu relativno visoke stope vjernosti replikacije. Cilj ovog seminara je bio objasniti kako DNA-polimeraze to postižu. Pokazalo se da ovi enzimi to postižu korištenjem različitih domena za polimerizaciju i korekciju, s antagonističkim katalitičkim funkcijama. Možemo izvući općeniti zaključak da su za visoku vjernost sinteze DNA odgovorni komplementarnost baza, inducirano pristajanje i 3’-5’ egzonukleazna aktivnost. Prvo, imamo početnu selekciju pravilnih parova baza na temelju geometrije. Zatim, vezanjem odgovarajućeg nukleotida nastaje konformacijska promjena koja pruža steričku provjeru geometrije para baza, nakon čega slijedi brza ugradnja nukleotida u rastući polimer. Ugradnjom krive baze dolazi do inhibicije ove konformacijske promjene kao i inhibicije polimerizacije, čime se omogućuje prebacivanje novosintetiziranog lanca u mjesto za popravljanje gdje se 3’-5’ egzonukleaznom aktivnošću odstranjuje krivo ugrađena baza. Sveukupna vjernost replikacije dolazi i do vrijednosti od jedne greške na 1010 ugrađenih nukleotida, što je kombinacija selektivnosti u polimerizaciji (105-106) i korektivnoj aktivnosti (103-106). Također, uz polimeraze koje postižu visoku vjernost replikacije imamo i one koje nisu toliko vjerne, ali ni specifične, te su stoga pogodne za replikaciju oštećenih molekula DNA, koju ne mogu provoditi obične DNA-polimeraze. Potrebno je napomenuti da nijedna DNA-polimeraza ne djeluje sama. Replikacija DNA uključuje ogromne komplekse DNA-polimeraza sa mnoštvom pomoćnih proteina koji na razne načine utječu na njenu procesivnost i efikasnost. Budući da kompleksnost polimerizacijskih reakcija in vitro nije ni približna onima u stanici, preostaju nam mnoga istraživanja koja će nam dati jasniju i detaljniju sliku kako zapravo stanice repliciraju svoj genom.DNA-polymerases are complex, multidomain enzymes that catalyze reactions of DNA replication. They achieve rates of synthesis that support physiological growth rates and yet preserve relatively high fidelity. The goal of this seminar was to explain how do they manage to do that. It has been shown that they achieve that by using distinct domains for polymerization and for proofreading, with antagonistic catalytic functions. We can draw general conclusion that high fidelity synthesis of DNA are driven by several factors: complementary base pairing, induced fit and 3’-5’ exonuclease activity. Firsty, initial selection of correct base pair is achieved on the basis of geometry. Then, binding of the correct nucleotide induces conformational change, which provides steric check for the proper base pair geometry, followed by a rapid incorporation of nucleotide into the growing polymer. Mismatch inhibits this conformational change as well as polymerization, allowing the transfer of newly synthesized chain into editing site, where the incorrect base is removed by 3’-5’ exonuclease. The overall fidelity approaches one error in 1010 by a combination of selectivity in polymerization (105-106) and in proofreading (103-104). Also, beside the high fidelity polymerases there are low fidelity ones, which are not so specific, and are therefore suitable for the replication of damaged DNA molecules, which can not be carried out by normal DNA-polymerases. It is necessary to note that no DNA-polymerase works alone. DNA replication involves huge complexes of DNA-polymerases with multitude accessory proteins, which in many ways affect its processivity and efficiency. Since the complexity of polymerization reactions in vitro does not even approximate those in the cell, many research remains to be done that will give us a clearer and more detailed picture of how do cells replicate their own genome

EDictionary: the Good, the Bad and the Ugly

On its own, learning a new language is an inherently daunting task. Combined with lacking or simply non-existent language resources, the task itself seems almost impossible. For some languages, this scarcity of available resources is even more obvious and further complicates the issue. With an interdisciplinary approach, a team of linguists, language teachers, information scientists, and students themselves undertook a task of developing a learner’s dictionary of Asian languages. With a great deal of care and discussion, an online e-dictionary was chosen as a platform for its ease of use, accessibility, and expandability, in lieu of a traditional printed dictionary. Since eDictionary is built as a website, it is established as a platform, agnostic and available to everyone with Internet access. Furthermore, such a design allows a link to resources hosted on other web portals. To that end, cooperation was initiated with Croatian Language Portal and their Croatian dictionary with the aim of hyperlinking all of our Croatian lemmas to their word definitions. With the added benefits of giving users the ability to request new resources while keeping track of the request internally and allowing the updates of the whole language database seamlessly, the proposed solution to eDictionary provides user engagement and continuous integration that should benefit us all

False-Positive Result of a Confirmatory Human Immunodeficiency Virus Line Immuno Assay in an Apparently Healthy Individual – A Case Report

A case of a false-positive result of human immunodeficiency virus (HIV) confirmatory immunoblot-based assay is described. Repeatedly borderline reactive anti-HIV screening enzyme immunoassay result obtained in a local hospital resulted in directing the sample to the Slovenian HIV/AIDS Reference Laboratory. In the Reference Laboratory, both anti- HIV screening assays and confirmatory Western blot were negative, while a confirmatory test INNO-LIA HIV I/II Score (Innogenetics, Ghent, Belgium) was anti-HIV-1 positive due to sgp120 and gp41 reactivity. The results of serological testing of the second sample obtained three weeks later were completely identical, while in the third sample obtained 5 months later, seroreversion was observed. Due to a negative dynamics in anti-HIV serological profile and repeatedly negative results of the molecular tests for HIV-1 and HIV-2, HIV infection was excluded and the results of test INNO-LIA HIV I/II Score were finally interpreted as false positive

Vertex elimination orderings for hereditary graph classes

We provide a general method to prove the existence and compute efficiently elimination orderings in graphs. Our method relies on several tools that were known before, but that were not put together so far: the algorithm LexBFS due to Rose, Tarjan and Lueker, one of its properties discovered by Berry and Bordat, and a local decomposition property of graphs discovered by Maffray, Trotignon and Vu\vskovi\'c. We use this method to prove the existence of elimination orderings in several classes of graphs, and to compute them in linear time. Some of the classes have already been studied, namely even-hole-free graphs, square-theta-free Berge graphs, universally signable graphs and wheel-free graphs. Some other classes are new. It turns out that all the classes that we study in this paper can be defined by excluding some of the so-called Truemper configurations. For several classes of graphs, we obtain directly bounds on the chromatic number, or fast algorithms for the maximum clique problem or the coloring problem

Clique cutsets beyond chordal graphs

Truemper configurations (thetas, pyramids, prisms, and wheels) have played an important role in the study of complex hereditary graph classes (e.g. the class of perfect graphs and the class of even-hole-free graphs), appearing both as excluded configurations, and as configurations around which graphs can be decomposed. In this paper, we study the structure of graphs that contain (as induced subgraphs) no Truemper configurations other than (possibly) universal wheels and twin wheels. We also study several subclasses of this class. We use our structural results to analyze the complexity of the recognition, maximum weight clique, maximum weight stable set, and optimal vertex coloring problems for these classes. We also obtain polynomial χ-bounding functions for these classes

The impact of sleep deprivation and nighttime light exposure on clock gene expression in humans

Aim To examine the effect of acute sleep deprivation under light conditions on the expression of two key clock genes, hPer2 and hBmal1, in peripheral blood mononuclear cells (PBMC) and on plasma melatonin and cortisol levels. Methods Blood samples were drawn from 6 healthy individuals at 4-hour intervals for three consecutive nights, including a night of total sleep deprivation (second night). The study was conducted in April-June 2006 at the University Medical Centre Ljubljana. Results We found a significant diurnal variation in hPer2 and hBmal1 expression levels under baseline (P < 0.001, F = 19.7, df = 30 for hPer2 and P < 0.001, F = 17.6, df = 30 for hBmal1) and sleep-deprived conditions (P < 0.001, F = 9.2, df = 30 for hPer2 and P < 0.001, F = 13.2, df = 30 for hBmal1). Statistical analysis with the single cosinor method revealed circadian variation of hPer2 under baseline and of hBmal1 under baseline and sleep-deprived conditions. The peak expression of hPer2 was at 13:55 ± 1:15 hours under baseline conditions and of hBmal1 at 16:08 ± 1:18 hours under baseline and at 17:13 ± 1:35 hours under sleep-deprived conditions. Individual cosinor analysis of hPer2 revealed a loss of circadian rhythm in 3 participants and a phase shift in 2 participants under sleep-deprived conditions. The plasma melatonin and cortisol rhythms confirmed a conventional alignment of the central circadian pacemaker to the habitual sleep/wake schedule. Conclusion Our results suggest that 40-hour acute sleep deprivation under light conditions may affect the expression of hPer2 in PBMC