Implementation of parallel algorithm for k-mer enrichment analysis of genomic sequences

The goal of this thesis was to implement a sequential algorithm that would search for subsequences in a genome. To accelerate the execution time of this algorithm we designed a parallel version and implemented the parallel version on a graphics card. The sequential algorithm had to search for predefined subsequences in a genome that was represented as a sequence of characters. It had to calculate the frequencies of sequence occurrences and the frequencies of interactions on predefined positions and on randomly modified positions in the genome, for each subsequence. Based on these frequencies it had to identify sequences that were more frequent on certain locations in a given genome. Based on data about protein-RNA interactions on certain locations in the genome, and based on the found character sequences, the algorithm had to calculate and statistically evaluate the frequencies of interactions. The sequential algorithm was implemented in the C programming language, while the parallelization was implemented on the OpenCL architecture

Creation of realistic spaces for visualization in virtual reality

The development of computer graphics has always been coupled with the desire to create realistic visualizations. In recent years, we have already been achieving results that are hard to distinguish from reality. However, we are constantly searching for ways to immerse the user even further. Virtual reality is an example of such technology. The purpose of this thesis was to create a realistic environment that a user can experience with a virtual reality system. We took a familiar setting for our scene, the Faculty of Computer and Information Science in Ljubljana. We began by modeling in Maya, and from there transferred the environment into Unreal Engine, where the implementation of the logic took place. Our target virtual reality system was HTC Vive. The user has the options of painting on surfaces and in 3D space, as well as arranging and interacting with objects in the scene. In addition to the implementations of the said functions, the thesis describes the tools, technologies and work ow, along with the main guidelines to be followed when developing these types of experiences

Implementation of parallel algorithm for k-mer enrichment analysis of genomic sequences

The goal of this thesis was to implement a sequential algorithm that would search for subsequences in a genome. To accelerate the execution time of this algorithm we designed a parallel version and implemented the parallel version on a graphics card. The sequential algorithm had to search for predefined subsequences in a genome that was represented as a sequence of characters. It had to calculate the frequencies of sequence occurrences and the frequencies of interactions on predefined positions and on randomly modified positions in the genome, for each subsequence. Based on these frequencies it had to identify sequences that were more frequent on certain locations in a given genome. Based on data about protein-RNA interactions on certain locations in the genome, and based on the found character sequences, the algorithm had to calculate and statistically evaluate the frequencies of interactions. The sequential algorithm was implemented in the C programming language, while the parallelization was implemented on the OpenCL architecture

Effect of carbon black nanomaterial on blood cell membranes

V doktorskem delu smo proučevali vpliv nanomateriala črnega ogljika (NM CB) na membrane krvnih celic ter orjaške unilamelarne fosfolipidne mehurčke (OUFM). Glavni namen je bilo ugotoviti, ali dodani NM CB vpliva na biološke membrane, tako plazemske celične membrane kot tudi membrane OUFM. Izolirane krvne celice, polno kri ter OUFM smo inkubirali z NM CB v različnih koncentracijah. Opazovali smo spremembo oblike eritrocitov zaradi prisotnosti NM CB v vzorcih. Ugotovili smo statistično pomembne razlike v razmerju povprečnega števila diskocitov, ehinocitov in stomatocitov glede na kontrolne vzorce. Dodani NM CB je v vzorcih povzročil tudi adhezijo eritrocitov na aglomerate nanomateriala. Pri populaciji trombocitov smo opazili tubularne izrastke po 3 in 24 urah inkubacije tako v testnih kot kontrolnih vzorcih, zato aktivacije ne moremo pripisati dodanemu NM CB. Statistično pomembne razlike so se pojavile pri populaciji levkocitov, saj so testni vzorci vsebovali v povprečju povečano število levkocitov, eozinofilcev ter bazofilcev in znižano število monocitov glede na kontrolo. Inkubacija OUFM z NM CB je povzročila znatno in statistično pomembno zmanjšanje števila OUFM že po 20 minutah pri preostalih OUFM pa povečano povprečno ekscentričnost, glede na kontrolo. Ugotovili smo, da prisotnost NM CB v vzorcih s krvnimi celicami ni povzročila hemolize ali drugih sprememb, ki bi lahko bile bistvene za delovanje krvnih celic, medtem ko je prišlo do disintegracije membran OUFM, kar smo, tako kot spremembo oblike eritrocitov, pripisali predvsem sekundarnim osmotskim učinkom v raztopini.We investigated the effect of carbon black nanomaterial (NM CB) on membranes of blood cells and of giant unilamelar phospholipid vesicles (GUV). The aim of the study was to determine whether NM CB effects the shape of blood cells and GUVs. The samples of isolated blood cells, full human blood and GUVs were incubated with different concentrations of NM CB. We observed the shape changes of erythrocytes due to the presence of NM CB in the samplesthe abundance of discocytes, echinocytes and stomatocytes in the treated samples was changed with respect to control samples. NM CB also affected the adhesion of erythrocytes to agglomerates of nanomaterial. Tubular protrusions on platelet membrane occurred after 3 and 24 hours both in the samples incubated with NM CB and in the control onesno differences were found in activation of platelets in the respective samples. However, statistically significant differences were observed in the average number of leukocytes as well as of eosinophils, basophils and monocytes with respect to control samples. Incubation of GUVs with NM CB caused a considerable and statistically significant decrease in their number while the contours of the remaining GUVs exhibited on average higher eccentricity than the control ones. It was concluded that the presence of NM CB in the samples with blood cells did not cause hemolysis. We did not detect hemolysis or changes in cell membranes due to the presence of NM CB that could impair the function of blood cells. We observed disintegration of GUV membranes which was, similarly to the erythrocyte shape change, interpreted as a secondary osmotic effect

Creation of realistic spaces for visualization in virtual reality

The development of computer graphics has always been coupled with the desire to create realistic visualizations. In recent years, we have already been achieving results that are hard to distinguish from reality. However, we are constantly searching for ways to immerse the user even further. Virtual reality is an example of such technology. The purpose of this thesis was to create a realistic environment that a user can experience with a virtual reality system. We took a familiar setting for our scene, the Faculty of Computer and Information Science in Ljubljana. We began by modeling in Maya, and from there transferred the environment into Unreal Engine, where the implementation of the logic took place. Our target virtual reality system was HTC Vive. The user has the options of painting on surfaces and in 3D space, as well as arranging and interacting with objects in the scene. In addition to the implementations of the said functions, the thesis describes the tools, technologies and work ow, along with the main guidelines to be followed when developing these types of experiences

DNA, spectroscopic and geochemical analyses of bone fragments and associated speleothems in Postojna cave, Slovenia

a loose/broken stalagmite containing small fragments of cemented bones were collected from the Postojna Cave to investigate whether deoxyribonucleic acid (DNA) can be determined. The study is complemented by the Fourier-transform infrared spectroscopy - attenuated total reflectance (FTIR-ATR) analysis in order to determine the alteration of the bones and to test whether this analysis can be used as an indicator of possible DNA preservation. In addition, geochemical analyses were conducted in order to determine whether the associated flowstone/stalagmite is suitable for elucidating the timing of bone thanatocoenosis and further palaeoenvironmental analyses. The organic matter (collagen) is poorly preserved. However, we succeeded in amplifying a 94 bp long fragment of the cytochrome b (Cyt b) gene of mitochondrial DNA (mtDNA) in polymerase chain reaction (PCR) for one sample, and in sequencing the amto that of the Cyt b of the cave bear (Ursus deningeri or Ursus spelaeus sensu lato). The uranium-thorium dating of the speleothem covering the bones revealed its thanatocoenosis occurred prior to 55 ka, most likely in the late marine isotope stage 4 or early marine isotope stage 3. High porosity and recrystallisation of the flowstone/stalagmite at this part of the cave prevent high-resolution palaeoclimatic interpretation; however, low-resolution stable isotope geochemistry suggests a steppe-like environment during the subsequent growth of the speleothem.Iz Postojnske jame so bili vzeti delci kosti, prevlečeni s kalcitno skorjo, vključno z odlomljenim stalagmitom, v katerem so zacementirani drobci kosti, da bi se ugotovilo, ali je mogoče določiti deoksiribonukleinsko kislino (DNA). Študijo dopolnjuje analiza s Fourierevo transformacijsko infrardečo spektroskopijo z zmanjšanim popolnim odbojem (FTIR-ATR), ki je bila izvedena, da se ugotovijo biokemične spremembe v kosteh in se preveri, ali je mogoče to analizo uporabiti kot kazalnik morebitne ohranjenosti DNA. Izvedene so bile tudi geokemijske analize, da bi ugotovili, ali je pripadajoča siga primerna za razlago časa kostne tanatocenoze in nadaljnje paleookoljske analize. Organska snov (kolagen) je slabo ohranjena. Pri enem vzorcu nam je z verižno reakcijo s polimerazo (PCR) uspelo pomnožiti 94 bp dolg fragment gena za citokrom b (Cyt b) mitohondrijske DNA (mtDNA) in pomnožene produkte smo uspešno sekvencirali. Dobljeno zaporedje dolžine 70 bp ustreza zaporedju Cytb jamskega medveda (Ursus deningeri ali Ursus spelaeus sensu lato). U-Th datacija sige, ki pokriva kosti, nakazuje, da se je tanatocenoza pojavila pred 55 ka, najverjetneje v fazi MIS 4 ali MIS 3. Visoka poroznost in rekristalizacija sige v tem delu jame preprečujeta paleoklimatsko interpretacijo visoke ločljivosti, geokemija stabilnih izotopov z nizko ločljivostjo pa nakazuje na stepi podobno okolje

Človeška in ptičja gripa: zakaj ptičja gripa ogroža človeštvo?

Gripa je pogost vzrok obolenj dihal, ki povzroča pomembno obolevnost in smrtnost predvsem pri starejših osebah in osebah s kroničnimi obolenji. Gripe ni mogoče izkoreniniti in se v obliki epidemije pojavlja sezonsko vsako zimo, vendar se proti njej lahko uspešno zaščitimo s pravočasnim cepljenjem. Cepljenje zelo priporočamo zdravstvenim delavcem, da okužbe ne prenašajo na svoje bolnike. V zadnjem času so na voljo protivirusna zdravila iz skupine zaviralcev nevraminidaze, s katerimi lahko preprečimo ali omilimo gripo. Kljub napredku nas nedavna obsežna epidemija ptičje gripe med perutnino v azijskih državah opozarja na ranljivost človeške vrste in tveganje za pojav nove pandemije, ki bi zahtevala več milijonov človeških žrtev. Zadnjo epidemijo ptičje gripe so v Aziji uspeli omejiti (ne pa tudi izkoreniniti) in ptičji virus se ni pomembno širil med ljudmi. Oboleli so le posamezniki, ki so bili v tesnem stiku z okuženo perutnino. V prihodnosti je pomembno zgodnje prepoznavanje epidemij ptičje gripe in takojšnji poboj vse okužene in obolele perutnine. Potrebno je pripraviti krizni načrt za primer izbruha epidemije, pripraviti cepivo in zalogo protivirusnih zdravil. Članek povzema značilnosti človeške in ptičje gripe, načine širjenje in zaščito