published_or_final_version / Pathology / Master / Master of Philosophy

Darbo tikslas buvo nustatyti Ternerio sindromo fenotipo ryšį su nustatyta chromosomine konstitucija ir jo įtaką šeiminei homeostazei. TS paplitimas, dažnis ir ligonių amžius diagnozavimo metu iki šiol nebuvo aprašytas mūsų tirtoje populiacijoje. KMU biologijos katedros citogenetikos laboratorijoje buvo ištirti kariotipai 1271 asmeniui, kuriam galima buvo įtarti TS: naujagimiai su įgimtomis sklaidos ydomis; mergaitės su fizinio vystymosi atsilikimais; mergaitės su brendimo atsilikimu; moterys su pirmine amenorėja; moterys su antrine amenorėja; moterys, tirtos dėl persileidimų ir nevaisingumo. Kariotipo pakitimai, būdingi TS, diagnozuoti 236 asmenims (18,6 proc.). Išskirti trys pagrindiniai kariotipo pakitimų variantai ir įvertinta, ar vienoda jų įtaka fenotipui. Tirta, ar yra skirtumas šių ligonių grupių fenotipe pagal tirtuosius parametrus: nėštumo trukmę, naujagimių kūno ilgį ir svorį, mergaičių ūgį ir svorį iki 18 metų amžiaus, tėvų amžių gimstant vaikui, sibsų amžių, paciento, kuriam įtariamas TS, amžių kariotipo tyrimo metu. Ištirta ir aprašyta keletas retų chromosomų disbalanso variantų. Nustatyta, kad monosominiai ligoniai dažniau vienintelę X chromosomą paveldi iš motinos (80,5 proc.), negu iš tėvo. Pirmą kartą atliktas šeiminis daugiaveiksniškai paveldimų požymių tyrimas (elektrokardiogramos ir gliukozės toleravimo mėginys) ne tik probandams, sergantiems TS, bet ir jų pirmosios eilės giminėms. Lietuvoje bent pusė TS atvejų lieka neatpažinti, todėl, siekiant kuo... [toliau žr. visą tekstą] / The aim of this study is to evaluate the link of chromosome constitution in Turner syndrome and in disruption of familial homeostasis. The distribution and incidence of TS in population nor the age of patients at the moment of diagnosis were not described previously. Cytogenetical laboratory at the Department of biology has investigated karyotypes for 1271. The number of abnormal karyotypes found is 236 (18.6%). We divided the patients into three groups according to logical, in our opinion, changes in their karyotypes. The aim of our research was to find out, if there were significant differences in phenotypes within those groups. Such traits were chosen for the comparison: the duration of pregnancy, length and weight of newborns, height and weight of the girls under 18 years old, the age of parents at birth of propositus, the age of the siblings, and the age at which TS was diagnosed for the patient. We predicted, that in a case of complete 45,X monosomy the clinical manifestation of the syndrome should be more severe, and this group of patients would differ from other karyological groups. We have found that in 80.5% of cases X chromosome had the maternal origin and in the rest 19.5% – paternal. To investigate the multifactorially inherited traits (electrocardiograms and glucose tolerance test) in relatives of Turner syndrome patients. We suggest that for the earlier diagnosis of TS, it is reasonable to investigate all girls, whose height is less than 3rd percentile.

The purpose of this study was to analyze the frequency distributions of alleles at the 3$ sp prime$HVR (hypervariable region) and 5$ sp prime$HVR, two highly polymorphic regions on chromosome 16p. About 300 DNA samples from individuals of East Asian, French Canadian, Greek, Italian, Jewish and Middle Eastern origin were analyzed by hybridization to probes for the 3$ sp prime$HVR and 5$ sp prime$HVR. / The distributions of alleles at both loci are skewed with the long tail towards the larger alleles. The observed heterozygosity at the 3$ sp prime$HVR locus for 281 individuals was 0.91, ranging from 0.85 in the Jewish group to 1.00 among French Canadians and East Asians. Statistical analysis demonstrated significant variation among some of the ethnic groups. / The observed heterozygosity at the 5$ sp prime$HVR locus in 225 individuals was 0.75. Heterozygosity varied from 0.91 in East Asians to 0.61 of Middle Eastern samples studied. 28% of samples also display a RsaI site polymorphism near the 5$ sp prime$HVR locus. / Genetic distance analysis demonstrated that the largest distance at these two loci exists between the Jews and East Asians (D = 0.119). / Both the 3$ sp prime$HVR and the 5$ sp prime$HVR are extremely variable in all the populations studied, and thus will serve as informative markers for chromosome 16p for clinical as well as population studies.

Proponents of the recognition concept of species hold that isolating mechanisms, including chromosome rearrangements, play no role in speciation while the more commonly accepted biological species concept proposes that isolation mechanisms are instrumental in the formation of new species. Moreover, some adherents of the biological concept of species, reject the hypothesis that chromosomal rearrangements can be instrumental in causing reproductive isolation and, hence, speciation. Evidence to the causative role played in speciation by chromosome changes can be obtained from cytogenetic investigations of sibling species, in parallel with analyses of gene products, DNA polymorphism and premating behaviour. This study reports the results of a cytogenetic investigation of 97 specimens of the vlei rat 0. irroratus, from 18 South African localities, and 11 samples of the Angoni vlei rat 0. angoniensis from two geographically distant populations. All 0. angoniensis individuals showed a constant karyotype with 56 acrocentric chromosomes but extensive variation was detected in 0. irroratus. Five cytotypes could be recognized within the latter. In the south-eastern parts of its South African range, 0. irroratus had a diploid number (2n) of 30 chromosomes in whicll all autosomes were acrocentric (cytotype A) while further east (cytotype A2), the diploid number was 30-32 with, again, acrocentric autosomes, A further acrocentric cytotype (AI) with 2n = 24-27 occupied the southern and south-eastern slopes of the Drakensberg range. A type with 2n = 28-30 (cytotype B), with eight pairs of biarmed autosomes, was found in the southern Cape region while in the Cape of Good Hope and in the north-eastern parts of South Africa, 0. irroratus had 2n = 28 with only four pairs of biarmed autosomes (cytotype C). Most of the numerical changes were due to variation in the number of copies of Bchromosomes which were small, biarmed and partly heterochromatic. C-banding analysis revealed that the short arms of bianned autosomes were totally heterochromatic. On the other hand, G-banding patterns of acrocentric autosomes were, with two exceptions (AI and A2 types), similar in all cytotypes while G~banding of the long arms VII of biarmed chromosomes matched the pattern of their homologues in acrocentric cytotypes. A potentially heterotic rearrangement was detected in the Al localities where a unique acrocentric autosome was identified as the product of a fusion between chromosomes 7 and 12. The geographic distribution of these groups of karyotypes correlated, by Discriminant Function Analysis, with bioclimatic regions of South Africa. The Al cytotype was shown to occupy the coldest and wettest region of the montane Drakensberg while the B type is found in the hot area of the eastern Cape with an unpredictable rainfall pattern: group C occupies regions of intermediate climate. Gene product analysis was carried out using the novel approach of subjecting liver homogenates to "Western blotting". This method was first assessed at supraspecilic level using specimens of various southern African rodents, and allowed the generation of phylogenies essentially similar to those produced by allozyme studies of the same taxa. At intraspecilic level, immunobloHing analysis did not reveal synapomorphies congruent with karyotype groups. This was interpreted, in conjunction with available allozyme data from the same populations, as evidence of low genetic differentiation between 0. irroratus cytotypes, A measure of genetic divergence was indicated in two populations from the Cape province and this was in agreement with existing data from allozyme electrophoresis and mitochondrial DNA polymorphism. The cytogenetic results were related to available data on breeding and premating behaviour concerning some of the O. irroratus populations investigated here. The presence of the 7/12 chromosome fusion in the Al cytotype correlated with a dramatic reproductive impairment of FI individuals originated from Al/A2 and Al/B cytotype crosses. Evidence of partial premating behavioural barriers has been reported by others, but information on premating behaviour between populations which are not chromosomally isolated is lacking. Therefore, it was not possible to establish if behavioural premating barriers preceded, or followed, the fixation of negatively heterotic chromosomal rearrangements. It was, nevertheless, suggested that the existence of such impaired mate recognition may be an example of reproductive character displacement which may have followed the fixation of the t(7: 12) typiVIII cal of the Al populations. In conclusion, the existence of chromosome changes in the AI, and possibly A2, populations accompanied by low genetic divergence and severely impaired hybrid reproductive success, are consistent with a hypothesis whereby chromosomal reproductive isolation causes speciation. Nonetheless, other speciation mechanisms mediated by genetic divergence and/or mate recognition failure, are possible in other populations where no chromosome changes of negatively heterotic potential were found. / Thesis (Ph.D.)-University of Natal, 1996.

In the B6.YTIR mouse strain, half of the XY progeny develop bilateral ovaries and the female phenotype. These XY females are infertile mainly due to the death of their embryos. This developmental failure has been attributed to a defect intrinsic to the XY oocyte. / The present study examined the transcriptional activity of the X and Y chromosomes in these oocytes. RT-PCR results show that the Ube1y gene is transcribed in the XY ovary at all stages examined and also in growing XY oocytes. The Sry gene was transcribed only at the onset of ovarian differentiation whereas the Zfy gene was undetectable at all stages during fetal life. The Xist gene, which is involved in X inactivation, was not expressed in XY oocytes. We speculate that expression of Y-encoded genes may have a deleterious effect on the quality of the oocytes and thus renders them incompetent for post-fertilization development.

Telomeres are nucleoprotein complexes located at the end of chromosomes. They have an essential role in protecting chromosome ends. Telomerase or ALT (alternative lengthening of telomeres) mechanisms maintain telomeres by compensating natural telomeric loss. We have set up a flow-FISH method and using mouse lymphoma cell lines we identified unexpectedly the presence of subpopulations of cells with different telomere lengths. Subpopulations of cells with different telomere lengths were also observed in a human ALT and non-ALT cell line. Differences in telomere length between subpopulations of cells were significant and we term this phenomenon TELEFLUCS (TElomere LEngth FLUctuations in Cell Subpopulations). By applying flow-FISH we could successfully measure telomere lengths during replicative senescence in human primary fibroblasts with different genetic defects that confer sensitivity to ionising radiation (IR). The results from this study, based on flow-FISH and Southern hybridisation measurements, revealed an accelerated rate of telomere shortening in radiosensitive fibroblasts. We also observed accelerated telomere shortening in murine BRCA1 deficient cells, another defect conferring radiosensitivity, in comparison with a BRCA1 proficient cell line. We transiently depleted BRCA1 by siRNAs in two human mammary epithelial cell lines but could not find changes in telomere length in comparison with control cells. Cytological evidence of telomere dysfunction was observed in all radiosensitive cell lines. These results suggest that mechanisms that confer sensitivity to IR may be linked with mechanisms that cause telomere dysfunction. Furthermore, we have been able to show that human ALT positive cell lines show dysfunctional telomeres as detected by either the presence of DSBs at their telomeres or cytogenetic analysis and usually cells with dysfunctional telomeres are sensitive to IR. Finally, we assessed hTERT mRNA splicing variants and telomerase activity in brain tumours, which exhibit considerable chromosome instability suggesting that DNA repair mechanisms may be impaired. We demonstrated that high levels of hTERT mRNAs and telomerase activity correlate with proliferation rate. The presence of hTERT splice variants did not strictly correlate with absence of telomerase activity but hTERT spliced transcripts were observed in some telomerase negative brain tumours suggesting that hTERT splicing may contribute to activation of ALT mechanisms.

Darbo uždaviniai: surinkti ir išanalizuoti mokslinę literatūrą apie chromosominius pakitimus ir jų poveikį galvijų reprodukcijai. Paruošti ir ištirti galvijų chromosomų preparatus. Įvertinti chromosomų skaičiaus ir struktūros pakitimus bei jų įtaką reprodukcinėms savybėms. Rezultatai ir aptarimas: ištyrus karves, kurioms nustatyti reprodukcijos sutrikimai, buvo identifikuoti ir chromosomų struktūros, ir chromosomų skaičiaus pakitimai. Didžiąją dalį chromosomų struktūros pakitimų, t. y. 38,2 proc., sudarė spragos vienoje chromatidėje (S1), 16,9 proc. spragos abiejose chromatidėse (S2) ir 16,9 proc. – chromatidžių trūkiai (D1). Fragmentai (F) sudarė 12,4 proc. Mažiausią dalį chromosomų struktūros aberacijų, t. y. 2,2 proc., sudarė žiedinės chromosomos (Ž) ir 2,2 proc. – chromosomų trūkiai (D2). Iš chromosomų skaičiaus pakitimų rasta 7,9 proc. poliploidijų (P). Ištyrus karves, kurioms nenustatyti reprodukcijos sutrikimai, taip pat buvo identifikuoti tiek chromosomų struktūros, tiek skaičiaus pakitimai. Iš chromosomų struktūros pakitimų nustatyta: 28,6 proc. spragų vienoje chromatidėje (S1), 11,4 proc. chromatidžių trūkių (D1), 11,4 proc. fragmentų (F), 8,6 proc. spragų abiejose chromatidėse (S2). Žiedinių chromosomų ir dicenrikų nenustatyta. Iš chromosomų skaičiaus pakitimų aptikta 34,3 proc. poliploidijų (P) ir 2,9 proc. trisomijų (Tr). Karvių grupėje, turinčių reprodukcijos sutrikimų, ląstelių su pakitimais pasitaiko 3,3 karto dažniau (p<0,001) nei kontrolinėje grupėje... [toliau žr. visą tekstą] / The Object of the work: cytogenetic analysis was performed on 26 cows from animal farm in Giraitė, 12 cows with reproductive disorder and 14 cows with no reproductive disorder (the control group). The research was performed by standard citogenetical approach modified in laboratory. The extent of the work: 48 pages. There are 4 tables and 10 pictures included. The aim of the work: to evaluate the influence of chromosomal aberrations on reproductive features of the cattle. The tasks of the work: to collect and analyze scientific literature on chromosomal changes and their impact on reproduction of cattle. To prepare and investigate the preparation of cattle chromosomes, estimate the structural and numeral variations of chromosomes and their influence on reproductive characteristics. The results and their discussion: after the examination of the cows with reproductive disorders the structural and numeral variations of chromosomes were identified. The major part of structural variations in chromosomes, i.e. 38.2%, consisted of gaps in one chromatid (S1), 16.9% of gaps in both chromatids (S2), 16.9% of cracks in chromatids (D1) and 12.4% of fragments (F). The least part (2.2%) of structural aberrations of chromosomes consisted of circular chromosomes (Ž) and 2.2% of cracks in chromosomes (D2). There were 7.9% of poliploidies (P) found in numeral variations of chromosomes. There were also identified both the structural and numerical variations of chromosomes after examining the... [to full text]

Darbo tikslas: ištirti karvių genomo nestabilumo ryšį su pieno produktyvumu. Darbo uždaviniai: 1. Surinkti ir išanalizuoti mokslinę literatūrą apie galvijų chromosomų skaičiaus ir struktūros pakitimus bei jų ryšį su produktyvumo savybėmis. 2. Paruošti karvių chromosomų preparatus. 3. Ištirti chromosomų skaičiaus ir struktūros pakitimus aukšto ir žemo produktyvumo pieninėms karvėms. 4. Apskaičiuoti chromosomų skaičiaus ir struktūros pakitimų dažnį ir spektrą aukšto ir žemo produktyvumo pieninėms karvėms. 5. Nustatyti ryšį tarp chromosomų skaičiaus ir struktūros pakitimų ir pieno produkcijos kiekio. Darbo metodai: mokslinės literatūros, straipsnių, statistinių duomenų analizė. Praktinėje dalyje atlikti karvių chromosomų tyrimai. Rezultatai aptarti juos apibendrinus. Darbe remtasi įvairiais užsienio ir lietuvių moksliniais darbais, straipsniais, tyrimų medžiaga, darbe analizuojama tema. Darbo objektas: citogenetinė analizė atlikta 20 karvių iš LSMU VA praktinio mokymo ir bandymų centro, 10 aukšto produktyvumo karvių ir 10 žemo produktyvumo karvių. Tyrimai atlikti standartiniu citogenetiniu metodu. Rezultatai ir aptarimas: žemo produktyvumo karvės turėjo žymiai daugiau chromosominių pakitimų. Daugiausiai chromosomų struktūros pakitimų, t.y. 37,5 proc., sudaro spragos vienoje chromatidėje (S1), 15,6 proc. – spragos abiejose chromatidėse (S2), 17,2 proc. – chromatidžių trūkiai (D1), 9,4 proc. – fragmentai (F). Mažiausią dalį chromosomų struktūros pakitimų, t. y. 3,1 proc. sudaro... [toliau žr. visą tekstą] / The Object of the work: cytogenetic analysis was performed on 20 cows from LSMU VA practice and research centre, 10 productive cows and 10 unproductive cows. The research was performed by standard citogenetical laboratory. The aim of the work: to evaluate the influence of chromosomal aberrations on cow high productivity. The tasks of the work: collect and analyze scientific literature on bovine chromosome number and structure of the environment and their relationship with performance traits. Prepared bovine chromosome preparations. To investigate the chromosome number and structure changes in high and low productivity of dairy cows. Calculate the number of chromosomes and structural changes in the frequency and range of high and low productivity of dairy cows. Determine the relationship between chromosome number and structure changes and milk production levels. The results and their discussion: after the examination of the unproductive cows the structural and numeral variations of chromosomes were identified. Most part of structural variations in chromosomes, i.e. 37,5 proc., consisted of gaps in one chromatid (S1), 15,6 proc.of gaps in both chromatids (S2), 17,2 proc. of cracks in chromatids (D1) .There were 10,9 proc. of poliploidies (P) found in numeral variations of chromosomes. There were also identified both the structural and numerical variations of chromosomes after examining the productive cows. These structural variations of chromosomes were identified: 34,6 proc... [to full text]

Thesis (Ph. D.)--University of Hawaii at Manoa, 2004. / Includes bibliographical references (leaves 198-219). / Also available by subscription via World Wide Web / xvii, 219 leaves, bound ill., some col. 29 cm

<p>With easy access to technology to generate expressed sequence tags (ESTs), several groups have sequenced from thousands to several thousands of ESTs. These ESTs benefit from consolidation and organization to deliver significant biological value. A number of EST projects are underway to extract maximum value from fragmented EST resources by constructing gene indices, where all transcripts are partitioned into index classes such that transcripts are put into the same index class if they represent the same gene. Therefore a gene index should ideally represent a non-redundant set of transcripts. Indeed, most gene indices aim to reconstruct the gene complement of a genome and their technological developments are directed at achieving this goal. The South African National Bioinformatics Institute (SANBI), on the other hand, embarked on the development of the sequence alignment and consensus knowledgebase (STACK) database that focused on the detection and visualisation of transcript variation in the context of developmental and pathological states, using all publicly available ESTs. Preliminary work on the STACK project employed an approach of partitioning the EST data into arbitrarily chosen tissue categories as a means of reducing the EST sequences to manageable sizes for subsequent processing. The tissue partitioning provided the template material for developing error-checking tools to analyse the information embedded in the error-laden EST sequences. However, tissue partitioning increases redundancy in the sequence data because one gene can be expressed in multiple tissues, with the result that multiple tissue partitioned transcripts will correspond to the same gene.</p> <p><br /> Therefore, the sequence data represented by each tissue category had to be merged in order to obtain a comprehensive view of expressed transcript variation across all available tissues. The need to consolidate all EST information provided the impetus for developing a STACK human gene index, also referred to as a whole-body index. In this dissertation, I report on the development of a STACK human gene index represented by consensus transcripts where all constituent ESTs sample single or multiple tissues in order to provide the correct development and pathological context for investigating sequence variation. Furthermore, the availability of a human gene index is assessed as a diseasecandidate gene discovery resource. A feasible approach to construction of a whole-body index required the ability to process error-prone EST data in excess of one million sequences (1,198,607 ESTs as of December 1998). In the absence of new clustering algorithms, at that time, we successfully ported D2_CLUSTER, an EST clustering algorithm, to the high performance shared multiprocessor machine, Origin2000. Improvements to the parallelised version of D2_CLUSTER included: (i) ability to cluster sequences on as many as 126 processors. For example, 462000 ESTs were clustered in 31 hours on 126 R10000 MHz processors, Origin2000. (ii) enhanced memory management that allowed for clustering of mRNA sequences as long as 83000 base pairs. (iii) ability to have the input sequence data accessible to all processors, allowing rapid access to the sequences. (iv) a restart module that allowed a job to be restarted if it was interrupted. The successful enhancements to the parallelised version of D2_CLUSTER, as listed above, allowed for the processing of EST datasets in excess of 1 million sequences. An hierarchical approach was adopted where 1,198,607 million ESTs from GenBank release 110 (October 1998) were partitioned into &quot / tissue bins&quot / and each tissue bin was processed through a pipeline that included masking for contaminants, clustering, assembly, assembly analysis and consensus generation. A total of 478,707 consensus transcripts were generated for all the tissue categories and these sequences served as the input data for the generation of the wholebody index sequences. The clustering of all tissue-derived consensus transcripts was followed by the collapse of each consensus sequence to its individual ESTs prior to assembly and whole-body index consensus sequence generation. The hierarchical approach demonstrated a consolidation of the input EST data from 1,198607 ESTs to 69,158 multi-sequence clusters and 162,439 singletons (or individual ESTs). Chromosomal locations were added to 25,793 whole-body index sequences through assignment of genetic markers such as radiation hybrid markers and g&eacute / n&eacute / thon markers. The whole-body index sequences were made available to the research community through a sequence-based search engine (http://ziggy.sanbi.ac.za/~alan/researchINDEX.html).</p>