Evidence against close linkage of the loci for fraXq of Martin-Bell syndrome and for factor IX.

Linkage between the loci for fraXq of Martin-Bell syndrome and factor IX was studied in nine families exhibiting this syndrome by means of a restriction fragment length polymorphism at the factor IX locus. Computer analysis of the data indicates there to be no evidence for close linkage between the syndrome and the factor IX locus.

Methods for construction and analysis of computational models in systems biology : applications to the modelling of the heat shock response and the self-assembly of intermediate filaments

Systems biology is a new, emerging and rapidly developing, multidisciplinary research field that aims to study biochemical and biological systems from a holistic perspective, with the goal of providing a comprehensive, system- level understanding of cellular behaviour. In this way, it addresses one of the greatest challenges faced by contemporary biology, which is to compre- hend the function of complex biological systems. Systems biology combines various methods that originate from scientific disciplines such as molecu- lar biology, chemistry, engineering sciences, mathematics, computer science and systems theory. Systems biology, unlike “traditional” biology, focuses on high-level concepts such as: network, component, robustness, efficiency, control, regulation, hierarchical design, synchronization, concurrency, and many others. The very terminology of systems biology is “foreign” to “tra- ditional” biology, marks its drastic shift in the research paradigm and it indicates close linkage of systems biology to computer science. One of the basic tools utilized in systems biology is the mathematical modelling of life processes tightly linked to experimental practice. The stud- ies contained in this thesis revolve around a number of challenges commonly encountered in the computational modelling in systems biology. The re- search comprises of the development and application of a broad range of methods originating in the fields of computer science and mathematics for construction and analysis of computational models in systems biology. In particular, the performed research is setup in the context of two biolog- ical phenomena chosen as modelling case studies: 1) the eukaryotic heat shock response and 2) the in vitro self-assembly of intermediate filaments, one of the main constituents of the cytoskeleton. The range of presented approaches spans from heuristic, through numerical and statistical to ana- lytical methods applied in the effort to formally describe and analyse the two biological processes. We notice however, that although applied to cer- tain case studies, the presented methods are not limited to them and can be utilized in the analysis of other biological mechanisms as well as com- plex systems in general. The full range of developed and applied modelling techniques as well as model analysis methodologies constitutes a rich mod- elling framework. Moreover, the presentation of the developed methods, their application to the two case studies and the discussions concerning their potentials and limitations point to the difficulties and challenges one encounters in computational modelling of biological systems. The problems of model identifiability, model comparison, model refinement, model inte- gration and extension, choice of the proper modelling framework and level of abstraction, or the choice of the proper scope of the model run through this thesis.

Diagnóstico de enteroparasitoses numa comunidade rural de Mirante da Serra, Rondônia, Brasil

As enteroparasitoses estão entre as infecções mais comuns no homem, apresentando-se com maior intensidade em países subdesenvolvidos por estarem diretamente relacionadas às condições higiênico-sanitárias. Este estudo tem por objetivo investigar a presença de enteroparasitas causadoras de doenças no homem, em uma comunidade do Movimento dos Trabalhadores Rurais Sem Terra (MST) no estado de Rondônia. No acampamento Pe. Ezequiel, município de Mirante da Serra, RO, foram utilizados os métodos direto e de sedimentação espontânea em água para detecção e identificação das formas parasitárias de protozoários e helmintos em material fecal de residentes do mesmo e o teste de ELISA (Ensaio imunoenzimático) para detecção de coprantígeno específico, anti-GIAP (proteina de aderência inibidora da galactose), de Entamoea histolytica (Tachlab, Blacksburg, VA, USA). Foram examinadas 313 amostras fecais pelos testes coproscópicos e 186 pelo teste de ELISA. A prevalência encontrada foi de 33,5% sendo a E. histolystica, Giárdia Lamblia e os ancilostomídeos os parasitas patogênicos mais frequentes. Não foram encontradas diferenças significativas entre parasitismo e idade, mas entre agente causador da infecção e sexo houve significância entre E. histolytica e sexo feminino. Não foi possível determinar fator (es) de risco relacionado (s) às infecções. Quanto ao resultado do ELISA, foi detectado um número maior de amébiase intestinal por este método do que por coproscopia. Considerando ser o acampamento uma área rural sem infra-estrutura ideal, o baixo parasitismo encontrado foi surpreendente. Todavia, a estrutura alternativa do local somado à organização social do grupo, consciência comunitária e formação básica em saúde, constitui fatores preponderantes para a aprovação e/ou controle das enteroparasitoses.

Analysis and mapping of CACNB4, CHRNA1, KCNJ3, SCN2A and SPG4, physiological candidate genes for porcine congenital progressive ataxia and spastic paresis

The cause of porcine congenital progressive ataxia and spastic paresis (CPA) is unknown. This severe neuropathy manifests shortly after birth and is lethal. The disease is inherited as a single autosomal recessive allele, designated cpa. In a previous study, we demonstrated close linkage of cpa to microsatellite SW902 on porcine chromosome 3 (SSC3), which corresponds syntenically to human chromosome 2. This latter chromosome contains ion channel genes (Ca(2+), K(+) and Na(+)), a cholinergic receptor gene and the spastin (SPG4) gene, which cause human epilepsy and ataxia when mutated. We mapped porcine CACNB4, KCNJ3, SCN2A and CHRNA1 to SSC15 and SPG4 to SSC3 with the INRA-Minnesota porcine radiation hybrid panel (IMpRH) and we sequenced the entire open reading frames of CACNB4 and SPG4 without finding any differences between healthy and affected piglets. An anti-epileptic drug treatment with ethosuximide did not change the severity of the disease, and pigs with CPA did not exhibit the corticospinal tract axonal degeneration found in humans suffering from hereditary spastic paraplegia, which is associated with mutations in SPG4. For all these reasons, the hypothesis that CACNB4, CHRNA1, KCNJ3, SCN2A or SPG4 are identical with the CPA gene was rejected.

Pteropod preservation on the Pakistan shelf and continental slope

Fifteen surface sediment samples from the Pakistan shelf and upper continental slope and a Late Quaternary high-sedimentation rate core (573 m water depth, Pakistan continental margin) have been analysed to improve the understanding of the factors influencing pteropod preservation. The aragonite compensation depth (ACD) is located at 250-400 m water depth, which corroborates previous observations of a very shallow ACD in the northern Arabian Sea. With the exception of the Hab transect off Karachi, the ACD coincides with the upper boundary of the OMZ located at 250 m water depth. The shell preservation index of the pteropod Limacina inflata (LDX) was applied on six surface sediment samples showing good to very good preservation (LDX: 2.2 to 1.3). The 30 000 yr long record of sediment core SO90 137KA is characterized by alternations between bioturbated and laminated sediments. Bioturbated sediments occurring in the Early Holocene, Younger Dryas and time-equivalents of Heinrich events contain well to perfectly preserved tests of L. inflata (LDX: 2.1-0.2), whereas only traces of pteropods are found in laminated intervals. The close linkage of pteropod preservation in the surface sediments and in core 137KA to well-oxygenated conditions can be explained by repetitive intermediate water formation in the Arabian Sea down to at least 600 m water depth in times of enhanced NE monsoons during stadials and H-equivalents. Low amounts of pteropods in laminated sediments (interstadials, Late Holocene) and in the present-day oxygen minimum zone (OMZ) indicate a weak NE monsoon, stable OMZ and shallow ACD.

Seawater Cd reconstruction for the western subtropical South Atlantic

Benthic foraminiferal Cd/Ca from an intermediate depth, western South Atlantic core documents the history of southward penetration of North Atlantic Intermediate Water (NAIW). Cd seawater estimates (CdW) for the last glacial are consistent with the production of NAIW and its export into the South Atlantic. At ~14.5 ka concurrently with the onset of the Bølling-Allerød to Younger Dryas cooling, the NAIW contribution to the South Atlantic began to decrease, marking the transition from a glacial circulation pattern to a Younger Dryas circulation. High CdW in both the deep North Atlantic and the intermediate South Atlantic imply reduced export of deep and intermediate water during the Younger Dryas and a significant decrease in northward oceanic heat transport. A modern circulation was achieved at ~9 ka, concurrently with the establishment of Holocene warmth in the North Atlantic region, further supporting a close linkage between deepwater variability and North Atlantic climate.

A single gene for lycopene cyclase, phytoene synthase, and regulation of carotene biosynthesis in Phycomyces

Previous complementation and mapping of mutations that change the usual yellow color of the Zygomycete Phycomyces blakesleeanus to white or red led to the definition of two structural genes for carotene biosynthesis. We have cloned one of these genes, carRA, by taking advantage of its close linkage to the other, carB, responsible for phytoene dehydrogenase. The sequences of the wild type and six mutants have been established, compared with sequences in other organisms, and correlated with the mutant phenotypes. The carRA and carB coding sequences are separated by 1,381 untranslated nucleotides and are divergently transcribed. Gene carRA contains separate domains for two enzymes, lycopene cyclase and phytoene synthase, and regulates the overall activity of the pathway and its response to physical and chemical stimuli from the environment. The lycopene cyclase domain of carRA derived from a duplication of a gene from a common ancestor of fungi and Brevibacterium linens; the phytoene synthase domain is similar to the phytoene and squalene synthases of many organisms; but the regulatory functions appear to be specific to Phycomyces.

Psychiatric genetics in Australia

Australian research in psychiatric genetics covers molecular genetic studies of depression, anxiety, alcohol dependence, Alzheimer's disease, bipolar disorder, schizophrenia, autism, and attention deficit hyperactivity disorder. For each disorder, a variety of clinical cohorts have been recruited including affected sib pair families, trios, case/controls, and twins from a large population-based twin registry. These studies are taking place both independently and in collaboration with international groups. Microarray studies now complement DNA investigations, while animal models are in development An Australian government genome facility provides a high throughput genotyping and mutation detection service to the Australian scientific community, enhancing the contribution of Australian psychiatric genetics groups to gene discovery. (C) 2003 Lippincott Williams Wilkins.

What May the Sheep safely know?

The relationship of knowledge and liberties in modern societies presents a multitude of fascinating issues that deserve to be explored more systematically. The production of knowledge is dynamic, and the conditions and practice of freedom is undergoing transformation. These changes ensure that the linkages between liberty and knowledge are always subject to changes. In the past, the connection between scientific knowledge, democracy, and emancipation seemed self-evident. More recently, the close linkage between democracy and knowledge has been viewed with skepticism. This volume explores the relationship between knowledge and democracy, Do they support each other, do they mutually depend on each other, or are they perhaps even in conflict with each other? Does knowledge increase the freedom to act? If additional knowledge contributes to individual and social well being, does it also enhance freedoms? Knowledge and Democracy focuses on the interpenetration of knowledge, freedom and democracy, and does so from various perspectives, theoretical as well as practical. Modern societies are transforming themselves into knowledge societies. This has a fundamental impact on political systems and the relationship of citizens to large social institutions. The contributors to this book systemically explore whether, and in what ways, these modern-day changes and developments are connected to expansion of the capacities of individual citizens to act. They focus on the interrelation of democracy and knowledge, and the role of democratic institutions, as well as on the knowledge and social conduct of actors within democratic institutions. In the process of investigation, they arrive at a newplatform for future research and theory, one that is sensitive to present-day societal conflicts, cleavages, and transformations generated by new knowledge.

(Table 1) Dissolved Hafnium and Neodymium in the South Atlantic measured on water bottle samples during POLARSTERN cruise ANT-XXIV/3

We present the first combined dissolved hafnium (Hf) and neodymium (Nd) concentrations and isotope compositions of deep water masses from the Atlantic sector of the Southern Ocean. Eight full depth profiles were analyzed for Hf and twelve for Nd. Hafnium concentrations are generally depleted in the upper few hundred meters ranging between 0.2 pmol/kg and 0.4 pmol/kg and increase to relatively constant values of around 0.6 pmol/kg in the deeper water column. At the stations north of the Polar Front (PF), Nd concentrations increase linearly from about 10 pmol/kg at depths of ~ 200 m to up to 31 pmol/kg close to the bottom indicating particle scavenging and release. Within the Weddell Gyre (WG), however, Nd concentrations are essentially constant at 25 pmol/kg at depths greater than ~ 1000 m. The distributions of both elements show a positive correlation with dissolved silicon implying a close linkage to diatom biogeochemistry. Hafnium essentially shows invariant isotope compositions with values averaging at epsilon-Hf = +4.6, whereas Nd isotopes mark distinct differences between water masses, such as modified North Atlantic Deep Water (NADW, epsilon-Nd = -11 to -10) and Antarctic Bottom Water (AABW, epsilon-Nd = -8.6 to -9.6), but also waters locally advected via the Agulhas Current can be identified by their unradiogenic Nd isotope compositions. Mixing calculations suggest that a small fraction of Nd is removed by particle scavenging during mixing of water masses north of the PF. Nevertheless, the Nd isotope composition has apparently not been significantly affected by uptake and release of Nd from particles, as indicated by mixing calculations. A mixing envelope of an approximated North Pacific and a North Atlantic end-member shows that Nd isotope and concentration patterns in the Lower Circumpolar Deep Water (LCDW) can be fully explained by ~ 30:70 percentage contributions of these respective end-members.

Linkage and Association Analysis of Radiation Damage Repair Genes XRCC3 and XRCC5 with Nevus Density in Adolescent Twins

Previous studies have shown that a deficiency in DNA damage repair is associated with increased cancer risk, and exposure to UV radiation is a major risk factor for the development of malignant melanoma. High density of common nevi (moles) is a major risk factor for cutaneous melanoma. A nevus may result from a mutation in a single UV-exposed melanocyte which failed to repair DNA damage in one or more critical genes. XRCC3 and XRCC5 may have an effect on nevus count through their function as components of DNA repair processes that may be involved directly or indirectly in the repair of DNA damage due to UV radiation. This study aims to test the hypothesis that the frequency of flat or raised moles is associated with polymorphism at or near these DNA repair genes, and that certain alleles are associated with less efficient DNA repair, and greater nevus density. Twins were recruited from schools in south eastern Queensland and were examined close to their 12th birthday. Nurses examined each individual and counted all moles on the entire body surface. A 10cM genome scan of 274 families (642 individuals) was performed and microsatellite polymorphisms in XRCC3 and adjacent to XRCC5 were also typed. Linkage and association of nevus count to these loci were tested simultaneously using a structural-equation modeling approach implemented in MX. There is weak evidence for linkage of XRCC5 to a QTL influencing raised mole count, and also weak association. There is also weak evidence for association between flat mole count and XRCC3. No tests were significant after correction for testing multiple alleles, nor were any of the tests for total association significant. If variation in XRCC3 or XRCC5 influences UV sensitivity, and indirectly affects nevus density, then the effects are small.

Linkage disequilibrium between a melanin-based colour polymorphism and tail length in the barn owl

A linkage disequilibrium between sexually selected and life history traits can be explained by three mutually non-exclusive mechanisms. Genes coding for two traits may be located close on the same chromosome, genes responsible for variation in one of the trait may pleiotropically alter the other, and non-random pairing with respect to two traits may generate a non-physical linkage disequilibrium between their genes. Knowledge of which of these three mechanisms is responsible for a covariation between two traits is of interest to understand why differently ornamented individuals differ in several phenotypic aspects. In Switzerland, barn owls Tyto alba mate randomly with respect to a colour polymorphism generating a large range of variants between reddish-brown and white, males being lighter coloured than females. Several studies have shown that plumage coloration is not neutral with respect to some life history components. To test whether coloration is genetically associated with body size, partial cross-fostering experiments were performed by exchanging some hatchlings between nests. These experiments showed that darker biological fathers produce longer-tailed offspring. This sex-specific pattern is consistent with the hypothesis of non-physical linkage disequilibrium. In line with this hypothesis, darker coloured males were mated with longer-tailed females, whereas female coloration was not associated with tail length of their mate. The finding that dark nestlings had a longer tail than their pale siblings also supports the physical linkage and pleiotropy hypotheses. Therefore, non-random pairing can generate or strengthen a genetic covariation between a secondary sexual character and a morphological trait.

Chromosomal organization and evolutionary conservation of the human chromosome 19q linkage group containing three DNA repair genes

A series of human-rodent somatic cell hybrids were investigated by Southern blot analysis for the presence or absence of twenty-six molecular markers and three isozyme loci from human chromosome 19. Based on the co-retention of these markers in the various independent hybrid clones containing portions of human chromosome 19 and on pulsed field mapping, chromosome 19 is divided into twenty ordered regions. The most likely marker order for the chromosome is: (LDLR, C3)-(cen-MANNB)-D19S7-PEPD-D19S9-GPI-TGF$ \beta$-(CYP2A, NCA, CGM2, BCKAD)-PSG1a-(D19S8, XRCC1)-(D19S19, ATP1A3)-(D19S37, APOC2)-CKMM-ERCC2-ERCC1-(D19S62, D19S51)-D19S6-D19S50-D19S22-(CGB, FTL)-qter.^ The region of 19q between the proximal marker D19S7 and the distal gene coding for the beta subunit of chorionic gonadotropin (CGB) is about 37 Mb in size and covers about 37 cM genetic distance. The ration of genetic to physical distance on 19q is therefore very close to the genomic average OF 1 cM/Mb. Estimates of physical distances for intervals between chromosome 19 markers were calculated using a mapping function which estimates distances based on the number of breaks in hybrid clone panels. The consensus genetic distances between individual markers (established at HBM10) were compared to these estimates of physical distances. The close agreement between the two estimates suggested that spontaneously broken hybrids are as appropriate for this type of study as radiation hybrids.^ All three DNA repair genes located on chromosome 19 were found to have homologues on Chinese hamster chromosome 9, which is hemizygous in CHO cells, providing an explanation for the apparent ease with which mutations at these loci were identified in CHO cells. Homologues of CKMM and TGF$\beta$ (from human chromosome 19q) and a mini-satellite DNA specific to the distal region of human chromosome 19q were also mapped to Chinese hamster 9. Markers from 19p did not map to this hamster chromosome. Thus the q-arm of chromosome 19, at least between the genes PEPD and ERCC1, appears to be a linkage group which is conserved intact between humans and Chinese hamsters. ^

LINKAGE RELATIONSHIPS AMONG PROTEIN-CODING LOCI IN FISHES OF THE GENUS XIPHOPHORUS

Inbred strains of three species of fishes of the genus Xiphophorus (platyfish and swordtails) were crossed to produce intra- and interspecific F(,1) hybrids, which were then backcrossed to one or both parental stocks. Backcross hybrids were used for the analysis of segregation and linkage of 33 protein-coding loci (whose products were visualized by starch gel electrophoresis) and a sex-linked pigment pattern gene. Segregation was Mendelian for all loci with the exception of one instance of segregation distortion. Six linkage groups of enzyme-coding loci were established: LG I, ADA --6%-- G(,6)PD --24%-- 6PGD; LG II, Est-2 --27%-- Est-3 --0%-- Est-5 --23%-- LDH-1 --16%-- MPI; LG III, AcPh --38%-- G(,3)PD-1 (GUK-2 --14%-- G(,3)PD-1 is also in LG III, but the position of GUK-2 with respect to AcPh has not yet been determined); LG IV, GPI-1 --41%-- IDH-1; LG V, Est-1 --38%-- MDH-2; and LG VI, P1P --7%-- UMPK-1 (P1P is a plasma protein, very probably transferrin).^ Sex-specific recombination appeared absent in LG II and LG IV locus pairs; significantly higher male recombination was demonstrated in LG I but significantly higher female recombination was detected in LG V. Only one significant population-specific difference in recombination was detected, in the G(,6)PD - 6PGD region of LG I; the notable absence of such effects implies close correspondence of the genomes of the species used in the study. Two cases of possible evolutionary conservation of linkage groups in fishes and mammals were described, involving the G(,6)PD - 6PGD linkage in LG I and the cluster of esterase loci in LG II. One clear case of divergence was observed, that of the linkage of ADA in LG I. It was estimated that a minimum of (TURN)50% of the Xiphophorus genome was marked by the loci studied. Therefore, the prior probability that a new locus will assort independently from the markers already established is estimated to be less than 0.5. A maximum of 21 of the 24 pairs of chromosomes could be marked with at least one locus.^ Only the two LG V loci showed a significant association with a postulated gene controlling the severity of a genetically controlled melanoma caused by abnormal proliferation of macromelanophore pigment pattern cells. The independence of melanotic severity from all other informative markers implies that one or at most a few major genes are involved in control of melanotic severity in this system. ^

The impact of childhood residential mobility on mental health outcomes in adolescence and early adulthood: a record linkage study.

Background Understanding the causes of poor mental health in early childhood and adolescence is important as this can be a significant determinant of mental well-being in later years. One potential and relatively unexplored factor is residential mobility in formative years. Previous studies have been relatively small and potentially limited due to methodological issues. The main aim of this study was to investigate the relationship between early residential instability and poor mental health among adolescents and young adults in Northern Ireland.

Methods A Census-based record linkage study of 28% of children aged 0–8 years in 2001 in Northern Ireland (n=49 762) was conducted, with six monthly address change assessments from health registration data and self-reported mental health status from the 2011 Census. Logistic regression models were built adjusting for socioeconomic status (SES), household composition and marital dissolution.

Results There was a graded relationship between the number of address changes and mental ill-health (adjusted OR 3.67, 95% CIs 2.11 to 6.39 for 5 or more moves). This relationship was not modified by SES or household composition. Marital dissolution was associated with poor mental health but did not modify the relationship between address change and mental health (p=0.206). There was some indication that movement after the age of five was associated with an increased likelihood of poor mental health.

Conclusions This large study clearly confirms the close relationship between address change in early years and later poor mental health. Residential mobility may be a useful marker for children at risk of poorer mental health in adolescence and early adulthood