Genetics publications

Permanent URI for this collection

https://hdl.handle.net/2440/11376

Browse

Now showing 1 - 20 of 446

Open Access
A conserved supergene locus controls colour pattern diversity in Heliconius butterflies
(Public Library of Science, 2006) Joron, M.; Papa, R.; Beltrán, M.; Chamberlain, N.; Mavárez, J.; Baxter, S.; Abanto, M.; Bermingham, E.; Humphray, S.J.; Rogers, J.; Beasley, H.; Barlow, K.; Ffrench-Constant, R.H.; Mallet, J.; McMillan, W.O.; Jiggins, C.D.; Noor, M.A.F.
We studied whether similar developmental genetic mechanisms are involved in both convergent and divergent evolution. Mimetic insects are known for their diversity of patterns as well as their remarkable evolutionary convergence, and they have played an important role in controversies over the respective roles of selection and constraints in adaptive evolution. Here we contrast three butterfly species, all classic examples of Müllerian mimicry. We used a genetic linkage map to show that a locus, Yb, which controls the presence of a yellow band in geographic races of Heliconius melpomene, maps precisely to the same location as the locus Cr, which has very similar phenotypic effects in its co-mimic H. erato. Furthermore, the same genomic location acts as a "supergene", determining multiple sympatric morphs in a third species, H. numata. H. numata is a species with a very different phenotypic appearance, whose many forms mimic different unrelated ithomiine butterflies in the genus Melinaea. Other unlinked colour pattern loci map to a homologous linkage group in the co-mimics H. melpomene and H. erato, but they are not involved in mimetic polymorphism in H. numata. Hence, a single region from the multilocus colour pattern architecture of H. melpomene and H. erato appears to have gained control of the entire wing-pattern variability in H. numata, presumably as a result of selection for mimetic "supergene" polymorphism without intermediates. Although we cannot at this stage confirm the homology of the loci segregating in the three species, our results imply that a conserved yet relatively unconstrained mechanism underlying pattern switching can affect mimicry in radically different ways. We also show that adaptive evolution, both convergent and diversifying, can occur by the repeated involvement of the same genomic regions.
Metadata only
A custom hybridisation enrichment forensic intelligence panel to infer biogeographic ancestry, hair and eye colour, and Y chromosome lineage
(Elsevier, 2022) Bardan, F.; Higgins, D.; Austin, J.J.
Massively parallel sequencing can provide genetic data for hundreds to thousands of loci in a single assay for various types of forensic testing. However, available commercial kits require an initial PCR amplification of short-to-medium sized targets which limits their application for highly degraded DNA. Development and optimisation of large PCR multiplexes also prevents creation of custom panels that target different suites of markers for identity, biogeographic ancestry, phenotype, and lineage markers (Y-chromosome and mtDNA). Hybridisation enrichment, an alternative approach for target enrichment prior to sequencing, uses biotinylated probes to bind to target DNA and has proven successful on degraded and ancient DNA. We developed a customisable hybridisation capture method, that uses individually mixed baits to allow tailored and targeted enrichment to specific forensic questions of interest. To allow collection of forensic intelligence data, we assembled and tested a custom panel of hybridisation baits to infer biogeographic ancestry, hair and eye colour, and paternal lineage (and sex) on modern male and female samples with a range of self-declared ancestries and hair/eye colour combinations. The panel correctly estimated biogeographic ancestry in 9/12 samples (75%) but detected European admixture in three individuals from regions with admixed demographic history. Hair and eye colour were predicted correctly in 83% and 92% of samples respectively, where intermediate eye colour and blond hair were problematic to predict. Analysis of Y-chromosome SNPs correctly assigned sex and paternal haplogroups, the latter complementing and supporting biogeographic ancestry predictions. Overall, we demonstrate the utility of this hybridisation enrichment approach to forensic intelligence testing using a combined suite of biogeographic ancestry, phenotype, and Y-chromosome SNPs for comprehensive biological profiling.
Open Access
A flexible brace maintains the assembly of a hexameric replicative helicase during DNA unwinding
(Oxford University Press, 2012) Whelan, F.; Stead, J.A.; Shkumatov, A.V.; Svergun, D.I.; Sanders, C.M.; Antson, A.A.
The mechanism of DNA translocation by papillomavirus E1 and polyomavirus LTag hexameric helicases involves consecutive remodelling of subunit-subunit interactions around the hexameric ring. Our biochemical analysis of E1 helicase demonstrates that a 26-residue C-terminal segment is critical for maintaining the hexameric assembly. As this segment was not resolved in previous crystallographic analysis of E1 and LTag hexameric helicases, we determined the solution structure of the intact hexameric E1 helicase by Small Angle X-ray Scattering. We find that the C-terminal segment is flexible and occupies a cleft between adjacent subunits in the ring. Electrostatic potential calculations indicate that the negatively charged C-terminus can bridge the positive electrostatic potentials of adjacent subunits. Our observations support a model in which the C-terminal peptide serves as a flexible 'brace' maintaining the oligomeric state during conformational changes associated with ATP hydrolysis. We argue that these interactions impart processivity to DNA unwinding. Sequence and disorder analysis suggest that this mechanism of hexamer stabilization would be conserved among papillomavirus E1 and polyomavirus LTag hexameric helicases.
Metadata only
A generic method of engagement to elicit regional coastal management options
(Elsevier, 2016) Dichmont, C.; Dutra, L.; Owens, R.; Jebreen, E.; Thompson, C.; Deng, R.; van Putten, E.; Pascual, R.; Dambacher, J.; Warne, M.; Quinn, R.; Thébaud, O.; Bennett, J.; Read, M.; Wachenfeld, D.; Davies, J.; Garland, A.; Dunning, M.; Collier, C.; Waycott, M.; et al.
Abstract not available
Open Access
A genome-wide association study of mitochondrial DNA copy number in two population-based cohorts
(BioMed Central, 2019) Guyatt, A.L.; Brennan, R.R.; Burrows, K.; Guthrie, P.A.I.; Ascione, R.; Ring, S.M.; Gaunt, T.R.; Pyle, A.; Cordell, H.J.; Lawlor, D.A.; Chinnery, P.F.; Hudson, G.; Rodriguez, S.
BACKGROUND:Mitochondrial DNA copy number (mtDNA CN) exhibits interindividual and intercellular variation, but few genome-wide association studies (GWAS) of directly assayed mtDNA CN exist. We undertook a GWAS of qPCR-assayed mtDNA CN in the Avon Longitudinal Study of Parents and Children (ALSPAC) and the UK Blood Service (UKBS) cohort. After validating and harmonising data, 5461 ALSPAC mothers (16-43 years at mtDNA CN assay) and 1338 UKBS females (17-69 years) were included in a meta-analysis. Sensitivity analyses restricted to females with white cell-extracted DNA and adjusted for estimated or assayed cell proportions. Associations were also explored in ALSPAC children and UKBS males. RESULTS:A neutrophil-associated locus approached genome-wide significance (rs709591 [MED24], β (change in SD units of mtDNA CN per allele) [SE] - 0.084 [0.016], p = 1.54e-07) in the main meta-analysis of adult females. This association was concordant in magnitude and direction in UKBS males and ALSPAC neonates. SNPs in and around ABHD8 were associated with mtDNA CN in ALSPAC neonates (rs10424198, β [SE] 0.262 [0.034], p = 1.40e-14), but not other study groups. In a meta-analysis of unrelated individuals (N = 11,253), we replicated a published association in TFAM (β [SE] 0.046 [0.017], p = 0.006), with an effect size much smaller than that observed in the replication analysis of a previous in silico GWAS. CONCLUSIONS:In a hypothesis-generating GWAS, we confirm an association between TFAM and mtDNA CN and present putative loci requiring replication in much larger samples. We discuss the limitations of our work, in terms of measurement error and cellular heterogeneity, and highlight the need for larger studies to better understand nuclear genomic control of mtDNA copy number.
Open Access
A genome-wide scan for signatures of selection in Azeri and Khuzestani buffalo breeds
(BMC, 2018) Mokhber, M.; Moradi-Shahrbabak, M.; Sadeghi, M.; Moradi-Shahrbabak, H.; Stella, A.; Nicolzzi, E.; Rahmaninia, J.; Williams, J.
Background: Identification of genomic regions that have been targets of selection may shed light on the genetic history of livestock populations and help to identify variation controlling commercially important phenotypes. The Azeri and Kuzestani buffalos are the most common indigenous Iranian breeds which have been subjected to divergent selection and are well adapted to completely different regions. Examining the genetic structure of these populations may identify genomic regions associated with adaptation to the different environments and production goals. Results: A set of 385 water buffalo samples from Azeri (N = 262) and Khuzestani (N = 123) breeds were genotyped using the Axiom® Buffalo Genotyping 90 K Array. The unbiased fixation index method (FST) was used to detect signatures of selection. In total, 13 regions with outlier FST values (0.1%) were identified. Annotation of these regions using the UMD3.1 Bos taurus Genome Assembly was performed to find putative candidate genes and QTLs within the selected regions. Putative candidate genes identified include FBXO9, NDFIP1, ACTR3, ARHGAP26, SERPINF2, BOLA-DRB3, BOLA-DQB, CLN8, and MYOM2. Conclusions: Candidate genes identified in regions potentially under selection were associated with physiological pathways including milk production, cytoskeleton organization, growth, metabolic function, apoptosis and domestication-related changes include immune and nervous system development. The QTL identified are involved in economically important traits in buffalo related to milk composition, udder structure, somatic cell count, meat quality, and carcass and body weight.
Open Access
A Genome-Wide survey of imprinted genes in rice seeds reveals imprinting primarily occurs in the endosperm
(Public Library Science, 2011) Luo, M.; Taylor, J.; Spriggs, A.; Zhang, H.; Wu, X.; Russell, S.; Singh, M.; Koltunow, A.; Kakutani, T.
Genomic imprinting causes the expression of an allele depending on its parental origin. In plants, most imprinted genes have been identified in Arabidopsis endosperm, a transient structure consumed by the embryo during seed formation. We identified imprinted genes in rice seed where both the endosperm and embryo are present at seed maturity. RNA was extracted from embryos and endosperm of seeds obtained from reciprocal crosses between two subspecies Nipponbare (Japonica rice) and 93-11 (Indica rice). Sequenced reads from cDNA libraries were aligned to their respective parental genomes using single-nucleotide polymorphisms (SNPs). Reads across SNPs enabled derivation of parental expression bias ratios. A continuum of parental expression bias states was observed. Statistical analyses indicated 262 candidate imprinted loci in the endosperm and three in the embryo (168 genic and 97 non-genic). Fifty-six of the 67 loci investigated were confirmed to be imprinted in the seed. Imprinted loci are not clustered in the rice genome as found in mammals. All of these imprinted loci were expressed in the endosperm, and one of these was also imprinted in the embryo, confirming that in both rice and Arabidopsis imprinted expression is primarily confined to the endosperm. Some rice imprinted genes were also expressed in vegetative tissues, indicating that they have additional roles in plant growth. Comparison of candidate imprinted genes found in rice with imprinted candidate loci obtained from genome-wide surveys of imprinted genes in Arabidopsis to date shows a low degree of conservation, suggesting that imprinting has evolved independently in eudicots and monocots.
Metadata only
A genomic Neolithic time transect of hunter-farmer admixture in central Poland
(Nature Publishing Group, 2018) Fernandes, D.M.; Strapagiel, D.; Borówka, P.; Marciniak, B.; Żądzińska, E.; Sirak, K.; Siska, V.; Grygiel, R.; Carlsson, J.; Manica, A.; Lorkiewicz, W.; Pinhasi, R.
Ancient DNA genome-wide analyses of Neolithic individuals from central and southern Europe indicate an overall population turnover pattern in which migrating farmers from Anatolia and the Near East largely replaced autochthonous Mesolithic hunter-gatherers. However, the genetic history of the Neolithic transition in areas lying north of the European Neolithic core region involved different levels of admixture with hunter-gatherers. Here we analyse genome-wide data of 17 individuals spanning from the Middle Neolithic to the Early Bronze Age (4300-1900 BCE) in order to assess the Neolithic transition in north-central Poland, and the local impacts of hunter-farmer contacts and Late Neolithic steppe migrations. We evaluate the influence of these on local populations and assess if and how they change through time, reporting evidence of recurrent hunter-farmer admixture over three millennia, and the co-existence of unadmixed hunter-gatherers as late as 4300 BCE. During the Late Neolithic we report the appearance of steppe ancestry, but on a lesser scale than previously described for other central European regions, with evidence of stronger affinities to hunter-gatherers than to steppe pastoralists. These results help understand the Neolithic palaeogenomics of another central European area, Kuyavia, and highlight the complexity of population interactions during those times.
Metadata only
A genotype-first approach identifies an intellectual disability-overweight syndrome caused by PHIP haploinsufficiency
(Nature, 2018) Jansen, S.; Hoischen, A.; Coe, B.; Carvill, G.; van Esch, H.; Bosch, D.; Andersen, U.; Baker, C.; Bauters, M.; Bernier, R.; van Bon, B.; Claahsen-van der Grinten, H.; Gecz, J.; Gilissen, C.; Grillo, L.; Hackett, A.; Kleefstra, T.; Koolen, D.; Kvarnung, M.; Larsen, M.; et al.
Genotype-first combined with reverse phenotyping has shown to be a powerful tool in human genetics, especially in the era of next generation sequencing. This combines the identification of individuals with mutations in the same gene and linking these to consistent (endo)phenotypes to establish disease causality. We have performed a MIP (molecular inversion probe)-based targeted re-sequencing study in 3,275 individuals with intellectual disability (ID) to facilitate a genotype-first approach for 24 genes previously implicated in ID. Combining our data with data from a publicly available database, we confirmed 11 of these 24 genes to be relevant for ID. Amongst these, PHIP was shown to have an enrichment of disruptive mutations in the individuals with ID (5 out of 3,275). Through international collaboration, we identified a total of 23 individuals with PHIP mutations and elucidated the associated phenotype. Remarkably, all 23 individuals had developmental delay/ID and the majority were overweight or obese. Other features comprised behavioral problems (hyperactivity, aggression, features of autism and/or mood disorder) and dysmorphisms (full eyebrows and/or synophrys, upturned nose, large ears and tapering fingers). Interestingly, PHIP encodes two protein-isoforms, PHIP/DCAF14 and NDRP, each involved in neurodevelopmental processes, including E3 ubiquitination and neuronal differentiation. Detailed genotype-phenotype analysis points towards haploinsufficiency of PHIP/DCAF14, and not NDRP, as the underlying cause of the phenotype. Thus, we demonstrated the use of large scale re-sequencing by MIPs, followed by reverse phenotyping, as a constructive approach to verify candidate disease genes and identify novel syndromes, highlighted by PHIP haploinsufficiency causing an ID-overweight syndrome.
Open Access
A global cline in a colour polymorphism suggests a limited contribution of gene flow towards the recovery of a heavily exploited marine mammal
(Royal Society, 2018) Hoffman, J.I.; Bauer, E.; Paijmans, A.J.; Humble, E.; Beckmann, L.M.; Kubetschek, C.; Christaller, F.; Kröcker, N.; Fuchs, B.; Moreras, A.; Shihlomule, Y.D.; Bester, M.N.; Cleary, A.C.; De Bruyn, P.J.N.; Forcada, J.; Goebel, M.E.; Goldsworthy, S.D.; Guinet, C.; Hoelzel, A.R.; Lydersen, C.; et al.
Evaluating how populations are connected by migration is important for understanding species resilience because gene flow can facilitate recovery from demographic declines. We therefore investigated the extent to which migration may have contributed to the global recovery of the Antarctic fur seal (Arctocephalus gazella), a circumpolar distributed marine mammal that was brought to the brink of extinction by the sealing industry in the eighteenth and nineteenth centuries. It is widely believed that animals emigrating from South Georgia, where a relict population escaped sealing, contributed to the re-establishment of formerly occupied breeding colonies across the geographical range of the species. To investigate this, we interrogated a genetic polymorphism (S291F) in the melanocortin 1 receptor gene, which is responsible for a cream-coloured phenotype that is relatively abundant at South Georgia and which appears to have recently spread to localities as far afield as Marion Island in the sub-Antarctic Indian Ocean. By sequencing a short region of this gene in 1492 pups from eight breeding colonies, we showed that S291F frequency rapidly declines with increasing geographical distance from South Georgia, consistent with locally restricted gene flow from South Georgia mainly to the South Shetland Islands and Bouvetøya. The S291F allele was not detected farther afield, suggesting that although emigrants from South Georgia may have been locally important, they are unlikely to have played a major role in the recovery of geographically more distant populations.
Metadata only
A high-resolution genetic map of the familial Mediterranean fever candidate region allows identification of haplotype-sharing among ethnic groups
(ACADEMIC PRESS INC ELSEVIER SCIENCE, 1997) Balow Jnr., J.; Shelton, D.; Orsborn, A.; Mangelsdorf, M.; Aksentijevich, I.; Blake, T.; Sood, R.; Gardner, D.; Liu, R.; Pras, E.; Levy, E.; Centola, M.; Deng, Z.; Zaks, N.; Wood, G.; Chen, X.; Richards, N.; Shohat, M.; Livneh, A.; Pras, M.; et al.
Familial Mediterranean fever (FMF) is a recessive disorder of inflammation caused by mutations in a gene (designated MEFV) on chromosome 16p13.3. We have recently constructed a 1-Mb cosmid contig that includes the FMF critical region. Here we show genotype data for 12 markers from our physical map, including 5 newly identified microsatellites, in FMF families. Intrafamilial recombinations placed MEFV in the approximately 285 kb between D16S468/D16S3070 and D16S3376. We observed significant linkage disequilibrium in the North African Jewish population, and historical recombinants in the founder haplotype placed MEFV between D16S3082 and D16S3373 (approximately 200 kb). In smaller panels of Iraqi Jewish, Arab, and Armenian families, there were significant allelic associations only for D16S3370 and D16S2617 among the Armenians. A sizable minority of Iraqi Jewish and Armenian carrier chromosomes appeared to be derived from the North African Jewish ancestral haplotype. We observed a unique FMF haplotype common to Iraqi Jews, Arabs, and Armenians and two other haplotypes restricted to either the Iraqi Jewish or the Armenian population. These data support the view that a few major mutations account for a large percentage of the cases of FMF and suggest that some of these mutations arose before the affected Middle Eastern populations diverged from one another.
Open Access
A hyperactive sleeping beauty transposase enhances transgenesis in zebrafish embryos
(BioMed Central Ltd., 2010) Newman, M.; Lardelli, M.
Background: Transposons are useful molecular tools for transgenesis. The 'sleeping beauty' transposon is a synthetic member of the Tc1/mariner transposon family. Davidson et al. (2003) previously described a vector for zebrafish transgenesis consisting of the inverted repeats of 'sleeping beauty' flanking the gene to be transposed. Subsequently, there have been attempts to enhance the transpositional activity of 'sleeping beauty' by increasing the activity of its transposase. Recently, Mates et al. (2009) generated a hyperactive transposase giving a 100-fold increased transposition rate in mouse embryos. Findings: The aim of this experiment was to determine whether this novel hyperactive transposase enhances transgenesis in zebrafish embryos. Using our previously characterised mitfa-amyloidβ-GFP transgene, we observed an eight-fold enhancement in transient transgenesis following detection of transgene expression in melanophores by whole mount in-situ hybridisation. However, high rates of defective embryogenesis were also observed. Conclusion: The novel hyperactive 'sleeping beauty' transposase enhances the rate of transgenesis in zebrafish embryos.
Metadata only
A hypervariable middle repetitive DNA sequence from citrus
(Springer-Verlag, 1995) Orford, S.; Scott, N.; Timmis, J.
The use of hypervariable sequences for DNA typing of plants is focussed on microsatellites and on amplification of regions defined by random (RAPD) or defined (AFLP) primers for PCR analysis of genomes. A hypervariable length of middle repetitive DNA has been isolated from citrus that contains no obvious hypervariable structures. The fingerprinting probe was shown to have an important commercial application in the separation of zygotic from nucellar progeny. A somatic variant of the sequence within one orange tree suggests that somatic variation in hypervariable markers may be a common event.
Open Access
A meta-analysis of gene expression signatures of blood pressure and hypertension
(Public Library of Science (PLoS), 2015) Huan, T.; Esko, T.; Peters, M.; Pilling, L.; Schramm, K.; Schurmann, C.; Chen, B.; Liu, C.; Joehanes, R.; Johnson, A.; Yao, C.; Ying, S.; Courchesne, P.; Milani, L.; Raghavachari, N.; Wang, R.; Liu, P.; Reinmaa, E.; Dehghan, A.; Hofman, A.; et al.; McCarthy, M.
Genome-wide association studies (GWAS) have uncovered numerous genetic variants (SNPs) that are associated with blood pressure (BP). Genetic variants may lead to BP changes by acting on intermediate molecular phenotypes such as coded protein sequence or gene expression, which in turn affect BP variability. Therefore, characterizing genes whose expression is associated with BP may reveal cellular processes involved in BP regulation and uncover how transcripts mediate genetic and environmental effects on BP variability. A meta-analysis of results from six studies of global gene expression profiles of BP and hypertension in whole blood was performed in 7017 individuals who were not receiving antihypertensive drug treatment. We identified 34 genes that were differentially expressed in relation to BP (Bonferroni-corrected p<0.05). Among these genes, FOS and PTGS2 have been previously reported to be involved in BP-related processes; the others are novel. The top BP signature genes in aggregate explain 5%-9% of inter-individual variance in BP. Of note, rs3184504 in SH2B3, which was also reported in GWAS to be associated with BP, was found to be a trans regulator of the expression of 6 of the transcripts we found to be associated with BP (FOS, MYADM, PP1R15A, TAGAP, S100A10, and FGBP2). Gene set enrichment analysis suggested that the BP-related global gene expression changes include genes involved in inflammatory response and apoptosis pathways. Our study provides new insights into molecular mechanisms underlying BP regulation, and suggests novel transcriptomic markers for the treatment and prevention of hypertension.
Metadata only
A method to exploit the structure of genetic ancestry space to enhance case-control studies
(Elsevier, 2016) Bodea, C.A.; Neale, B.M.; Ripke, S.; Barclay, M.; Peyrin-Biroulet, L.; Chamaillard, M.; Colombel, J.F.; Cottone, M.; Croft, A.; D'Incà, R.; Halfvarson, J.; Hanigan, K.; Henderson, P.; Hugot, J.P.; Karban, A.; Kennedy, N.A.; Khan, M.A.; Lémann, M.; Levine, A.; Massey, D.; et al.
One goal of human genetics is to understand the genetic basis of disease, a challenge for diseases of complex inheritance because risk alleles are few relative to the vast set of benign variants. Risk variants are often sought by association studies in which allele frequencies in case subjects are contrasted with those from population-based samples used as control subjects. In an ideal world we would know population-level allele frequencies, releasing researchers to focus on case subjects. We argue this ideal is possible, at least theoretically, and we outline a path to achieving it in reality. If such a resource were to exist, it would yield ample savings and would facilitate the effective use of data repositories by removing administrative and technical barriers. We call this concept the Universal Control Repository Network (UNICORN), a means to perform association analyses without necessitating direct access to individual-level control data. Our approach to UNICORN uses existing genetic resources and various statistical tools to analyze these data, including hierarchical clustering with spectral analysis of ancestry; and empirical Bayesian analysis along with Gaussian spatial processes to estimate ancestry-specific allele frequencies. We demonstrate our approach using tens of thousands of control subjects from studies of Crohn disease, showing how it controls false positives, provides power similar to that achieved when all control data are directly accessible, and enhances power when control data are limiting or even imperfectly matched ancestrally. These results highlight how UNICORN can enable reliable, powerful, and convenient genetic association analyses without access to the individual-level data.
Metadata only
A molecular and evolutionary study of the β-globin gene family of the Australian marsupial Sminthopsis Crassicaudata
(SOC MOLECULAR BIOLOGY EVOLUTION, 1996) Cooper, S.; Murphy, R.; Dolman, G.; Hussey, D.; Hope, R.
Beta-globin gene families in eutherians (placental mammals) consist of a set of four or more developmentally regulated genes which are closely linked and, in general, arranged in the order 5'-embryonic/fetal genes-adult genes-3'. This cluster of genes is proposed to have arisen by tandem duplication of ancestral beta-globin genes, with the first duplication occurring 200 to 155 MYBP just prior to a period in mammalian evolution when eutherians and marsupials diverged from a common ancestor. In this paper we trace the evolutionary history of the beta-globin gene family back to the origins of these mammals by molecular characterization of the beta-globin gene family of the Australian marsupial Sminthopsis crassicaudata. Using Southern and restriction analysis of total genomic DNA and bacteriophage clones of beta-like globin genes, we provide evidence that just two functional beta-like globin genes exist in this marsupial, including one embryonic-expressed gene (S.c-epsilon) and one adult-expressed gene (S.c-beta), linked in the order 5'-epsilon-beta-3'. The entire DNA sequence of the adult beta-globin gene is reported and shown to be orthologous to the adult beta-globin genes of the North American marsupial Didelphis virginiana and eutherian mammals. These results, together with results from a phylogenetic analysis of mammalian beta-like globin genes, confirm the hypothesis that a two-gene cluster, containing an embryonic- and an adult-expressed beta-like globin gene, existed in the most recent common ancester of marsupials and eutherians. Northern analysis of total RNA isolated from embryos and neonatals indicates that a switch from embryonic to adult gene expression occurs at the time of birth, coinciding with the transfer of the marsupial from a uterus to a pouch environment.
Metadata only
A monophyletic origin of the B chromosomes of Brachycome dichromosomatica (Asteraceae)
(SPRINGER WIEN, 1999) Houben, A.; Thompson, N.; Ahne, R.; Leach, C.; Verlin, D.; Timmis, J.
The A and B chromosomes of different karyotype variants(cytodemes A1, A2, A3 and A4) of Brachycome dichromosomatica were analysed by computer-aided chromosome image analysis and fluorescence in situ hybridisation (FISH). Ribosomal DNA and the B chromosome-specific sequence Bd49 were detected on all B chromosomes. In addition to minor size variation of the Bs, polymorphism of the rDNA and Bd49 position and copy number revealed two major types of B chromosomes. The B chromosomes of all the cytodemes were indistinguishable from each other in length, but that of A3 showed evidence of rearrangements consistent with its long-term geographic isolation. The results presented suggest a monophyletic origin of the B chromosomes of B. dichromosomatica.
Open Access
A multidisciplinary review of the Inka imperial resettlement policy and implications for future investigations
(MDPI, 2021) Davidson, R.; Fehren-Schmitz, L.; Llamas, B.
The rulers of the Inka empire conquered approximately 2 million km² of the South American Andes in just under 100 years from 1438-1533 CE. Inside the empire, the elite conducted a systematic resettlement of the many Indigenous peoples in the Andes that had been rapidly colonised. The nature of this resettlement phenomenon is recorded within the Spanish colonial ethnohistorical record. Here we have broadly characterised the resettlement policy, despite the often incomplete and conflicting details in the descriptions. We then review research from multiple disciplines that investigate the empirical reality of the Inka resettlement policy, including stable isotope analysis, intentional cranial deformation morphology, ceramic artefact chemical analyses and genetics. Further, we discuss the benefits and limitations of each discipline for investigating the resettlement policy and emphasise their collective value in an interdisciplinary characterisation of the resettlement policy.
Metadata only
A myelopoiesis gene signature during remission in anti-neutrophil cytoplasm antibody-associated vasculitis does not predict relapses but seems to reflect ongoing prednisolone therapy
(Wiley, 2014) Kurz, T.; Weiner, M.; Skoglund, C.; Basnet, S.; Eriksson, P.; Segelmark, M.
A myelopoiesis gene signature in circulating leucocytes, exemplified by increased myeloperoxidase (MPO) and proteinase 3 (PR3) mRNA levels, has been reported in patients with active anti-neutrophil cytoplasm antibody-associated vasculitis (AAV), and to a lesser extent during remission. We hypothesized that this signature could predict disease relapse. mRNA levels of PR3, MPO, selected myelopoiesis transcription factors [CCAAT/enhancer binding protein α (CEBP-α), CCAAT/enhancer binding protein β (CEBP-β), SPI1/PU.1-related transcription factor (SPIB), spleen focus forming virus proviral integration oncogene, PU.1 homologue (SPI1)] and microRNAs (miRNAs) from patient and control peripheral blood mononuclear cells (PBMC) and polymorphonuclear cells (PMN) were analysed and associated with clinical data. Patients in stable remission had higher mRNA levels for PR3 (PBMC, PMN) and MPO (PBMC). PR3 and SPIB mRNA correlated positively in controls but negatively in patient PBMC. Statistically significant correlations existed between PR3 mRNA and several miRNAs in controls, but not in patients. PR3/MPO mRNA levels were not associated with previous or future relapses, but correlated with steroid treatment. Prednisolone doses were negatively linked to SPIB and miR-155-5p, miR-339-5p (PBMC) and to miR-221, miR-361 and miR-505 (PMN). PR3 mRNA in PBMC correlated with time since last flare, blood leucocyte count and estimated glomerular filtration rate. Our results show that elevated leucocyte PR3 mRNA levels in AAV patients in remission do not predict relapse. The origin seems multi-factorial, but to an important extent explainable by prednisolone action. Gene signatures in patients with AAV undergoing steroid treatment should therefore be interpreted accordingly.
Open Access
A nearly complete skeleton of a new eusphenodontian from the Upper Jurassic Morrison Formation, Wyoming, USA, provides insight into the evolution and diversity of Rhynchocephalia (Reptilia: Lepidosauria)
(Informa UK Limited, 2022) DeMar, D.G.; Jones, M.E.H.; Carrano, M.T.
We describe a new, small-bodied rhynchocephalian reptile, Opisthiamimus gregori gen. et sp. nov., from the Upper Jurassic Morrison Formation of Wyoming, USA. Whereas many fossil rhynchocephalians are based on isolated incomplete jaws, the holotype of O. gregori includes most of the skull and postcranium and therefore represents one of the most complete specimens of Rhynchocephalia known from North America. We used micro-computed tomography to examine its skeletal anatomy in detail and to develop a three-dimensional reconstruction of the skull. The skull of O. gregori is similar to that of several non-neosphenodontian rhynchocephalians such as Planocephalosaurus (e.g. large orbits) and Clevosaurus (e.g. parietal parasagittal crests) yet exhibits a suite of other features related to the proal shearing mechanism that becomes increasingly elaborated among more phylogenetically nested taxa such as Sphenodon (e.g. lateral palatine tooth row parallels maxillary tooth row along its entire length, pyramidal dentary teeth with mesial shearing crests). The postcranial skeleton of O. gregori exhibits characteristics typical of a terrestrial rhynchocephalian. Our phylogenetic analyses use a substantially updated data set of 118 characters and 46 taxa, and both maximum parsimony and Bayesian frameworks. Results place O. gregori inside Eusphenodontia but outside Neosphenodontia, and therefore in a key position for contributing to character polarity for more deeply nested clades such as Clevosauridae, Sphenodontidae and Pleurosauridae. We also erect Leptorhynchia taxon nov., composed primarily of aquatically adapted taxa (e.g. Pleurosaurus, Sapheosaurus), which is supported by both cranial and postcranial characters. Because O. gregori is not particularly closely related to the other named Morrison rhynchocephalians (e.g. Opisthias rarus), it increases both the alpha and beta taxonomic diversities within the formation. Similarly, major differences in body size and inferred diet of the Morrison taxa imply considerable concomitant palaeoecological diversity just prior to a major global decline in rhynchocephalian diversity around the close of the Jurassic.

Browse

Browsing Genetics publications by Title

Results Per Page

Sort Options