Theory Summary and Future Directions

Summary talk at the Lepton-Photon Symposium, Cornell University, Aug. 10-15, 1993.Comment: (Talk presented at the Lepton-Photon Symposium, Cornell University, Aug. 10-15, 1993.) 19 page

An SNP-Based Linkage Map for Zebrafish Reveals Sex Determination Loci

A surprising diversity of mechanisms controls sex determination of vertebrate organisms, even among closely related species. Both genetic and temperature-dependent systems of sex determination have been described in teleost fish. In the common zebrafish model organism, heteromorphic sex chromosomes are not observed, and the potential role of a genetic component of sex determination remains largely unknown. Here we report a genome-wide linkage study of sex determination in zebrafish using a novel SNP genetic map. We identified loci on zebrafish chromosomes 5 (LOD score 7.9) and 16 (LOD score 9.3) governing sex determination as a complex trait, rather than as an XY or ZW genetic system. Each of these loci contains a prominent candidate gene with a conserved role in sex determination across additional species that suggest potential mechanisms of sex determination in zebrafish. The chromosome 5 locus harbors dmrt1, a key gene in sex determination from fruit flies to humans; mutation of the human DMRT1 ortholog is a cause of complete sex reversal of XY individuals. The chromosome 16 locus harbors cyp21a2; mutation of the human CYP21A2 ortholog is one of the more common causes of pseudohermaphroditism. Mutation detection at each of these candidate genes within the zebrafish cross identified hypomorphic variants on the female-associated allele of each locus. The two loci together accounted for 16% of variance of the trait. Interacting environmental cues are likely to be an additional important component of sex determination in zebrafish

Sec24D-Dependent Transport of Extracellular Matrix Proteins Is Required for Zebrafish Skeletal Morphogenesis

Protein transport from endoplasmic reticulum (ER) to Golgi is primarily conducted by coated vesicular carriers such as COPII. Here, we describe zebrafish bulldog mutations that disrupt the function of the cargo adaptor Sec24D, an integral component of the COPII complex. We show that Sec24D is essential for secretion of cartilage matrix proteins, whereas the preceding development of craniofacial primordia and pre-chondrogenic condensations does not depend on this isoform. Bulldog chondrocytes fail to secrete type II collagen and matrilin to extracellular matrix (ECM), but membrane bound receptor β1-Integrin and Cadherins appear to leave ER in Sec24D-independent fashion. Consequently, Sec24D-deficient cells accumulate proteins in the distended ER, although a subset of ER compartments and Golgi complexes as visualized by electron microscopy and NBD C6-ceramide staining appear functional. Consistent with the backlog of proteins in the ER, chondrocytes activate the ER stress response machinery and significantly upregulate BiP transcription. Failure of ECM secretion hinders chondroblast intercalations thus resulting in small and malformed cartilages and severe craniofacial dysmorphology. This defect is specific to Sec24D mutants since knockdown of Sec24C, a close paralog of Sec24D, does not result in craniofacial cartilage dysmorphology. However, craniofacial development in double Sec24C/Sec24D-deficient animals is arrested earlier than in bulldog/sec24d, suggesting that Sec24C can compensate for loss of Sec24D at initial stages of chondrogenesis, but Sec24D is indispensable for chondrocyte maturation. Our study presents the first developmental perspective on Sec24D function and establishes Sec24D as a strong candidate for cartilage maintenance diseases and craniofacial birth defects

A major zebrafish polymorphism resource for genetic mapping

645,088 candidate polymorphisms in zebrafish were identified and positioned on genetic and physical maps as a resource for positional cloning

Visualizing spatially correlated dynamics that directs RNA conformational transitions

RNAs fold into three- dimensional ( 3D) structures that subsequently undergo large, functionally important, conformational transitions in response to a variety of cellular signals(1-3). RNA structures are believed to encode spatially tuned flexibility that can direct transitions along specific conformational pathways(4,5). However, this hypothesis has proved difficult to examine directly because atomic movements in complex biomolecules cannot be visualized in 3D by using current experimental methods. Here we report the successful implementation of a strategy using NMR that has allowed us to visualize, with complete 3D rotational sensitivity, the dynamics between two RNA helices that are linked by a functionally important trinucleotide bulge over timescales extending up to milliseconds. The key to our approach is to anchor NMR frames of reference onto each helix and thereby directly measure their dynamics, one relative to the other, using 'relativistic' sets of residual dipolar couplings ( RDCs)(6,7). Using this approach, we uncovered super- large amplitude helix motions that trace out a surprisingly structured and spatially correlated 3D dynamic trajectory. The two helices twist around their individual axes by approximately 536 and 1106 in a highly correlated manner ( R = 0.97) while simultaneously ( R = 0.81 - 0.92) bending by about 94 degrees. Remarkably, the 3D dynamic trajectory is dotted at various positions by seven distinct ligand- bound conformations of the RNA. Thus even partly unstructured RNAs can undergo structured dynamics that directs ligand- induced transitions along specific predefined conformational pathways.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62506/1/nature06389.pd

Fanny Copeland and the geographical imagination

Raised in Scotland, married and divorced in the English south, an adopted Slovene, Fanny Copeland (1872 – 1970) occupied the intersection of a number of complex spatial and temporal conjunctures. A Slavophile, she played a part in the formation of what subsequently became the Kingdom of Yugoslavia that emerged from the First World War. Living in Ljubljana, she facilitated the first ‘foreign visit’ (in 1932) of the newly formed Le Play Society (a precursor of the Institute of British Geographers) and guided its studies of Solčava (a then ‘remote’ Alpine valley system) which, led by Dudley Stamp and commended by Halford Mackinder, were subsequently hailed as a model for regional studies elsewhere. Arrested by the Gestapo and interned in Italy during the Second World War, she eventually returned to a socialist Yugoslavia, a celebrated figure. An accomplished musician, linguist, and mountaineer, she became an authority on (and populist for) the Julian Alps and was instrumental in the establishment of the Triglav National Park. Copeland’s role as participant observer (and protagonist) enriches our understanding of the particularities of her time and place and illuminates some inter-war relationships within G/geography, inside and outside the academy, suggesting their relative autonomy in the production of geographical knowledge

Brain volumes and functional outcomes in children without cerebral palsy after therapeutic hypothermia for neonatal hypoxic-ischaemic encephalopathy

Aim: To investigate whether brain volumes were reduced in children aged 6 to 8 years without cerebral palsy, who underwent therapeutic hypothermia for neonatal hypoxic-ischaemic encephalopathy (patients), and matched controls, and to examine the relation between subcortical volumes and functional outcome.   Method: We measured regional brain volumes in 31 patients and 32 controls (median age 7 years and 7 years 2 months respectively) from T1-weighted magnetic resonance imaging (MRI). We assessed cognition using the Wechsler Intelligence Scales for Children, Fourth Edition and motor ability using the Movement Assessment Battery for Children, Second Edition (MABC-2).  Results: Patients had lower volume of whole-brain grey matter, white matter, pallidi, hippocampi, and thalami than controls (false discovery rate-corrected p < 0.05). Differences in subcortical grey-matter volumes were not independent of total brain volume (TBV). In patients, hippocampal and thalamic volumes correlated with full-scale IQ (hippocampi, r = 0.477, p = 0.010; thalami, r = 0.452, p = 0.016) and MABC-2 total score (hippocampi, r = 0.526, p = 0.004; thalami, r = 0.505, p = 0.006) independent of age, sex, and TBV. No significant correlations were found in controls. In patients, cortical injury on neonatal MRI was associated with reduced volumes of hippocampi (p = 0.001), thalami (p = 0.002), grey matter (p = 0.015), and white matter (p = 0.013).  Interpretation: Children who underwent therapeutic hypothermia have reduced whole-brain grey and white-matter volumes, with associations between hippocampal and thalamic volumes and functional outcomes

β-delayed γ-proton decay in 56Zn: analysis of the charged-particle spectrum

A study of the beta decay of the proton-rich T-z = 2 nucleus Zn-56 has been reported in a recent publication. A rare and exotic decay mode, beta-delayed gamma-proton decay, has been observed there for the first time in the fp shell. Here, we expand on some of the details of the data analysis, focussing on the charged particle spectrum