A highly polymorphic locus cloned from the breakpoint of a chromosome 11p13 deletion associated with the WAGR syndrome

Children with constitutional deletions of chromosome 11p13 suffer from aniridia, genitourinary malformations, and mental retardation and are predisposed to develop bilateral Wilms tumor (the WAGR syndrome). The critical region for these defects has been narrowed to a segment of band 11p13 between the catalase and the beta-follicle-stimulating hormone genes. In this report, we have cloned the endpoints from a WAGR patient whose large cytogenetic deletion, del(11)(p14.3::p13), does not include the catalase gene. The deletion was characterized using DNA polymorphisms and found to originate in the paternally derived chromosome 11. The distal endpoint was identified as a rearrangement of locus D11S21 in conventional Southern blots of the patient's genomic DNA, but was not detected in leukocyte DNA from either parent or in sperm DNA from the father. The proximal endpoint was isolated by cloning the junction fragment and was mapped in relation to other markers and breakpoints. It defines a new locus in 11p13-delta J, which is close to the Wilms tumor gene and the breakpoint cluster region (TCL2) of the frequent t(11;14)(p13;q11) translocation in acute T-cell leukemia. An unusual concentration of base pair substitutions was discovered at delta J, in which 9 of 44 restriction sites tested (greater than 20%) vary in the population. This property makes delta J one of the most polymorphic loci on chromosome 11 and may reflect an underlying instability that contributed to the original mutation. The breakpoint extends the genetic map of this region and provides a useful marker for linkage studies and the analysis of allelic segregation in tumor cells.     

Alcaloïdes d'Alstonia vitiensis var. Novo ebudica monachino

Five alkaloids have been isolated from Alstonia vitiensis: pleïocarpamine, vincorine, cabucraline, alstovine (11-methoxycompactinervine) and quaternoxine; the latter two are new alkaloids.     

Ultrastructure of trichoblasts in the red alga Osmundea spectabilis var. spectabilis (Rhodomelaceae,Ceramiales)

The apex of the tetrasporangial branches of Osmundea spectabilis var. spectabilis (= Laurencia spectabilis var. spectabilis) exhibits cavities in which tufts of multicellular trichoblasts occur. Trichoblast development in Osmundea spectabilis var. spectabilis begins with the differentiation of an epidermal cell within the crypt. This cell differentiates into a trichoblast mother cell (TMC). The TMC divides to form a two-celled incipient trichoblast. Successive periclinal divisions of the apical cell of the young trichoblast result in the formation of a multicellular developing trichoblast. With the exception of the apical cell all trichoblast cells are at the same developmental stage. They possess a large nucleus, abundant plastids with peripheral and some internal thylakoids and dictyosomes. Daughter chloroplasts result from one constriction or multiple fission of a single chloroplast. Dictyosomal cisternae and mucilage sacs contribute material to wall formation. Each differentiating trichoblast cell is surrounded by a bi-layered wall. The outer wall layer represents the trichoblast mother cell wall and the inner wall layer is the trichoblast cell wall. Mature trichoblast cells have thin walls, probably as a consequence of mucilage extrusion, the most likely function of trichoblasts in Osmundea.     

Exome sequencing discloses <Emphasis Type="Italic">KALRN</Emphasis> homozygous variant as likely cause of intellectual disability and short stature in a consanguineous pedigree

Background

The recent availability of whole-exome sequencing has opened new possibilities for the evaluation of individuals with genetically undiagnosed intellectual disability.

Results

We report two affected siblings, offspring of first-cousin parents, with intellectual disability, hypotonia, short stature, growth hormone deficiency, and delayed bone age. All members of the nuclear family were genotyped, and exome sequencing was performed in one of the affected individuals. We used an in-house algorithm (CATCH v1.1) that combines homozygosity mapping with exome sequencing results and provides a list of candidate variants. One identified novel homozygous missense variant in KALRN (NM_003947.4:c.3644C>A: p.(Thr1215Lys)) was predicted to be pathogenic by all pathogenicity prediction software used (SIFT, PolyPhen, Mutation Taster). KALRN encodes the protein kalirin, which is a GTP-exchange factor protein with a reported role in cytoskeletal remodeling and dendritic spine formation in neurons. It is known that mice with ablation of Kalrn exhibit age-dependent functional deficits and behavioral phenotypes.

Conclusion

Exome sequencing provided initial evidence linking KALRN to monogenic intellectual disability in man, and we propose that KALRN is the causative gene for the autosomal recessive phenotype in this family.

     

Exome sequences and multi‐environment field trials elucidate the genetic basis of adaptation in barley

Broadening the genetic base of crops is crucial for developing varieties to respond to global agricultural challenges such as climate change. Here, we analysed a diverse panel of 371 domesticated lines of the model crop barley to explore the genetics of crop adaptation. We first collected exome sequence data and phenotypes of key life history traits from contrasting multi‐environment common garden trials. Then we applied refined statistical methods, including some based on exomic haplotype states, for genotype‐by‐environment (G×E) modelling. Sub‐populations defined from exomic profiles were coincident with barley's biology, geography and history, and explained a high proportion of trial phenotypic variance. Clear G×E interactions indicated adaptation profiles that varied for landraces and cultivars. Exploration of circadian clock‐related genes, associated with the environmentally adaptive days to heading trait (crucial for the crop's spread from the Fertile Crescent), illustrated complexities in G×E effect directions, and the importance of latitudinally based genic context in the expression of large‐effect alleles. Our analysis supports a gene‐level scientific understanding of crop adaption and leads to practical opportunities for crop improvement, allowing the prioritisation of genomic regions and particular sets of lines for breeding efforts seeking to cope with climate change and other stresses.     

Toward a better understanding of the "Transverse Range break": lineage diversification in southern California

The Transverse Ranges in southern California have been identified as having a prominent phylogeographic role. Numerous studies have identified distinct north-south and/or east-west lineage breaks involving the Transverse Ranges. However, in evaluating their findings, most authors have regarded this complex system somewhat simplistically. In this study we more deeply investigate these breaks using two approaches: first we examine the phylogeographic history of Sepedophilus castaneus (Coleoptera: Staphylinidae) and then implement a comparative phylogeography approach applying Brooks parsimony analysis to the topologies of nine additional taxa. Phylogenetic analysis, nested clade analysis, and AMOVAs for S. castaneus agree that there is a major lineage break between the eastern and western Transverse Ranges, localized between the Sierra Pelona and the San Gabriel Mountains. The comparative phylogeographic analysis supports a generally strong concordance of area relationships with geographic proximity. It is notable, however, that the Transverse Ranges as a group do not show phylogenetic cohesion, but rather they are split into three main regions: an eastern region (San Gabriel, San Bernardino, and San Jacinto Mountains), a central region (central Transverse Ranges and Sierra Pelona) that is often grouped with the Tehachapi and Sierra Nevada populations, and a western region (northwestern Transverse Ranges and Santa Ynez Mountains) that is consistently grouped with coast range areas to the north. The lineage break between east and west Transverse Ranges is attributable to the presence of a marine embayment in what is now the Santa Clara River valley 5-2.5 million years ago.     

Early history of mammals is elucidated with the ENCODE multiple species sequencing data

Understanding the early evolution of placental mammals is one of the most challenging issues in mammalian phylogeny. Here, we addressed this question by using the sequence data of the ENCODE consortium, which include 1% of mammalian genomes in 18 species belonging to all main mammalian lineages. Phylogenetic reconstructions based on an unprecedented amount of coding sequences taken from 218 genes resulted in a highly supported tree placing the root of Placentalia between Afrotheria and Exafroplacentalia (Afrotheria hypothesis). This topology was validated by the phylogenetic analysis of a new class of genomic phylogenetic markers, the conserved noncoding sequences. Applying the tests of alternative topologies on the coding sequence dataset resulted in the rejection of the Atlantogenata hypothesis (Xenarthra grouping with Afrotheria), while this test rejected the second alternative scenario, the Epitheria hypothesis (Xenarthra at the base), when using the noncoding sequence dataset. Thus, the two datasets support the Afrotheria hypothesis; however, none can reject both of the remaining topological alternatives.     

Generation of dwarf goat (Capra hircus) clones following nuclear transfer with transfected and nontransfected fetal fibroblasts and in vitro-matured oocytes

The developmental potential of caprine fetal fibroblast nuclei after in vitro transfection and nuclear transfer (NT) into enucleated, in vitro-matured oocytes was evaluated. Fetal fibroblasts were isolated from Day 27 to Day 30 fetuses from a dwarf breed of goat (BELE: breed early lactate early). Cells were transfected with constructs containing the enhanced green fluorescent protein (eGFP) and neomycin resistance genes and were selected with G418. Three eGFP lines and one nontransfected line were used as donor cells in NT. Donor cells were cultured in Dulbecco minimum Eagle medium plus 0.5% fetal calf serum for 4-8 days prior to use in NT. Immature oocytes were recovered by laparoscopic ovum pick-up and matured for 24 h prior to enucleation and NT. Reconstructed embryos were transferred as cleaved embryos into synchronized recipients. A total of 27 embryos derived from transgenic cells and 70 embryos derived from nontransgenic cells were transferred into 13 recipients. Five recipients (38%) were confirmed pregnant at Day 35 by ultrasound. Of these, four recipients delivered five male kids (7.1% of embryos transferred) derived from the nontransfected line. One recipient delivered a female kid derived from an eGFP line (7.7% of embryos transferred for that cell line). Presence of the eGFP transgene was confirmed by polymerase chain reaction, Southern blotting, and fluorescent in situ hybridization analyses. Nuclear transfer derivation from the donor cells was confirmed by single-strand confirmation polymorphism analysis. These results demonstrate that both in vitro-transfected and nontransfected caprine fetal fibroblasts can direct full-term development following NT.     

Production of recombinant human type I procollagen homotrimer in the mammary gland of transgenic mice

The large scale production of recombinant collagen for use in biomaterials requires an efficient expression system capable of processing a large (>400Kd) multisubunit protein requiring post-translational modifications. To investigate whether the mammary gland of transgenic animals fulfills these requirements, transgenic mice were generated containing the S1-casein mammary gland-specific promoter operatively linked to 37Kb of the human 1(I) procollagen structural gene and 3 flanking region. The frequency of transgenic lines established was 12%. High levels of soluble triple helical homotrimeric [(1)₃] type I procollagen were detected (up to 8mg/ml) exclusively in the milk of six out of 9 lines of lactating transgenic mice. The transgene-derived human procollagen chains underwent efficient assembly into a triple helical structure. Although proline or lysine hydroxylation has never been described for any milk protein, procollagen was detected with these post-translational modifications. The procollagen was stable in mil; minimal degradation was observed. These results show that the mammary gland is capable of expressing a large procollagen gene construct, efficiently assembling the individual polypeptide chains into a stable triple helix, and secreting the intact molecule into the milk.