Deep evolutionary diversification of semicircular canals in archosaurs

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RICE‐PAPER PLANT –TETRAPANAX PAPYRIFER

From the 1820s pith became a familiar material in Europe, under the name of rice‐paper, as a raw material for artificial flowers, and as a medium for export paintings from China. The structure of pith sheets was early recognised as different to that of paper, but it was not until 1852 that William Jackson Hooker was able to describe the source plant, as Aralia papyrifera Hook., now Tetrapanax papyrifer (Hook.) K. Koch. Using his consular contacts, Hooker was able to build up a remarkable collection of pith, as raw materials, artificial flowers and Chinese paintings. Many are described and illustrated in this article, in the context of recent work on the history and conservation of pith paintings.     

A system of nomenclature for band patterns of mouse chromosomes

Mouse chromosomes banded by quinacrine mustard staining, by the ASG technique, or by Giemsa staining following trypsinization or chymotrypsinization are described in detail. Three hundred and twelve regions within the mouse karyotype can be distinguished and a simple system of nomenclature is proposed for naming these regions. This nomenclature is applied to discussion of the locations of the breakpoints of twenty translocations and of many specific gene loci.Dedicated to the memory of Dr. Stanley W. Wright, in gratitude for his support of, and interest in, our work.Supported by Cancer Research Funds of the University of California and USPHS Grant HD 04608.     

Dok-2 Adaptor Protein Regulates the Shear-dependent Adhesive Function of Platelet Integrin αIIbβ3 in Mice

The Dok proteins are a family of adaptor molecules that have a well defined role in regulating cellular migration, immune responses, and tumor progression. Previous studies have demonstrated that Doks-1 to 3 are expressed in platelets and that Dok-2 is tyrosine-phosphorylated downstream of integrin α_IIbβ₃, raising the possibility that it participates in integrin α_IIbβ₃ outside-in signaling. We demonstrate that Dok-2 in platelets is primarily phosphorylated by Lyn kinase. Moreover, deficiency of Dok-2 leads to dysregulated integrin α_IIbβ₃-dependent cytosolic calcium flux and phosphatidylinositol(3,4)P₂ accumulation. Although agonist-induced integrin α_IIbβ₃ affinity regulation was unaltered in Dok-2^−/− platelets, Dok-2 deficiency was associated with a shear-dependent increase in integrin α_IIbβ₃ adhesive function, resulting in enhanced platelet-fibrinogen and platelet-platelet adhesive interactions under flow. This increase in adhesion was restricted to discoid platelets and involved the shear-dependent regulation of membrane tethers. Dok-2 deficiency was associated with an increased rate of platelet aggregate formation on thrombogenic surfaces, leading to accelerated thrombus growth in vivo. Overall, this study defines an important role for Dok-2 in regulating biomechanical adhesive function of discoid platelets. Moreover, they define a previously unrecognized prothrombotic mechanism that is not detected by conventional platelet function assays.     

FLCN,a novel autophagy component,interacts with GABARAP and is regulated by ULK1 phosphorylation

Birt-Hogg-Dubé (BHD) syndrome is a rare autosomal dominant condition caused by mutations in the FLCN gene and characterized by benign hair follicle tumors, pneumothorax, and renal cancer. Folliculin (FLCN), the protein product of the FLCN gene, is a poorly characterized tumor suppressor protein, currently linked to multiple cellular pathways. Autophagy maintains cellular homeostasis by removing damaged organelles and macromolecules. Although the autophagy kinase ULK1 drives autophagy, the underlying mechanisms are still being unraveled and few ULK1 substrates have been identified to date. Here, we identify that loss of FLCN moderately impairs basal autophagic flux, while re-expression of FLCN rescues autophagy. We reveal that the FLCN complex is regulated by ULK1 and elucidate 3 novel phosphorylation sites (Ser406, Ser537, and Ser542) within FLCN, which are induced by ULK1 overexpression. In addition, our findings demonstrate that FLCN interacts with a second integral component of the autophagy machinery, GABA(A) receptor-associated protein (GABARAP). The FLCN-GABARAP association is modulated by the presence of either folliculin-interacting protein (FNIP)-1 or FNIP2 and further regulated by ULK1. As observed by elevation of GABARAP, sequestome 1 (SQSTM1) and microtubule-associated protein 1 light chain 3 (MAP1LC3B) in chromophobe and clear cell tumors from a BHD patient, we found that autophagy is impaired in BHD-associated renal tumors. Consequently, this work reveals a novel facet of autophagy regulation by ULK1 and substantially contributes to our understanding of FLCN function by linking it directly to autophagy through GABARAP and ULK1.     

Identifying novel genes in <Emphasis Type="Italic">C. elegans</Emphasis> using SAGE tags

Background  

Despite extensive efforts devoted to predicting protein-coding genes in genome sequences, many bona fide genes have not been found and many existing gene models are not accurate in all sequenced eukaryote genomes. This situation is partly explained by the fact that gene prediction programs have been developed based on our incomplete understanding of gene feature information such as splicing and promoter characteristics. Additionally, full-length cDNAs of many genes and their isoforms are hard to obtain due to their low level or rare expression. In order to obtain full-length sequences of all protein-coding genes, alternative approaches are required.     

Recovery of scrap iron metal value using biogenerated ferric iron

The utility of employing biogenerated ferric iron as an oxidant for the recycling of scrap metal has been demonstrated using continuously growing cells of the extremophilic organism Acidithiobacillus ferrooxidans. A ferric iron rich (70 mol%) lixiviant resulting from bioreactor based growth of A. ferrooxidans readily solubilized target scrap metal with the resultant generation of a leachate containing elevated ferrous iron levels and solubilized copper previously resident in the scrap metal. Recovery of the copper value was easily accomplished via a cementation reaction and the clarified leachate containing a replenished level of ferrous iron as growth substrate was shown to support the growth of A. ferrooxidans and be fully recyclable. The described process for scrap metal recycling and copper recovery was shown to be efficient and economically attractive. Additionally, the utility of employing the E(h) of the growth medium as a means for monitoring fluctuations in cell density in cultures of A. ferrooxidans is demonstrated.     

QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species

Background  

Single nucleotide polymorphisms (SNPs) are important tools in studying complex genetic traits and genome evolution. Computational strategies for SNP discovery make use of the large number of sequences present in public databases (in most cases as expressed sequence tags (ESTs)) and are considered to be faster and more cost-effective than experimental procedures. A major challenge in computational SNP discovery is distinguishing allelic variation from sequence variation between paralogous sequences, in addition to recognizing sequencing errors. For the majority of the public EST sequences, trace or quality files are lacking which makes detection of reliable SNPs even more difficult because it has to rely on sequence comparisons only.