Modeling the MHC class I pathway by combining predictions of proteasomal cleavage,TAP transport and MHC class I binding

Epitopes presented by major histocompatibility complex (MHC) class I molecules are selected by a multi-step process. Here we present the first computational prediction of this process based on in vitro experiments characterizing proteasomal cleavage, transport by the transporter associated with antigen processing (TAP) and MHC class I binding. Our novel prediction method for proteasomal cleavages outperforms existing methods when tested on in vitro cleavage data. The analysis of our predictions for a new dataset consisting of 390 endogenously processed MHC class I ligands from cells with known proteasome composition shows that the immunological advantage of switching from constitutive to immunoproteasomes is mainly to suppress the creation of peptides in the cytosol that TAP cannot transport. Furthermore, we show that proteasomes are unlikely to generate MHC class I ligands with a C-terminal lysine residue, suggesting processing of these ligands by a different protease that may be tripeptidyl-peptidase II (TPPII).Received 26 November 2004; received after revision 4 February 2005; accepted 4 March 2005S. Tenzer and B. Peters contributed equally to this work.     

Genetic mapping with SNP markers in Drosophila.

Map-based positional cloning of Drosophila melanogaster genes is hampered by both the time-consuming, error-prone nature of traditional methods for genetic mapping and the difficulties in aligning the genetic and cytological maps with the genome sequence. The identification of sequence polymorphisms in the Drosophila genome will make it possible to map mutations directly to the genome sequence with high accuracy and resolution. Here we report the identification of 7,223 single-nucleotide polymorphisms (SNPs) and 1,392 insertions/deletions (InDels) in common laboratory strains of Drosophila. These sequence polymorphisms define a map of 787 autosomal marker loci with a resolution of 114 kb. We have established PCR product-length polymorphism (PLP) or restriction fragment-length polymorphism (RFLP) assays for 215 of these markers. We demonstrate the use of this map by delimiting two mutations to intervals of 169 kb and 307 kb, respectively. Using a local high-density SNP map, we also mapped a third mutation to a resolution of approximately 2 kb, sufficient to localize the mutation within a single gene. These methods should accelerate the rate of positional cloning in Drosophila.     

Morphology of tube-like threads related to Limnochares aquatica (L., 1758) (Acariformes: Hydrachnidia: Limnocharidae) in the laboratory

Water mites Limnochares aquatica (L., 1758) during maintenance in the laboratory for a long period of time in constant conditions periodically produced certain whitish flocculent material consisting of long rigid unbranched tube-like threads 1.3 ± 0.3 µm in diameter crossing freely. These threads were studied using light-optical as well as transmission electron microscopical and scanning electron microscopical methods. Microbiological staining was also applied to the threads to exclude their bacterial or fungal origin. The thread wall is built of fine fibrils arranged at different angles to the long axis of threads that is reflected in a certain stratification of the wall. Threads are mostly hollow or may contain electron-dense homogeneous material. No cell components are present in the thread composition. Numerous dermal glands with their small slit-like orifice scattered throughout the mite body surface are thought to produce these threads. Most probably the thread formation is a reaction of mites to stress under laboratory conditions, and this is expected to be a type of defensive reaction.     

The ontogeny ofa-foetoprotein in the chicken

Summary The ontogeny ofa-foetoprotein (AFP) has been studied in the chicken using polyacrylamide gel gradient electrophoresis and electroimmunoassay from 7 days of incubation until after hatching. The results are discussed in the light of previous on the ontogeny of AFP in mammals.     

有机硫对维多利亚褐煤液化的催化作用之穆斯堡尔研究

我们以Morwell和Coolungoolun两种维多利亚褐煤进行实验,对铁和锡在煤的液化中的催化作用进行了比较,发现锡对低硫的Morwell煤较为有效,而铁则更适合于高硫的Coolungoolun煤。对液化余渣的穆斯堡尔分析的结果,使我们可以用低硫煤中元素态锡的形成以及在高硫煤中磁黄铁矿（Fe_(0.92)S）的形成来对观察到的现象作出解释。硫的损耗数据表明,磁黄铁矿的存在使得煤中的硫转化为气相的量增加了。     

Synthesis of rhodotorucine A,the inducing factor of mating tube formation ofRhodosporidium toruloides

Summary The inducing factor of mating tube formation ofRhodosporidium turuloides, named rhodotorucine A (H-Tyr-Pro-Glu-Ile-Ser-Trp-Thr-Arg-Asn-Gly-Cys(S-farnesyl)-OH), has been synthesized to confirm the structure proposed for the natural lipopeptide. The synthetic S-farnesyl undecapeptide has identical Rf values on TLC using several different solvents, and also the same biological activity as the natural hormone.Acknowledgments. We wish to express our thanks to Drs E. Ohmura, M. Nishikawa and M. Yoneda of Takeda Chemical Industries and Dr I. Banno of Institute for Fermentation, Osaka, for their encouragement throughout this work.     

Fibronectin peptide DRVPHSRNSIT and fibronectin receptor peptide DLYYLMDL arrest gastrulation ofRana pipiens

Gastrulation is characterized by dramatic cell migration which is thought to require the interaction of cell adhesion molecules with extracellular molecules. We have tested two novel peptides, a fibronectin peptide and a fibronectin receptor peptide, for their effects on gastrulation of the leopard frogRana pipiens. The fibronectin peptide DRVPHSRNSIT corresponds to residues 1373–1383 of the cell-binding domain of fibronectin; the receptor peptide DLYYLMDL corresponds to residues 124–131 of 1 subunit of a variety of integrins including 51. Either of these peptides significantly inhibited gastrulation after being microinjected into mid-blastulae. These results indicate that these sequences may correspond to the ligand/receptor interaction sites of fibronectin and its receptor(s).     

Exemplification and the use-values of cases and case studies

This paper provides an account of the ‘use-value’ of case-based research by showing how social scientists exploit cases, and case studies, in a variety of practices of inference and extension. The critical basis for making such extensions relies on the power of a case, or the account given of a case (the case-study account), to exemplify certain features of the social world in ways which prove valuable for further analysis: either of the same case, or in many domains beyond the original case study. Framing use-values in terms of exemplification compares favourably with understanding reasoning beyond the case either as a form of analogical reasoning or in taking cases as experimentable objects.