Alignment of a 1.2-Mb chromosomal region from three strains of Rhodobacter capsulatus reveals a significantly mosaic structure.

High-resolution physical maps of the genomes of three Rhodobacter capsulatus strains, derived from ordered cosmid libraries, were aligned. The 1.2-Mb segment of the SB1003 genome studied here is adjacent to a 1-Mb region analyzed previously [Fonstein, M., Nikolskaya, T. & Haselkorn, H. (1995) J. Bacteriol. 177, 2368-2372]. Probes derived from the ordered cosmid set of R. capsulatus SB1003 were used to link cosmids from the St. Louis and 2.3.1 strain libraries. Cosmids selected this way did not merge into a single contig but formed several unlinked groups. EcoRV restriction maps of the ordered cosmids were then constructed using lambda terminase and fused to derive fragments of the chromosomal map. In order to link these fragments, their ends were transcribed to produce secondary probes for hybridization to gridded cosmid libraries of the same strains. This linking reduced the number of subcontigs to three for the St. Louis strain and one for the 2.3.1 strain. Hybridization of the same probes back to the ordered cosmid set of SB1003 positioned the subcontigs on the high-resolution physical map of SB1003. The final alignment of the restriction maps shows numerous large and small translocations in this 1.2-Mb chromosomal region of the three Rhodobacter strains. In addition, the chromosomes of the three strains, whose fine-structure maps can now be compared over 2.2 Mb, are seen to contain regions of 15-80 kb in which restriction sites are highly polymorphic, interspersed among regions in which the positions of restriction sites are highly conserved.

Isolation of small polarized bile duct units.

Fragments of small interlobular bile ducts averaging 20 microns in diameter can be isolated from rat liver. These isolated bile duct units form luminal spaces that are impermeant to dextran-40 and expand in size when cultured in 10 microM forskolin for 24-48 hr. Secretion is Cl- and HCO3- dependent and is stimulated by forskolin > dibutyryl cAMP > secretion but not by dideoxyforskolin, as assessed by video imaging techniques. Secretin stimulates Cl-/HCO3- exchange activity, and intraluminal pH increases after forskolin administration. These studies establish that small polarized physiologically intact interlobular bile ducts can be isolated from rat liver. These isolated bile duct units should be useful preparations for assessing the transport properties of small bile duct segments, which are the primary site of injury in cholestatic liver disorders, known as "vanishing bile duct syndromes."

Folding of a nascent polypeptide chain in vitro: cooperative formation of structure in a protein module.

We have prepared a family of peptide fragments of the 64-residue chymotrypsin inhibitor 2, corresponding to its progressive elongation from the N terminus. The growing polypeptide chain has little tendency to form stable structure until it is largely synthesized, and what structures are formed are nonnative and lack, in particular, the native secondary structural elements of alpha-helix and beta-sheet. These elements then develop as sufficient tertiary interactions are made in the nearly full-length chain. The growth of structure in the small module is highly cooperative and does not result from the hierarchical accretion of substructures.

Transendothelial migration of neutrophils involves integrin-associated protein (CD47).

Inflammation is a primary pathological process. The development of an inflammatory reaction involves the movement of white blood cells through the endothelial lining of blood vessels into tissues. This process of transendothelial cell migration of neutrophils has been shown to involve neutrophil beta 2 integrins (CD18) and endothelial cell platelet-endothelium cell adhesion molecules (PECAM-1; CD31). We now show that F(ab')2 fragments of the monoclonal antibody B6H12 against integrin-associated protein (IAP) blocks the transendothelial migration of neutrophils stimulated by an exogenous gradient of the chemokine interleukin 8 (IL-8; 60% inhibition), by the chemotactic peptide N-formyl-methionylleucylphenylalanine (FMLP; 76% inhibition), or by the activation of the endothelium by the cytokine tumor necrosis factor alpha (98% inhibition). The antibody has two mechanisms of action: on neutrophils it prevents the chemotactic response to IL-8 and FMLP, and on endothelium it prevents an unknown but IL-8-independent process. Blocking antibodies to IAP do not alter the expression of adhesion proteins or production of IL-8 by endothelial cells, and thus the inhibition of neutrophil transendothelial migration is selective. These data implicate IAP as the third molecule essential for neutrophil migration through endothelium into sites of inflammation.

Computer determination of peptide conformations in water: different roads to structure.

Fragments of proteins (short peptides) that "fold" suggest a mechanism of how complete conformational search in protein folding is avoided. We used a computational method to determine structures of two foldable peptides in explicit water: RVEW and CSVTC. The optimization starts from random structures and no experimental constraints are used. In agreement with NMR data, the simulations find a hydrophobic pair (Val/Trp) in REVW. The structure of CSVTC is induced by a surface water that bridges two amide hydrogens, a drive to structure hypothesized by Ben-Naim [Ben-Naim, A. (1990) J. Chem. Phys. 93, 8196-8210] that is largely ignored in studies of folding. Tendency to structure in short peptide chains suggests a mechanism for the formation of short-range nucleation sites in protein folding.

B-cell activation by crosslinking of surface IgM or ligation of CD40 involves alternative signal pathways and results in different B-cell phenotypes.

Treatment of small resting B cells with soluble F(ab')2 fragments of anti-IgM, an analogue of T-independent type 2 antigens, induced activation characterized by proliferation and the expression of surface CD5. In contrast, B cells induced to proliferate in response to thymus-dependent inductive signals provided by either fixed activated T-helper 2 cells or soluble CD40 ligand-CD8 (CD40L) recombinant protein displayed elevated levels of CD23 (Fc epsilon II receptor) and no surface CD5. Treatment with anti-IgM and CD40L induced higher levels of proliferation and generated a single population of B cells coexpressing minimal amounts of CD5 and only a slight elevation of CD23. Anti-IgM- but not CD40L-mediated activation was highly sensitive to inhibition by cyclosporin A and FK520. Sp-cAMPS, an analogue of cAMP, augmented CD40L and suppressed surface IgM-mediated activation. Taken together these results are interpreted to mean that there is a single population of small resting B cells that can respond to either T-independent type 2 (surface IgM)- or T-dependent (CD40)-mediated activation. In response to different intracellular signals these cells are induced to enter alternative differentiation pathways.

Suppression and promotion of tumor growth by monoclonal antibodies to ErbB-2 differentially correlate with cellular uptake.

Amplification and overexpression of the erbB-2/neu protooncogene are frequently associated with aggressive clinical course of certain human adenocarcinomas, and therefore the encoded surface glycoprotein is considered a candidate target for immunotherapy. We previously generated a series of anti-ErbB-2 monoclonal antibodies (mAbs) that either accelerate or inhibit the tumorigenic growth of erbB-2-transformed murine fibroblasts. The present study extended this observation to a human tumor cell line grown as xenografts in athymic mice and addressed the biochemical differences between the two classes of mAbs. We show that the inhibitory effect is dominant in an antibody mixture, and it depends on antibody bivalency. By using radiolabeled mAbs we found that all of three tumor-inhibitory mAbs became rapidly inaccessible to acid treatment when incubated with tumor cells. However, a tumor-stimulatory mAb remained accessible to extracellular treatments, indicating that it did not undergo endocytosis. In addition, intracellular fragments of the inhibitory mAbs, but not of the stimulatory mAb, were observed. Electron microscopy of colloidal gold-antibody conjugates confirmed the absence of endocytosis of the stimulatory mAb but detected endocytic vesicles containing an inhibitory mAb. We conclude that acceleration of cell growth by ErbB-2 correlates with cell surface localization, whereas inhibition of tumor growth is associated with an intrinsic ability of anti-ErbB-2 mAbs to induce endocytosis. These conclusions are relevant to the selection of optimal mAbs for immunotherapy and may have implications for the mechanism of cellular transformation by an overexpressed erbB-2 gene.

Total chemical synthesis of a ribozyme derived from a group I intron.

We describe the complete chemical synthesis of a ribozyme that catalyzes template-directed oligonucleotide ligation. The specific activity of the synthetic ribozyme is nearly identical to that of the same enzyme generated by in vitro transcription with T7 RNA polymerase. The ribozyme is derived from a group I intron and consists of three RNA fragments of 36, 43, and 59 nt that self-assemble to form a catalytically active complex. We have site-specifically substituted ribonucleotide analogs into this enzyme and have identified two 2'-hydroxyl groups that are required for full catalytic activity. In contrast, neither the 2'-hydroxyl nor the exocyclic amino group of the conserved guanosine in the guanosine binding site is necessary for catalysis. By allowing the ribozyme to be modified as easily as its substrates, this synthetic ribozyme system should be useful for testing specific hypotheses concerning ribozyme-substrate interactions and tertiary interactions within the ribozyme.

Fate of a redundant gamma-globin gene in the atelid clade of New World monkeys: implications concerning fetal globin gene expression.

Conclusive evidence was provided that gamma 1, the upstream of the two linked simian gamma-globin loci (5'-gamma 1-gamma 2-3'), is a pseudogene in a major group of New World monkeys. Sequence analysis of PCR-amplified genomic fragments of predicted sizes revealed that all extant genera of the platyrrhine family Atelidae [Lagothrix (woolly monkeys), Brachyteles (woolly spider monkeys), Ateles (spider monkeys), and Alouatta (howler monkeys)] share a large deletion that removed most of exon 2, all of intron 2 and exon 3, and much of the 3' flanking sequence of gamma 1. The fact that two functional gamma-globin genes were not present in early ancestors of the Atelidae (and that gamma 1 was the dispensible gene) suggests that for much or even all of their evolution, platyrrhines have had gamma 2 as the primary fetally expressed gamma-globin gene, in contrast to catarrhines (e.g., humans and chimpanzees) that have gamma 1 as the primary fetally expressed gamma-globin gene. Results from promoter sequences further suggest that all three platyrrhine families (Atelidae, Cebidae, and Pitheciidae) have gamma 2 rather than gamma 1 as their primary fetally expressed gamma-globin gene. The implications of this suggestion were explored in terms of how gene redundancy, regulatory mutations, and distance of each gamma-globin gene from the locus control region were possibly involved in the acquisition and maintenance of fetal, rather than embryonic, expression.

Do psicólogo no programa de residência multiprofissional em saúde: posição-sujeito, análise de discurso e psicanálise lacaniana

A residência multiprofissional em saúde é uma modalidade de ensino de pós graduação lato sensu, voltada para a educação em serviço. Emerge no contexto brasileiro como uma proposta complementar a fim de se atingir as metas e os princípios preconizados pelo sistema único de saúde (SUS), principalmente quanto à integralidade. Além de trazer implicações e lançar desafios ao exercício profissional do psicólogo, inserindo-o no entrelaçamento de campos densos e complexos (saúde, educação e políticas públicas), a modalidade propõe que profissionais com formações diferentes atuem num mesmo campo, com discussões e intervenções conjuntas. A questão que move a pesquisa é a posição-sujeito no programa de residência multiprofissional face ao modelo de educação-saúde vinculado. Assevera-se que a posição-sujeito é objeto discursivo deslizante (de tessitura simbólica) que toma em consideração o sujeito constituído no claudicar da linguagem e interpelado pelo inconsciente e que se manifesta como efeito de significantes em direção ao grande Outro. Para tal, vale-se da interface dos aportes teóricos da análise de discurso pêchetiana e da psicanálise lacaniana. A análise de discurso sustenta o discurso como efeito de sentidos mediados pela ideologia e ocupa-se, especialmente, da incursão da alteridade do discurso-outro sobre o mesmo. A psicanálise lacaniana, por sua vez, reitera a primazia do inconsciente estruturado como linguagem diante de um eu imaginário e versa para o sujeito marcado como falta que, dividido, faz do discurso o estatuto do significado. Assim, é proeminente na análise do objeto a metodologia indiciária dada ao caráter simbólico e cambiante da posição-sujeito no discurso. A análise se realizou mediante o dispositivo da interpretação como gesto analítico, que acompanha as elações próprias do objeto. O corpora é constituído por uma materialidade escrita e por uma oral. A escrita compõe-se de recortes de leis, portarias e resoluções que fundam a modalidade de residência multiprofissional e reforçam os ideias do sistema único de saúde; a materialidade oral compõe-se de recortes e fragmentos discursivos advindos da transcrição de supervisões realizadas mediante a prática clínica do psicólogo-residente na cena hospitalar. Da análise, conclui-se que a materialidade escrita se posta como campo-Outro que ordena a estrutura política da residência multiprofissional e direciona a manutenção da ordem e reprodução das relações hierárquicas mediante ideologia assujeitante. Essa materialidade, por sua vez, age como intradiscurso e reverbera-se na memória discursiva e na prática clínica. A posição-sujeito, no plano da articulação significante, faz deslizar e produzir sentidos que denotam ora a manutenção e reprodução de uma posição fusionada ao discurso médico, científico-positivista; ora a posição-sujeito é marcada pelo saber condicionado ao fetiche da mercadoria, deflagrando a ordem do capital nas insígnias da multiprofissionalidade e da educação permanente. O trabalho propiciou, enfim, acompanhar as transmutações da posição-sujeito, independentemente do indivíduo ou da naturalização de sentidos provenientes da função que exerce. O objeto posição-sujeito reiterou a construção da realidade a partir da condição faltante. É essa condição faltante e incompleta que outorga ao desejo o modo de o sujeito se posicionar desta e outra maneira - na formação, no trabalho, na vida.

“Fall” and Redemption in the Thought of Martin Heidegger and Jacques Lacan

This dissertation examines and develops Martin Heidegger’s concept of “falling” as a significant historical-philosophical principle. Falling, however, is primarily understood as a concept of the early Heidegger, whereas I argue that Heidegger continues to rely upon it, both explicitly and implicitly, throughout his career. Falling is a description ofphilosophical and Western history, known as metaphysics, and the description of man’s relationship to Being. Thus, falling relates to the most significant streams in Heidegger’s later thought, too, including the truth of Being, the death of God, the gods, the overcoming of metaphysics, and meditative thinking. I then reinterpret the traditional theology of the Fall narrative from Genesis in light of falling as philosophical concept, extending Heidegger’s own “destruction” of Western metaphysics in relation to one of its grounding myths. I move on to demonstrate the significance of a falling understanding in a rereading of the death of God and the end of metaphysics by examining Heidegger’s engagement with Nietzsche. I conclude by incorporating Jacques Lacan’s psychoanalysis as a further extension of Heidegger’s discourse on falling, showing that the subject’s discourse and relationship to the truth of Being is at the core of his constitution and neurosis.

Library catalogue notes of Isaac Smith, ca. 1789

Thirteen slips of paper with fragments of handwritten alphabetical lists created by Isaac Smith presumably in his capacity as Harvard Librarian. Most of the entries are surnames or single-word subjects. For example, one slip with "M" entries includes: milway, miracles, miraculous, Mitchell, and Mitchell. Some of the lists have struck-through words or have entries annotated with numbers and the abbreviations "o" and "bk." The verso of one leaf has a brief, undated note regarding the transfer of books between Mr. Hilliard and Mr. Smith.

Repurposing Globalization: Discourse and Political Strategy in New Labour Britain. ACES Working Papers, 2012

As elsewhere in Europe and around the world, the discourse of globalization in the United Kingdom—the particular representation of the world as undergoing an epochal shift away from the traditional autonomy of the nation-state—has powerfully reshaped political debate. And this has had important distributional effects on the balance of power in the political party system, most notably in the return to power of the Labour Party as “New Labour” under the leadership of Tony Blair and Gordon Brown. But while it is known that articulations of globalization are embedded in the political system, a systematic analysis linking such discourse with party competition is lacking. In this paper, I propose that many features of the globalist language invoked by New Labour can be explained in terms of concrete strategic aims. Working with concepts of “heresthetics” and “bricolage” drawn from a synthesis of literatures, I illustrate this approach through several representative texts. These findings are then used to make predictions about the kind of globalization discourse to expect in the communications of two nationalist parties in the UK—“least likely” cases for globalism—which can be explored further as part of a larger research program.

Geochemistry and isotopic ratios of basalts from ODP Leg 163 sites

Voluminous, subaerial magmatism resulted in the formation of extensive seaward-dipping reflector sequences (SDRS) along the Paleogene Southeast Greenland rifted margin. Drilling during Leg 163 recovered basalts from the SDRS at 66ºN (Site 988) and 63ºN (Sites 989 and 990). The basalt from Site 988 is light rare-earth-element (REE) enriched (La(n)/Yb(n) = 3.4), with epsilon-Nd(t=60) = 5.3, 87Sr/86Sr = 0.7034, and 206Pb/204Pb = 17.98. It is similar to tholeiites recovered from the Irminger Basin during Leg 49 and to light-REE-enriched tholeiites from Iceland. Drilling at Site 989, the innermost of the sites on the 63ºN transect, was proposed to extend recovery of the earliest part of the SDRS initiated during Leg 152. These basalts are, however, younger than those from Site 917 and are compositionally similar to basalts from the more seaward Sites 990 and 915. Many of the basalts from Sites 989 and 990 show evidence of contamination by continental crust (e.g., epsilon-Nd(t=60) extends down to -3.7, 206Pb/204Pb extends down to 15.1). We suggest that the contaminant is a mixture of Archean granulite and amphibolite and that the most contaminated basalts have assimilated ~5% of crust. Uncontaminated basalts are isotopically similar to basalts from Site 918, on the main body of the SDRS, and are light-REE depleted. Consistent with previous models of the development of this margin, we show that at the time of formation of the basalts from Sites 989 and 990 (1) melting was at relatively shallow levels in a fully-fledged rift zone; (2) fragments of continental crust were present in the lithosphere above the zones of melt generation; and (3) the sublithospheric mantle was dominated by a depleted Icelandic plume component.

Analysis of Mn-deposits from Lake Eningi-Lampi

The processes of formation of iron-manganese nodules and crusts have been studied on an example of the Eningi-Lampi lake, Central Karelia, where the relationships between the source of the ore, sedimentary materials and areas of their accumulation prove relatively simple and apparent. Nodules and crusts are composed mostly by birnessite, amorphous hydrous ferric oxides and hydro-goethite. They occur, as a rule, on the surface of relatively coarse-grained sediments, at the ground-water interface. Considerably in a lesser extent are found the nodules in the upper part (0ó5 cm) of the red-brown flooded watery mud covering dark-green, black muds. The nucleus of nodules, or the basis of crusts of iron-manganese hydroxides are various, frequently altered, fragments of rocks, sometimes pieces of wood. Distribution of Mn and Fe in sediments and waters of the lake is considered. It is shown that the Mn/Fe ratio decreases considerably in waters, sediments and nodules of the lake while moving off a distance from the source. The main role in the process of formation of iron-manganese nodules belongs to the selective chemosorption interaction (with auto-catalytic oxidation) of component-bearing solutions with active surfaces.