Cruise 4 of the M/V N.B. Scofield for 1957.

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Cruise 5 of the N.B. Scofield for 1957.

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Cruise Report 64-S-6: N. B. Scofield, September 29 to October 25, 1964

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Sequence specific complexation of b DNA at sites containing g,c base pairs

A series of eight related analogs of distamycin A has been synthesized. Footprinting and affinity cleaving reveal that only two of the analogs, pyridine-2- car box amide-netropsin (2-Py N) and 1-methylimidazole-2-carboxamide-netrops in (2-ImN), bind to DNA with a specificity different from that of the parent compound. A new class of sites, represented by a TGACT sequence, is a strong site for 2-PyN binding, and the major recognition site for 2-ImN on DNA. Both compounds recognize the G•C bp specifically, although A's and T's in the site may be interchanged without penalty. Additional A•T bp outside the binding site increase the binding affinity. The compounds bind in the minor groove of the DNA sequence, but protect both grooves from dimethylsulfate. The binding evidence suggests that 2-PyN or 2-ImN binding induces a DNA conformational change.

In order to understand this sequence specific complexation better, the Ackers quantitative footprinting method for measuring individual site affinity constants has been extended to small molecules. MPE•Fe(II) cleavage reactions over a 10^5 range of free ligand concentrations are analyzed by gel electrophoresis. The decrease in cleavage is calculated by densitometry of a gel autoradiogram. The apparent fraction of DNA bound is then calculated from the amount of cleavage protection. The data is fitted to a theoretical curve using non-linear least squares techniques. Affinity constants at four individual sites are determined simultaneously. The distamycin A analog binds solely at A•T rich sites. Affinities range from 10^(6)- 10^(7)M^(-1) The data for parent compound D fit closely to a monomeric binding curve. 2-PyN binds both A•T sites and the TGTCA site with an apparent affinity constant of 10^(5) M^(-1). 2-ImN binds A•T sites with affinities less than 5 x 10^(4) M^(-1). The affinity of 2-ImN for the TGTCA site does not change significantly from the 2-PyN value. At the TGTCA site, the experimental data fit a dimeric binding curve better than a monomeric curve. Both 2-PyN and 2-ImN have substantially lower DNA affinities than closely related compounds.

In order to probe the requirements of this new binding site, fourteen other derivatives have been synthesized and tested. All compounds that recognize the TGTCA site have a heterocyclic aromatic nitrogen ortho to the N or C-terminal amide of the netropsin subunit. Specificity is strongly affected by the overall length of the small molecule. Only compounds that consist of at least three aromatic rings linked by amides exhibit TGTCA site binding. Specificity is only weakly altered by substitution on the pyridine ring, which correlates best with steric factors. A model is proposed for TGTCA site binding that has as its key feature hydrogen bonding to both G's by the small molecule. The specificity is determined by the sequence dependence of the distance between G's.

One derivative of 2-PyN exhibits pH dependent sequence specificity. At low pH, 4-dimethylaminopyridine-2-carboxamide-netropsin binds tightly to A•T sites. At high pH, 4-Me_(2)NPyN binds most tightly to the TGTCA site. In aqueous solution, this compound protonates at the pyridine nitrogen at pH 6. Thus presence of the protonated form correlates with A•T specificity.

The binding site of a class of eukaryotic transcriptional activators typified by yeast protein GCN4 and the mammalian oncogene Jun contains a strong 2-ImN binding site. Specificity requirements for the protein and small molecule are similar. GCN4 and 2-lmN bind simultaneously to the same binding site. GCN4 alters the cleavage pattern of 2-ImN-EDTA derivative at only one of its binding sites. The details of the interaction suggest that GCN4 alters the conformation of an AAAAAAA sequence adjacent to its binding site. The presence of a yeast counterpart to Jun partially blocks 2-lmN binding. The differences do not appear to be caused by direct interactions between 2-lmN and the proteins, but by induced conformational changes in the DNA protein complex. It is likely that the observed differences in complexation are involved in the varying sequence specificity of these proteins.

Experimental chemical physics of droplets and clusters

Time-of-flight measurements of energetic He atoms, field ionization of cryogenic liquid helium clusters, and time-of-flight and REMPI spectroscopy of radical salt clusters were investigated experimentally. The excited He atoms were generated in a corona discharge. Two strong neutral peaks were observed, accompanied by a prompt photon peak and a charged peak. All peaks were correlated with the pulsing of the discharge. The neutral hyperthermal and metastable atoms were formed by different mechanisms at different stages of the corona discharge. Positively charged helium droplets were produced by ionization of liquid helium in an electrostatic spraying experiment. The fluid emerging from a thin glass capillary was ionized by a high voltage applied to a needle inside the capillary. Fine droplets (less than 10 µm in diameter) were produced in showers with currents as high as 0.4 µA at 2-4 kV. The high currents resulting from field ionization in helium and the low surface tension of He I, led to charge densities that greatly exceeded the Rayleigh limit, thus resulting in coulombic explosion of the liquid. In contrast, liquid nitrogen formed a well-defined Taylor cone with droplets having diameters comparable to the jet (≈100 µm) at lower currents (10 nA) and higher voltages (8 kV). The metal-halide clusters of calcium and chlorine were generated by laser ablation of calcium metal in a Ar/CCl₄ expansion. A visible spectrum of the Ca<sub>2b>Cl₃ cluster was observed from 651 to 630 nm by 1 +1' REMPI. The spectra were composed of a strong origin band at 15 350.8 cm^-1 and several weak vibronic bands. Density functional calculations predicted three minimum energy isomers. The spectrum was assigned to the ²B₂ ← X ²A₁ transition of a planar C_2V structure having a ring of two Cl and two Ca atoms and a terminal Cl atom. The ring isomer of Ca<sub>2b>Cl₃ has the unpaired electron localized on one Ca<sup>2+ ion to form a Ca<sup>+ chromophore. A second electronic band of Ca<sub>2b>Cl₃ was observed at 720 nm. The band is sharply different from the 650 nm band and likely due to a different isomer.

A study of T = 2 states in ^(12)B, ^(12)C, ^(20)F and ^(28)Al

The lowest T = 2 states have been identified and studied in the nuclei ¹²C, ¹²B, ²⁰F and and ²⁸Al. The first two of these were produced in the reactions ¹⁴C(p,t)¹²C and ¹⁴C (p,³He)¹²B, at 50.5 and 63.4 MeV incident proton energy respectively, at the Oak Ridge National Laboratory. The T = 2 states in ²⁰F and ²⁸Al were observed in (³He,p) reactions at 12-MeV incident energy, with the Caltech Tandem accelerator.

The results for the four nuclei studied are summarized below:

(1) ¹²C: the lowest T = 2 state was located at an excitation energy of 27595 ± 20 keV, and has a width less than 35 keV.

(2) ¹²B: the lowest T = 2 state was found at an excitation energy of 12710 ± 20 keV. The width was determined to be less than 54 keV and the spin and parity were confirmed to be 0⁺. A second ¹²B state (or doublet) was observed at an excitation energy of 14860 ± 30 keV with a width (if the group corresponds to a single state) of 226 ± 30 keV.

(3) ²⁰F: the lowest T = 2 state was observed at an excitation of 6513 ± 5 keV; the spin and parity were confirmed to be 0⁺. A second state, tentatively identified as T = 2 from the level spacing, was located at 8210 ± 6 keV.

(4) ²⁸Al: the lowest T = 2 state was identified at an excitation of 5997 ± 6 keV; the spin and parity were confirmed to be 0⁺. A second state at an excitation energy of 7491 ± 11 keV is tentatively identified as T = 2, with a corresponding (tentative) spin and parity assignment J^π = 2⁺.

The results of the present work and the other known masses of T = 2 states and nuclei for 8 ≤ A ≤ 28 are summarized, and massequation coefficients have been extracted for these multiplets. These coefficients were compared with those from T = 1 multiplets, and then used to predict the mass and stability of each of the unobserved members of the T = 2 multiplets.

Desenvolvimento de técnica de análise de imagens digitais para avaliação do estágio da fibrose em biópsias hepáticas de pacientes portadores de hepatite crônica por vírus da hepatite B e C

As hepatites crônicas por vírus são as mais frequentes, destacando-se os vírus das hepatites B (VHB) e C (VHC). O estudo anatomopatológico da biópsia hepática é considerado o padrão ouro para avaliar com precisão a distorção arquitetural e o grau de fibrose do parênquima do fígado, importantes fatores prognósticos para os pacientes portadores de hepatites crônicas virais. Na avaliação histopatológica atual, em adição aos relatos subjetivos das alterações histológicas, escores semiquantitativos que correlacionam achados morfológicos com graus numéricos são usados, tais como os reconhecidos escores de Ishak e METAVIR. Entretanto, em todos estes sistemas há a desvantagem da subjetividade do examinador e da incorporação de alterações categóricas, sem referências às mudanças quantitativas do colágeno hepático. Técnicas de análise de imagens digitais (AID) que fornecem quantifica��ão objetiva dos graus de fibrose em amostras histológicas têm sido desenvolvidas. Todavia, o alto custo e dificuldade ao acesso das tecnologias descritas restringem seu uso a poucos centros especializados. Este estudo visa o desenvolvimento de uma técnica de custo acessível para a análise de imagens digitais da fibrose hepática em hepatites crônicas virais. Foram estudadas 304 biópsias de pacientes com hepatite crônica por vírus B e C, obtidas através de agulhas Menghini. Todas as amostras tinham pelo menos 15 mm de comprimento ou cinco espaços-porta completos e foram coradas pelo método Tricrômico de Masson. O estadiamento foi feito por um único hepatopatologista experiente, sem o conhecimento dos dados clínicos dos pacientes. Os escores de Ishak e METAVIR foram aplicados. As imagens microscópicas foram digitalizadas. Os índices de fibrose foram determinados de forma automatizada, em técnica desenvolvida no programa Adobe Photoshop. Para o escore de Ishak, observamos os seguintes índices de Fibrose (IF) médios: 0,8% 0,0 (estágio 0), 2.4% 0,6 (estágio 1), 4,7% 1,6 (estágio 2), 7,4% 1,4 (estágio 3), 14,9% 3,7 (estágio 4), 23,4% 2,9 (estágio 5) e 34,5% 1,5 (estágio 6). Para a classifica��ão METAVIR: 0,8% 0,1 (estágio F0), 3,8% 1,8 (estágio F1), 7,4% 1,4 (estágio F2), 20,4% 5,2 (estágio F3) e 34,5% 1,5 (estágio F4). Observamos uma excelente correlação entre os índices de fibrose da AID e os escores de Ishak (r=0,94; p<0,001) e METAVIR (r=0,92; p<0,001). Em relação à indica��ão de tratamento antiviral, foi observado IF médio de 16,4%. Em relação ao diagnóstico de cirrose, foi observado IF médio de 26,9%, para o escore de Ishak, e 34,5% para a classifica��ão METAVIR. A reprodutibilidade intra-observador foi excelente. Este novo método de análise de imagens digitais para a quantifica��ão de fibrose hepática tem custo acessível e foi desenvolvido com tecnologia que está disponível em todo o mundo, permitindo identificar com precisão todos os estágios de fibrose, com excelente reprodutibilidade intra-observador.

Binding of the molecular chaperone αB-crystallin to Aβ amyloid fibrils inhibits fibril elongation.

The molecular chaperone αB-crystallin is a small heat-shock protein that is upregulated in response to a multitude of stress stimuli, and is found colocalized with Aβ amyloid fibrils in the extracellular plaques that are characteristic of Alzheimer's disease. We investigated whether this archetypical small heat-shock protein has the ability to interact with Aβ fibrils in vitro. We find that αB-crystallin binds to wild-type Aβ(42) fibrils with micromolar affinity, and also binds to fibrils formed from the E22G Arctic mutation of Aβ(42). Immunoelectron microscopy confirms that binding occurs along the entire length and ends of the fibrils. Investigations into the effect of αB-crystallin on the seeded growth of Aβ fibrils, both in solution and on the surface of a quartz crystal microbalance biosensor, reveal that the binding of αB-crystallin to seed fibrils strongly inhibits their elongation. Because the lag phase in sigmoidal fibril assembly kinetics is dominated by elongation and fragmentation rates, the chaperone mechanism identified here represents a highly effective means to inhibit fibril proliferation. Together with previous observations of αB-crystallin interaction with α-synuclein and insulin fibrils, the results suggest that this mechanism is a generic means of providing molecular chaperone protection against amyloid fibril formation.

Southern California's megaflood event of ca. 1605 AD linked to large-scale atmospheric forcing

A distinct, 1- to 2-cm-thick flood deposit found in Santa Barbara Basin with a varve-date of 1605 AD ± 5 years testifies to an intensity of precipitation that remains unmatched for later periods when historical or instrumental records can be compared against the varve record. The 1605 AD ± 5 event correlates well with Enzel's (1992) finding of a Silver Lake playa perennial lake at the terminus of the Mojave River (carbon-14-dated 1560 AD ± 90 years), in relative proximity to the rainfall catchment area draining into Santa Barbara Basin. According to Enzel, such a persistent flooding of the Silver Lake playa occurred only once during the last 3,500 years and required a sequence of floods, each comparable in magnitude to the largest floods in the modern record. To gain confidence in dating of the 1605 AD ± 5 event, we compare Southern California's sedimentary evidence against historical reports and multi-proxy time-series that indicate unusual climatic events or are sensitive to changes in large-scale atmospheric circulation patterns. The emerging pattern supports previous suggestions that the first decade of the 17th century was marked by a rapid cooling of the Northern Hemisphere, with some indications for global coverage. A burst of volcanism and the occurrence of El Nino seem to have contributed to the severity of the events. The synopsis of the 1605 AD ± 5 years flood deposit in Santa Barbara Basin, the substantial freshwater body at Silver Lake playa, and much additional paleoclimatic, global evidence testifies for an equatorward shift of global wind patterns as the world experienced an interval of rapid, intense, and widespread cooling.