History of grazing; a circular offering suggestions on a technique for compiling data, writing, and editing material for a history of grazing.

Mimeographed.

"It could be one thing or another" - on the construction of an archaeological category

This article explores the history of the archaeological category Sámi circular offering sites, which refers to certain dry wall structures in Finnmark and Troms in northern Norway. In recent years the term has been used more frequently outside this geographical area too, at times to refer to structures vastly different from those originally labelled as circular offering sites. Such interpretations may be questioned, but perhaps it is the category itself that needs to be re-evaluated; a study ofthe research history suggests that the term is a result of a mid-19th century hypothesis that was established due to a lack of other plausible explanations rather than based on indicative finds or on local traditions. This interpretation has later been adopted by key researchers and has never really been challenged by any alternative hypothesis. This article proposes that the stone structures in question could represent other cultural phenomena, and that this needs further investigation.

Albumin-induced circular dichroism in Congo red: applications for studies of amyloid-like fibril aggregates and binding sites

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

A mobile app offering distractions and tips to cope with cigarette craving: A qualitative study

Background Despite considerable effort, most smokers relapse within a few months after quitting due to cigarette craving. The widespread adoption of mobile phones presents new opportunities to provide support during attempts to quit. Objective To design and pilot a mobile app "DistractMe" to enable quitters to access and share distractions and tips to cope with cigarette cravings. Methods A qualitative study with 14 smokers who used DistractMe on their mobiles during the first weeks of their quit attempt. Based on interviews, diaries, and log data, we examined how the app supported quitting strategies. Results Three distinct techniques of coping when using DistractMe were identified: diversion, avoidance, and displacement. We further identified three forms of engagement with tips for coping: preparation, fortification, and confrontation. Overall, strategies to prevent cravings and their effects (avoidance, displacement, preparation, and fortification) were more common than immediate coping strategies (diversion and confrontation). Tips for coping were more commonly used than distractions to cope with cravings, because they helped to fortify the quit attempt and provided opportunities to connect with other users of the application. However, distractions were important to attract new users and to facilitate content sharing. Conclusions Based on the qualitative results, we recommend that mobile phone-based interventions focus on tips shared by peers and frequent content updates. Apps also require testing with larger groups of users to assess whether they can be self-sustaining.

Solution NMR studies of acetohydroxy acid synthase I: Identification of the sites of inter-subunit interactions using multidimensional NMR methods

The novel multidomain organization in the multimeric Escherichia coli AHAS I (ilvBN) enzyme has been dissected to generate polypeptide fragments. These fragments when cloned, expressed and purified reassemble in the presence of cofactors to yield a catalytically competent enzyme. Structural characterization of AHAS has been impeded due to the fact that the holoenzyme is prone to dissociation leading to heterogeneity in samples. Our approach has enabled the structural characterization using high-resolution nuclear magnetic resonance methods. Near complete sequence specific NMR assignments for backbone H-N, N-15, C-13 alpha and C-13(beta) atoms of the FAD binding domain of ilvB have been obtained on samples isotopically enriched in H-2, C-13 and N-15. The secondary structure determined on the basis of observed C-13(alpha) secondary chemical shifts and sequential NOEs indicates that the secondary structure of the FAD binding domain of E. coli AHAS large Subunit (ilvB) is similar to the structure of this domain in the catalytic subunit of yeast AHAS. Protein-protein interactions involving the regulatory subunit (ilvN) and the domains of the catalytic subunit (ilvB) were studied using circular dichroic and isotope edited solution nuclear magnetic resonance spectroscopic methods. Observed changes in circular dichroic spectra indicate that the regulatory subunit (ilvN) interacts with ilvB alpha and ilvB beta domains of the catalytic subunit and not with the ilvB gamma domain. NMR chemical shift mapping methods show that ilvN binds close to the FAD binding site in ilvB beta and proximal to the intrasubunit ilvB alpha/ilvB beta domain interface. The implication of this interaction on the role of the regulatory subunit oil the activity of the holoenzyme is discussed. NMR studies of the regulatory domains show that these domains are structured in solution. Preliminary evidence for the interaction of ilvN with the metabolic end product of the pathway, viz., valine is also presented.

The RecA intein of Mycobacterium tuberculosis promotes cleavage of ectopic DNA sites. Implications for the dispersal of inteins in natural populations

The RecA intein of Mycobacterium tuberculosis, a novel double-stranded DNA endonuclease, requires both Mn(2+) and ATP for efficient cleavage of the inteinless recA allele. In this study, we show that Mg(2+) alone was sufficient to stimulate PI-MtuI to cleave double-stranded DNA at ectopic sites. In the absence of Mg(2+), PI-MtuI formed complexes with topologically different forms of DNA containing ectopic recognition sequences with equal affinity but failed to cleave DNA. We observed that PI-MtuI was able to inflict double-strand breaks robustly within the ectopic recognition sequence to generate either a blunt end or 1-2-nucleotide 3'-hydroxyl overhangs. Mutational analyses of the presumptive metal ion-binding ligands (Asp(122), Asp(222), and Glu(220)) together with immunoprecipitation assays provided compelling evidence to link both the Mg(2+)- and Mn(2+) and ATP-dependent endonuclease activities to PI-MtuI. The kinetic mechanism of PI-MtuI promoted cleavage of ectopic DNA sites proceeded through a sequential mechanism with transient accumulation of nicked circular duplex DNA as an intermediate. Together, these data suggest that PI-MtuI, like group II introns, might mediate ectopic DNA transposition and hence its lateral transfer in natural populations.

I. The structure and properties of closed circular duplex DNA. II. Chemically interacting systems at equilibrium in a buoyant density gradient

I. The binding of the intercalating dye ethidium bromide to closed circular SV 40 DNA causes an unwinding of the duplex structure and a simultaneous and quantitatively equivalent unwinding of the superhelices. The buoyant densities and sedimentation velocities of both intact (I) and singly nicked (II) SV 40 DNAs were measured as a function of free dye concentration. The buoyant density data were used to determine the binding isotherms over a dye concentration range extending from 0 to 600 µg/m1 in 5.8 M CsCl. At high dye concentrations all of the binding sites in II, but not in I, are saturated. At free dye concentrations less than 5.4 µg/ml, I has a greater affinity for dye than II. At a critical amount of dye bound I and II have equal affinities, and at higher dye concentration I has a lower affinity than II. The number of superhelical turns, τ, present in I is calculated at each dye concentration using Fuller and Waring's (1964) estimate of the angle of duplex unwinding per intercalation. The results reveal that SV 40 DNA I contains about -13 superhelical turns in concentrated salt solutions.

The free energy of superhelix formation is calculated as a function of τ from a consideration of the effect of the superhelical turns upon the binding isotherm of ethidium bromide to SV 40 DNA I. The value of the free energy is about 100 kcal/mole DNA in the native molecule. The free energy estimates are used to calculate the pitch and radius of the superhelix as a function of the number of superhelical turns. The pitch and radius of the native I superhelix are 430 Å and 135 Å, respectively.

A buoyant density method for the isolation and detection of closed circular DNA is described. The method is based upon the reduced binding of the intercalating dye, ethidium bromide, by closed circular DNA. In an application of this method it is found that HeLa cells contain in addition to closed circular mitochondrial DNA of mean length 4.81 microns, a heterogeneous group of smaller DNA molecules which vary in size from 0.2 to 3.5 microns and a paucidisperse group of multiples of the mitochondrial length.

II. The general theory is presented for the sedimentation equilibrium of a macromolecule in a concentrated binary solvent in the presence of an additional reacting small molecule. Equations are derived for the calculation of the buoyant density of the complex and for the determination of the binding isotherm of the reagent to the macrospecies. The standard buoyant density, a thermodynamic function, is defined and the density gradients which characterize the four component system are derived. The theory is applied to the specific cases of the binding of ethidium bromide to SV 40 DNA and of the binding of mercury and silver to DNA.

Investigation of Human Albumin-Induced Circular Dichroism in Dansylglycine

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Deconstructing the DGAT1 enzyme: Binding sites and substrate interactions

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

A Faster Circular Binary Segmentation Algorithm for the Analysis of Array CGH Data

Motivation: Array CGH technologies enable the simultaneous measurement of DNA copy number for thousands of sites on a genome. We developed the circular binary segmentation (CBS) algorithm to divide the genome into regions of equal copy number (Olshen {\it et~al}, 2004). The algorithm tests for change-points using a maximal $t$-statistic with a permutation reference distribution to obtain the corresponding $p$-value. The number of computations required for the maximal test statistic is $O(N^2),$ where $N$ is the number of markers. This makes the full permutation approach computationally prohibitive for the newer arrays that contain tens of thousands markers and highlights the need for a faster. algorithm. Results: We present a hybrid approach to obtain the $p$-value of the test statistic in linear time. We also introduce a rule for stopping early when there is strong evidence for the presence of a change. We show through simulations that the hybrid approach provides a substantial gain in speed with only a negligible loss in accuracy and that the stopping rule further increases speed. We also present the analysis of array CGH data from a breast cancer cell line to show the impact of the new approaches on the analysis of real data. Availability: An R (R Development Core Team, 2006) version of the CBS algorithm has been implemented in the ``DNAcopy'' package of the Bioconductor project (Gentleman {\it et~al}, 2004). The proposed hybrid method for the $p$-value is available in version 1.2.1 or higher and the stopping rule for declaring a change early is available in version 1.5.1 or higher.

Calcareous nannofossil stratigraphy and datums of sediments from ODP Leg 198 sites

During Ocean Drilling Program Leg 198, Sites 1207, 1208, 1212, 1213, and 1214 were drilled on Shatsky Rise, coring Lower to mid-Cretaceous successions of nannofossil chalk, porcellanite, and chert. Although recovery was poor, these sites yielded an outstanding record of calcareous nannoplankton, providing valuable data concerning the evolutionary succession and paleobiogeography of the largest Cretaceous marine habitat. Mid-Cretaceous sections (Aptian-Cenomanian) were recovered at all sites, and Site 1213 includes an apparently complete Berriasian-Hauterivian section. Biostratigraphic dating is problematic in places because of the absence or rarity of zonal fossils of both Boreal and Tethyan affinity. The majority of nannofossil assemblages are relatively typical of this age, but there are clear differences that set them apart from coeval epicontinental assemblages: for example, Lithraphidites carniolensis is common to abundant throughout and was most likely an oceanic-adapted taxon; the cold- to temperate-water species Crucibiscutum salebrosum, Repagulum parvidentatum, and Seribiscutum primitivum are entirely absent, indicating the persistence of tropical, warm surface water temperatures; and the warm-water species Hayesites irregularis is common. Most striking, however, is the virtual absence of Nannoconus and Micrantholithus, both taxa that were conspicuous and often common components of many Tethyan and Atlantic nannofloras. These forms were almost certainly neritic adapted and usually absent in deep open-ocean settings away from guyots and platforms. Other Tethyan taxa are also absent or rare and sporadically distributed (e.g., Calcicalathina oblongata, Conusphaera spp., Tubodiscus verenae, and Lithraphidites bollii), and factors related to neritic environments presumably controlled their distribution. Site 1213 also records extended Early Cretaceous ranges for species previously thought to have become extinct during the Late Jurassic (e.g., Axopodorhabdus cylindratus, Hexapodorhabdus cuvillieri, and Biscutum dorsetensis), suggesting these species became Pacific-restricted prior to their extinction. Watznaueria britannica may also have been a species with Pacific affinities before reexpansion of its biogeography in the early Aptian. One new genus (Mattiolia) and thirteen new species (Zeugrhabdotus clarus, Zeugrhabdotus petrizzoae, Helicolithus leckiei, Rhagodiscus amplus, Rhagodiscus robustus, Rhagodiscus sageri, Rhagodiscus adinfinitus, Tubodiscus bellii, Tubodiscus frankiae, Gartnerago ponticula, Haqius peltatus, Mattiolia furva, and Kokia stellata) are described from the Shatsky Rise Lower Cretaceous section.

Preliminary ichthyolith biostratigraphy and age profiles at DSDP Sites 91-595 and 91-596

Seventy meters of Cenozoic and Mesozoic pelagic clay cored at DSDP Sites 595 and 596 provide the basis for a preliminary analysis of ichthyolith biostratigraphy in the southwest Pacific. A most likely order of the more reliable ichthyolith events is compared with a synthesis of ichthyolith biostratigraphy in the North Pacific and with dated composite ranges. The resultant preliminary ichthyolith stratigraphy suggests that the Cenozoic is represented by the upper 20 m at Site 596 and 16 to 22 m at Site 595. Mixing of taxa precludes a clear recognition of the Cretaceous/Tertiary boundary at Site 595. The occurrence of 13 newly described subtypes is recorded in Mesozoic sediments at Sites 595 and 596. These new subtypes and previously described Mesozoic forms may be useful for recognizing Mesozoic subdivisions when their occurrences in sequences dated by other microfossils are investigated.

Calcareous nannofossils of ODP sites 177-1088 and 177-1090

During ODP Leg 177, a Miocene to Pliocene calcareous nannofossil record was recovered at Sites 1088 and 1090. Site 1088, located at 41°8'S, shows a continuous middle-upper Miocene to Pliocene carbonate sequence that was deposited at relatively high sedimentation rates (Shipboard Scientific Party, 1999a, doi:10.2973/odp.proc.ir.177.103.1999). Moreover, Site 1088 proved suitable for calcareous nannofossil analysis as a means to improve the biostratigraphy at this southern latitude. Site 1090 was drilled at 42°54'S; a tephra layer marks a significant disconformity at the Miocene/Pliocene boundary of this sequence (Shipboard Scientific Party, 1999b, doi:10.2973/odp.proc.ir.177.105.1999). Although nannofossil assemblages are poorly preserved at this site (Shipboard Scientific Party, 1999b), they may help in determining the age of the disconformity and its paleoceanographic significance.

Paleomagnetic reconstructions of sediments at ODP Sites 135-840 and 135-841

The geometry of the Tonga Arc implies that it has rotated approximately 17° clockwise away from the Lau Ridge as the Lau Basin formed in between. Questions have arisen about the timing of the opening, whether the arc behaved rigidly, and whether the opening occurred instead from motion of the Lau Ridge, the remanent arc. We undertook to address these questions by taking paleomagnetic samples from sediment cores drilled on the Tonga Arc at Sites 840 and 841, orienting the samples in azimuth, and comparing the paleodeclinations to expected directions. Advanced hydraulic piston corer (APC) cores from Holes 840C and 841A were oriented during drilling with a tool based on a magnetic compass and attached to the core barrel. Samples from Hole 841B were drilled with a rotary core barrel (RCB) and therefore are azimuthally unoriented. They were oriented by identifying faults and dipping beds in the core and aligning them with the same features in the Formation MicroScanner (FMS) wireline logs, which were themselves oriented with a three-axis magnetometer in the FMS tool. The best results came from the APC cores, which yielded a mean pole at -69.0°S, 112.2°E for an age of 4 Ma. This pole implies a declination anomaly of 20.8° ± 12.6° (95% confidence limit), which appears to have occurred by tectonic rotation of the Tonga Arc. This value is almost exactly that expected from the geometry of the arc and implies that it did indeed rotate clockwise as a rigid body. The large uncertainty in azimuth results from core orientation errors, which have an average standard deviation of 18.6°. The youngest cores used to calculate the APC pole contain sediments deposited during Subchron 2A (2.48-3.40 Ma), and their declinations are indistinguishable from the others. This observation suggests that most of the rotation occurred after their deposition; this conclusion must be treated with caution, however, because of the large azimuthal orientation errors. Poles from late and early Miocene sediments of Hole 841B are more difficult to interpret. Samples from this hole are mostly normal in polarity, fail a reversal test, and yield poles that suggest that the normal-polarity directions may be a recent overprint. Late Miocene reversed-polarity samples may be unaffected by this overprint; if so, they imply a declination anomaly of 51.1° ± 11.5°. This observation may indicate that, for older sediments, Tonga forearc rotations are larger than expected.

Paleomagnetic of ODP Leg 101 sites

Paleomagnetic measurements were made on 913 samples from 11 holes (626B, 626C, 627B, 628A, 630A, 631A, 632A, 632B, 633A, 634A, and 635B) drilled in and around the Bahamas carbonate bank during Ocean Drilling Program Leg 101. These samples displayed a wide range of magnetic intensities (from about 1.0 A/m to 1.6 * 10**- 6 A/m) and magnetic behavior. Most samples were weakly magnetized and had low mean destructive fields; however, sediments from sections of several holes were strongly magnetic with stable magnetizations. Magnetic-polarity interpretations were made on a Campanian unit from Hole 627B, a mid-Oligocene unit from Hole 628A, and a Plio-Pleistocene section from Hole 633A. Sediments in the upper parts of Holes 627B, 632A, and 633A have high magnetic intensities that decay 2 to 3 orders of magnitude over depths of 5 to 18 mbsf. The pattern of decline of the magnetism and the change in mean destructive fields and geochemical conditions in these holes are consistent with diagenetic dissolution of the magnetic minerals in a suboxic or anoxic-sulfidic environment. Paleolatitudes were calculated from samples from 16 time units in 7 holes and compared to the apparent polar wander path of the North American plate.