An Sp1/Sp3 site polymorphism associated with hypermethylation of the candidate tumor suppressor gene RIL in cancer

Gene silencing due to promoter methylation is an alternative to mutations and deletions, which inactivate tumor suppressor genes (TSG) in cancer. We identified RIL by Methylated CpG Island Amplification technique as a novel aberrantly methylated gene. RIL is expressed in normal tissues and maps to the 5q31 region, frequently deleted in leukemias. We found methylation of RIL in 55/80 (69%) cancer cell lines, with highest methylation in leukemia and colon. We also observed methylation in 46/80 (58%) primary tumors, whereas normal tissues showed substantially lower degrees of methylation. RIL expression was lost in 13/16 cancer cell lines and was restored by demethylating agent. Screening of 38 cell lines and 13 primary cancers by SSCP revealed no mutations in RIL, suggesting that methylation and LOH are the primary inactivation mechanisms. Stable transfection of RIL into colorectal cancer cells resulted in reduction in cell growth, clonogenicity, and increased apoptosis upon UVC treatment, suggesting that RIL is a good candidate TSG. ^ In searching for a cause of RIL hypermethylation, we identified a 12-bp polymorphic sequence around the transcription start site of the gene that creates a long allele containing 3CTC repeat. Evolutionary studies suggested that the long allele appeared late in evolution due to insertion. Using bisulfite sequencing, in cancers heterozygous for RIL, we found that the short allele is 4.4-fold more methylated than the long allele (P = 0.003). EMSA results suggested binding of factor(s) to the inserted region of the long allele, but not to the short. EMSA mutagenesis and competition studies, as well as supershifts using nuclear extracts or recombinant Sp1 strongly indicated that those DNA binding proteins are Sp1 and Sp3. Transient transfections of RIL allele-specific expression constructs showed less than 2-fold differences in luciferase activity, suggesting no major effects of the additional Sp1 site on transcription. However, stable transfection resulted in 3-fold lower levels of transcription from the short allele 60 days post-transfection, consistent with the concept that the polymorphic Sp1 site protects against time-dependent silencing. Thus, an insertional polymorphism in the RIL promoter creates an additional Sp1/Sp3 site, which appears to protect it from silencing and methylation in cancer. ^

Safety, pharmacokinetics, and antiretroviral activity of multiple doses of ibalizumab (formerly TNX-355), an anti-CD4 monoclonal antibody in HIV-1 infected adults

Context: Despite tremendous strides in HIV treatment over the past decade, resistance remains a major problem. A growing number of patients develop resistance and require new therapies to suppress viral replication. ^ Objective: To assess the safety of multiple administrations of the anti-CD4 receptor (anti-CD4) monoclonal antibody ibalizumab given as intravenous (IV) infusions, in three dosage regimens, in subjects infected with human immunodeficiency virus (HIV-1). ^ Design: Phase 1, multi-center, open-label, randomized clinical trial comparing the safety, pharmacokinetics and antiviral activity of three dosages of ibalizumab. ^ Setting: Six clinical trial sites in the United States. ^ Participants: A total of twenty-two HIV-positive patients on no anti-retroviral therapy or a stable failing regimen. ^ Intervention: Randomized to one of two treatment groups in Arms A and B followed by non-randomized enrollment in Arm C. Patients randomized to Arm A received 10 mg/kg of ibalizumab every 7 days, for a total of 10 doses; patients randomized to Arm B received a total of six doses of ibalizumab; a single loading dose of 10 mg/kg on Day 1 followed by five maintenance doses of 6 mg/kg every 14 days, starting at Week 1. Patients assigned to Arm C received 25 mg/kg of ibalizumab every 14 days for a total of 5 doses. All patients were followed for safety for an additional 7 to 8 weeks. ^ Main Outcome Measures: Clinical and laboratory assessments of safety and tolerability of multiple administrations of ibalizumab in HIV-infected patients. Secondary measures of efficacy include HIV-1 RNA (viral load) measurements. ^ Results: 21 patients were treatment-experienced and 1 was naïve to HIV therapy. Six patients were failing despite therapy and 15 were on no current HIV treatment. Mean baseline viral load (4.78 log 10; range 3.7-5.9) and CD4+ cell counts (332/μL; range 89-494) were similar across cohorts. Mean peak decreases in viral load from baseline of 0.99 log10(1.11 log10, and 0.96 log 10 occurred by Wk 2 in Cohorts A, B and C, respectively. Viral loads decreased by >1.0 log10 in 64%; 4 patients viral loads were suppressed to < 400 copies/mL. Viral loads returned towards baseline by Week 9 with reduced susceptibility to ibalizumab. CD4+ cell counts rose transiently and returned toward baseline. Maximum median elevations above BL in CD4+ cell counts for Cohorts A, B and C were +257, +198 and +103 cells/μL, respectively and occurred within 3 Wks in 16 of 22 subjects. The half-life of ibalizumab was 3-3.5 days and elimination was characteristic of capacity-limited kinetics. Administration of ibalizumab was well tolerated. Four serious adverse events were reported during the study. None of these events were related to study drug. Headache, nausea and cough were the most frequently reported treatment emergent adverse events and there were no laboratory abnormalities related to study drug. ^ Conclusions: Ibalizumab administered either weekly or bi-weekly was safe, well tolerated, and demonstrated antiviral activity. Further studies with ibalizumab in combination with standard antiretroviral treatments are warranted.^

Sediment geochemistry of ODP Leg 127 sites

The relative effects of paleoceanographic and paleogeographic variations, sediment lithology, and diagenetic processes on the final preserved chemistry of Japan Sea sediments are evaluated by investigating the rare earth element (REE), major element, and trace element concentrations in 59 squeeze-cake whole-round and 27 physical-property sample residues from Sites 794, 795, and 797, cored during ODP Leg 127. The most important variation in sedimentary chemical composition is the increase in SiO2 concentration through the Pliocene diatomaceous sequences, which dilutes most other major and trace element components by various degrees. This biogenic input is largest at Site 794 (Yamato Basin), moderately developed at Site 797 (Yamato Basin), and of only minor importance at Site 795 (Japan Basin), potentially reflecting basinal contrasts in productivity with the Yamato Basin recording greater biogenic input than the Japan Basin and with the easternmost sequence of Site 794 lying beneath the most productive waters. There are few systematic changes in solid-phase chemistry resulting from the opal-A/opal-CT or opal-CT/quartz silica phase transformations. Most major and trace element concentrations are controlled by the aluminosilicate fraction of the sediment, although the effects of diagenetic silica phases and manganese carbonates are of localized importance. REE total abundances (Sum REE) in the Japan Sea are strongly dependent upon the paleoceanographic position of a given site with respect to terrigenous and biogenic sources. REE concentrations at Site 794 overall correspond well to aluminosilicate chemical indices and are strongly diluted by SiO2 within the upper Miocene-Pliocene diatomaceous sequence. Eu/Eu* values at Site 794 reach a maximum through the diatomaceous interval as well, most likely suggesting an association of Eu/Eu* with the siliceous component, or reflecting slight incorporation of a detrital feldspar phase. SumREE at Site 795 also is affiliated strongly with aluminosilicate phases and yet is diluted only slightly by siliceous input. At Site 797, SumREE is not as clearly associated with the aluminosilicate fraction, is correlated moderately to siliceous input, and may be sporadically influenced by detrital heavy minerals originating from the nearby rifted continental fragment composing the Yamato Rise. Ce/Ce* profiles at all three sites increase essentially monotonically with depth and record progressive diagenetic LREE fractionation. The observed Ce/Ce* increases are not responding to changes in the paleoceanographic oxygenation state of the overlying water, as there is no independent evidence to suggest the proper oceanographic conditions. Ce/Ce* correlates slightly better with depth than with age at the two Yamato Basin sites. The downhole increase in Ce/Ce* at Sites 794 and 797 is a passive response to the diagenetic transfer of LREE (except Ce) from sediment to interstitial water. At Site 795, the overall lack of correlation between Ce/Ce* and Lan/Ybn suggests that other processes mask the diagenetic behavior of all LREEs. First-order calculations of the Ce budget in Japan Sea waters and sediment indicate that ~20% of the excess Ce adsorbed by settling particles is recycled within the water column and that an additional ~38% is recycled at or near the seafloor. Thus, because the remaining excess Ce is only ~10% of the total Ce, there is not a large source of Ce to the deeply buried sediment, further suggesting that the downhole increase in Ce/Ce* is a passive response to diagenetic behavior of the other LREEs. The REE chemistry of Japan Sea sediment therefore predicts successive downhole addition of LREEs to deeply buried interstitial waters.

Rare earth element data for sediments from ODP Leg 127

The relative effects of paleoceanographic and paleogeographic variations, sediment lithology, and diagenetic processes on the recorded rare earth element (REE) chemistry of Japan Sea sediments are evaluated by investigating REE total abundances and relative fractionations in 59 samples from Ocean Drilling Program Leg 127. REE total abundances (Sum REE) in the Japan Sea are strongly dependent upon the paleoceanographic position of a given site with respect to terrigenous and biogenic sources. REE concentrations at Site 794 (Yamato Basin) overall correspond well to aluminosilicate chemical indices and are strongly diluted by SiO2 within the late Miocene-Pliocene diatomaceous sequence. Eu/Eu* values at Site 794 reach a maximum through the diatomaceous interval as well, most likely suggesting an association of Eu/Eu* with the siliceous component, or reflecting slight incorporation of a detrital feldspar phase. Sum REE at Site 795 (Japan Basin) also is affiliated strongly with aluminosilicate phases, yet is diluted only slightly by siliceous input. At Site 797 (Yamato Basin), REE is not as clearly associated with the aluminosilicate fraction, is correlated moderately to siliceous input, and may be sporadically influenced by detrital heavy minerals originating from the nearby rifted continental fragment composing the Yamato Rise. The biogenic influence is largest at Site 794, moderately developed at Site 797, and of only minor importance at Site 795, reflecting basinal contrasts in productivity such that the Yamato Basin records greater biogenic input than the Japan Basin, while the most productive waters overlie the easternmost sequence of Site 794. Ce/Ce* profiles at all three sites increase monotonically with depth, and record progressive diagenetic LREE fractionation. The observed Ce/Ce* record does not respond to changes in oxygenation state of the overlying water, and Ce/Ce* correlates slightly better with depth than with age. The downhole increase in Ce/Ce* at Site 794 and Site 797 is a passive response to diagenetic transfer of LREE (except Ce) from sediment to interstitial water. At Site 795, the overall lack of correlation between Ce/Ce* and La_n/Yb_n suggests that other processes are occurring which mask the diagenetic behavior of all LREEs. First-order calculations of the Ce budget in Japan Sea waters and sediment indicate that ~20% of the excess Ce adsorbed by settling particles is recycled within the water column, and that an additional ~38% is recycled at or near the seafloor (data from Masuzawa and Koyama, 1989). Thus, because the remaining excess Ce is only ~10% of the total Ce, there is not a large source of Ce to the deeply buried sediment, further suggesting that the downhole increase in Ce/Ce* is a passive response to diagenetic behavior of the other LREEs. The REE chemistry of Japan Sea sediment therefore predicts successive downhole addition of LREEs to deeply-buried interstitial waters.

Clay mineralogy of Cape Roberts sediment cores

The clay mineral assemblages of the ca. 1600 m thick Cenozoic sedimentary succession recovered at the CRP-1, CRP-2/2A and CRP-3 drill sites off Cape Roberts on the McMurdo Sound shelf, Antarctica, were analysed in order to reconstruct the palaeoclimate and the glacial history of this part of Antarctica. The sequence can be subdivided into seven clay mineral units that reflect the transition from humid to subpolar and polar conditions. Unit I (35-33.6 Ma) is characterised by an almost monomineralic assemblage consisting of well crystalline, authigenic smectite, and therefore does not allow a palaeoclimatic reconstruction. Unit II (33.6-33.1 Ma) has also a monomineralic clay mineral composition. However, the assemblage consists of variably crystallized smectite that, at least in part, is of detrital origin and indicates chemical weathering under a humid climate. The main source area for the clays was in the Transantarctic Mountains. Minor amounts of illite and chlorite appear for the first time in Unit III (33.1-31 Ma) and suggest subordinate physical weathering. The sediments of Unit IV (31-30.5 Ma) have strongly variable smectite and illite concentrations indicating an alternation of chemical weathering periods and physical weathering periods. Unit V (30.5-24.2 Ma) shows a further shift towards physical weathering. Unit VI (24.2-18.5 Ma) indicates strong physical weathering under a cold climate with persistent and intense illite formation. Unit VII (18.5 Ma to present) documents an additional input of smectite derived from the McMurdo Volcanic Group in the south.

Calcium isotopes of planktonic foraminifera

Measurements of the calcium isotopic composition (d44/40Ca) of planktonic foraminifera from the western equatorial Pacific and the Indian sector of the Southern Ocean show variations of about 0.6 per mil over the past 24 Myr. The stacked d44/40Ca record of Globigerinoides trilobus and Globigerina bulloides indicates a minimum in d44/40Casw (seawater calcium) at 15 to 16 Ma and a subsequent general increase toward the present, interrupted by a second minimum at 3 to 5 Ma. Applying a coupled calcium/carbon cycle model, we find two scenarios that can explain a large portion of the observed d44/40Casw variations. In both cases, variations in the Ca input flux to the ocean without proportional changes in the carbonate flux are invoked. The first scenario increases the riverine calcium input to the ocean without a proportional increase of the carbonate flux. The second scenario generates an additional calcium flux from the exchange of Ca by Mg during dolomitization. In both cases the calcium flux variations lead to drastic changes in the seawater Ca concentrations on million year timescales. Our d44/40Casw record therefore indicates that the global calcium cycle may be much more dynamic than previously assumed.

(Table 2) Concentrations of particulate chemical elements in waters of the Pechora Sea

Mineralogy of suspended matter from surface and bottom waters has been studied at two sites in the Barents Sea. Along with terrigenous minerals, particulate matter samples contain authigenic mineral phases of iron and manganese oxyhydroxides. Mn-feroxyhite, Fe-vernadite, goethite, and proto-ferrihydrite have been identified in samples from the surface waters, whereas birnessite and non-ferruginous vernadite have been found in samples from the bottom waters. Formation of suspended manganese minerals in the bottom waters is explained by an additional Mn supply from underlying reduced sediments during their early diagenesis and oxygen depletion in the near-bottom nepheloid layer. Bacteria are supposed to take part in the authigenic mineral formation.

Halogene concentrations and iodine isotopic composition in pore water on Hydrare Ridge, Cascadia continental margin

We report iodine and bromine concentrations in a total of 256 pore water samples collected from all nine sites of Ocean Drilling Program Leg 204, Hydrate Ridge. In a subset of these samples, we also determined iodine ages in the fluids using the cosmogenic isotope 129I (T1/2 = 15.7 Ma). The presence of this cosmogenic isotope, combined with the strong association of iodine with methane, allows the identification of the organic source material responsible for iodine and methane in gas hydrates. In all cores, iodine concentrations were found to increase strongly with depth from values close to that of seawater (0.0004 mM) to concentrations >0.5 mM. Several of the cores taken from the northwest flank of the southern summit show a pronounced maximum in iodine concentrations at depths between 100 and 150 meters below seafloor in the layer just above the bottom-simulating reflector. This maximum is especially visible at Site 1245, where concentrations reach values as high as 2.3 mM, but maxima are absent in the cores taken from the slope basin sites (Sites 1251 and 1252). Bromine concentrations follow similar trends, but enrichment factors for Br are only 4-8 times that of seawater (i.e., considerably lower than those for iodine). Iodine concentrations are sufficient to allow isotope determinations by accelerator mass spectrometry in individual pore water samples collected onboard (~5 mL). We report 129I/I ratios in a few samples from each core and a more complete profile for one flank site (Site 1245). All 129I/I ratios are below the marine input ratio (Ri = 1500x10**-15). The lowest values found at most sites are between 150 and 250x10**-15, which correspond to minimum ages between 40 and 55 Ma, respectively. These ages rule out derivation of most of the iodine (and, by association, of methane) from the sediments hosting the gas hydrates or from currently subducting sediments. The iodine maximum at Site 1245 is accompanied by an increase in 129I/I ratios, suggesting the presence of an additional source with an age younger than 10 Ma; there is indication that younger sources also contribute at other sites, but data coverage is not yet sufficient to allow a definitive identification of sources there. Likely sources for the older component are formations of early Eocene age close to the backstop in the overriding wedge, whereas the younger sources might be found in recent sediments underlying the current locations of the gas hydrates.

(Table 1) Estimated e-Nd(0) input calculated using the relative fraction of ODP Hole 105-647A amphibole grains originated from different provinces of the North America

Many marine radiogenic isotope records show both spatial and temporal variations, reflecting both the degree of mixing of distinct sources in the oceans and changes in the distribution of chemical weathering on the continents. However, changes in weathering and transport processes may themselves affect the composition of radiogenic isotopes released into seawater. The provenance of physically weathered material in the Labrador Sea, constrained through the use of Ar-Ar ages of individual detrital minerals, has been used to estimate the relative contributions of chemically weathered terranes releasing radiogenic isotopes into the Labrador Sea. A simple box-model approach for balancing observed Nd-isotope variations has been used to constrain the relative importance of localised input in the Labrador Sea, and the subsequent mixing of Labrador Sea Water into North Atlantic Deep-Water. The long-term pattern of erosion and deep-water formation around the North Atlantic seems to have been a relatively stable feature since 1.5 Ma, although there has been a dramatic shift in the nature of physical and chemical weathering affecting the release of Hf and Pb isotopes. The modelled Nd isotopes imply a relative decrease in water mass advection into the Labrador Sea between 2.4 and 1.5 Ma, accompanied by a decrease in the rate of overturning, possibly caused by an increased freshwater input into the Labrador Sea.

Documentation of Graf-Wilczek-Knoll

During Leg ANT-XXIII/9 on the 31st March 2007 the German research vessel Polarstern mapped a significant bathymetric feature with its swath sonar system at the north-west margin of the Kerguelen Plateau. Due to the fact, that the feature was discovered just a month after the third IPY 2007/2008 has started, it was named after Graf Wilczek who, together with Carl Weyprecht, had promoted the first IPY. The undersea feature name proposal was officialy accepted by the GEBCO Sub-Committee on Undersea Feature Names (SCUFN) at its 20th meeting in late July and was added to the GEBCO Gazetteer of UFN (http://www.iho.shom.fr/COMMITTEES/GEBCO/SCUFN/scufn_intro.htm). ______________ Graf Hans Wilczek (Notation of the name from the book of Wilczek's daughter Elisabeth Kinsky- Wilczek). The Austrian naval hero Tegetthoff in 1871 planned an expedition to the southern hemisphere. The geophysicist G. Neumayer (1826-1909) already was selected as its chief scientist. Also the naval officer Carl Weyprecht (1838-1881) and the mountaineer Julius Payer (1841-1915) were to participate. Because of the sudden death of Tegettoff the project came to a halt and eventually was cancelled. By support of the well known geographer August Petermann (1822-1878) Weyprecht and Payer made a voyage into the Barents Sea which made them believe having seen the "open polar sea". An additional undertaking to confirm and to extend the find was obvious. At this stage of the affair count Hans Wilczek (1837-1922) got involved. He not only fostered a new expedition with a considerable sum of money, but he participated in commanding a support vessel to Novaya Zemlya. Wilczek managed to get home but the expedition vessel under Weyprecht's command became imprisoned in the pack for two years and at least had to be abandoned. After an adventurous trip back to civilisation Weyprecht changed his mind in what he considered the best way of polar research. Together with Wilczek in 1875 he started the promotion of international station-based polar exploration - the IPY was born. Wilczek guaranteed the constitution of an Austrian station on Novaya Zemlya and was ready to winter over there personally. Because of several political and other obstructions the beginning of the IPY was delayed till 1882. Wilczek's friend Weyprecht had passed away already. The command of the Austrian station, eventually erected on Jan Mayen, was given to Emil v. Wohlgemuth (1843-1896). Wilczek financed the main part of the Austrian IPY participation. Wilczek is described as honest and popular. On the one hand acquainted with the most prominent persons of his days, he respected everybody and had many relationships with scientists and artists. There is a kind of autobiography under the title: Hans Wilczek erzählt seinen Enkeln Erinnerungen aus seinem Leben (Hans Wilczek tells his grandchildren reminiscences from his life); edited by his daughter Elisabeth Kinsky-Wilczek, Graz 1933, 502 p. The book is available in an English version: Happy Retrospect - the Reminiscences of Count Wilczek 1837-1922, Bell and Sons, London 1934, 295 p.

Investigation of time series stations along a productivity gradient north of the Canary Islands

Three stations along a productivity gradient north of the Canary Islands were investigated for surface-water properties, particle flux, and composition (biogenic and lithogenic components, and stable nitrogen isotope composition, delta15N) and export production. Investigation sites along the east-west transect off the NW African upwelling margin included the European Station for Time-Series in the Ocean, Canary Islands (ESTOC), one location contiguous to the NW African upwelling zone in the Eastern Boundary Current (EBC) and one station north of the island La Palma (LP). The seasonality of surface-water properties along the transect was mainly influenced by the winter cooling and simultaneous phytoplankton maximum and, in addition at EBC, by nearby upwelling. Accordingly, particle flux and composition along the transect were closely linked to the winter bloom sedimentation and upwelling related enhanced plankton biomass stemming from the primary upwelling and the Cape Yubi filament at EBC. During all seasons, particle flux was highest at EBC and had the highest contribution of biogenic opal and lithogenic components, and the lowest delta15N compared to the offshore stations. But contrary to what would be expected from the productivity gradient, particle flux did not decrease from ESTOC to LP. Below the upper several hundred meters, particle flux was enhanced by additional particle input along the entire transect, manifested by an increase of flux with depth and lower delta15N values. We offer a scenario in which intermediate nepheloid layers originating from the primary upwelling as well as particle dispersion from upwelling filaments, mainly the Cape Ghir filament, impact on the trap stations as far as 700 km into the open ocean. This study contributes to our understanding of the poorly resolved biogeochemical transition between the productive shelf and subtropical gyre provinces.

Swift thermal reaction norm evolution in a key coccolithopore species: Reaction norm assay data from an experiment in Kiel from December 2012 to June 2015

Temperature has a profound effect on the species composition and physiology of marine phytoplankton, a polyphyletic group of microbes responsible for half of global primary production. Here, we ask whether and how thermal reaction norms in a key calcifying species, the coccolithophore Emiliania huxleyi, change as a result of 2.5 years of experimental evolution to a temperature about 2°C below its upper thermal limit. Replicate experimental populations derived from a single genotype isolated from Norwegian coastal waters were grown at two temperatures for 2.5 years before assessing thermal responses at 6 temperatures ranging from 15 to 26°C, with pCO2 (400/1100/2200 ?atm) as a fully factorial additional factor. The two selection temperatures (15°/26.3°C) led to a marked divergence of thermal reaction norms. Optimal growth temperatures were 0.7°C higher in experimental populations selected at 26.3°C than those selected at 15.0°C. An additional negative effect of high pCO2 on maximal growth rate (8% decrease relative to lowest level) was observed. Finally, the maximum persistence temperature (Tmax) differed by 1-3°C between experimental treatments, as a result of an interaction between pCO2 and the temperature selection. Taken together, we demonstrate that several attributes of thermal reaction norms in phytoplankton may change faster than the predicted progression of ocean warming.

PREVIRNEC A new platform for cognitive tele-rehabilitation

Acquired Brain Injury (ABI), either caused by vascular or traumatic nature, is one of the most important causes for neurological disabilities. People who suffer ABI see how their quality of life decreases, due to the affection of one or some of the cognitive functions (memory, attention, language or executive functions). The traditional cognitive rehabilitation protocols are too expensive, so every help carried out in this area is justified. PREVIRNEC is a new platform for cognitive tele-rehabilitation that allows the neuropsychologist to schedule rehabilitation sessions consisted of specifically designed tasks, plus offering an additional way of communication between neuropsychologists and patients. Besides, the platform offers a knowledge management module that allows the optimization of the cognitive rehabilitation to this kind of patients.

PWM Control of a Buck Converter with an Amorphous Core Coil

Pulse-width modulation is widely used to control electronic converters. One of the most topologies used for high DC voltage/low DC voltage conversion is the Buck converter. It is obtained as a second order system with a LC filter between the switching subsystem and the load. The use of a coil with an amorphous magnetic material core instead of air core lets design converters with smaller size. If high switching frequencies are used for obtaining high quality voltage output, the value of the auto inductance L is reduced throughout the time. Then, robust controllers are needed if the accuracy of the converter response must not be affected by auto inductance and load variations. This paper presents a robust controller for a Buck converter based on a state space feedback control system combined with an additional virtual space variable which minimizes the effects of the inductance and load variations when a not-toohigh switching frequency is applied. The system exhibits a null steady-state average error response for the entire range of parameter variations. Simulation results are presented.