Dynamical principles in biological processes: A model of charge migration in proteins and DNA

The generalized master equations (GMEs) that contain multiple time scales have been derived quantum mechanically. The GME method has then been applied to a model of charge migration in proteins that invokes the hole hopping between local amino acid sites driven by the torsional motions of the floppy backbones. This model is then applied to analyze the experimental results for sequence-dependent long-range hole transport in DNA reported by Meggers et al. [Meggers, E., Michel-Beyerle, M. E., & Giese, B. (1998) J. Am. Chem. Soc. 120, 12950–12955]. The model has also been applied to analyze the experimental results of femtosecond dynamics of DNA-mediated electron transfer reported by Zewail and co-workers [Wan, C., Fiebig, T., Kelley, S. O., Treadway, C. R., Barton, J. K. & Zewail, A. H. (1999) Proc. Natl. Acad. Sci. USA 96, 6014–6019]. The initial events in the dynamics of protein folding have begun to attract attention. The GME obtained in this paper will be applicable to this problem.

(Table T2) Integrated intensity (peak area) of matrix minerals of ODP Hole 173-1068A

Mass-wasting deposits characterize the Upper Jurassic(?) to Lower Cretaceous sedimentary record of the Iberia Abyssal Plain. These deposits include olistostromes at Site 897, olistostromes and/or possible rock-fall deposits at Site 899, a breccia succession at Site 1068, slumped and fractured deposits at Site 1069, and a breccia succession at Site 1070. Whereas the exact origin of these deposits is uncertain, the regional common occurrence of middle to upper Mesozoic mass-wasting deposits suggests that they record the early rifting evolution of the west Iberia margin. This data report presents both qualitative and semiquantitative results from XRD analyses of the breccia matrix at Site 1068. In this study the matrix is defined as the fine-grained particles (as viewed through a binocular microscope) plus cement. Results are based on analytical methods that aimed to isolate the desired matrix from larger clast contamination prior to XRD analyses. In addition, the breccia was sampled at a higher resolution than was conducted aboard ship, producing a more complete description of downcore matrix mineralogical changes. The data presented here may be used to (1) further justify the subunit designation of Unit IV made aboard ship, (2) help determine to what degree the matrix and the larger clasts (studied in thin section aboard ship; Shipboard Scientific Party, 1998, doi:10.2973/odp.proc.ir.173.106.1998) are compositionally distinct, (3) help identify the extent of hydrothermal fluid migration in the breccia, and (4) support the proposed shipboard hypothesis that the Site 1068 breccia succession resulted from multiple mass-wasting.

Late Miocene and Pliocene dinoflagellate cysts, acritarchs and terrestrial palynomorphs from ODP Hole 642B, Vøring Plateau, Norwegian Sea

The globally warm climate of the early Pliocene gradually cooled from 4 million years ago, synchronous with decreasing atmospheric CO2 concentrations. In contrast, palaeoceanographic records indicate that the Nordic Seas cooled during the earliest Pliocene, before global cooling. However, a lack of knowledge regarding the precise timing of Nordic Seas cooling has limited our understanding of the governing mechanisms. Here, using marine palynology, we show that cooling in the Nordic Seas was coincident with the first trans-Arctic migration of cool-water Pacific mollusks around 4.5 million years ago, and followed by the development of a modern-like Nordic Seas surface circulation. Nordic Seas cooling precedes global cooling by 500,000 years; as such, we propose that reconfiguration of the Bering Strait and Central American Seaway triggered the development of a modern circulation in the Nordic Seas, which is essential for North Atlantic Deep Water formation and a precursor for more widespread Greenland glaciation in the late Pliocene.

Geochemistry of hydrate gas and water at DSDP Hole 84-570

Molecular and isotopic measurements of gas and water obtained from a gas hydrate at Site 570, DSDP Leg 84, are reported. The hydrate appeared to be Structure I and was composed of a solid framework of water molecules enclosing methane and small amounts of ethane and carbon dioxide. Carbon isotopic values for the hydrate-bound methane, ethane, and carbon dioxide were -41 to about -44, -27, and -2.9 per mil, respectively. The d13C-C1 values are consistent with void gas values that were determined to have a biogenic source. A significant thermogenic source was discounted because of high C1/C2 ratios and because the d13C-CO2 values in these sections were also anomalously heavy (or more positive) isotopically, suggesting that the methane was formed biogenically by reduction of heavy CO2 . The isotopically heavy hydrate d13C-C2 is also similar to void gas isotopic compositions and is either a result of low-temperature diagenesis producing heavy C2 in these immature sediment sections or upward migration of deeper thermogenic gas. The salinity of the hydrate water was 2.6 per mil with dDH2O and d18OH2O values of +1 and +2.2 per mil, respectively.

Major and trace element composition of clinopyroxenes from an olivine gabbro of ODP Hole 176-735B (Table 1)

Major and trace element profiles of clinopyroxene grains in oceanic gabbros from ODP Hole 735B have been investigated by a combined in situ analytical study with ion probe, and electron microprobe. In contrast to the homogeneous major element compositions, trace elements (REE, Y, Cr, Sr, and Zr) show continuous core to rim zoning profiles. The observed trace element systematics in clinopyroxene cannot be explained by a simple diffusive exchange between melts and gabbros along grain boundaries. A simultaneous modification of the melt composition is required to generate the zoning, although Rayleigh fractional crystallization modelling could mimic the general shape of the profiles. Simultaneous metasomatism between the cumulate crystal and the porous melt during crystal accumulation is the most likely process to explain the zoning. Deformation during solidification of the crystal mush could have caused squeezing out of the incompatible element enriched residual melts (interstitial liquid). Migration of the melt along grain boundaries might carry these melt out of the system. This process named as synkinematic differentiation or differentiation by deformation (Natland and Dick, 2001, doi:10.1016/S0377-0273(01)00211-6) may act as an important magma evolution mechanism in the oceanic crust, at least at slow-spreading ridges.

High-resolution pore-water and solid-phase analyses of sediment cores GeoB6520-3 (Hydrate Hole) and GeoB6521-2 (Worm Hole) of the northern Congo Fan

The geochemical cycling of barium was investigated in sediments of pockmarks of the northern Congo Fan, characterized by surface and subsurface gas hydrates, chemosynthetic fauna, and authigenic carbonates. Two gravity cores retrieved from the so-called Hydrate Hole and Worm Hole pockmarks were examined using high-resolution pore-water and solid-phase analyses. The results indicate that, although gas hydrates in the study area are stable with respect to pressure and temperature, they are and have been subject to dissolution due to methane-undersaturated pore waters. The process significantly driving dissolution is the anaerobic oxidation of methane (AOM) above the shallowest hydrate-bearing sediment layer. It is suggested that episodic seep events temporarily increase the upward flux of methane, and induce hydrate formation close to the sediment surface. AOM establishes at a sediment depth where the upward flux of methane from the uppermost hydrate layer counterbalances the downward flux of seawater sulfate. After seepage ceases, AOM continues to consume methane at the sulfate/methane transition (SMT) above the hydrates, thereby driving the progressive dissolution of the hydrates "from above". As a result the SMT migrates downward, leaving behind enrichments of authigenic barite and carbonates that typically precipitate at this biogeochemical reaction front. Calculation of the time needed to produce the observed solid-phase barium enrichments above the present-day depths of the SMT served to track the net downward migration of the SMT and to estimate the total time of hydrate dissolution in the recovered sediments. Methane fluxes were higher, and the SMT was located closer to the sediment surface in the past at both sites. Active seepage and hydrate formation are inferred to have occurred only a few thousands of years ago at the Hydrate Hole site. By contrast, AOM-driven hydrate dissolution as a consequence of an overall net decrease in upward methane flux seems to have persisted for a considerably longer time at the Worm Hole site, amounting to a few tens of thousands of years.

Experimental and analytical investigation of refrigerant and lubricant migration

The off-cycle refrigerant mass migration has a direct influence on the on-cycle performance since compressor energy is necessary to redistribute the refrigerant mass. No studies, as of today, are available in the open literature which experimentally measured the lubricant migration within a refrigeration system during cycling or stop/start transients. Therefore, experimental procedures measuring the refrigerant and lubricant migration through the major components of a refrigeration system during stop/start transients were developed and implemented. Results identifying the underlying physics are presented. The refrigerant and lubricant migration of an R134a automotive A/C system-utilizing a fixed orifice tube, minichannel condenser, plate and fin evaporator, U-tube type accumulator and fixed displacement compressor-was measured across five sections divided by ball valves. Using the Quick-Closing Valve Technique (QCVT) combined with the Remove and Weigh Technique (RWT) using liquid nitrogen as the condensing agent resulted in a measurement uncertainty of 0.4 percent regarding the total refrigerant mass in the system. The determination of the lubricant mass distribution was achieved by employing three different techniques-Remove and Weigh, Mix and Sample, and Flushing. To employ the Mix and Sample Technique a device-called the Mix and Sample Device-was built. A method to separate the refrigerant and lubricant was developed with an accuracy-after separation-of 0.04 grams of refrigerant left in the lubricant. When applying the three techniques, the total amount of lubricant mass in the system was determined to within two percent. The combination of measurement results-infrared photography and high speed and real time videography-provide unprecedented insight into the mechanisms of refrigerant and lubricant migration during stop-start operation. During the compressor stop period, the primary refrigerant mass migration is caused by, and follows, the diminishing pressure difference across the expansion device. The secondary refrigerant migration is caused by a pressure gradient as a result of thermal nonequilibrium within the system and causes only vapor phase refrigerant migration. Lubricant migration is proportional to the refrigerant mass during the primary refrigerant mass migration. During the secondary refrigerant mass migration lubricant is not migrating. The start-up refrigerant mass migration is caused by an imbalance of the refrigerant mass flow rates across the compressor and expansion device. The higher compressor refrigerant mass flow rate was a result of the entrainment of foam into the U-tube of the accumulator. The lubricant mass migration during the start-up was not proportional to the refrigerant mass migration. The presence of water condensate on the evaporator affected the refrigerant mass migration during the compressor stop period. Caused by an evaporative cooling effect the evaporator held 56 percent of the total refrigerant mass in the system after three minutes of compressor stop time-compared to 25 percent when no water condensate was present on the evaporator coil. Foam entrainment led to a faster lubricant and refrigerant mass migration out of the accumulator than liquid entrainment through the hole at the bottom of the U-tube. The latter was observed for when water condensate was present on the evaporator coil because-as a result of the higher amount of refrigerant mass in the evaporator before start-up-the entrainment of foam into the U-tube of the accumulator ceased before the steady state refrigerant mass distribution was reached.

Ankhd1 Silencing Inhibits Stathmin 1 Activity, Cell Proliferation And Migration Of Leukemia Cells.

ANKHD1 is highly expressed in human acute leukemia cells and potentially regulates multiple cellular functions through its ankyrin-repeat domains. In order to identify interaction partners of the ANKHD1 protein and its role in leukemia cells, we performed a yeast two-hybrid system screen and identified SIVA, a cellular protein known to be involved in proapoptotic signaling pathways. The interaction between ANKHD1 and SIVA was confirmed by co-imunoprecipitation assays. Using human leukemia cell models and lentivirus-mediated shRNA approaches, we showed that ANKHD1 and SIVA proteins have opposing effects. While it is known that SIVA silencing promotes Stathmin 1 activation, increased cell migration and xenograft tumor growth, we showed that ANKHD1 silencing leads to Stathmin 1 inactivation, reduced cell migration and xenograft tumor growth, likely through the inhibition of SIVA/Stathmin 1 association. In addition, we observed that ANKHD1 knockdown decreases cell proliferation, without modulating apoptosis of leukemia cells, while SIVA has a proapoptotic function in U937 cells, but does not modulate proliferation in vitro. Results indicate that ANKHD1 binds to SIVA and has an important role in inducing leukemia cell proliferation and migration via the Stathmin 1 pathway. ANKHD1 may be an oncogene and participate in the leukemia cell phenotype.

Paracoccidioides brasilinsis-Induced Migration of Dendritic Cells and Subsequent T-Cell Activation in the Lung-Draining Lymph Nodes

Paracoccidioidomycosis is a mycotic disease caused by a dimorphic fungus, Paracoccidioides brasiliensis (Pb), that starts with inhalation of the fungus; thus, lung cells such as DC are part of the first line of defense against this microorganism. Migration of DC to the lymph nodes is the first step in initiating T cell responses. The mechanisms involved in resistance to Pb infection are poorly understood, but it is likely that DC play a pivotal role in the induction of effector T cells that control Pb infection. In this study, we showed that after Pb Infection, an important modification of lung DC receptor expression occurred. We observed an increased expression of CCR7 and CD103 on lung DC after infection, as well as MHC-II. After Pb infection, bone marrow-derived DC as well lung DC, migrate to lymph nodes. Migration of lung DC could represent an important mechanism of pathogenesis during PCM infection. In resume our data showed that Pb induced DC migration. Furthermore, we demonstrated that bone marrow-derived DC stimulated by Pb migrate to the lymph nodes and activate a T helper (Th) response. To the best of our knowledge, this is the first reported data showing that Pb induces migration of DC and activate a T helper (Th) response.