Non-Destructive Global and Localized 2D T1/T2 NMR Relaxometry to Resolve Microstructure in Apples Affected by Watercore

Apples can be considered as having a complex system formed by several structures at different organization levels: macroscale (>100 μm) and microscale (<100 μm). This work implements 2D T1/T2 global and localized relaxometry sequences on whole apples to be able to perform an intensive non-destructive and non-invasive microstructure study. The 2D T1/T2 cross-correlation spectroscopy allows the extraction of quantitative information about the water compartmentation in different subcellular organelles. A clear difference is found as sound apples show neat peaks for water in different subcellular compartments, such as vacuolar, cytoplasmatic and extracellular water, while in watercore-affected tissues such compartments appear merged. Localized relaxometry allows for the predefinition of slices in order to understand the microstructure of a particular region of the fruit, providing information that cannot be derived from global 2D T1/T2 relaxometry.

Antibody catalysis of peptidyl-prolyl cis-trans isomerization in the folding of RNase T1

An antibody generated to an α-keto amide containing hapten 1 catalyzes the cis-trans isomerization of peptidyl-prolyl amide bonds in peptides and in the protein RNase T1. The antibody-catalyzed peptide isomerization reaction showed saturation kinetics for the cis-substrate, Suc-Ala-Ala-Pro-Phe-pNA, with a kcat/Km value of 883 s−1⋅M−1; the reaction was inhibited by the hapten analog 13 (Ki = 3.0 ± 0.4 μM). Refolding of denatured RNase T1 to its native conformation also was catalyzed by the antibody, with the antibody-catalyzed folding reaction inhibitable both by the hapten 1 and hapten analog 13. These results demonstrate that antibodies can catalyze conformational changes in protein structure, a transformation involved in many cellular processes.

T1/ST2 is preferentially expressed on murine Th2 cells, independent of interleukin 4, interleukin 5, and interleukin 10, and important for Th2 effector function

T helper (Th) cells can be categorized according to their cytokine expression. The differential induction of Th cells expressing Th1 and/or Th2 cytokines is key to the regulation of both protective and pathological immune responses. Cytokines are expressed transiently and there is a lack of stably expressed surface molecules, significant for functionally different types of Th cells. Such molecules are of utmost importance for the analysis and selective functional modulation of Th subsets and will provide new therapeutic strategies for the treatment of allergic or autoimmune diseases. To this end, we have identified potential target genes preferentially expressed in Th2 cells, expressing interleukin (IL)-4, IL-5, and/or IL-10, but not interferon-γ. One such gene, T1/ST2, is expressed stably on both Th2 clones and Th2-polarized cells activated in vivo or in vitro. T1/ST2 expression is independent of induction by IL-4, IL-5, or IL-10. T1/ST2 plays a critical role in Th2 effector function. Administration of either a mAb against T1/ST2 or recombinant T1/ST2 fusion protein attenuates eosinophilic inflammation of the airways and suppresses IL-4 and IL-5 production in vivo following adoptive transfer of Th2 cells.

The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small

In the maximum parsimony (MP) and minimum evolution (ME) methods of phylogenetic inference, evolutionary trees are constructed by searching for the topology that shows the minimum number of mutational changes required (M) and the smallest sum of branch lengths (S), respectively, whereas in the maximum likelihood (ML) method the topology showing the highest maximum likelihood (A) of observing a given data set is chosen. However, the theoretical basis of the optimization principle remains unclear. We therefore examined the relationships of M, S, and A for the MP, ME, and ML trees with those for the true tree by using computer simulation. The results show that M and S are generally greater for the true tree than for the MP and ME trees when the number of nucleotides examined (n) is relatively small, whereas A is generally lower for the true tree than for the ML tree. This finding indicates that the optimization principle tends to give incorrect topologies when n is small. To deal with this disturbing property of the optimization principle, we suggest that more attention should be given to testing the statistical reliability of an estimated tree rather than to finding the optimal tree with excessive efforts. When a reliability test is conducted, simplified MP, ME, and ML algorithms such as the neighbor-joining method generally give conclusions about phylogenetic inference very similar to those obtained by the more extensive tree search algorithms.

Expression of a dominant negative TrkB receptor, T1, reveals a requirement for presynaptic signaling in BDNF-induced synaptic potentiation in cultured hippocampal neurons

We have developed a method to analyze the relative contributions of pre- and postsynaptic actions of a particular gene product in neurons in culture and potentially in slices using adenovirus-mediated gene transfer. A recombinant virus directed the expression of both a GFP reporter protein and TrkB.T1, a C-terminal truncated dominant negative TrkB neurotrophin receptor. When expressed in the presynaptic cell at synapses between embryonic hippocampal neurons in culture, the dominant negative TrkB.T1 inhibited two forms of synaptic potentiation induced by the neurotrophin brain-derived neurotrophic factor (BDNF): (i) greater evoked synaptic transmission and (ii) higher frequency of spontaneous miniature synaptic currents. These inhibition effects are not seen if the transgene is expressed only in the postsynaptic cell. We conclude that BDNF-TrkB signal transduction in the presynaptic terminal leads to both types of potentiation and is therefore the primary cause of synaptic enhancement by BDNF in these neurons.

Oxidative/reductive conjugation of mannan to antigen selects for T1 or T2 immune responses.

The induction of CD8+ cytotoxic T lymphocytes (CTLs) is desirable for immunization against many diseases, and recombinant-synthetic peptide antigens are now favored agents to use. However, a major problem is how to induce CTLs, which requires a T1-type response to such synthetic antigens. We report that T1-type (generating high CTL, low antibody) or T2-type (the reciprocal) responses can be induced by conjugation of the antigen to the carbohydrate polymer mannan: T1 responses are selected by using oxidizing conditions; T2 responses are selected by using reducing conditions for the conjugation. Using human MUC1 as a model antigen in mice, immunization with oxidized mannan-MUC1 fusion protein (ox-M-FP) led to complete tumor protection (challenge up to 5 x 10(7) MUC1+ tumor cells), CTLs, and a high CTL precursor (CTLp) frequency (1/6900), whereas immunization with reduced mannan-MUC1 FP (red-M-FP) led to poor protection after challenge with only 10(6) MUC1+ tumor cells, no CTLs, and a low CTLp frequency (1/87,800). Ox-M-FP selects for a T1 response (mediated here by CD8+ cells) with high interferon gamma (IFN-gamma) secretion, no interleukin 4 (IL-4), and a predominant IgG2a antibody response; red-M-FP selects for a T2-type response with IL-4 production and a high predominant IgG1 antibody response but no IFN-gamma.

α-sarcin and RNase T1 based immunoconjugates: the role of intracellular trafficking in cytotoxic efficiency

Toxins have been thoroughly studied for their use as therapeutic agents in search of an improvement in toxic efficiency together with a minimization of their undesired side effects. Different studies have shown how toxins can follow different intracellular pathways which are connected with their cytotoxic action inside the cells. The work herein presented describes the different pathways followed by the ribotoxin a-sarcin and the fungal RNase T1,as toxic domains of immunoconjugates with identical binding domain, the single chain variable fragment of a monoclonal antibody raised against the glycoprotein A33. According to the results obtained both immunoconjugates enter the cells via early endosomes and, while a-sarcin can translocate directly into the cytosol to exert its deathly action, RNase T1 follows a pathway that involves lysosomes and the Golgi apparatus. These facts contribute to explaining the different cytotoxicity observed against their targeted cells, and reveal how the innate properties of the toxic domain, apart from its catalytic features, can be a key factor to be considered for immunotoxin optimization.

(Table T1) Calcium carbonate mineralogy and stable isotopic composition of ODP Hole 182-1132C sediments

Petrographic observation and carbonate mineralogic and stable isotopic investigation were conducted on lower Oligocene to middle Miocene sediments recovered during Ocean Drilling Program Leg 182 from Site 1132, located at a water depth of 218.5 m immediately seaward of the shelf-slope break of the eastern Eyre Terrace in the western Great Australian Bight. The middle Miocene section consists of bioclastic packstone and grainstone with an interval of partially silicified nannofossil-foraminiferal chalk and is slightly to densely dolomitized. By contrast, the lower Oligocene to lower Miocene section is characterized by a predominance of planktonic and benthic foraminifers, high porosity, absence of chert, and weak dolomitization. The carbon and oxygen isotopic composition of calcites and dolomites between two sections, however, shows no significant difference.

(Table T1) Strontium isotopic composition and ages of limestone samples from ODP Hole 180-1118A

Limestone from Unit VI (857.1-859.15 meters below seafloor) collected at Site 1118 contains a planktonic foraminiferal fauna indicating a latest Miocene to early Pliocene age. Globorotalia tumida is recorded in Sample 180-1118A-68R-4, 46-48 cm, indicating an early Pliocene (N18) age at this level (J. Resig, pers. comm., 2000). Based on their known range in the western Papuan Basin, the presence of (rare) Lepidocyclina and common Amphistegina in some samples suggests that abundant shallow-water bioclastic debris present in these limestones may be reworked from older, possibly middle or early late Miocene sediments. Four samples were selected for whole-rock strontium isotopic analysis to further investigate this possibility. A petrographic examination of samples analyzed was also conducted.

(Table T1) Bulk calcium carbonate content of ODP Hole 194-1198A sediments

Weight percent calcium carbonate (wt% CaCO3) content was determined on 328 samples from Ocean Drilling Program Hole 1198A. Two intervals were analyzed, one within lithologic Subunit IA between 14.52 and 41.13 meters below seafloor (mbsf) (25 cm sampling interval) and one within Subunit IB between 67.42 and 100.12 mbsf (15-30 cm interval), allowing the comparison of the nature of cyclic siliciclastic-carbonate variations during the late and early Pleistocene. Overlap with a previously analyzed interval in Hole 1198A illustrates the good agreement in data generated by differing methodologies and extends the continuous record of bulk wt% CaCO3 from 0 to 41.13 mbsf. Although Subunits 1A and 1B exhibit nearly the same variability, from 93% to 63% and 94% to 68%, respectively, Subunit 1A is characterized by a longer cycle length.

(Table T1) Porosity and permeability of samples from ODP Leg 180 sites

Woodlark Basin, an area of continental extension, is an ideal location to study the evolution of permeability and the development of overpressures within an active rift basin. In this investigation, we measured sediment permeabilities of cores from Woodlark Basin and used numerical modeling to determine if pore fluid overpressures are likely at the base of the rift basin. Constant-rate flow tests were conducted on cores from Site 1108, located in the rift basin, and Sites 1115 and 1118, located on the northern margin of the basin. Results of the laboratory tests indicated permeabilities that range from 1.5 x 10**-18 to 1 x 10**-16 m**2. Results of the numerical modeling of Site 1108 suggest that overpressures due to sedimentation are unlikely.

(Table T1) Physical properties of minicores from ODP Leg 193 sites, PACMANUS field

Permeability of the ocean crust is one of the most crucial parameters for constraining submarine fluid flow systems. Active hydrothermal fields are dynamic areas where fluid flow strongly affects the geochemistry and biology of the surrounding environment. There have been few permeability measurements in these regions, especially in felsic-hosted hydrothermal systems. We present a data set of 38 permeability and porosity measurements from the PACMANUS hydrothermal field, an actively venting, felsic hydrothermal field in the eastern Manus Basin. Permeability was measured using a complex transient method on 2.54-cm minicores. Permeability varies greatly between the samples, spanning over five orders of magnitude. Permeability decreases with both depth and decreasing porosity. When the alteration intensity of individual samples is considered, relationships between depth and porosity and permeability become more clearly defined. For incompletely altered samples (defined as >5% fresh rock), permeability and porosity are constant with depth. For completely altered samples (defined as <5% fresh rock), permeability and porosity decrease with depth. On average, the permeability values from the PACMANUS hydrothermal field are greater than those in other submarine environments using similar core-scale laboratory measurements; the average permeability, 4.5 x 10-16 m**2, is two to four orders of magnitude greater than in other areas. Although the core-scale permeability is higher than in other seafloor environments, it is still too low to obtain the fluid velocities observed in the PACMANUS hydrothermal field based on simplified analytical calculations. It is likely that core-scale permeability measurements are not representative of bulk rock permeability of the hydrothermal system overall, and that the latter is predominantly fracture controlled.

(Table T1) Ice rafted debris characteristics of ODP Site 177-1092

We have carried out a multiphase analysis of samples from ODP Site 177-1092, Meteor Rise, subantarctic South Atlantic. Samples were analyzed for ice-rafted debris (IRD [see Table T1]) and stable isotopes from benthic foraminifera [see Murphy et al., 2002, doi:10.1016/S0031-0182(01)00495-3]. Both analyses were performed on the same samples. Additional work was performed to identify the paleomagnetic stratigraphy. The analyzed samples range in age from about 2.6(?) Ma to 4.6 Ma, a time span that saw considerable global warmth, but witnessed overall global refrigeration and the transition to truly bipolar glaciations. IRD arrived frequently during the Early and early Late Pliocene, but only as 'background rafting' (occasional grains per sample). The first identifiable IRD above background rafting is associated with marine isotope stage (MIS) KM4 (~3.18 Ma). Successive IRD peaks become larger, the same pattern as noted at nearby Site 114-704. A very large peak near the top of the record, approximately 2.8 Ma, is considered to represent a hiatus. Peaks below 51.3 meters composite depth (mcd) coincide with positive excursions of the oxygen isotopic record, and with negative excursions of the carbon isotopic curve, a pattern also noted at Site 114-704. However, the reasonably large IRD peak at 51 mcd (tentatively identified with MIS G11) coincides with a positive excursion on the carbon isotopic curve and negative excursion on the oxygen isotopic curve. This relationship suggests a northern hemisphere interglacial, rising sea level, destabilization of the Antarctic margin, and delivery of Antarctic icebergs to the Southern Ocean. Such a mechanism has recently been suggested by Kanfoush et al. (2000, doi:10.1126/science.288.5472.1815) for latest Pleistocene stadial/interstadial oscillations. Here we suggest that such a mechanism may have been in place on glacial/interglacial time scales as early as the Late Pliocene.