Antifreeze Proteins in Winter Rye Leaves Form Oligomeric Complexes1

Antifreeze proteins (AFPs) similar to three pathogenesis-related proteins, a glucanase-like protein (GLP), a chitinase-like protein (CLP), and a thaumatin-like protein (TLP), accumulate during cold acclimation in winter rye (Secale cereale) leaves, where they are thought to modify the growth of intercellular ice during freezing. The objective of this study was to characterize the rye AFPs in their native forms, and our results show that these proteins form oligomeric complexes in vivo. Nine proteins were separated by native-polyacrylamide gel electrophoresis from apoplastic extracts of cold-acclimated winter rye leaves. Seven of these proteins exhibited multiple polypeptides when denatured and separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. After isolation of the individual proteins, six were shown by immunoblotting to contain various combinations of GLP, CLP, and TLP in addition to other unidentified proteins. Antisera produced against individual cold-induced winter rye GLP, CLP, and TLP all dramatically inhibited glucanase activity in apoplastic extracts from cold-acclimated winter rye leaves, and each antiserum precipitated all three proteins. These results indicate that each of the polypeptides may be exposed on the surface of the protein complexes. By forming oligomeric complexes, AFPs may form larger surfaces to interact with ice, or they may simply increase the mass of the protein bound to ice. In either case, the complexes of AFPs may inhibit ice growth and recrystallization more effectively than the individual polypeptides.

Caracterização da farinha e do amido isolado da semente de jaca e comportamento reológico de dispersões de amido

O amido é um ingrediente com grande versatilidade de aplicação, e as sementes de jaca, fruto bem difundido, porém pouco aproveitado no Brasil, contêm uma quantidade considerável de amido, sendo ainda fonte de ferro e proteínas. Dessa maneira, os objetivos desse projeto foram a obtenção da farinha de sementes de jaca das variedades mole e dura, a extração do amido utilizando diferentes solventes, e a caracterização de suas propriedades físico-químicas, estruturais e funcionais, bem como a caracterização reológica de dispersões/géis de amido em cisalhamento estacionário e oscilatório. A extração alcalina do amido, além de reduzir significativamente o conteúdo de lipídeos e proteínas, deixando o amido mais puro, promoveu um aumento no teor de amilose e influenciou diretamente as características de inchamento e solubilidade, que apresentaram aumento significativo a partir da temperatura de 70 °C. O aumento da temperatura ocasionou aumento no poder de inchamento e solubilidade, que foi mais pronunciado para a variedade dura, porém esses valores ainda foram considerados baixos (< 17%). Os amidos de sementes de jaca apresentaram grânulos lisos, arredondados e em forma de sino, com formato mais truncado para o amido extraído com hidróxido de sódio. O diâmetro médio dos grânulos de amido foi menor para a extração alcalina, mas sempre com comportamento monomodal. Foi observado um padrão de difração de Raios-X do tipo A para todas as amostras estudadas, e o índice de cristalinidade foi maior para os amidos de sementes de jaca dura, com uma redução estimada em 70% para os amidos obtidos por extração alcalina. A temperatura de gelatinização dos amidos de semente de jaca foi considerada alta (70-100 °C). Os amidos de sementes de jaca dura obtidos na extração com água apresentaram maiores valores de viscosidade de pico e de Breakdown, que representa menor resistência mecânica. A extração com solução de NaOH 0,1 M aumentou a tendência a retrogradação de ~36% (extração aquosa) para 64% e 45% dos amidos de sementes de jaca das variedades mole e dura, respectivamente. Todas as amostras apresentaram comportamento pseudoplástico (n < 1) nas concentrações e temperaturas estudadas, e as dispersões e/ou géis de amido obtidos pela extração alcalina com NaOH apresentaram menor tixotropia e maiores valores de viscosidade. Os modelos Lei da Potência e Herschel Bulkley apresentaram ótimos ajustes aos pontos experimentais (R² ~0,998) para as amostras com 2 e 6 % de amido, respectivamente, porém para a concentração de 5%, o melhor modelo foi função da variedade do fruto usado na obtenção do amido. A dependência das propriedades reológicas com a temperatura foi analisada pela equação de Arrhenius e a energia de ativação foi baixa (15-25 kJ/mol). Quanto ao comportamento viscoelástico, as amostras com 5 e 6% de amido apresentaram comportamento de gel fraco e o aumento da concentração desse polissacarídeo produziu um aumento na elasticidade do material. Os módulos de armazenamento (G\') associados à elasticidade do gel de amido aumentaram durante o seu resfriamento nos ensaios de varredura de temperatura, o que pode ser relacionado à recristalização da amilose durante esse processo e mantiveram-se praticamente constantes no aquecimento isotérmico a 80 °C, sugerindo boa estabilidade térmica do gel. A farinha isolada da semente de jaca pode ser considerada fonte de fibras e apresentou elevados teores de proteínas (~14-16%) e ferro (~85-150 mg/kg). A distribuição do tamanho de partículas da farinha apresentou comportamento bimodal, com grânulos arredondados, presença de fibras e uma matriz proteica envolvendo os grânulos de amido. As propriedades de pasta revelaram maior pico de viscosidade para a farinha de semente de jaca mole. As características encontradas sugerem que os amidos de semente de jaca poderiam ser aplicados na produção de filmes biodegradáveis, e a farinha da semente de jaca poderia ser utilizada em substituição parcial à farinha convencional na fabricação de bolos e biscoitos.

Phosphoramidite-Cu(OTf)2 complexes as chiral catalysts for 1,3-dipolar cycloaddition of iminoesters and nitroalkenes

Chiral complexes formed by phosphoramidites such as (Sa,R,R)-9 and Cu(OTf)2 are excellent catalysts for the general 1,3-dipolar cycloaddition between azomethine ylides and nitroalkenes affording the corresponding tetrasubstituted proline esters mainly as exo-cycloadducts in high er at room temperature. The exo-cycloadducts can be obtained in enantiomerically pure form just after simple recrystallization. DFT calculations support the stereochemical results.

Efficient Diastereo- and Enantioselective Synthesis of exo-Nitroprolinates by 1,3-Dipolar Cycloadditions Catalyzed by Chiral Phosphoramidite⋅Silver(I) Complexes

Chiral complexes formed by privileged phosphoramidites and silver triflate or silver benzoate are excellent catalysts for the general 1,3-dipolar cycloaddition between azomethine ylides generated from α-amino acid-derived imino esters and nitroalkenes affording with high dr the exo-cycloadducts 4,5-trans-2,5-cis-4-nitroprolinates in high ee at room temperature. In general, better results are obtained using silver rather than copper(II) complexes. In many cases the exo-cycloadducts can be obtained in enantiomerically pure form just after simple recrystallization. The mechanism and the justification of the experimentally observed stereodiscrimination of the process are supported by DFT calculations. These enantiomerically enriched exo-nitroprolinates can be used as reagents for the synthesis of nitropiperidines, by ester reduction and ring expansion, which are inhibitors of farnesyltransferase.

Structural evolution of the Lesser Himalayan fold-thrust belt of west central Nepal

The Lesser Himalayan fold-thrust belt on the south flank of the Jajarkot klippe in west central Nepal was mapped in detail between the Main Central thrust in the north and the Main Boundary thrust in the south. South of the Jajarkot klippe, the fold-thrust belt involves sandstone, shale and carbonate rocks that are unmetamorphosed in the foreland and increase in metamorphic grade with higher structural position to sub-greenschist facies towards the hinterland. The exposed stratigraphy is correlative with the Proterozoic Ranimata, Sangram, Galyang, Syangia Formations and Lakharpata Group of Western Nepal and overlain by the Paleozoic Tansen and Kali Gandaki Groups. Based on field mapping and cross-section construction, three distinct thrust sheets were identified separated by top-to-the-south thrust faults. From the foreland (south) to the hinterland (north), the first thrust sheet in the immediate hanging wall of the Main Boundary thrust defines an open syncline. The second thrust sheet contains a very broad synformal duplex, which is structurally stacked against the third thrust sheet containing a homoclinal panel of the oldest exposed Proterozoic stratigraphy. Outcrop scale folds throughout the study area are predominantly south vergent, open, and asymmetric reflecting the larger regional scale folding style, which corroborate the top-to-the-south deformation style seen in the faults of the region. Field techniques were complemented with microstructural and quartz crystallographic c-axis preferred orientation analyses using a petrographic microscope and a fabric analyzer, respectively. Microstructural analysis identified abundant strain-induced recrystallization textures and occasional occurrences of top-to-the-south shear-sense indicators primarily in the hinterland rocks in the immediate footwall of the Main Central Thrust. Top-to-the-south shearing is also supported by quartz crystallographic c-axis preferred orientations. Quartz recrystallization textures indicate an increase in deformation temperature towards the Main Central thrust. A line balance estimate indicates that approximately 15 km of crustal shortening was accommodated by folding and faulting in the fold-thrust belt south of the Jajarkot klippe. Additionally, estimations of shortening velocity suggest that the shortening velocity operating in this section of the fold-thrust belt between 23 to 14 Ma was slower than what is currently observed as a result of the ongoing deformation of the Sub-Himalayan fold-thrust belt.

Exploring several nonconventional interactions of ice-binding proteins

Traditionally, ice-binding proteins (IBPs), also known as antifreeze proteins (AFPs), have been defined by two universal activities: ice recrystallization inhibition and thermal hysteresis. However, there remains the possibility IBPs have other complementary functions given the diversity found within this protein group. This thesis explores some of these in both natural and applied settings, in the hopes of furthering our understanding of this remarkable group of proteins. Plant IBPs could function as part of a defensive strategy against ice nucleators produced by certain pathogens. To assess this hypothesis, recombinant IBPs from perennial ryegrass and purple false brome were combined with the ice nucleation protein (INP) from the plant pathogen, Pseudomonas syringae. Strikingly, the plant proteins depressed the freezing point of the bacterial INP, while a fish AFP could not, nor did the INPs have any effect on IBP activity. Thus, the interaction between these two different proteins suggests a role in plant defensive strategies against pathogenic bacteria as another IBP function. In addition, the potential use of hyperactive insect IBPs in organ preservation was investigated. Current kidney preservation techniques involve storing the organ at 4 °C for a maximum of 24 h prior to transplantation. Extending this “safe” time would have profound effects on renal transplants, however, ischemic injury is prevalent when storage periods are prolonged. Experiments described here allowed subzero preservation for 72 h with the addition of a beetle IBP to CryoStasis® solution. Kidneys stored using the traditional technique for 24 h and the method developed here for 72 h showed similar levels of biomarker enzymes, underscoring the potential utility of insect IBPs for future transplant purposes. Finally, IBP function in the freeze-tolerant gall fly, Eurosta solidaginis, was examined. Larvae representing the mid-autumn stage displayed ice-binding activity, suggesting an IBP is being expressed, possibly as a protective measure against freezing damage when fall temperatures can unpredictably drop. IBP activity was also observed in the larvae’s host plant, Solidago spp. Mass spectrometry analysis of ice-affinity purified plant extracts provided three candidate pathogenesis-related proteins that could be responsible for the detected activity, further demonstrating additional functions of IBPs.

Rare earth and trace elements in igneous and metamorphic minerals of oceanic gabbros from the Mid-Atlantic Ridge

SIMS analyses have been carried out on clinopyroxenes, plagioclases and amphiboles of six gabbroic samples from Holes 921-924 of the Ocean Drilling Program Leg 153 sited in the MARK area of the Mid-Atlantic Ridge at the ridge-transform intersection, to investigate the rare earth, trace and volatile element distribution in the lower ocean crust during igneous crystallization and higher grade metamorphic conditions. The metagabbros underwent granulite to subgreenschist facies conditions through three main tectono-metamorphic phases: (1) ductile regime (750 < T < 1000 °C and P = 0.3 GPa); (2) transitional regime (600 < T < 700 °C and P = 0.2 GPa); (3) brittle regime (350 < T < 600 °C and P < 0.2 GPa). Igneous clinopyroxenes show Cl-chondrite normalized patterns depleted in LREE, and nearly flat for HREE. The rare earth and trace element distributions in igneous clinopyroxenes and plagioclases indicate that these minerals act as REE reservoirs, and comprise the main contribution to the overall rock content. The abundances in igneous minerals reflect the degree of fractionation of the parent liquids. In metamorphic clinopyroxenes recrystallized in anhydrous assemblages, the REE and trace elements patterns mimic those of the primary ones. Conversely, clinopyroxerie re-equilibrated in amphibolebearing assemblages shows a significant increase in REE, Ti, Zr, Y and V, a negative Eu anomaly, and slight decreases in Sr and Ba. An overall increase of REE and some trace elements is evident in hydrous assemblages, with preferential partitioning in the amphibole. It shows high Ti (18196-22844 ppm), LREE depleted patterns and LaN/SmN = 0.10-0.33, LaN/YbN = 0.10-0.30. Amphiboles from granoblastic assemblages show homogeneous patterns with no or a positive anomaly for TiN and negative anomalies for SrN and ZrN. Volatiles in amphibole are low, with Cl/F < 1; H2O% is significantly lower than the stoichiometric ratio (1.33-1.53%). The composition of the clinopyroxene and amphibole recrystallized in low-strain domains records evidence of incomplete re-equilibration, and element diffusion and partitioning is in part controlled by the textural site. The possible origins of the fluids involved in the metamorphic recrystallization are discussed: (1) remobilization from igneous amphibole; (2) exsolution from evolved melts; (3) introduction of seawater-derived fluids modified in rock-dominated systems; (4) injection of highly evolved hydrous melts during the metamorphic process.

Geochemistry and strontium isotopic composition of interstitial waters of marine carbonates

The concentrations and isotopic compositions of strontium in interstitial waters from several DSDP sites, where sediments consist chiefly of carbonate oozes and chalks, are used as indicators of carbonate diagenesis by reference to a recently-produced curve showing detailed variations in the 87Sr/86Sr ratio of seawater with time. Carbonate sediments of the Walvis Ridge show increases in interstitial Sr[2+] concentrations in the upper carbonate-ooze sections with the highest concentrations near the ooze-chalk boundary where maximum rates of carbonate recrystallization occur. Below this, in situ production of Sr[2+] diminishes and there is a diffusive flux of Sr to an underlying sink, presumably volcanogenic sediments or basalts, leading to Sr isotopic disequilibrium between carbonates and interstitial waters. In some other sites, however, there is no apparent Sr sink at depth and isotopic equilibrium is retained. Overall, diffusive smoothing of profiles exerts an important control on the 87Sr/86Sr ratios, although lower ratios than contemporaneous seawater values in the carbonate oozes often correlate with zones of Mg[2+] loss and reflect a combination of a flux of Sr[2+] from the zone of maximum recrystallization rates together with a contribution from the in situ alteration of volcanic matter.

Interstitial water chemistry of DSDP Leg 85 sites

The concentration changes in pore waters of dissolved calcium, magnesium, sulfate, strontium, and silica and of alkalinity are controlled by diagenetic reactions occurring within the biogenic sediments of DSDP Sites 572, 573, and 574. Downcore increases in dissolved Sr2 + indicate recrystallization of calcite, and increases in dissolved SiO2 reflect dissolution of amorphous silica. Minor gradients in dissolved Ca(2+) and Mg(2+) suggest little if any influence from reactions involving volcanic sediments or basalt. Differences in interstitial water profiles showing the downhole trends of these chemical species mark variations in carbonate and silica diagenesis, sediment compositions, and sedimentation rate histories among the sites. The location and extent of carbonate diagenesis in these sediments are determined from Sr/Ca distributions between the interstitial waters and the bulk carbonate samples. Pore water strontium increases in the upper 100 to 250 m of sediment are assumed to reflect diffusion from underlying zones where calcite recrystallization has occurred. On the basis of calculations of dissolved strontium production and comparisons between observed and calculated "equilibrium" Sr/Ca ratios of the solids, approximately 30 to 50% of the carbonate has recrystallized in these deeper intervals. These estimates agree with the observed amounts of chalk at these sites. Variations in Sr/Ca ratios of these carbonates reflect differences in calcareous microfossil content, in diagenetic history, and, possibly, in changes in seawater Sr/Ca with time. Samples of porcelanite recovered below 300 m at Site 572 suggest formation at temperatures 20 to 30° C greater than ones estimated assuming oceanic geothermal gradients from sedimentary sections similar to those recovered on Leg 85. The higher temperatures may partially account for higher Sr/Ca ratios determined for recrystallized carbonates from this site.

Geochemistry of labile organic matter in sediments and interstitial waters of ODP Sites 107-651 and 107-653

Sediment and interstitial water from Sites 651 and 653 (ODP Leg 107) were investigated by organic geochemical methods to characterize labile organic compound classes (amino compounds and carbohydrates) and to evaluate their progressive diagenetic and thermal degradation in deep-sea sediments. Downhole distribution of dissolved organic carbon (DOC) appears related to redox zones associated with bacterial activity and of diagenetic recrystallization of biogenic tests and not so much to organic matter concentrations in ambient sediments. DOC ranges from 250 to 8300 µmol/L (3-100.1 ppm). Amino acids contribute 10%-0.3% of DOC; carbohydrates range from 78 to 5 µmol/L. Rate of degradation of amino acids by thermal effects and/or bacterial activity at both sites (significantly different in sedimentation rates: average 41 cm/1000 yr in the top 300 m at Site 651, average 3.9 cm/1000 yr in the Pliocene/Quaternary sequence at Site 653 to 220 mbsf) is more dependent on exposure time rather than on the depth within the sediment column. Variability in neutral, acidic, and basic amino acid fractions of total amino acids (with a range of 1.1-0.02 µmol/g sediment; up to 2.5% of organic carbon) varies with carbonate content and by differences in thermal stability of amino acids. Distribution patterns of monosaccharides are interpreted to result from differences in organic matter sources, sedimentation rates, and the degree of organic matter decomposition prior to and subsequent to burial. Total particulate carbohydrates range from 1.82 to 0.21 µmol/g sediment and contribute about 8% to the sedimentary organic matter. Investigation of trace metals in the interstitial waters did not show any correlation of either DOC, amino compounds, or carbohydrates.

Elemental and stable isotopic composition of fine fraction samples of ODP Site 115-709 (Table 1)

Stable isotopic and minor element compositions were measured on the fine fraction of pelagic carbonate sediments from Ocean Drilling Program Site 709 in the central Indian Ocean. This section ranges in age from 47 Ma to the present. The observed compositional variations are the result of either paleoceanographic changes (past oceanic chemical or temperature variations) or diagenetic changes. The CaCO3 record is little affected by diagenesis. From previous work, carbonate content is known to be determined by the interplay of biological productivity, water column dissolution, and dilution. The carbon isotopic record is generally similar to previously published curves. A good correlation was observed between sea-level high stands and high 13C/12C ratios. This supports Shackleton's hypothesis that as the proportion of organic carbon buried in marine sediments becomes larger, oceanic-dissolved inorganic carbon becomes isotopically heavier. This proportion appears to be higher when sea level is higher and organic carbon is buried in more extensive shallow-shelf sediments. The strontium content and oxygen isotopic composition of carbonate sediments are much more affected by burial diagenesis. Low strontium concentrations are invariably associated with high values of d18O, probably indicating zones of greater carbonate recrystallization. Nevertheless, there is an inverse correlation between strontium concentration and sea level that is thought to be a result of high-strontium aragonitic sedimentation on shallow banks and shelves during high stands. Iron and manganese concentrations and, to a lesser extent, magnesium and strontium concentrations and carbon isotopic ratios are affected by early diagenetic reactions. These reactions are best observed in a slumped interval of sediments that occurs between 13.0 and 17.5 Ma. As a result of microbial reduction of manganese and iron oxides and dissolved sulfate, it is hypothesized that small amounts of mixed-metal carbonate cements are precipitated. These have low carbon isotopic ratios and high concentrations of metals.

Benthic foraminiferal stable isotope record for the equatorial Pacific

Stable oxygen and carbon isotope (d18O and d13C) values measured in foraminiferal calcite are one of the primary tools used in paleoceanography. Diagenetic recrystallization of foraminiferal calcite can act to reset primary isotopic values, but its effects are typically poorly quantified. Here we test the impact of early stage diagenesis on stable isotope records generated from a suite of drill sites in the equatorial Pacific Ocean recovered during Ocean Drilling Program Leg 199 and Integrated Ocean Drilling Program Expedition 320. Our selected sites form paleowater and burial depth transects, with excellent stratigraphic control allowing us to confidently correlate our records. We observe large intersite differences in the preservation state of benthic foraminiferal calcite, implying very different recrystallization histories, but negligible intersite offsets in benthic d18O and d13C values. We infer that diagenetic alteration of benthic foraminiferal calcite (in sedimentary oozes) must predominantly occur at shallow burial depths (<100 m) where offsets in both the temperature and isotopic composition of waters in which the foraminifera calcified and pore waters in which diagenesis occurs are small. Our results suggest that even extensive recrystallization of benthic foraminiferal calcite results in minimal shifts from primary d18O and d13C values. This finding supports the long-held suspicion that diagenetic alteration of foraminiferal calcite is less problematic in benthic than in planktic foraminifera and that in deep-sea sediments routinely employed for paleoceanographic studies benthic foraminifera are robust recorders of stable isotope values in the fossil record.

(Table 1) Calcium carbonate and <2 µm fractions of bulk sample and insoluble residue at DSDP Hole 92-597

Particles of red brown to yellow brown semiopaque oxides (RSO) dominate the insoluble residue fraction of the sediments at Site 597. Unlike the X-ray amorphous particles in the Bauer Deep sediments, these particles are composed of mainly goethite; the amount of X-ray amorphous ferric hydroxide and poorly crystalline ferromanganese oxyhydroxides is generally small relative to the amount of goethite. A qualitative goethite crystallinity index was established. The variations observed in the crystallinity of goethite with increasing depth and changes in lithology suggest that aging and long-term exposure to seawater in a high water/sediment regime influence and increase the rate of recrystallization of the Fe-oxyhydroxides of the RSO particles. The percentage of organic carbon is low in these sediments; it varies primarily between 0.2 and 0.4 wt.%. Phillipsite is present throughout the sediment column and is more concentrated in the youngest clay layer and in the oldest basal sediments.