Identification of peptides that bind with thymidylate synthase RNA using mRNA display technique

Using in vitro selection method to isolate nucleic acids, peptides and proteins has been studied intensively in recent years. In vitro mRNA display is a new and effective technique for peptides selection, and the rationale of this technique is that a synthetic mRNA with puromycin could covalently link with the protein that it encodes, thus an mRNA-protein fusion is formed. This approach has been used in identification of many functional peptides. The peptides binding with thymidylate synthase RNA were isolated using mRNA display technique from a large peptide library (>10(13) different sequences). The selection scheme was constructed, and the experimental conditions, including library synthesis, formation of RNA-peptide fusion and RNA immobilization were optimized. Eight cycles have been processed and the results confirmed that the selected peptides could bind with thymidylate synthase mRNA specifically. Compared the amino acid sequences of the selected peptides with those from the initial random library, the basic and aromatic residues in selected peptides were enriched significantly, suggesting these peptide regions may be important in the peptide-TS mRNA interaction. As a novel in vitro selection approach, mRNA display technique would be developed as a powerful tool for isolation of functional peptides and proteins that could interact with immobilized targets with high affinity and specificity.

Transient expression of lacZ in particle bombarded Gracilaria changii (Gracilariales, Rhodophyta)

Using a Biolistic PDS 1000/He system, healthy thalli of Gracilaria changii were bombarded with gold particles coated with plasmid DNA containing the lacZ reporter gene. Transient expression of lacZ was observed in bombarded thalli under the rupture-disc pressures of 4482, 6206, 7584 and 8963 KPa, two days after bombardment. Although G. changii exhibits a slight blue background, positive expression and the background colour can be clearly differentiated. The results indicate that lacZ could be a useful reporter gene and that SV40 promoter could be an effective promoter for Gracilaria transformation.

In vitro selected peptides bind with thymidylate synthase mRNA and inhibit its translation

Thymidylate synthase (TS), an essential enzyme for catalyzing the biosynthesis of thymidylate, is a critical therapeutic target in cancer therapy. Recent studies have shown that TS functions as an RNA-binding protein by interacting with two different sequences on its own mRNA, thus, repressing translational efficiency. In this study, peptides binding TS RNA with high affinity were isolated using mRNA display from a large peptide library (>10(13) different sequences). The randomized library was subjected up to twelve rounds of in vitro selection and amplification. Comparing the amino acid composition of the selected peptides (12th round, R12) with those from the initial random library (round zero, R0), the basic and aromatic residues in the selected peptides were enriched significantly, suggesting that these peptide regions might be important in the peptide-TS mRNA interaction. Categorizing the amino acids at each random position based on their physicochemical properties and comparing the distributions with those of the initial random pool, an obvious basic charge characteristic was found at positions 1, 12, 17 and 18, suggesting that basic side chains participate in RNA binding. Secondary structure prediction showed that the selected peptides of R12 pool represented a helical propensity compared with R0 pool, and the regions were rich in basic residues. The electrophoretic gel mobility shift and in vitro translation assays showed that the peptides selected using mRNA display could bind TS RNA specifically and inhibit the translation of TS mRNA. Our results suggested that the identified peptides could be used as new TS inhibitors and developed to a novel class of anticancer agents.

Distribution and their pollution assessment of heavy metals in the sediments of the Yalu River Estuary and its adjacent coastal waters

The present paper deals with the distribution patterns of heavy metals and the associated influencing factors in the Yalu River Estuary and its adjacent coastal waters. Based upon the analysis of the surficial and core sediments measurements, the pollution of heavy metal and potential ecological risk were evaluated. The burial flux and contents of heavy metals (except for copper) have been continuously increasing since the 1920s. Therefore, the gross potential ecological risk for the sediments was high or very high, and the study area was endangered by heavy metals contamination. Heavy metals originated mainly from upstream pollutant input, correlation analysis showed that chromium, nickel, zinc, cadmium, lead, arsenic, and mercury in the sediments of the middle and west channels as well as the sea area of the western Yalu River Estuary concentrations were most probably derived from similar sources. In contrast, the metal of copper most probably originated from sources different from the other metals. Preliminary studies indicate that copper contamination was most likely the result of emission from mining activities situated at the upstream of the river. The contents of heavy metals in the sediments of estuarine turbidity maximum zone of Yalu River were larger than those of any other areas in the middle channel. With large portion of fine sediments, weaker hydrodynamics, and richer sources of heavy metals, the sediments of the west channel, were even more enriched with heavy metals than those of the middle channel.

Methane-derived authigenic carbonates from the Ulleung basin sediments, East Sea of Korea

Authigenic carbonates were sampled in methane-enriched piston core sediments collected from gas venting sites on the western continental slope of the Ulleung Basin, East Sea of Korea. Multidisciplinary investigations on these carbonates, including the scanning electronic microscope (SEM) observations and mineralogical-geochemical compositions, were carried out to identify the carbon and oxygen sources and the forming mechanism of these carbonates. The authigenic carbonates from the study area correspond to semi-consolidated, compact concretions or nodules ranging from 2 to 9 cm in size. X-ray diffraction and electron microprobe analyses showed that most of the sampled carbonate concretions were composed of almost purely authigenic high-Mg calcite (10.7-14.3 mol% MgCO3). Characteristically, microbial structures such as filaments and rods, which were probably associated with the authigenic minerals, were abundantly observed within the carbonate matrix. The carbonates were strongly depleted in delta C-13 (-33.85 parts per thousand to -39.53 parts per thousand Peedee Belemnite (PDB)) and were enriched in delta O-18 (5.16-5.60 parts per thousand PDB), indicating that the primary source of carbon is mainly derived from the anaerobic oxidation of methane. Such methane probably originated from the destabilization of the underlying gas hydrates as strongly supporting from the enriched O-18 levels. Furthermore, the strongly depleted delta C-13 values (-60.7 parts per thousand to -61.6 parts per thousand PDB) of the sediment void gases demonstrate that the majority of the gas venting at the Ulleung Basin is microbial methane by CO2 reduction. This study provides another example for the formation mechanism of methane-derived authigenic carbonates associated with gas-hydrate decomposition in gas-seeping pockmark environments. (c) 2009 Elsevier Ltd. All rights reserved.

Enrichment of lanthanides in aragonite

Using the constant addition technique, the coprecipitation of lanthanum, gadolinium, and lutetium with aragonite in seawater was experimentally investigated at 25 degrees C. Their concentrations in aragonite overgrowths were determined by inductive coupled plasma mass spectrometer. All these lanthanides were strongly enriched in aragonite overgrowths. The amount of lanthanum, gadolinium, and lutetium incorporated into aragonite accounted for 57%-99%, 50%-89%, and 40%-91% of their initial total amount, respectively. With the increase of aragonite precipitation rate, more lanthanides were incorporated into aragonite while their relative fraction in aragonite overgrowths decreased consistently. It indicated that the coprecipitation of lanthanides with aragonite was controlled by the kinetics of aragonite precipitation.

Rare earth elements in bottom sediments of major rivers around the Yellow Sea: implications for sediment provenance

Rare earth elements (REEs) of 91 fine-grained bottom sediment samples from five major rivers in Korea (the Han, Keum, and Yeongsan) and China (the Changjiang and Huanghe) were studied to investigate their potential as source indicator for Yellow Sea shelf sediments, this being the first synthetic report on REE trends for bottom sediments of these rivers. The results show distinct differences in REE contents and their upper continental crust (UCC)-normalized patterns: compared to heavy rare earth elements (HREEs), light rare earth elements (LREEs) are highly enriched in Korean river sediments, in contrast to Chinese river sediments that have a characteristic positive Eu anomaly. This phenomenon is observed also in primary source rocks within the river catchments. This suggests that source rock composition is the primary control on the REE signatures of these river sediments, due largely to variations in the levels of chlorite and monazite, which are more abundant in Korean bottom river sediments. Systematic variations in I LREE pound/I HREE pound ratios, and in (La/Yb)-(Gd/Yb)(UCC) but also (La/Lu)-(La/Y)(UCC) and (La/Y)-(Gd/Lu)(UCC) relations have the greatest discriminatory power. These findings are consistent with, but considerably expand on the limited datasets available to date for suspended sediments. Evidently, the REE fingerprints of these river sediments can serve as a useful diagnostic tool for tracing the provenance of sediments in the Yellow Sea, and for reconstructing their dispersal patterns and the circulation system of the modern shelf, as well as the paleoenvironmental record of this and adjoining marginal seas.

Element enrichment and U-series isotopic characteristics of the hydrothermal sulfides at Jade site in the Okinawa Trough

The geochemical and U-series isotopic characteristics of hydrothermal sulfide samples from the Jade site (127A degrees 04.5'E, 27A degrees 15'N, water depth 1300-1450 m) at Jade site in the Okinawa Trough were analyzed. In the hydrothermal sulfide samples bearing sulfate (samples HOK1 and HOK2), the LREEs are relatively enriched. All the hydrothermal sulfide samples except HOK1 belong to Zn-rich hydrothermal sulfide. In comparison with Zn-rich hydrothermal sulfides from other fields, the contents of Zn, Pb, Ag, Cd, Au and Hg are higher, the contents of Fe, Al, Cr, Co, Ni, Sr, Te, Cs, Ti and U lower, and the Pb-210 radioactivity ratios and Pb-210/Pb ratios very low. In the hydrothermal sulfide mainly composed of sphalerite, the correlations between rare elements Hf and U, and Hf and Mn as well as that between dispersive elements Ga and Zn, are strongly positive; also the contents of Au and Ag are related to Fe-sulfide, because the low temperature promotes enrichment of Au and Ag. Meanwhile, the positive correlations between Fe and Bi and between Zn and Cd are not affected by the change of mineral assemblage. Based on the Pb-210/Pb ratios of hydrothermal sulfide samples (3.99x10(-5)-5.42x10(-5)), their U isotopic composition (U-238 content 1.15-2.53 ppm, U-238 activity 1.07-1.87 dpm/g, U-234 activity 1.15-2.09 dpm/g and U-234/U-238 ratio 1.07-1.14) and their Th-232 and Th-230 contents are at base level, and the chronological age of hydrothermal sulfide at Jade site in the Okinawa Trough is between 200 and 2000 yr.

He, Ne and Ar isotopic composition of Fe-Mn crusts from the western and central Pacific Ocean and implications for their genesis

The noble gas nuclide abundances and isotopic ratios of the upmost layer of Fe-Mn crusts from the western and central Pacific Ocean have been determined. The results indicate that the He and Ar nuclide abundances and isotopic ratios can be classified into two types: low He-3/He-4 type and high He-3/He-4 type. The low He-3/He-4 type is characterized by high He-4 abundances of 191x10(-9) cm(3.)STP(.)g(-1) on average, with variable He-4, Ne-20 and Ar-40 abundances in the range (42.8-421)x10(-9) cm(3.)STP(.)g(-1), (5.40-141)x10(-9)cm(3.)STP(.)g(-1), and (773-10976)x10(-9) cm(3.)STP(.)g(-1), respectively. The high He-3/He-4 samples are characterized by low He-4 abundances of 11.7x10(-9) cm(3.)STP(.)g(-1) on average, with He-4, Ne-20 and Ar-40 abundances in the range of (7.57-17.4)x10(-9) cm(3.)STP(.)g(-1), (110.4-25.5)x10(-9) cm(3.)STP(.)g(-1) and (5354-9050)x10(-9) cm(3.)STP(.)g(-1), respectively. The low He-3/He-4 samples have He-3/He-4 ratios (with RIRA ratios of 2.04-2.92) which are lower than those of MORB (R/R-A=8 +/- 1) and Ar-40/Ar-36 ratios (447-543) which are higher than those of air (295.5). The high He-3/He-4 samples have He-3/He-4 ratios (with R/R-A ratios of 10.4-12.0) slightly higher than those of MORB (R/R-A=8 +/- 1) and Ar-40/Ar-36 ratios (293-299) very similar to those of air (295.5). The Ne isotopic ratios (Ne-20/Ne-22 and Ne-21/Ne-22 ratios of 10.3-10.9 and 0.02774-0.03039, respectively) and the Ar-38/Ar-36 ratios (0.1886-0.1963) have narrow ranges which are very similar to those of air (the Ne-20/Ne-22, Ne-21/Ne-22, Ar-38/Ar-36 ratios of 9.80, 0.029 and 0.187, respectively), and cannot be differentiated into different groups. The noble gas nuclide abundances and isotopic ratios, together with their regional variability, suggest that the noble gases in the Fe-Mn crusts originate primarily from the lower mantle. The low He-3/He-4 type and high He-3/He-4 type samples have noble gas characteristics similar to those of HIMU (High U/Pb Mantle)- and EM (Enriched Mantle)-type mantle material, respectively. The low He-3/He-4 type samples with HIMU-type noble gas isotopic ratios occur in the Magellan Seamounts, Marcus-Wake Seamounts, Marshall Island Chain and the Mid-Pacific Seamounts whereas the high He-3/He-4 type samples with EM-type noble gas isotopic ratios occur in the Line Island Chain. This difference in noble gas characteristics of these crust types implies that the Magellan Seamounts, Marcus-Wake Seamounts, Marshall Island Chain, and the Mid-Pacific Seamounts originated from HIMU-type lower mantle material whereas the Line Island Chain originated from EM-type lower mantle material. This finding is consistent with variations in the Pb-isotope and trace element signatures in the seamount lavas. Differences in the mantle surce may therefore be responsible for variations in the noble gas abundances and isotopic ratios in the Fe-Mn crusts. Mantle degassing appears to be the principal factor controlling noble gas isotopic abundances in Fe-Mn crusts. Decay of radioactive isotopes has a negligible influence on the nuclide abundances and isotopic ratios of noble gases in these crusts on the timescale of their formation.

Geochemistry of the lava and its implications in Musicians Seamounts

Chemical and isotopic data of the lava samples dredged in the southern Bach Ridge and the northern Italian Ridge of the Musicians Seamounts province, northeast of Hawaii. Although most of the samples analyzed are generally altered, a few are fresh. The latter exhibits similar geochemical and isotopic characteristics to normal MORB (Mid-Ocean Ridge Basalts). There are systematic geochemical trends from hotspot to mid-ocean ridge in the province. Incompatible element and isotopic variations suggest that the flow field had at least two distinct parental magmas, one with higher and one with lower MgO concentrations. The two parental magmas could be related by a magma mixing model. The major and trace element modeling shows that the two parental magmas could not have been produced by different degrees of melting of a homogeneous mantle source, but they are consistent with melting of a generally depleted mantle containing variable volumes of embedded enriched heterogeneity enriched interbeds.

Major element, trace element, and Sr, Nd and Pb isotope studies of Cenozoic basalts from the South China Sea

The whole rock K-Ar ages of basalts from the South China Sea basin vary from 3.8 to 7.9 Ma, which suggest that intra-plate volcanism after the cessation of spreading of the South China Sea (SCS) is comparable to that in adjacent regions around the SCS, i.e., Leiqiong Peninsula, northern margin of the SCS, Indochina block, and so on. Based on detailed petrographic studies, we selected many fresh basaltic rocks and measured their major element, trace element, and Sr-Nd-Pb isotope compositions. Geochemical characteristics of major element and trace element show that these basaltic rocks belong to alkali basalt magma series, and are similar to OIB-type basalt. The extent of partial melting of mantle rock in source region is very low, and magma may experience crystallization differentiation and cumulation during the ascent to or storing in the high-level magma chamber. Sr-Nd-Pb isotopic data of these basaltic rocks imply an inhomogeneous mantle below the South China Sea. The nature of magma origin has a two end-member mixing model, one is EM2 (Enriched Mantle 2) which may be originated from mantle plume, the other is DMM (Depleted MORB Mantle). Pb isotopic characteristics show the Dupal anomaly in the South China Sea, and combined with newly found Dupal anomaly at Gakkel ridge in Arctic Ocean, this implies that Dupal anomaly is not only limited to South Hemisphere. In variation diagrams among Sr, Nd and Pb, the origin nature of mantle below the SCS is similar to those below Leiqiong peninsula, northern margin of the SCS and Indochina peninsula, and is different from those below north and northeast China. This study provides geochemical constraints on Hainan mantle plume.

Geochemical and isotopic characteristics of volcanic rocks from the northern East China Sea shelf margin and the Okinawa Trough

Volcanic rocks both from the northern East China Sea (NECS) shelf margin and the northern Okinawa Trough are subalkaline less aluminous, and lower in High Field Strength Elements (HFSE). These rocks are higher in Large Ion Lithophile Elements (LILE), thorium and uranium contents, positive lead anomalies, negative Nb-Ta anomalies, and enrichment in Light Rare Earth Elements (LREE). Basalts from the NECS shelf margin are akin to Indian Ocean Mid-Ocean Ridge Basalt (MORB), and rhyolites from the northern Okinawa Trough have the highest Pb-207/Pb-208 and Pb-208/Pb-204 ratios. The NECS shelf margin basalts have lower Sr-87/Sr-86 ratios, epsilon(Nd) and sigma O-18 than the northern Okinawa Trough silicic rocks. According to K-40-Ar-40 isotopic ages of basalts from the NECS shelf margin, rifting of the Okinawa Trough may have been active since at least 3.65-3.86 Ma. The origin of the NECS shelf margin basalt can be explained by the interaction of melt derived from Indian Ocean MORB-like mantle with enriched subcontinental lithosphere. The basalts from both sides of the Okinawa Trough may have a similar origin during the initial rifting of the Okinawa Trough, and the formation of basaltic magmas closely relates to the thinning of continental crust. The source of the formation of the northern Okinawa Trough silicic rocks was different from that of the middle Okinawa Trough, which could have been generated by the interaction of basaltic melt with an enriched crustal component. From the Ryukyu island arc to East China, the Cenozoic basalts have apparently increasing trends of MgO contents and ratios of LREE to Heavy Rare Earth Elements (HREE), suggesting that the trace element variabilities of basalts may have been influenced by the subduction of the Philippine Sea plate, and that the effects of subduction of the Philippine Sea plate on the chemical composition of basaltic melts have had a decreasing effect from the Ryukyu island arc to East China.

Relationships between nitrogen and phosphorus forms and ratios and the development of dinoflagellate blooms in the East China Sea

During late spring and early summer of 2005, large-scale (> 15 000 km(2)), mixed dinoflagellate blooms developed along the the coast of the East China Sea. Karenia mikimotoi was the dominant harmful algal bloom species in the first stage of the bloom (late May) and was succeeded by Prorocentrum donghaiense approximately 2 wk later. Samples were collected from different stations along both north-south and west-east transects, from the Changjiang River estuary to the south Zhejiang coast, during 3 cruises of the Chinese Ecology and Oceanography of Harmful Algal Blooms Program, before and during the bloom progression. Nitrogen isotope tracer techniques were used to measure rates of NO3-, NH4+, urea, and glycine uptake during the blooms. High inorganic nitrogen (N), but low phosphorus (P) loading from the Changjiang River led to high dissolved inorganic N:dissolved inorganic P ratios in the sampling area and indicate the development of P limitation. The rates of N-15-uptake experiments enriched with PO43- were enhanced compared to unamended samples, suggesting P limitation of the N-uptake rates. The bloom progression was related to the change in availability of both organic and inorganic N and P. Reduced N forms, especially NH4+, were preferentially taken up during the blooms, but different bloom species had different rates of uptake of organic N substrates. K mikimotoi had higher rates of urea uptake, while P. donghaiense had higher rates of glycine uptake. Changes in the availability of reduced N and the ratios of N:P in inorganic and organic forms were suggested to be important in the bloom succession. Nutrient ratios and specific uptake rates of urea were similar when compared to analogous blooms on the West Florida Shelf.

The nitrogen isotopic composition of dissolved nitrate in the Yangtze River (Changjiang) estuary, China

The nitrogen isotopic composition of dissolved nitrate (delta N-15-NO3-) in surface water of the Yangtze River estuary was determined in four seasons of 2006. delta N-15-NO3- ranged from 0.4 parts per thousand to 6.5 parts per thousand and varied with seasons and geographic regions, reflecting the dynamics of nitrogen cycling in the estuarine ecosystem. delta N-15-NO3- was markedly lower in February than in other seasons and exhibited conservative mixing, which was probably attributed to the NO3- being sourced from the atmospheric deposition and agricultural fertilizer. In the upper estuary, the influence of riverine inputs was important during all surveys. in the turbidity maximum zone, nitrification was found with nitrate depleted in N-15 in May, whereas denitrification resulting in heavy delta N-15-NO3- played an important role in August. More enriched delta N-15-NO3- values coinciding with losses of nitrate concentrations based on the conservative mixing model were found in the adjacent marine area in May, and may reflect obvious phytoplankton assimilation of dissolved nitrate. In this manner, delta N-15-NO3- may be a sensitive indicator of nitrogen sources and biogeochemical processing existing in this estuary in conjunction with the variations of dissolved nitrate and other environmental factors. (C) 2009 Elsevier Ltd. All rights reserved.

Stable carbon and nitrogen isotopic compositions of high molecular weight dissolved organic matter from four US estuaries

High molecular weight dissolved organic matter (HMW-DOM) represents an important component of dissolved organic carbon (DOC) in seawater and fresh-waters. In this paper, we report measurements of stable carbon (delta(13)C) isotopic compositions in total lipid, total hydrolyzable amino acid (THAA), total carbohydrate (TCHO) and acid-insoluble "uncharacterized" organic fractions separated from fourteen HMW-DOM samples collected from four U.S. estuaries. In addition, C/N ratio, delta(13) C and stable nitrogen (delta(15)N) isotopic compositions were also measured for the bulk HMW-DOM samples. Our results indicate that TCHO and THAA are the dominant organic compound classes, contributing 33-46% and 13-20% of the organic carbon in HMW-DOM while total lipid accounts for only <2% of the organic carbon in the samples. In all samples. a significant fraction (35-49%) of HMW-DOM was included in the acid-insoluble fraction. Distinct differences in isotopic compositions exist among bulk samples, the compound classes and the acid-insoluble fractions. Values of delta(13)C and delta(15)N measured for bulk HMW-DOM varied from -22.1 to -30.1parts per thousand and 2.8 to 8.9parts per thousand, respectively and varied among the four estuaries studied as well. Among the Compound classes, TCHO was more enriched in C-13 (delta(13)C = -18.5 to -22.8parts per thousand) compared with THAA (delta(13)C = -20.0 to -29.6parts per thousand) and total lipid (delta(13)C = -25.7 to -30.7parts per thousand). The acid-insoluble organic fractions, in general, had depleted C-13 values (delta(13)C = -23.0 to -34.4parts per thousand). Our results indicate that the observed differences in both delta(13)C and delta(15)N were mainly due to the differences in sources of organic matter and nitrogen inputs to these estuaries in addition to the microbial processes responsible for isotopic fractionation among the compound classes. Both terrestrial sources and local sewage inputs contribute significantly to the HMW-DOM pool in the estuaries studied and thus had a strong influence on its isotopic signatures. Copyright (C) 2004 Elsevier Ltd.