Stable Isotope Probing:Linking Functional Activity to Specific Members of Microbial Communities

Linking organisms or groups of organisms to specific functions within natural environments is a fundamental challenge in microbial ecology. Advances in technology for manipulating and analyzing nucleic acids have made it possible to characterize the members of microbial communities without the intervention of laboratory culturing. Results from such studies have shown that the vast majority of soil organisms have never been cultured, highlighting the risks of culture-based approaches in community analysis. The development of culture-independent techniques for following the flow of substrates through microbial communities therefore represents an important advance. These techniques, collectively known as stable isotope probing (SIP), involve introducing a stable isotope-labeled substrate into a microbial community and following the fate of the substrate by extracting diagnostic molecular species such as fatty acids and nucleic acids from the community and determining which specific molecules have incorporated the isotope. The molecules in which the isotope label appears provide identifying information about the organism that incorporated the substrate. Stable isotope probing allows direct observations of substrate assimilation in minimally disturbed communities, and thus represents an exciting new tool for linking microbial identity and function. The use of lipids or nucleic acids as the diagnostic molecule brings different strengths and weaknesses to the experimental approach, and necessitates the use of significantly different instrumentation and analytical techniques. This short review provides an overview of the lipid and nucleic acid approaches, discusses their strengths and weaknesses, gives examples of applications in various settings, and looks at prospects for the future of SIP technology.

Aliphatic Poly(ester-carbonate)s Bearing Amino Groups and Its RGD Peptide Grafting

This article deals with (1) synthesis of novel cyclic carbonate monomer (2-oxo [1,3]dioxan-5-yl)carbamic acid benzyl ester (CAB) containing protected amino groups; (2) ring-opening copolymerization of the cyclic monomer with L-lactide (LA) to provide novel degradable poly(ester-carbonate)s with functional groups; (3) removal of the protective benzyloxycarbonyl (Cbz) groups by catalytic hydrogenation to afford the corresponding poly(ester-co-carbonate)s with free amino groups; (4) grafting of oligopeptide Gly-Arg-Gly-Asp-Ser-Tyr (GRGDSY, abbreviated as RGD) onto the copolymer pendant amino groups in the presence of 1,1'-carbonyldiimidazole (CDI).

Synthesis and characterization of functional poly(gamma-benzyl-L-glutamate) (PBLG) as a hydrophobic precursor

Four kinds of functional poly(gamma-benzyl-L-glutamate) (PBLG) copolymers containing chloro, azido, allyl or propargyl groups on the side chains were synthesized through ester exchange reactions of PBLG with functional alcohols without any protection and de-protection process. Hydrolysis of PBLG, which was found during the ester exchange reaction under low ratios of alcohol to the repeat units of PBLG, was thoroughly investigated, and could be successfully depressed by addition of certain amount of benzyl alcohol to the reaction system. Click chemistry reactions of the azidized or propargylated copolymers, thiol-ene reaction of the allyllated copolymer were taken successfully, indicating that the functional groups on the copolymers were still reactive.

Structures and elastic properties of OsN2 investigated via first-principles density functional calculations

The structure, elastic, and electronic properties of OsN2 at various space groups: cubic Fm-3m, Pa-3, and orthorhombic Pnnm were studied by first-principles calculations based on density functional theory. Our calculation indicates that the structure in orthorhombic Pnnm phase is energetically more stable compared with cubic systems. It is metallic, mechanically stable and contains diatomic N-N units with the bond distance 1.418 A. These characters are consistent with experimental facts that OsN2 is orthorhombic and metallic. The calculated bulk modulus 394 GPa is also the highest among the considered space groups, slightly larger than previous value 358 GPa. The calculated elastic anisotropic factors and directional bulk modulus showed that OsN2 possess high elastic anisotropy.

Naphthyl and thionaphthyl end-capped oligothiophenes as organic semiconductors: Effect of chain length and end-capping groups

Two series of oligothiophenes (OThs), NaTn and TNTn (n = 2-6 represents the number of thiophene rings), end-capped with naphthyl and thionaphthyl units have been synthesized by means of Stille coupling. Their thermal properties, optical properties, single crystal structures, and organic field-effect transistor performance have been characterized. All oligomers display great thermal stability and crystallinity. ne crystallographic structures of NaT2, NaT3, TNT2, and TNT3 have been determined. The crystals of NaT2 and NaT3 are monoclinic with space group P2(1)/C, while those of TNT2 and TNT3 are triclinic and orthorhombic with space groups P-1(-) and P2(1)2(1)2(1), respectively. All oligomers adopt the well-known herringbone packing-mode in crystals with packing parameters dependent on the structure of the end-capping units and the number of thiophene rings. The shorter intermolecular distance in NaT3 compared to NaT2 indicates that the intermolecular interaction principally increases with increasing molecular length. X-ray diffraction and atomic force microscopy (AFM) characterization indicate that the NaTn oligomers can form films with better morphology and high molecular order than TNTn oligomers with the same number of thiophene rings. The NaTn oligomers exhibit mobilities that are much higher than those for TNTn oligomers (0.028-0.39 cm(2) V-1 s(-1) versus 0.010-0.055 cm(2) V-1 s(-1), respectively).

Synthesis of novel functional polyolefin containing carboxylic acid via Friedel-Crafts acylation reaction

The strong polar group, carboxylic acid, has triumphantly been introduced into ethylene and allylbenzene copolymers without obvious degradation or crosslinking via Friedel-Crafts (F-C) acylation reaction with glutaric anhydride (GA), succinic anhydride (SA) and phthalic anhydride (PA) in the presence of anhydrous aluminum chloride in carbon disulfide. Some important reaction parameters were examined in order to optimize the acylation process. In the optimum reaction conditions, almost all of the phenyls can be acylated with any anhydride. The microstructure of acylated copolymer was characterized by Fr-IR, H-1 NMR and H-1-H-1 COSY. All the peaks of acylated copolymers can be accurately attributed, which indicates that all the acylation reactions occur only at the para-positions of the substituent of the aromatic rings. The thermal behavior was studied by differential scanning calorimetry (DSC), showing that the melting temperatures (T(m)s) of acylated copolymers with GA firstly decrease slowly and then increase significantly with the increase of the amount of carboxyl acid groups.

Liquid crystalline and light emitting polyacetylenes: Synthesis and properties of biphenyl-containing poly(1-alkynes) with different functional bridges and spacer lengths

Biphenyl- (Biph-) containing 1-alkynes (3 and 4) and their polymers (1 and 2) with varying bridge groups and spacer lengths were synthesized and the effects of the structural variation on their properties, especially their mesomorphism and photoluminescence behaviors, were studied. The acetylene monomers 3(3) [HCdropC(CH2)(3)O-Biph-OCO(CH2)(10)CH3] and 4(m) [HCdropC(CH2)(m)OCO-Biph-OCO(CH2)(10)-CH3, m = 3, 4] were prepared by sequential etherization and esterification reactions of 1-alkynes. While 3(3) exhibits enantiotropic crystal E and SmB mesophases, its structural cousin 4(3) displays only a monotropic SmB phase. Enantiotropic SmA and SmB mesophases are, however, developed when the spacer length is increased to 4. Polymerizations of the monomers are effected by Mo-, W-, Rh-, and Fe-based catalysts, with the WCl6-Ph4Sn catalyst giving the best results (isolation yield up to 85% and M-w up to 59000). The polymers were characterized by IR, UV, NMR, TGA, DSC, POM, XRD, and PL analyses. Compared to 1(3), 2(3) shows a red-shifted absorption, a higher T-i, and a better packed interdigitated bilayer SmA(d) structure, while the mesophase of 2(4) involves monolayer-packing arrangements of the mesogens. Upon photoexcitation, 1(3) emits almost no light but 2(m) gives a strong ultraviolet emission (lambda(max) similar to 350 nm), whose intensity increases with the spacer length.

Polymer-supported zirconocene catalyst for ethylene polymerization

The use of crosslinked poly(styrene-co-4-vinylpyridine) having functional groups as the support for zirconocene catalysts in ethylene polymerization was studied. Several factors affecting the activity of the catalysts were examined. Conditions like time, temperature, Al/N (molar ratio), Al/Zr (molar ratio), and the mode of feeding were found having no significant influence on the activity of the catalysts, while the state of the supports had a great effect on the catalytic behavior. The activity of the catalysts sharply increased with either the degree of crosslinking or the content of 4-vinylpyridine in the support. Via aluminum compounds, AlR3 or methylaluminoxane (MAO), zirconocene was attached on the surface of the support. IR spectra showed an intensified and shifted absorption bands of C-N in the pyridine ring, and a new absorption band appeared at about 730 cm(-1) indicating a stable bond Al-N formed in the polymer-supported catalysts. The formation of cationic active centers was hypothesized and the performance of the polymer-supported zirconocene was discussed as well. (C) 1999 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 37: 37-46, 1999.

Characterization of the structural and functional changes of hemoglobin in dimethyl sulfoxide by spectroscopic techniques

Circular dichroism (CD), fourier transform infrared (FTIR), and fluorescence spectroscopy were used to explore the effect of dimethyl sulfoxide (DMSO) on the structure and function of hemoglobin (Hb). The native tertiary structure was disrupted completely when the concentration of DMSO reached 50% (v/v), which was determined by loss of the characteristic Soret CD spectrum. Loss of the native tertiary structure could be mainly caused by breaking the hydrogen bonds, between the heme propionate groups and nearby surface amino acid residues, and by disorganizing the hydrophobic interior of this protein. Upon exposure of Hb to 52% DMSO for ca. 12 h in a D2O medium no significant change in 1652 cm(-1) band of the FTIR spectrum was produced, which demonstrated that alpha-helical structure predominated. When the concentration of DMSO increased to 57%: (1) the band at 1652 cm(-1) disappeared with the appearance of two new bands located at 1661 and 1648 cm(-1); (2) another new band at 1623 cm(-1) was attributed to the formation of intermolecular beta-sheet or aggregation, which was the direct consequence of breaking of the polypeptide chain by the competition of S=O groups in DMSO with C=O groups in amide bonds. Further increasing the DMSO concentration to 80%, the intensity at 1623 cm(-1) increased, and the bands at 1684, 1661 and 1648 cm(-1) shifted to 1688, 1664 and 1644 cm(-1), respectively. These changes showed that the native secondary structure of Hb was last and led to further aggregation and increase of the content of 'free' amide C=O groups. In pure DMSO solvent, the major band at 1664 cm(-1) indicated that almost all of both the intermolecular beta-sheet and any residual secondary structure were completely disrupted. The red shift of the fluorescence emission maxima showed that the tryptophan residues were exposed to a greater hydrophilic environment as the DMSO content increased. GO-binding experiment suggested that the biological function of Hb was disrupted seriously even if the content of DMSO was 20%. (C) 1998 Elsevier Science B.V. All rights reserved.

Functional biosynthesis of an allophycocyan beta subunit in Escherichia coli

Allophycocyanin is a phycobiliprotein with various biological and pharmacological properties. An expression vector was constructed using CpeS as the bilin lyase for the allophycocyanin beta subunit, resulting in overexpression of a fluorescent allophycocyanin beta-subunit in Escherichia coli. A high-density cell culture was developed using a continuous feeding strategy. After 16 h of culture, the dry cell density reached 21.4 g 1(-1), the expression of the allophycocyanin beta-subunit was 0.86 g l(-1) broth, and the relative chromoprotein yield was 81.4%. The recombinant protein showed spectral features similar to native allophycocyanin, which provide an efficient methodology for large-scale production of this valuable fluorescent protein. (C) 2008, The Society for Biotechnology, Japan. All rights reserved.

Molecular cloning and functional analysis of cathepsin B in nutrient metabolism during larval development in Meretrix meretrix

Seed rearing is an important part in large scale clam culture industry. Since the nutritional history affects early development in bivalve, the condition of larval nutrition plays a key role in successful seed rearing. So far, the molecular mechanism of nutrient uptake in bivalve larvae is unclear. As one of the important proteolytic enzymes, cathepsin B of several organisms has been reported to be involved in digestion. We intended to analyze whether cathepsin B is involved in larval nutrient metabolism in the economic bivalve, clam Meretrix meretrix. The full length of M. meretrix cathepsin B (MmeCB) cDNA was cloned, which is 1647 bp with an open reading frame of 1014 bp. The deduced amino acid sequence encoded a preproenzyme of 337 residues with Cys-114, His-282 and Asn-302 composing cathepsin B activity center. The temporal and spatial expressions of MmeCB mRNA were examined from trochophore to post larva stages by whole mount in situ hybridization. In trochophore stage, no detectable signal was found. In the later three stages, MmeCB mRNA was detected in the digestive gland, suggesting a possible role of MmeCB in digestion. Moreover, MmeCB mRNA was also observed in the epidermal cells in D-veligers. Cathepsin B specific inhibitor (CA074 methyl ester) was applied to block the activity of cathepsin B in unfed larvae. The average shell lengths of treated larvae were smaller than that in control groups. The results of mRNA epidermal distribution and inhibitor treatment in D-veligers indicated that MmeCB may be also associated with other pathway of nutrient metabolism in larval epidermis. The overall results in this paper revealed that MmeCB might play a role in larval nutrient metabolism. (C) 2008 Elsevier B.V. All rights reserved.

Feeding level-scaled retention efficiency, growth and energy partitioning of a marine detritivorous fish, redlip mullet (Liza haematocheila T. & S.)

The effects of feeding level on growth, retention efficiency, faeces production and energy partitioning of redlip mullet were studied. A practical diet was used and fed at six levels from starvation, 1%, 2%, 3%, 4% of body weight (BW) to satiation for 3 weeks. The temperature was kept at 24 +/- 1 degrees C. Reducing the feeding amount resulted in significantly lower weight gain, and retention efficiency was significantly affected by feeding levels and attained the maximum at maximum feeding intake. Feeding 2% BW was the minimum required for fish to maintain growth. Fish carcass composition under different feeding levels could be divided into three groups: (1) starvation and FL1; (2) FL2 and FL3 and (3) FL4 and satiation, with significant differences among the groups but no differences in the groups except that ash content remained at constant value. Body composition of fish of group 2 was close to initial fish. The thermal-unit coefficient was 0.0381 at satiation, and significantly increased with increasing feeding levels. In order to accurately estimate basal metabolism (HeE), another trial on the relationship between HeE (kJ) and BW (g) was carried out. An exponential curve as HeE=0.1255BW(0.8386) explained this relationship. Intake energy (IE) increased from 11.30 to 63.08 kJ per fish, matching with different feeding levels. Energy allocated to growth of IE decreased with reducing feeding amount. There was a linear relationship between metabolism energy and retention energy in percentage.

Summer feeding activities of zooplankton in Prydz Bay, Antarctica

Grazing of dominant zooplankton copepods (Calanoides acutus. and Metridia gerlachei), salps (Salpa thompsoni) and microzooplankton was determined during the austral summer of 1998/1999 at the seasonal ice zone of the Prydz Bay region. The objective was to measure the ingestion rates of zooplankton at the seasonal ice zone, so as to evaluate the importance of different groups of zooplankton in their grazing impact on phytoplankton standing stock and primary production. Grazing by copepods was low, and accounted for less than or equal to 1% of phytoplankton standing stocks and 3.8-12.5% of primary production for both species during this study, even the ingestion rates of individuals were at a high level compared with previous reports. S. thompsoni exhibited a relatively high grazing impact on primary production (72%) in the north of our investigation area. The highest grazing impact on phytoplankton was exerted by microzooplankton during this investigation, and accounted for 10-65% of the standing stock of phytoplankton and 34-100% of potential daily primary production. We concluded that microzooplankton was the dominant phytoplankton consumer in this study area. Salps also played an important role in control of phytoplankton where swarming occurred. The grazing of copepods had a relatively small effect on phytoplankton biomass development.

Feeding activities of zooplankton in the Bohai Sea

The Bohai Sea was the site of the Chinese national GLOBEC programme. During the June 1997 cruises of R/V Science No.1, observations and experiments on zooplankton feeding were conducted. At five 48 h time-series stations the following observations and measurements on zooplankton were carried out: (1) diurnal vertical migration, by collecting samples at different layers every 3 h with a closing net; (2) diurnal feeding rhythms, by gut pigment analysis; and (3) ingestion rate, by both gut pigment analysis and the dilution method. A classification by body size was used to deal with the diversity of species and developmental stages of zooplankton assemblages. Samples were separated into three size groups: small (200-500 mu m), medium (500-1000 mu m) and large (> 1000 mu m). The results showed that the copepods (Calanus sinicus, Paracalanus parvus, Acartia bifilosa and Centropages mcmurrichi) performed clear diurnal vertical migrations. However, their behaviour was different at different stations. The variation in gut pigment content over the 24 h cycle showed strong diurnal feeding rhythms, particularly for the large size group. Gut pigment contents reached their daily maximum during the time from dusk to midnight (18:00-24:00). The peak value was about 10 times the minimum observed in the daytime. The in situ daily grazing rate, based on gut pigment contents and evacuation experiments, was 4.00-12.65 ng chla ind(-1) day(-1) for the small size group, 5.99-66.58 ng chla ind(-1) day(-1) for the medium size group and 31.31-237.13 ng chla ind(-1) day(-1) for the large size group. The copepods consumed only a small part (2.90-13.52%) of the phytoplankton biomass hut about 77% of the daily production. The grazing mortality rate of phytoplankton by microzooplankton (<200 mu m) measured by the dilution method ranged from 0.43 to 0.69 day(-1) The calculated daily consumption of phytoplankton biomass was 35-50%, and 85-319% of the potential production.