scholarly journals Production and transformation of dissolved neutral sugars and amino acids by bacteria in seawater

2014 ◽  
Vol 11 (19) ◽  
pp. 5349-5363 ◽  
Author(s):  
L. Jørgensen ◽  
O. J. Lechtenfeld ◽  
R. Benner ◽  
M. Middelboe ◽  
C. A. Stedmon
Keyword(s):  
Amino Acids ◽  
Unknown Origin ◽  
Molecular Composition ◽  
Bacterial Degradation ◽  
The Arctic ◽  
Striking Similarity ◽  
Neutral Sugar ◽  
Natural Seawater ◽  
Glucose Content ◽  
Neutral Sugars

Abstract. Dissolved organic matter (DOM) in the ocean consists of a heterogeneous mixture of molecules, most of which are of unknown origin. Neutral sugars and amino acids are among the few recognizable biomolecules in DOM, and the molecular composition of these biomolecules is shaped primarily by biological production and degradation processes. This study provides insight into the bioavailability of biomolecules as well as the chemical composition of DOM produced by bacteria. The molecular compositions of combined neutral sugars and amino acids were investigated in DOM produced by bacteria and in DOM remaining after 32 days of bacterial degradation. Results from bioassay incubations with natural seawater (sampled from water masses originating from the surface waters of the Arctic Ocean and the North Atlantic Ocean) and artificial seawater indicate that the molecular compositions following bacterial degradation are not strongly influenced by the initial substrate or bacterial community. The molecular composition of neutral sugars released by bacteria was characterized by a high glucose content (47 mol %) and heterogeneous contributions from other neutral sugars (3–14 mol %). DOM remaining after bacterial degradation was characterized by a high galactose content (33 mol %), followed by glucose (22 mol %) and the remaining neutral sugars (7–11 mol %). The ratio of D-amino acids to L-amino acids increased during the experiments as a response to bacterial degradation, and after 32 days, the D/L ratios of aspartic acid, glutamic acid, serine and alanine reached around 0.79, 0.32, 0.30 and 0.51 in all treatments, respectively. The striking similarity in neutral sugar and amino acid compositions between natural (representing marine semi-labile and refractory DOM) and artificial (representing bacterially produced DOM) seawater samples, suggests that microbes transform bioavailable neutral sugars and amino acids into a common, more persistent form.

scholarly journals Bacterial production and transformation of dissolved neutral sugars and amino acids in seawater

2014 ◽  
Vol 11 (4) ◽  
pp. 6151-6184 ◽  
Author(s):  
L. Jørgensen ◽  
O. Lechtenfeld ◽  
R. Benner ◽  
M. Middelboe ◽  
C. A. Stedmon
Keyword(s):  
Amino Acids ◽  
Unknown Origin ◽  
Artificial Seawater ◽  
Molecular Composition ◽  
Bacterial Degradation ◽  
Striking Similarity ◽  
Neutral Sugar ◽  
Glucose Content ◽  
Carbon Pump ◽  
Neutral Sugars

Abstract. Dissolved organic matter (DOM) in the ocean consists of a heterogeneous mixture of molecules, most of which are of unknown origin. Neutral sugars and amino acids are among the few recognizable biomolecules in DOM, and the molecular composition of these biomolecules is shaped primarily by biological production and degradation processes. This study provides insight into the bioavailability of biomolecules as well as the chemical composition of DOM produced by bacteria. The molecular compositions of neutral sugars and amino acids were investigated in DOM produced by bacteria and in DOM remaining after long-term bacterial degradation. Results from bioassay incubations (32 days) with natural and artificial seawater, indicate that the molecular compositions following bacterial degradation are not strongly influenced by the initial substrate or bacterial community. The molecular composition of neutral sugars released by bacteria was characterized by a high glucose content (47 mol%) and heterogeneous contributions from other neutral sugars (3–14 mol%). DOM remaining after bacterial degradation was characterized by a high galactose content (33 mol%), followed by glucose (22 mol%) and the remaining neutral sugars (7–11 mol%). The ratio of D-amino acids to L-amino acids increased during the experiments as a response to bacterial degradation, and after 32 days the D/L ratios of aspartic acid, glutamic acid, serine and alanine reached around 0.79, 0.32, 0.30 and 0.51 in all treatments, respectively. The striking similarity in neutral sugar and amino acid compositions between natural and artificial seawater samples, suggests that the microbial carbon pump also applies for neutral sugars and amino acids and that bacterially-produced biomolecules persist for long periods in the ocean.

Studies on soil polysaccharides. II. The composition and properties in soils under pasture and under a fallow-wheat rotation

Soil Research ◽  
1968 ◽  
Vol 6 (2) ◽  
pp. 225 ◽  
Author(s):  
GD Swincer ◽  
JM Oades ◽  
DJ Greenland
Keyword(s):  
Amino Acids ◽  
Molecular Weight ◽  
Extraction Procedure ◽  
Gel Filtration ◽  
Wheat Crop ◽  
Low Molecular Weight ◽  
Neutral Sugar ◽  
Sugar Composition ◽  
High Molecular Weight Material ◽  
Neutral Sugars

After the removal of light fraction from soils under old pasture and under continuous fallow-wheat rotation, carbohydrates were extracted using IN HC1 followed by 0.5N NaOH and finally an acidic acetylation procedure, or by a single extraction with 0.2N NaOH only. The sequential extraction procedure removed 70-80 % of the carbohydrate from the soil under both agronomic systems. 0.2N NaOH removed a larger proportion of the carbohydrates from soil under fallow-wheat rotation (43-52%) than from soil under old pasture (35-38%). The composition of the carbohydrates in a given extract from the soil under pasture or fallow-wheat was similar. This similarity extended even to the neutral sugar composition of fractions obtained by gel filtration of the purified extracts. Generally, low molecular weight materials were rich in amino acids and compounds such as glucose, ribose, and glycerol. Polymers of molecular weight 4000-100,000 contained relatively high proportions of uronic acids and amino acids. Least amino acids were present in materials of molecular weight greater than 100,000 which contained appreciable quantities of deoxyhexoses (up to 20% of the total neutral sugars) indicative of their microbial origin. Against this background of similarity, certain differences between the carbohydrates from soils under pasture and fallow-wheat rotation were apparent. 1N HCl extracts contained more high molecular weight material from the old pasture soils than from the cultivated soil. The composition of these extracts indicated that they comprised the easily extractable recently synthesized microbial polysaccharides. The proportion of such polymers was lower in the cropped soil. A higher proportion of materials of small size was present in soils under a wheat crop. Maximum amounts of these compounds were present during periods of maximum plant and microbial activity. Extracts from soils under fallow-wheat rotation contained a higher proportion of uronic and amino acids and less ribose, arabinose, and deoxysugars than the extracts from soils under pasture. Based on relative deoxysugar contents it was calculated that the pasture soil contains about four times as much microbial polysaccharide as the soil under fallow-wheat.

scholarly journals Transcriptional activation and repression by Fos are independent functions: the C terminus represses immediate-early gene expression via CArG elements.

1990 ◽  
Vol 10 (8) ◽  
pp. 4243-4255 ◽  
Author(s):  
D Gius ◽  
X M Cao ◽  
F J Rauscher ◽  
D R Cohen ◽  
T Curran ◽  
...  
Keyword(s):  
Gene Expression ◽  
Amino Acids ◽  
Transcriptional Activation ◽  
Leucine Zipper ◽  
Regulatory Element ◽  
Regulatory Elements ◽  
Early Gene ◽  
Immediate Early ◽  
Striking Similarity ◽  
Independent Functions

The Fos-Jun complex has been shown to activate transcription through the regulatory element known as the AP-1 binding site. We show that Fos down regulates several immediate-early genes (c-fos, Egr-1, and Egr-2) after mitogenic stimulation. Specifically, we demonstrate that the target for this repression is a sequence of the form CC(A/T)6GG, also known as a CArG box. Whereas Fos bound to the AP-1 site through a domain rich in basic amino acids and associated with Jun via a leucine zipper interaction, mutant Fos proteins lacking these structures were still capable of causing repression. Furthermore, Jun neither enhanced nor inhibited down regulation by Fos. Critical residues required for repression are located within the C-terminal 27 amino acids of c-Fos, since v-Fos and C-terminal truncations of c-Fos did not down regulate. In addition, transfer of 180 c-Fos C-terminal amino acids to Jun conferred upon it the ability to repress. Finally, Fra-1, a Fos-related protein which has striking similarity to Fos in its C-terminal 40 amino acids, also down regulated Egr-1 expression. Thus, Fos is a transcriptional regulator that can activate or repress gene expression by way of two separate functional domains that act on distinct regulatory elements.

scholarly journals A COMPARISON OF METABOLITES IN WOOD-FORMING TISSUES FROM EIGHT COMMERCIAL TIMBER TREE SPECIES OF HEILONGJIANG PROVINCE IN CHINA

Wood Research ◽  
2021 ◽  
Vol 66 (5) ◽  
pp. 746-761
Author(s):  
JIANGTAO SHI ◽  
JUNYI PENG ◽  
CHONGYANG XIA ◽  
JIAN LI
Keyword(s):  
Malic Acid ◽  
Tree Species ◽  
Wood Formation ◽  
Deciduous Trees ◽  
Glucose Content ◽  
Coniferous Trees ◽  
Timber Tree ◽  
Neutral Sugars ◽  
The Mean ◽  
Species Specific

Four coniferous and four deciduous commercial tree species from Northeastern ofChina were selected to investigate the differences ofmetabolites in wood-forming tissues bygas chromatography-mass spectrometry. The results showed that the identified metabolites mainly consisted of neutral sugars, lipids, and organic acids. The mean contents of both arabinofuranose and 1-cyclohexene-1-carboxylic acid were higher in coniferous trees thanin deciduous ones. Similarly, the D-fructose and D-glucose content was significantly higherin coniferous trees than deciduous trees, but the total contents of these two sugars was roughly equal among most tree species. The mean content of lactic acid, glycerol and malic acid was lowerin coniferous trees than deciduous trees. The malic acid content decreased in later-stages of wood formation than in early-stagefor all tree species. The content of L-proline and myo-inositol was greater in later-stage of wood formation than early-stage.The contentof octadecanoic acid, D-fructose and D-glucose decreased in later-stage of wood formationfor most tree species. All of thissuggested that the metabolites in wood-forming tissues showed the significance of species-specific and seasonal dynamic differences among the eight tree species.

scholarly journals Multi-molecular tracers of terrestrial carbon transfer across the pan-Arctic – Part 1: Comparison of hydrolysable components with plant wax lipids and lignin phenols

2015 ◽  
Vol 12 (6) ◽  
pp. 4721-4767 ◽  
Author(s):  
X. Feng ◽  
Ö. Gustafsson ◽  
R. M. Holmes ◽  
J. E. Vonk ◽  
B. E. van Dongen ◽  
...  
Keyword(s):  
Higher Plants ◽  
River Sediments ◽  
Molecular Composition ◽  
The Arctic ◽  
Benchmark Assessment ◽  
Lignin Phenols ◽  
Carbon Transfer ◽  
North American Arctic ◽  
Arctic Rivers ◽  
Plant Wax

Abstract. Hydrolysable organic carbon (OC) comprises a significant component of sedimentary particulate matter transferred from land into oceans via rivers. Its abundance and nature are however not well studied in the arctic river systems, and yet may represent an important pool of carbon whose fate remains unclear in the context of mobilization and related processes associated with changing climate. Here, we examine the molecular composition and source of hydrolysable compounds isolated from surface sediments derived from nine rivers across the pan-Arctic. Bound fatty acids (b-FAs), hydroxy FAs, n-alkane-α, ω-dioic acids (DAs) and phenols were the major components released upon hydrolysis of these sediments. Among them, b-FAs received considerable inputs from bacterial and/or algal sources, whereas ω-hydroxy FAs, mid-chain substituted acids, DAs, and hydrolysable phenols were mainly derived from cutin and suberin of higher plants. We further compared the distribution and fate of suberin- and cutin-derived compounds with those of other terrestrial biomarkers (plant wax lipids and lignin phenols) from the same arctic river sediments and conducted a benchmark assessment of several biomarker-based indicators of OC source and extent of degradation. While suberin-specific biomarkers were positively correlated with plant-derived high-molecular-weight (HMW) FAs, lignin phenols were correlated with cutin-derived compounds. These correlations suggest that, similar to leaf-derived cutin, lignin was mainly derived from litter and surface soil horizons, whereas suberin and HMW FAs incorporated significant inputs from belowground sources (roots and deeper soil). This conclusion is supported by the negative correlation between lignin phenols and the ratio of suberin-to-cutin biomarkers. Furthermore, the molecular composition of investigated biomarkers differed between Eurasian and North American arctic rivers: while lignin dominated in the terrestrial OC of Eurasian river sediments, hydrolysable OC represented a much larger fraction in the sedimentary particles from Colville River. Hence, studies exclusively focusing on either plant wax lipids or lignin phenols will not be able to fully unravel the mobilization and fate of bound OC in the arctic rivers. More comprehensive, multi-molecular investigations are needed to better constrain the land-ocean transfer of carbon in the changing Arctic, including further research on the degradation and transfer of both free and bound components in the arctic river sediments.

scholarly journals Distribution and bacterial availability of dissolved neutral sugars in the South East Pacific

2008 ◽  
Vol 5 (4) ◽  
pp. 1165-1173 ◽  
Author(s):  
R. Sempéré ◽  
M. Tedetti ◽  
C. Panagiotopoulos ◽  
B. Charrière ◽  
F. Van Wambeke
Keyword(s):  
Organic Carbon ◽  
Dissolved Organic Carbon ◽  
Surface Waters ◽  
Detectable Effect ◽  
Neutral Sugar ◽  
The South ◽  
East Pacific ◽  
Significant Stimulation ◽  
Order Of Magnitude ◽  
Neutral Sugars

Abstract. The distribution and bacterial availability of dissolved neutral sugars were studied in the South East Pacific from October to December 2004 during the BIOSOPE cruise. Four contrasting stations were investigated: Marquesas Islands (MAR), the hyper-oligotrophic South Pacific Gyre (GYR), the eastern part of the Gyre (EGY), and the coastal waters associated to the upwelling area off Chile (UPW). Total (free and combined) dissolved neutral sugar (TDNS) concentrations were in the same order of magnitude at MAR (387±293 nM), GYR (206±107 nM), EGY (269±175 nM), and UPW (231±73 nM), with the highest and lowest concentrations found at MAR (30 m, 890 nM) and EGY (250 m, 58 nM), respectively. Their contribution to dissolved organic carbon (TDNS-C×DOC−1%) was generally low for all sites varying from 0.4% to 6.7% indicating that South East Pacific surface waters were relatively poor in neutral sugars. Free dissolved neutral sugar (FDNS; e.g. sugars analyzed without hydrolysis) concentrations were very low within the detection limit of our method (5–10 nM) accounting for <5% of the TDNS. In general, the predominant sugars within the TDNS pool were glucose, xylose, arabinose, and galactose, while in the FDNS pool only glucose was present. TDNS stock to bacterial production ratios (integrated values from the surface to the deep chlorophyll maximum) were high at GYR with respect to the low primary production, whereas the opposite trend was observed in the highly productive area of UPW. Intermediate situations were observed for MAR and EGY. Bioavailability of dissolved organic matter (DOM) exposed to natural solar radiation was also experimentally studied and compared to dark treatments. Our results showed no or little detectable effect of sunlight on DOM bacterial assimilation in surface waters of UPW and GYR, while a significant stimulation was found in MAR and EGY. The overall results clearly suggest that DOM is less labile at GYR compared to UPW, which is consistent with the observed accumulation of dissolved organic carbon and the elevated C/N ratios reported by Raimbault et al. (2008).

scholarly journals The composition and distribution of labile dissolved organic matter across the south west Pacific

2018 ◽  
Author(s):  
Christos Panagiotopoulos ◽  
Mireille Pujo Pay ◽  
Mar Benavides ◽  
France Van Wambeke ◽  
Richard Sempéré
Keyword(s):  
Organic Matter ◽  
Residence Time ◽  
Surface Waters ◽  
Austral Summer ◽  
Bacterial Degradation ◽  
The South ◽  
Long Period ◽  
South West ◽  
Neutral Sugars ◽  
South Pacific Gyre

Abstract. The distribution and dynamics of dissolved organic carbon (DOC) and dissolved combined neutral sugars (DCNS) were studied across an increasing oligotrophic gradient (−18 to −22° N latitude) spanning from the Melanesian Archipelago (MA) area to the western part of the south Pacific gyre (WGY), in austral summer, as a part of the OUTPACE project. Our results showed DOC and DCNS concentrations exhibited little differences among the MA and WGY areas (0–200 m: 55–78 µMC for DOC and 1.5–2 µMC for DCNS), however, a deeper penetration of DOC was noticeable at 150 m depth at the WGY area. This finding was also reflected to the DOC and semi-labile DOC (DOCSL) stocks values (integration 0–200 m) for which we found higher values in the WGY than the MA area. The high excess DOCSL measured in WGY was characterized by a high residence time (130 ± 31 days (n = 3)) about three times higher than the MA region (Tr = 40 ± 7 days (n = 8)) suggesting an accumulation of the semi-labile DOM in the surface waters of WGY. DCNS yields (DCNS-C x DOC−1 %) also followed this pattern with higher values recorded in the WGY (3.2 ± 1.3 %) than MA (2.8 ± 0.8 %) highlighting the presence of semi-labile dissolved organic material (DOM) in the form of polysaccharides. These polysaccharides also exhibited a higher residence time in WGY (Tr = 8 ± 4 days, n = 3) than in MA (Tr = 3 ± 1days, n = 8) suggesting that this DCNS pool persists longer in the surface waters of the WGY. The accumulation of DOCSL in the surface waters of WGY is probably due to the very slow bacterial degradation due to nutrient limitation indicating that biologically produced DOC can be stored in the euphotic layer for a very long period.

scholarly journals Investigation of the Effect of Nanocrystalline Calcium Carbonate-Substituted Hydroxyapatite and L-Lysine and L-Arginine Surface Interactions on the Molecular Properties of Dental Biomimetic Composites

Biomimetics ◽  
2021 ◽  
Vol 6 (4) ◽  
pp. 70
Author(s):  
Dmitry Goloshchapov ◽  
Vladimir Kashkarov ◽  
Kirill Nikitkov ◽  
Pavel Seredin
Keyword(s):  
Amino Acids ◽  
Fourier Transform ◽  
Infrared Spectroscopy ◽  
Fourier Transform Infrared ◽  
Surface Interactions ◽  
Molecular Composition ◽  
Alkaline Media ◽  
Hydroxyl Groups ◽  
X Ray Diffraction ◽  
X Ray

Differences in the surface interactions of non-stoichiometric nanocrystalline B-type carbonate-substituted hydroxyapatite (n-cHAp) with the amino acids L-Lysine hydrochloride (L-LysHCl) and L-Arginine hydrochloride (L-ArgHCl) in acidic and alkaline media were determined using structural and spectroscopic analysis methods. The obtained data confirm that hydroxyapatite synthesized using our technique, which was used to develop the n-cHAp/L-LysHCl and n-cHAp/L-ArgHCl composites, is nanocrystalline. Studies of molecular composition of the samples by Fourier transform infrared spectroscopy under the change in the charge state of L-Lysine in environments with different alkalinity are consistent with the results of X-ray diffraction analysis, as evidenced by the redistribution of the modes’ intensities in the spectra that is correlated with the side chains, i.e., amide and carboxyl groups, of the amino acid. During the formation of a biomimetic composite containing L-Lysine hydrochloride and n-cHAp, the interaction occurred through bonding of the L-Lysine side chain and the hydroxyl groups of hydroxyapatite, which created an anionic form of L-Lysine at pH ≤ 5. In contrast, in biocomposites based on L-Arginine and n-cHAp, the interaction only slightly depends on pH value, and it proceeds by molecular orientation mechanisms. The X-ray diffraction and infrared spectroscopy results confirm that changes in the molecular composition of n-cHAp/L-ArgHCl biomimetic composites are caused by the electrostatic interaction between the L-ArgHCl molecule and the carbonate-substituted calcium hydroxyapatite. In this case, the bond formation was detected by Fourier transform infrared (FTIR) spectroscopy; the vibrational modes attributed to the main carbon chain and the guanidine group of L-Arginine are shifted during the interaction. The discovered interaction mechanisms between nanocrystalline carbonate-substituted hydroxyapatite that has physicochemical properties characteristic of the apatite in human dental enamel and specific amino acids are important for selecting the formation conditions of biomimetic composites and their integration with the natural dental tissue.

scholarly journals Organic molecular composition of marine aerosols over the Arctic Ocean in summer: contributions of primary emission and secondary aerosol formation

2012 ◽  
Vol 9 (8) ◽  
pp. 10429-10465
Author(s):  
P. Q. Fu ◽  
K. Kawamura ◽  
J. Chen ◽  
B. Charrière ◽  
R. Sempéré
Keyword(s):  
Organic Carbon ◽  
Arctic Ocean ◽  
Organic Compounds ◽  
Fungal Spores ◽  
Organic Aerosols ◽  
Molecular Composition ◽  
The Arctic ◽  
Marine Aerosols ◽  
Aerosol Formation ◽  
The Arctic Ocean

Abstract. Organic molecular composition of marine aerosol samples collected during the MALINA cruise in the Arctic Ocean was investigated by gas chromatography/mass spectrometry. More than 110 individual organic compounds were determined in the samples and were grouped into different compound classes based on the functionality and sources. The concentrations of total quantified organics ranged from 7.3 to 185 ng m−3 (mean 47.6 ng m−3), accounting for 1.8–11.0% (4.8%) of organic carbon in the marine aerosols. Primary saccharides were found to be dominant organic compound class, followed by secondary organic aerosol (SOA) tracers formed from the oxidation of biogenic volatile organic compounds (VOCs) such as isoprene, α-pinene and β-caryophyllene. Mannitol, the specific tracer for airborne fungal spores, was detected as the most abundant organic species in the samples with a concentration range of 0.052–53.3 ng m−3 (9.2 ng m−3), followed by glucose, arabitol, and the isoprene oxidation products of 2-methyltetrols. Biomass burning tracers such as levoglucosan are evident in all samples with trace levels. On the basis of the tracer-based method for the estimation of fungal-spore OC and biogenic secondary organic carbon (SOC), we estimate that an average of 10.7% (up to 26.2%) of the OC in the marine aerosols was due to the contribution of fungal spores, followed by the contribution of isoprene SOC (mean 3.8%) and α-pinene SOC (2.9%). In contrast, only 0.19% of the OC was due to the photooxidation of β-caryophyllene. This study indicates that primary organic aerosols from biogenic emissions, both from long-range transport of mid-latitude aerosols and from sea-to-air emission of marine organics, as well as secondary organic aerosols formed from the photooxidation of biogenic VOCs are important factors controlling the organic chemical composition of marine aerosols in the Arctic Ocean.

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