Gedeelde zorg: De rol van de Nederlandse Hervormde Kerk / Protestantse Kerk in Nederland bij de bestrijding van armoede in relatie tot de overheidstaak

Brinkman, M.E. [Promotor]Vonk, G.J. [Copromotor

Developing a genetic approach to target cyanobacterial producers of heterocyte glycolipids in the environment

Heterocytous cyanobacteria are important players in the carbon and nitrogen cycle. They can fix dinitrogen by using heterocytes, specialized cells containing the oxygen-sensitive nitrogenase enzyme surrounded by a thick polysaccharide and glycolipid layer which prevents oxygen diffusion and nitrogenase inactivation. Heterocyte glycolipids can be used to detect the presence of heterocytous cyanobacteria in present-day and past environments, providing insight into the functioning of the studied ecosystems. However, due to their good preservation throughout time, heterocyte glycolipids are not ideal to detect and study living communities, instead methods based on DNA are preferred. Currently cyanobacteria can be detected using untargeted genomic approaches such as metagenomics, or they can be specifically targeted by, for example, the use of primers that preferentially amplify their 16S rRNA gene or their nifH gene in the case of nitrogen fixing cyanobacteria. However, since not all cyanobacterial nitrogen fixers are heterocytous, there is currently no fast gene-based method to specifically detect and distinguish heterocytous cyanobacteria. Here, we developed a PCR-based method to specifically detect heterocytous cyanobacteria by designing primers targeting the gene (hglT) encoding the enzyme responsible for the last step in the biosynthesis of heterocyte glycolipid (i.e., a glycosyltransferase). We designed several primer sets using the publicly available sequences of 23 heterocytous cyanobacteria, after testing them on DNA extracts of 21 heterocyte-forming and 7 non-heterocyte forming freshwater cyanobacteria. The best primer set was chosen and successfully used to confirm the presence of heterocytous cyanobacteria in a marine environmental sample

Molecular analysis of intact preen waxes of Calidris canutus (Aves:Scolopacidae) by gas chromatography/mass spectrometry

The intact preen wax esters of the red knot Calidris canutus were studied with gas chromatography/mass spectrometry (GC/MS) and GC/MS/MS. In this latter technique, transitions from the molecular ion to fragment ions representing the fatty acid moiety of the wax esters were measured, providing additional resolution to the analysis of wax esters. The C-21-C-32 wax esters are composed of complex mixtures of hundreds of individual isomers. The odd carbon-numbered wax esters are predominantly composed of even carbon-numbered n-alcohols (C-14, C-16, and C-18) esterified predominantly with odd carbon-numbered 2-methyl fatty acids (C-7, C-9, C-11, and C-13), resulting in relatively simple distributions. The even carbon-numbered wax esters show a far more complex distribution due to a number of factors: (i) Their n-alcohol moieties are not dominated by even carbon-numbered n-alcohols esterified with odd carbon-numbered 2-methyl fatty acids, but odd and even carbon-numbered n-alcohols participate in approximately equal amounts; (ii) odd carbon-numbered methyl-branched alcohols participate abundantly in these wax ester clusters; and (iii) with increasing molecular weight, various isomers of the 2,6-, 2,8-, and 2,10-dimethyl branched fatty acids also participate in the even carbon-numbered wax esters. The data demonstrate that there is a clear biosynthetic control on the wax ester composition although the reasons for the complex chemistry of the waxes are not yet understood

Developing a genetic approach to target cyanobacterial producers of heterocyte glycolipids in the environment

Heterocytous cyanobacteria are important players in the carbon and nitrogen cycle. They can fix dinitrogen by using heterocytes, specialized cells containing the oxygen-sensitive nitrogenase enzyme surrounded by a thick polysaccharide and glycolipid layer which prevents oxygen diffusion and nitrogenase inactivation. Heterocyte glycolipids can be used to detect the presence of heterocytous cyanobacteria in present-day and past environments, providing insight into the functioning of the studied ecosystems. However, due to their good preservation throughout time, heterocyte glycolipids are not ideal to detect and study living communities, instead methods based on DNA are preferred. Currently cyanobacteria can be detected using untargeted genomic approaches such as metagenomics, or they can be specifically targeted by, for example, the use of primers that preferentially amplify their 16S rRNA gene or their nifH gene in the case of nitrogen fixing cyanobacteria. However, since not all cyanobacterial nitrogen fixers are heterocytous, there is currently no fast gene-based method to specifically detect and distinguish heterocytous cyanobacteria. Here, we developed a PCR-based method to specifically detect heterocytous cyanobacteria by designing primers targeting the gene (hglT) encoding the enzyme responsible for the last step in the biosynthesis of heterocyte glycolipid (i.e., a glycosyltransferase). We designed several primer sets using the publicly available sequences of 23 heterocytous cyanobacteria, after testing them on DNA extracts of 21 heterocyte-forming and 7 non-heterocyte forming freshwater cyanobacteria. The best primer set was chosen and successfully used to confirm the presence of heterocytous cyanobacteria in a marine environmental sample

Rapid sulfurisation of highly branched isoprenoid (HBI) alkenes in sulfidic Holocene sediments from Ellis Fjord, Antarctica

Author Posting. © Elsevier B.V., 2007. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Organic Geochemistry 38 (2007): 128-139, doi:10.1016/j.orggeochem.2006.08.003.Samples of particulate organic matter from the water column and anoxic Holocene sediment layers from the Small Meromictic Basin (SMB) in Ellis Fjord (eastern Antarctica) were analyzed to study the early incorporation of reduced inorganic sulfur species into highly branched isoprenoid (HBI) alkenes. HBIs were not detected in the water column samples from austral winter, whereas compounds containing the C25 HBI skeleton were abundant in all analyzed Holocene sediment layers. The structure of the C25:2 HBI alkene together with its enriched stable carbon isotopic composition suggest that the HBI alkene is produced by a diatom or diatoms probably belonging to the Navicula genus present in the sea-ice which covers the area most of the year. Within just 500 years of deposition, all of the HBI alkene was sulfurised. A mixture of products was formed, including components tentatively identified as a C25 HBI thiane and three S-containing dimers composed of two C25:1 HBI skeletons linked together by a sulfide bond. Most of the HBI alkene, however, was converted to polar S-containing compounds. The observed reaction rate for sulfurisation the C25:2 HBI alkene is the highest observed so far in natural systems. Sterols and other lipids known to be prone to sulfurisation were only minimally sulfurised under these depositional conditions. The reason for this is presently unclear.Funding for the collection of the sediment and water samples (by MJLC and CW) was provided by ASAC grant 1166 to JKV. This work was further supported by a grant from the Netherlands Organization for Scientific Research (NWO; Netherlands Antarctic Research Proposals 851.20.006 to JSSD)

Holocene subsurface temperature variability in the eastern Antarctic continental margin

We reconstructed subsurface (∼45-200m water depth) temperature variability in the eastern Antarctic continental margin during the late Holocene, using an archaeal lipid-based temperature proxy (TEX 86 L). Our results reveal that subsurface temperature changes were probably positively coupled to the variability of warmer, nutrient-rich Modified Circumpolar Deep Water (MCDW, deep water of the Antarctic circumpolar current) intrusion onto the continental shelf. The TEX 86 L record, in combination with previously published climatic records, indicates that this coupling was probably related to the thermohaline circulation, seasonal variability in sea ice extent, sea temperature, and wind associated with high frequency climate dynamics at low-latitudes such as internal El Nio Southern Oscillation (ENSO). This in turn suggests a linkage between centennial ENSO-like variability at low-latitudes and intrusion variability of MCDW into the eastern Antarctic continental shelf, which might have further impact on ice sheet evolution. Copyright 2012 by the American Geophysical Union

Biophysical properties of membrane lipids of anammox bacteria:I. Ladderane phospholipids form highly organized fluid membranes

AbstractAnammox bacteria that are capable of anaerobically oxidizing ammonium (anammox) with nitrite to nitrogen gas produce unique membrane phospholipids that comprise hydrocarbon chains with three or five linearly condensed cyclobutane rings. To gain insight into the biophysical properties of these ‘ladderane’ lipids, we have isolated a ladderane phosphatidylcholine and a mixed ladderane phosphatidylethanolamine/phosphatidylglycerol lipid fraction and reconstituted these lipids in different membrane environments. Langmuir monolayer experiments demonstrated that the purified ladderane phospholipids form fluid films with a relatively high lipid packing density. Fluid-like behavior was also observed for ladderane lipids in bilayer systems as monitored by cryo-electron microscopy on large unilamellar vesicles (LUVs) and epi-fluorescence microscopy on giant unilamellar vesicles (GUVs). Analysis of the LUVs by fluorescence depolarization revealed a relatively high acyl chain ordering in the hydrophobic region of the ladderane phospholipids. Micropipette aspiration experiments were applied to study the mechanical properties of ladderane containing lipid bilayers and showed a relatively high apparent area compressibility modulus for ladderane containing GUVs, thereby confirming the fluid and acyl chain ordered characteristics of these lipids. The biophysical findings in this study support the previous postulation that dense membranes in anammox cells protect these microbes against the highly toxic and volatile anammox metabolites

Rapid Climate Changes in the Westernmost Mediterranean (Alboran Sea) Over the Last 35 kyr: New Insights From Four Lipid Paleothermometers (UK'37, TEXH86, RI-OH', and LDI)

The westernmost Mediterranean is one of the most sensitive areas to global climate change and high sedimentation rates allow recording high frequency variability. We present a high-resolution paleotemperature reconstruction over the last 35 kyr using, for the first time, four independent organic sea surface temperature (SST) proxies (U-37(K'), TEX86H, RI-OH' and LDI) based on alkenones, (hydroxy) isoprenoid GDGTs, and long-chain diols. We also generated a delta O-18 of planktonic foraminifera G. bulloides record together with records of bulk parameters (total organic carbon content, delta C-13(org)) and the accumulation rates of different biomarkers to provide insights into terrestrial input and primary producers. All derived-SST records showed similar trends over the last 35 kyr, revealing abrupt temperature variations during the last seven Dansgaard-Oeschger (D/O) cycles, the three Heinrich (H) events, the Last Glacial Maximum, and the Younger Dryas. H3 is recognized as the coldest event, while H1 was recorded by all SST proxies as the most abrupt one. In general, TEX86H-, RI-OH'- and LDI-SST estimates were lower than those obtained from U-37(K'). The LDI paleothermometer recorded the largest range of absolute SSTs over the whole period (ca. 20 degrees C) followed by RI-OH' (ca. 16 degrees C). TEX86H, RI-OH' and LDI proxies reflected sudden SST changes during the D/O 6 and 5 particularly well. Low BIT values and the abundance of C-32 1,15-diol in range with typical marine values indicated only minor input of continental organic matter. Accumulation rates of different lipid biomarkers were generally modulated by D/O cycles, suggesting enhanced productivity during D/O interstadials and the Bolling-Allerod period