Carbon Mineralization and Labile Organic Carbon Pools in the Sandy Soils of a North Florida Watershed

The large pool of actively cycling carbon (C) held in soils is susceptible to release due to changes in landuse, management, or climate. Yet, the amount and distribution of potentially mineralizable C present in soils of various types and the method by which this soil C fraction can best be quantified, are not well established. The distribution of total organic C (TOC), extractable C pools (hot-water-extractable and acid-hydrolyzable), and in vitro mineralizable C in 138 surface soils across a north Florida watershed was found to be quite heterogeneous. Thus, these C quality parameters could not statistically distinguish the eight landuses or four major soil orders represented. Only wetland and upland forest soils, with the largest and smallest C pool size, respectively, were consistently different from the soils of other landuse types. Variations in potential C mineralization were best explained by TOC (62%) and hot-water-extractable C (59%), whereas acid-hydrolyzable C (32%) and clay content (35%) were generally not adequate indicators of C bioavailability. Within certain landuse and soil orders (Alfisol, Wetland and Rangeland, all with >3% clay content), however, C mineralization and clay content were directly linearly correlated, indicating a possible stimulatory effect of clay on microbial processing of C. Generally, the sandy nature of these surface soils imparted a lack of protection against C mineralization and likely resulted in the lack of landuse/soil order differences in the soil C pools. If a single parameter is to be chosen to quantify the potential for soil C mineralization in southeastern U.S. coastal plain soils, we recommend TOC as the most efficient soil variable to measure. Author Contributions  Conceived of or designed study: Sabine Grunwald, Nick Comerford, and James Sickman—Performed research: Mi-Youn Ahn—Analyzed data: Mi-Youn Ahn, Andrew Zimmerman, and Nick Comerford—Contributed new methods or models: Andrew Zimmerman, Nick Comerford, and James Sickman—Wrote the paper: Mi-Youn Ahn, Andrew Zimmerman, and Nick Comerford.     

Oxidized alkyl phospholipids are specific, high affinity peroxisome proliferator-activated receptor gamma ligands and agonists

Synthetic high affinity peroxisome proliferator-activated receptor (PPAR) agonists are known, but biologic ligands are of low affinity. Oxidized low density lipoprotein (oxLDL) is inflammatory and signals through PPARs. We showed, by phospholipase A(1) digestion, that PPARgamma agonists in oxLDL arise from the small pool of alkyl phosphatidylcholines in LDL. We identified an abundant oxidatively fragmented alkyl phospholipid in oxLDL, hexadecyl azelaoyl phosphatidylcholine (azPC), as a high affinity ligand and agonist for PPARgamma. [(3)H]azPC bound recombinant PPARgamma with an affinity (K(d)((app)) approximately 40 nm) that was equivalent to rosiglitazone (BRL49653), and competition with rosiglitazone showed that binding occurred in the ligand-binding pocket. azPC induced PPRE reporter gene expression, as did rosiglitazone, with a half-maximal effect at 100 nm. Overexpression of PPARalpha or PPARgamma revealed that azPC was a specific PPARgamma agonist. The scavenger receptor CD36 is encoded by a PPRE-responsive gene, and azPC enhanced expression of CD36 in primary human monocytes. We found that anti-CD36 inhibited azPC uptake, and it inhibited PPRE reporter induction. Results with a small molecule phospholipid flippase mimetic suggest azPC acts intracellularly and that cellular azPC accumulation was efficient. Thus, certain alkyl phospholipid oxidation products in oxLDL are specific, high affinity extracellular ligands and agonists for PPARgamma that induce PPAR-responsive genes.     

Duffy-null promoter heterozygosity reduces DARC expression and abrogates adhesion of the P. vivax ligand required for blood-stage infection

The Duffy blood group antigen is an essential receptor for Plasmodium vivax entry into erythrocytes in a process mediated by the parasite ligand, the Duffy binding protein (DBP). Recently, individuals living in a malaria endemic region of Papua New Guinea were identified as heterozygous for a new allele conferring Duffy negativity, which results in 50% less Duffy antigen on their erythrocytes. We demonstrate that DBP adherence to erythrocytes is significantly reduced for erythrocytes from heterozygous individuals who carry one Duffy antigen negativity allele. These data provide evidence that emergence of this new allelic form of Duffy negativity is correlated with resistance against vivax malaria.     

Congenital hypotrichosis in a white-tailed deer fawn from South Dakota

On 1 October 2001, a 4-mo-old male white-tailed deer (Odocoileus virginianus) fawn was collected in Day County, South Dakota (USA), by South Dakota Department of Game, Fish and Parks personnel. The fawn had sparse hair development on the ventral thorax, the lateral caudal and caudal aspects of the rear legs, the muzzle, around the eyes, and inside the ears. Remaining skin surfaces were devoid of hair. Histologic examination revealed normal hair follicle density although follicles were empty or contained keratin debris and fragments of hair shaft. The epidermis of the fawn was mildly thickened and melanin pigment was prominent within deep layers of the epidermis. Based on histologic examination, the deer was diagnosed with congenital hypotrichosis. Although this condition has been reported in domestic species and humans, this specimen represents the first documented case of congenital hypotrichosis in a cervid.     

Studies on the compaction of isolated nucleoids from Escherichia coli

The genomic DNA of Escherichia coli is contained in one or two compact bodies known as nucleoids. Isolation of typically shaped nucleoids requires control of DNA expansion, accomplished here by a modification of the polylysine-spermidine procedure. The ability to control expansion of in vitro nucleoids has application in nucleoid purification and in preparation of samples for high-resolution imaging, and may allow an increased resolution in gene localization studies. Polylysine of relatively low average molecular weight (approximately 3 kDa) is used to produce lysates containing nucleoids that are several-fold expanded relative to the sizes of in vivo nucleoids. These expanded forms can be converted to compact forms similar in dimensions to the cellular nucleoids by either a further addition of polylysine or by incubation of diluted lysates at 37 degrees C. The incubation at 37 degrees C is accompanied by autolytic degradation of most ribosomal RNA. Hyperchromism and circular dichroism spectra indicate that polylysine-DNA complexes are modified during the incubation. Compact forms of the nucleoid can be progressively reexpanded by exposure to salt solutions. Nucleoid compaction was similar in lysates made from rapidly or slowly growing cells or from cells that had been briefly treated with chloramphenicol to reduce linkages between DNA and cell envelope.     

Solution measurement of DNA curvature in papillomavirus E2 binding sites

‘Indirect readout’ refers to the proposal that proteins can recognize the intrinsic three-dimensional shape or flexibility of a DNA binding sequence apart from direct protein contact with DNA base pairs. The differing affinities of human papillomavirus (HPV) E2 proteins for different E2 binding sites have been proposed to reflect indirect readout. DNA bending has been observed in X-ray structures of E2 protein–DNA complexes. X-ray structures of three different E2 DNA binding sites revealed differences in intrinsic curvature. DNA sites with intrinsic curvature in the direction of protein-induced bending were bound more tightly by E2 proteins, supporting the indirect readout model. We now report solution measurements of intrinsic DNA curvature for three E2 binding sites using a sensitive electrophoretic phasing assay. Measured E2 site curvature agrees well the predictions of a dinucleotide model and supports an indirect readout hypothesis for DNA recognition by HPV E2.     

Rab11b resides in a vesicular compartment distinct from Rab11a in parietal cells and other epithelial cells

The Rab11 family of small GTPases is composed of three members, Rab11a, Rab11b, and Rab25. While recent work on Rab11a and Rab25 has yielded some insights into their function, Rab11b has received little attention. Therefore, we sought to examine the distribution of endogenous Rab11b in epithelial cells. In rabbit gastric parietal cells, unlike Rab11a, Rab11b did not colocalize or coisolate with H(+)/K(+)-ATPase. In MDCK cells, endogenous Rab11b localized to an apical pericentrisomal region distinct from Rab11a. The microtubule agents nocodazole and taxol dramatically alter Rab11a's localization in the cell, while effects on Rab11b's distribution were less apparent. These results indicate that in contrast to Rab11a, the Rab11b compartment in the apical region is not as dependent upon microtubules. While Rab11a is known to regulate transferrin trafficking in nonpolarized cells and IgA trafficking in polarized cells, Rab11b exhibited little colocalization with either of these cargoes. Thus, while Rab11a and Rab11b share high sequence homology, they appear to reside within distinct vesicle compartments.     

Platelet-activating factor acetylhydrolase,and not paraoxonase-1, is the oxidized phospholipid hydrolase of high density lipoprotein particles

Paraoxonase-1 (PON1), an high density lipoprotein (HDL)-associated organophosphate triesterase, suppresses atherosclerosis in an unknown way. Purified PON1 protects lipoprotein particles from oxidative modification and hydrolyzes pro-atherogenic oxidized phospholipids and the inflammatory mediator platelet-activating factor (PAF). We find human PON1 acted as a phospholipase A(2) but not as a phospholipase C or D through cleavage of phosphodiester bonds as expected. PON1 requires divalent cations, but EDTA did not block the phospholipase A(2) activity of PON1. In contrast, a serine esterase inhibitor abolished phospholipase activity even though PON1 has no active-site serine residues. PAF acetylhydrolase, an oxidized phospholipid phospholipase A(2), is a serine esterase associated with specific HDL particles. Western blotting did not reveal detectable amounts of PAF acetylhydrolase in PON1 preparations, although very low amounts of PAF acetylhydrolase might still account for PON1 phospholipase A(2) activity. We revised the standard PON1 purification by first depleting HDL of PAF acetylhydrolase to find PON1 purified in this way no longer hydrolyzed oxidized phospholipids or PAF. Serum from a donor with an inactivating mutation in the PAF acetylhydrolase gene did not hydrolyze oxidized phospholipids or PAF, yet displayed full paraoxonase activity. We conclude that PAF acetylhydrolase is the sole phospholipase A(2) of HDL and that PON1 has no phospholipase activity toward PAF or pro-atherogenic oxidized phospholipids.