Microbial Communities Involved in Fe Reduction and Mobility During Soil Organic Matter (SOM) Mineralization in Two Contrasted Paddy Soils

Lowland rice fields of West Africa (Ivory Coast) and South Asia (Thailand) are affected by ferrous toxicity or salinity, respectively, and their soil waters contain large amounts of ferrous iron, depending on reducing irrigation condition and suggesting occurrence of bacterial reducing processes. To determine the involvement, dynamic and activities of bacterial communities in Fe(III) reduction and mobilization during anaerobic degradation and mineralization of soil organic matter (SOM), different experiments and analyses have been performed. Results demonstrated that the utilization of SOM as sole carbon, nutrient and energy sources favored the presence of large bacterial communities: facultative anaerobic and anaerobic bacteria, Fe(III)-reducing bacteria (FeRB) (fermentative and Fe respiring), sulfate reducing bacteria (SRB) which are involved in carbon, nitrogen, iron and sulfur cycling. The larger functional diversity is observed in the Ivory Coast paddy soils containing larger amounts of organic matter and sulfur compounds. These communities contained complementary populations (chemoorganotrophic, chemolitotrophic, aerobic, facultative anaerobic and anaerobic) that can be active at different steps of iron solubilization with simultaneous organic matter mineralization. Our results indicate that the pH controlled by bacterial activity, the nature much more than the content of organic matter, and consequently the structure and activity of bacterial communities influence significantly the availability and dynamic of iron in paddy fields which affect the soil quality.     

Nucleotide-dependent self-assembly of Nucleoside Diphosphate Kinase (NDPK) in vitro

In addition to their role in nucleotide homeostasis, members of the Nucleoside Diphosphate Kinase (NDPK) family have been implicated in tumor metastasis, cell migration and vesicle trafficking. Although its role in most cases depends on nucleotide catalysis, a precise understanding of how the catalytic activity of NDPK supports its function in diverse processes is lacking. Here we report that wild type, but not catalytically inactive (H118C) NDPKB, undergoes dynamic self-assembly into ordered 20-25 nm diameter filaments in vitro. Self-assembly is nucleoside triphosphate dependent, GTP being most effective at promoting polymer formation. In addition, polymerization appears to depend on formation of the phosphoryl-Histidine intermediate of the enzyme, suggesting a previously unappreciated conformational change in NDPK during its catalytic cycle. We hypothesize that the observed nucleotide-dependent self-assembly property of NDPKB may reflect a key feature of NDPK enzymes that enables their function in diverse processes.     

Localization of PTP-1B, SHP-2, and Src exclusively in rat brain mitochondria and functional consequences

An immunodetection study of protein tyrosine phosphatase 1B (PTP-1B), SHP-2, and Src in isolated mitochondria from different rat tissues (brain, muscle, heart, liver, and kidney) revealed their exclusive localization in the brain. Given this result, we sought whether mitochondria respond to ATP and to the general tyrosine phosphatase inhibitor orthovanadate and found little or no change in the tyrosine phosphorylation profile of mitochondria from muscle, heart, liver, and kidney. In contrast, ATP induced an enhancement in the tyrosine-phosphorylated protein profile of brain mitochondria, which was further greatly enhanced with orthovanadate and which disappeared when Src was inhibited with two inhibitors: PP2 and PP1. Importantly, we found that in brain mitochondria, ATP addition induced Src autophosphorylation at Tyr-416 in its catalytic site, leading to its activation, whereas the regulatory Tyr-527 site remained unphosphorylated. Functional implications were addressed by measurements of the enzymatic activity of each of the oxidative phosphorylation complexes in brain mitochondria in the presence of ATP. We found an increase in complex I, III, and IV activity and a decrease in complex V activity, partially reversed by Src inhibition, demonstrating that the complexes are Src substrates. These results complemented and reinforced our initial study showing that respiration of brain mitochondria was partially dependent on tyrosine phosphorylation. Therefore, the present data suggest a possible control point in the regulation of respiration by tyrosine phosphorylation of the complexes mediated by Src auto-activation.     

X-inactivation reveals epigenetic anomalies in most hESC but identifies sublines that initiate as expected

The clinical and research value of human embryonic stem cells (hESC) depends upon maintaining their epigenetically naïve, fully undifferentiated state. Inactivation of one X chromosome in each cell of mammalian female embryos is a paradigm for one of the earliest steps in cell specialization through formation of facultative heterochromatin. Mouse ES cells are derived from the inner cell mass (ICM) of blastocyst stage embryos prior to X‐inactivation, and cultured murine ES cells initiate this process only upon differentiation. Less is known about human X‐inactivation during early development. To identify a human ES cell model for X‐inactivation and study differences in the epigenetic state of hESC lines, we investigated X‐inactivation in all growth competent, karyotypically normal, NIH approved, female hESC lines and several sublines. In the vast majority of undifferentiated cultures of nine lines examined, essentially all cells exhibit hallmarks of X‐inactivation. However, subcultures of any hESC line can vary in X‐inactivation status, comprising distinct sublines. Importantly, we identified rare sublines that have not yet inactivated Xi and retain competence to undergo X‐inactivation upon differentiation. Other sublines exhibit defects in counting or maintenance of XIST expression on Xi. The few hESC sublines identified that have not yet inactivated Xi may reflect the earlier epigenetic state of the human ICM and represent the most promising source of NIH hESC for study of human X‐inactivation. The many epigenetic anomalies seen indicate that maintenance of fully unspecialized cells, which have not formed Xi facultative heterochromatin, is a delicate epigenetic balance difficult to maintain in culture. J. Cell. Physiol. 216: 445–452, 2008. © 2008 Wiley‐Liss, Inc.     

Nucleoside diphosphate kinase B (NDKB) scaffolds endoplasmic reticulum membranes in vitro

The mechanisms that structure the mammalian endoplasmic reticulum (ER) network are not fully understood. Here we show that salt extraction of semi-intact normal rat kidney (NRK) fibroblasts and subsequent incubation of the extracted cells with ATP resulted in dramatic ER network retraction. Under these conditions, addition of a single protein, Nucleoside Diphosphate Kinase B (NDKB), was sufficient to reverse the retraction and to promote ER network extension. The underlying mechanism of membrane extension involved direct lipid binding, as NDKB bound phosphatidylinositol (PtdIns)(4)P, PtdIns(4,5)P₂ and phosphatidic acid (PA); binding to these anionic lipids required clusters of basic residues on the surface of the NDKB hexamer; and amino acid changes in NDKB that blocked lipid binding also blocked ER network extension. Remarkably, purified NDKB transformed a uniform population of synthetic lipid vesicles into extensive membrane networks, and this also required its phospholipid-binding activity. Altogether these results identify a protein sufficient to scaffold extended membrane networks, and suggest a possible role for NDKB-like proteins, as well as phosphoinositides and/or acidic phospholipids, in modulating ER network morphogenesis.     

Founding Swarms in a Tropical Social Wasp: Adult Mortality, Emigration Distance, and Swarm Size

When colonies of swarm-founding wasps lose their nests to predation or accident, the entire adult population escapes, emigrates as an absconding swarm, and renests elsewhere. Such an event causes a reduction in the adult population due to losses during the emigration itself and to adult attrition without replacement during the subsequent preemergence growth period in the new nest. We addressed the first of these sources of mortality for 27 absconding swarms of Polybia occidentalis in Costa Rica. Adult mortality over the day that included swarm emigration averaged 0.044 ± 0.039 (SD) of the original population and was a weak positive function of distance moved, but not of swarm size. A larger data set showed that emigration distance increased with swarm size. This is the first study to measure mortality rates during emigration in a swarm-founding social insect.     

Gastrointestinal Parasites in Free-Ranging Kenyan Baboons (Papio cynocephalus and P. anubis)

We screened fecal samples from 3 groups of wild-living baboons (Papio cynocephalus and P. anubis), involved in longitudinal behavioral studies, for evidence of gastrointestinal parasites. The two objectives of the study were: 1) to compare parasites from two of the groups with different foraging behavior from the same area and 2) to obtain fecal parasitic data on 3 groups of baboons to provide baseline reference data. We sampled individual baboons opportunistically from Lodge and Hook's groups, Amboseli National Park and from Mpala Group, Mpala Wildlife Research Centre, Kenya. Lodge Group baboons supplemented foraging on wild foods by daily foraging in human-source refuse, whereas Hook's and Mpala groups did not. We collected fecal samples from 55, 30 and 42 individuals in Hook's, Lodge and Mpala groups, respectively, and processed them via ether sedimentation. We identified strongylids, Streptopharagus sp., Physaloptera sp., Trichuris sp., Enterobius sp., and Strongyloides sp., in the feces, but no parasite directly attributable to exposure to people. Garbage- and wild-feeding Amboseli baboons differed in the prevalence of Streptopharagus sp., Physaloptera sp. and Trichuris sp.