Major limitations to achieving “4 per 1000” increases in soil organic carbon stock in temperate regions: Evidence from long‐term experiments at Rothamsted Research,United Kingdom

We evaluated the “4 per 1000” initiative for increasing soil organic carbon (SOC) by analysing rates of SOC increase in treatments in 16 long‐term experiments in southeast United Kingdom. The initiative sets a goal for SOC stock to increase by 4‰ per year in the 0–40 cm soil depth, continued over 20 years. Our experiments, on three soil types, provided 114 treatment comparisons over 7–157 years. Treatments included organic additions (incorporated by inversion ploughing), N fertilizers, introducing pasture leys into continuous arable systems, and converting arable land to woodland. In 65% of cases, SOC increases occurred at >7‰ per year in the 0–23 cm depth, approximately equivalent to 4‰ per year in the 0–40 cm depth. In the two longest running experiments (>150 years), annual farmyard manure (FYM) applications at 35 t fresh material per hectare (equivalent to approx. 3.2 t organic C/ha/year) gave SOC increases of 18‰ and 43‰ per year in the 23 cm depth during the first 20 years. Increases exceeding 7‰ per year continued for 40–60 years. In other experiments, with FYM applied at lower rates or not every year, there were increases of 3‰–8‰ per year over several decades. Other treatments gave increases between zero and 19‰ per year over various periods. We conclude that there are severe limitations to achieving the “4 per 1000” goal in practical agriculture over large areas. The reasons include (1) farmers not having the necessary resources (e.g. insufficient manure); (2) some, though not all, practices favouring SOC already widely adopted; (3) practices uneconomic for farmers—potentially overcome by changes in regulations or subsidies; (4) practices undesirable for global food security. We suggest it is more realistic to promote practices for increasing SOC based on improving soil quality and functioning as small increases can have disproportionately large beneficial impacts, though not necessarily translating into increased crop yield.     

The function of Alr1p of <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis> in cadmium detoxification: Insights from phylogenetic studies and particle-induced X-ray emission

Two genes in Saccharomyces cerevisiae, ALR1 and ALR2, encode transmembrane proteins involved in Mg²⁺ uptake. The present study investigates the phylogenetic relationship of Alr1p/Alr2p with bacterial CorA proteins and some proteins related to Mg²⁺influx/efflux transport in mitochondrial and bacterial zinc transporters; including hydrophobic cluster analysis (HCA). The phylogenetic results indicate that the Alrp sequences of S. cerevisiae share a common carboxy-terminus with proteins related to zinc efflux transport. We also analyse the intracellular metal content by particle-induced X-ray emission (PIXE) after cell exposure to cadmium. The PIXE analysis of cadmium-exposed ALR mutants and wild-type yeast cells suggests that Alrp has a central role in cell survival in a cadmium-rich environment. Published online December 2004 Ana Lúcia Kern, Diego Bonatto: Both authors contributed equally to this work.     

Performance comparison of protein A affinity resins for the purification of monoclonal antibodies

During the selection of protein A affinity resin for the purification of monoclonal antibodies, dynamic binding capacity (Q(dyn10%)), volumetric production rate (Pr(vol)) and 'process robustness' are essential parameters to be evaluated. In this article, empirical mathematical models describe these parameters as a function of antibody concentration in load (C0), load flow rate (u(load)) and bed height (L). These models allow us to select optimal process conditions for each of the evaluated protein A affinity resins. C0, u(load) and L largely affect dynamic binding capacity (Q(dyn10%)) and volumetric production rate (Pr(vol)). Maximum Q(dyn10%) is generally obtained at high C0 and at low u(load). Maximum Pr(vol) is obtained at high C0 and at lowest L, run at high u(load). All evaluated resins have a relatively high robustness against variations in C0. |DeltaQ(dyn10%)/deltaC0| ranges from 0.0 to 7.8. It is clear that Q(dyn10%), Pr(vol) and 'process robustness' cannot be maximized all at the same time. Furthermore, some other aspects like IgG recovery, protein A leaching, easiness to pack, easiness to clean, number of re-uses and cost of production might be important to be taken into the equation. Certain evaluation parameters may be more important than others, depending on the specific situation. Therefore, a case-by-case evaluation is recommended.     

The ubiquitin-selective chaperone CDC-48/p97 links myosin assembly to human myopathy

Protein degradation in eukaryotes often requires the ubiquitin-selective chaperone p97 for substrate recruitment and ubiquitin-chain assembly. However, the physiological relevance of p97, and its role in developmental processes, remain unclear. Here, we discover an unanticipated function for CDC-48/p97 in myosin assembly and myofibril organization, both in Caenorhabditis elegans and humans. The developmentally regulated assembly of a CDC-48-UFD-2-CHN-1 complex links turnover of the myosin-directed chaperone UNC-45 to functional muscle formation. Our data suggest a similarly conserved pathway regulating myosin assembly in humans. Remarkably, mutations in human p97, known to cause hereditary inclusion-body myopathy, abrogate UNC-45 degradation and result in severely disorganized myofibrils, detrimental towards sarcomeric function. These results identify a key role for CDC-48/p97 in the process of myofibre differentiation and maintenance, which is abolished during pathological conditions leading to protein aggregation and inclusion-body formation in human skeletal muscle.     

Ablation of ceramide synthase 2 strongly affects biophysical properties of membranes

Little is known about the effects of altering sphingolipid (SL) acyl chain structure and composition on the biophysical properties of biological membranes. We explored the biophysical consequences of depleting very long acyl chain (VLC) SLs in membranes prepared from lipid fractions isolated from a ceramide synthase 2 (CerS2)-null mouse, which is unable to synthesize C22-C24 ceramides. We demonstrate that ablation of CerS2 has different effects on liver and brain, causing a significant alteration in the fluidity of the membrane and affecting the type and/or extent of the phases present in the membrane. These changes are a consequence of the depletion of VLC and unsaturated SLs, which occurs to a different extent in liver and brain. In addition, ablation of CerS2 causes changes in intrinsic membrane curvature, leading to strong morphological alterations that promote vesicle adhesion, membrane fusion, and tubule formation. Together, these results show that depletion of VLC-SLs strongly affects membrane biophysical properties, which may compromise cellular processes that critically depend on membrane structure, such as trafficking and sorting.     

A Galactoglycerolipid Lipase Is Required for Triacylglycerol Accumulation and Survival Following Nitrogen Deprivation in Chlamydomonas reinhardtii

Following N deprivation, microalgae accumulate triacylglycerols (TAGs). To gain mechanistic insights into this phenomenon, we identified mutants with reduced TAG content following N deprivation in the model alga Chlamydomonas reinhardtii. In one of the mutants, the disruption of a galactoglycerolipid lipase-encoding gene, designated PLASTID GALACTOGLYCEROLIPID DEGRADATION1 (PGD1), was responsible for the primary phenotype: reduced TAG content, altered TAG composition, and reduced galactoglycerolipid turnover. The recombinant PGD1 protein, which was purified from Escherichia coli extracts, hydrolyzed monogalactosyldiacylglycerol into its lyso-lipid derivative. In vivo pulse-chase labeling identified galactoglycerolipid pools as a major source of fatty acids esterified in TAGs following N deprivation. Moreover, the fatty acid flux from plastid lipids to TAG was decreased in the pgd1 mutant. Apparently, de novo–synthesized fatty acids in Chlamydomonas reinhardtii are, at least partially, first incorporated into plastid lipids before they enter TAG synthesis. As a secondary effect, the pgd1 mutant exhibited a loss of viability following N deprivation, which could be avoided by blocking photosynthetic electron transport. Thus, the pgd1 mutant provides evidence for an important biological function of TAG synthesis following N deprivation, namely, relieving a detrimental overreduction of the photosynthetic electron transport chain.     

Cross-species vascular endothelial growth factor (VEGF)-blocking antibodies completely inhibit the growth of human tumor xenografts and measure the contribution of stromal VEGF

To fully assess the role of VEGF-A in tumor angiogenesis, antibodies that can block all sources of vascular endothelial growth factor (VEGF) are desired. Selectively targeting tumor-derived VEGF overlooks the contribution of host stromal VEGF. Other strategies, such as targeting VEGF receptors directly or using receptor decoys, result in inhibiting not only VEGF-A but also VEGF homologues (e.g. placental growth factor, VEGF-B, and VEGF-C), which may play a role in angiogenesis. Here we report the identification of novel anti-VEGF antibodies, B20 and G6, from synthetic antibody phage libraries, which block both human and murine VEGF action in vitro. Their affinity-improved variants completely inhibit three human tumor xenografts in mice of skeletal muscle, colorectal, and pancreatic origins (A673, HM-7, and HPAC). Avastin, which only inhibits the tumor-derived human VEGF, is approximately 90% effective at inhibiting HM-7 and A673 growth but is <50% effective at inhibiting HPAC growth. Indeed, HPAC tumors contain more host stroma invasion and stroma-derived VEGF than other tumors. Thus, the functional contribution of stromal VEGF varies greatly among tumors, and systemic blockade of both tumor and stroma-derived VEGF is sufficient for inhibiting the growth of tumor xenografts.     

Phospholipase A2-activating protein (PLAA) enhances cisplatin-induced apoptosis in HeLa cells

Phospholipase A₂ (PLA₂)-activating protein (PLAA) is a novel signaling molecule that regulates eicosanoid production and participates in inflammatory responses. In our current study, we revealed that PLAA production was induced by the chemotherapeutic drug cisplatin in HeLa cervical carcinoma cells. To determine the potential pro-apoptotic effects of PLAA induction by cisplatin, we utilized HeLa (Tet-off) cells overexpressing the plaa gene (plaa ^high) and compared them with control (plaa ^low) cells, which produce endogenous plaa from the chromosome. Cisplatin-stimulated plaa ^high cells contained significantly higher levels of DNA fragmentation, caspase 3, 8 and 9 activities, PLA₂ enzyme activity, and cytochrome c leakage from mitochondria than did the cisplatin-stimulated plaa ^low cells. Importantly, siRNA against PLAA (siRNA–PLAA) reduced the levels of cisplatin-induced PLAA, DNA fragmentation, and PLA₂ activation, while promoting cell viability in both plaa ^high and plaa ^low cells. Cisplatin-induced-cytochrome c leakage in plaa ^high cells was reduced by siRNA–PLAA and restored by the addition of exogenous arachidonic acid (AA), suggesting to us that PLAA induction by cisplatin promoted cytochrome c leakage/mitochondrial damage partially by accumulating AA. In addition, cisplatin-stimulated plaa ^high cells produced less cytoprotective clusterin than did the cisplatin-stimulated plaa ^low cells, and siRNA–PLAA promoted clusterin production from both plaa ^high and plaa ^low cells. We showed that clusterin reduced DNA fragmentation in cisplatin-stimulated plaa ^high and plaa ^low cells, which is consistent with the notion that clusterin promotes cancer chemoresistance. Furthermore, cisplatin-stimulated plaa ^high cells produced more IL-32 (a pro-apoptotic protein) than did cisplatin-stimulated plaa ^low cells, and siRNA–PLAA reduced IL-32 production from both plaa ^high and plaa ^low cells. Finally, our proteomic analysis revealed that cisplatin-stimulated plaa ^high cells contained higher levels of phosphorylated JNK/c-Jun and FasL than did plaa ^low cells treated the same way. In summary, our data indicated that PLAA induction enhanced cisplatin-induced-apoptosis through four pathways, namely by: 1) accumulation of AA and mitochondrial damage, 2) downregulation of the cytoprotective clusterin, 3) upregulation of the pro-apoptotic IL-32, and 4) induction of JNK/c-Jun signaling and FasL expression.