The Effect of Heat Treatment of Forages on Degradation Kinetics and Escape Protein Concentration

An in situ study was conducted to evaluate the effects of heat treatments on the degradation kinetics and escape protein concentrations of forages (alfalfa and berseem clover). Alfalfa collected at 4 and 7 weeks post-harvest and berseem clover collected at 5 and 7 weeks postharvest were freeze-dried and then heated to 100, 125, and 150o C for 2 hours. Heat treatment effects were determined by placing two bags of sample (for each treatment, maturity, and forage species for a given incubation times) into the rumen of one fistulated steer fed alfalfa hay. Bags were incubated for periods of 0 to 48 hours. Increasing levels of heat treatments of forages increased concentrations of neutral detergent fiber (NDF), acid detergent fiber (ADF), and acid detergent insoluble nitrogen (ADIN) and non-degradable protein (NDP), potentially degradable protein proportion (PDP), and protein escaping rumen degradation (PEP) while decreasing water soluble protein (WSP) and the rates of crude protein (CP), except immature berseem clover and cell wall (CW) degradation. PEP was greater and rate of CP degradation was lower at 100 and 150o C compared to 125o C in immature berseem clover.

The Effect of Maturity and Frost Killing of Forages on Degradation Kinetics and Escape Protein Concentration

Two consecutive in situ studies were conducted to determine the effects of maturity and frost killing of forages (alfalfa and berseem clover) on degradation kinetics and escape protein concentrations. Four maturities (3, 5, 7, and 9 weeks after second harvest) of forages collected from three locations were used to determine the effects of maturity. Four weeks after a killing frost (-2o C), berseem clover was harvested from the same locations previously sampled. To evaluate maturity, 336 DacronÒ bags containing all maturities of either alfalfa or berseem clover were placed into the rumen of two fistulated steers fed alfalfa-grass hay. Frost killing effects of berseem clover were compared with maturecut berseem clover by placing DacronÒ bags into the rumen of one fistulated steer fed alfalfa hay. Bags were incubated for periods of 0 to 48 hours. With increasing maturity, the proportion of non-degradable protein (NDP) and the rate of crude protein (CP) degradation increased in both forages. While the rate of neutral detergent fiber (NDF) degradation and potentially degradable protein proportion (PDP) increased with increasing maturity in alfalfa, the rate of NDF degradation and PDP proportion decreased and proportion of water soluble protein (WSP) increased in berseem clover. The proportion of protein escaping rumen degradation (PEP) was greater in berseem clover than alfalfa, but was not affected by maturity. Frost killing of mature berseem clover decreased WSP proportion and increased PDP proportion compared to mature berseem clover harvested live. Even though ADIN concentration was higher for frost-killed berseem clover, PEP and total escape protein concentration (CEP) was also higher for frostkilled berseem clover than mature berseem clover harvested live, due to decreases in the rate of ruminal N degradation with frost-killing.

Mechanism of malarial haem detoxification inhibition by chloroquine

The haem detoxification pathway of the malaria parasite Plasmodium falciparum is a potential biochemical target for drug development. Free haem, released after haemoglobin degradation, is polymerized by the parasite to form haemozoin pigment. Plasmodium falciparum histidine-rich protein-2 (Pfhrp-2) has been implicated as the catalytic scaffold for detoxification of haem in the malaria parasite. Previously we have shown that a hexapeptide repeat sequence (Ala-His-His-Ala-Ala-Asp), which appears 33 times in Pfhrp-2, may be the major haem binding site in this protein. The haem binding studies carried out by ourselves indicate that up to 18 equivalents of haem could be bound by this protein with an observed K(d) of 0.94 microM. Absorbance spectroscopy provides evidence that chloroquine is capable of extracting haem bound to Pfhrp-2. This was supported by the K(d) value, of 37 nM, observed for the haem-chloroquine complex. The native PAGE studies reveal that the formation of the haem-Pfhrp-2 complex is disrupted by chloroquine. These results indicate that chloroquine may be acting by inhibiting haem detoxification/binding to Pfhrp-2. Moreover, the higher affinity of chloroquine for haem than Pfhrp-2 suggests a possible mechanism of action for chloroquine; it may remove the haem bound to Pfhrp-2 and form a complex that is toxic to the parasite.

Tools for better SLM knowledge management and informed decision-making in addressing land degradation at different scales: the WOCAT–LADA–DESIRE methodology

Desertification research conventionally focuses on the problem – that is, degradation – while neglecting the appraisal of successful conservation practices. Based on the premise that Sustainable Land Management (SLM) experiences are not sufficiently or comprehensively documented, evaluated, and shared, the World Overview of Conservation Approaches and Technologies (WOCAT) initiative (www.wocat.net), in collaboration with FAO’s Land Degradation Assessment in Drylands (LADA) project (www.fao.org/nr/lada/) and the EU’s DESIRE project (http://www.desire-project.eu/), has developed standardised tools and methods for compiling and evaluating the biophysical and socio-economic knowledge available about SLM. The tools allow SLM specialists to share their knowledge and assess the impact of SLM at the local, national, and global levels. As a whole, the WOCAT–LADA–DESIRE methodology comprises tools for documenting, self-evaluating, and assessing the impact of SLM practices, as well as for knowledge sharing and decision support in the field, at the planning level, and in scaling up identified good practices. SLM depends on flexibility and responsiveness to changing complex ecological and socioeconomic causes of land degradation. The WOCAT tools are designed to reflect and capture this capacity of SLM. In order to take account of new challenges and meet emerging needs of WOCAT users, the tools are constantly further developed and adapted. Recent enhancements include tools for improved data analysis (impact and cost/benefit), cross-scale mapping, climate change adaptation and disaster risk management, and easier reporting on SLM best practices to UNCCD and other national and international partners. Moreover, WOCAT has begun to give land users a voice by backing conventional documentation with video clips straight from the field. To promote the scaling up of SLM, WOCAT works with key institutions and partners at the local and national level, for example advisory services and implementation projects. Keywords: Sustainable Land Management (SLM), knowledge management, decision-making, WOCAT–LADA–DESIRE methodology.

THE UBIQUITIN LIGASE UBE4B IS REQUIRED FOR EFFICIENT EPIDERMAL GROWTH FACTOR RECEPTOR DEGRADATION

The length of time that integral membrane proteins reside on the plasma membrane is regulated by endocytosis, a process that can inactivate these proteins by removing them from the membrane and may ultimately result in their degradation. Proteins are internalized and pass through multiple distinct intracellular compartments where targeting decisions determine their fate. Membrane proteins initially enter early endosomes, and subsequently late endosomes/multivesicular bodies (MVBs), before being degraded in the lysosome. The MVB is a subset of late endosomes characterized by the appearance of small vesicles in its luminal compartment. These vesicles contain cargo proteins sorted from the limiting membrane of the MVB. Proteins not sorted into luminal vesicles remain on the MVB membrane, from where they may be recycled back to the plasma membrane. In the case of receptor tyrosine kinases (RTKs), such as epidermal growth factor (EGF) receptor, this important sorting step determines whether a protein returns to the surface to participate in signaling, or whether its signaling properties are inactivated through its degradation in the lysosome. Hrs is a protein that resides on endosomes and is known to recruit sorting complexes that are vital to this sorting step. These sorting complexes are believed to recognize ubiquitin as sorting signals. However, the link between MVB sorting machinery and the ubiquitination machinery is not known. Recently, Hrs was shown to recruit and bind an E3 ubiquitin ligase, UBE4B, to endosomes. In an assay that is able to measure cargo movement, the disruption of the Hrs-UBE4B interaction showed impaired sorting of EGF receptor into MVBs. My hypothesis is that UBE4B may be the connection between MVB sorting and ubiquitination. This study addresses the role of UBE4B in the trafficking and ubiquitination of EGF receptor. I created stable cell lines that either overexpresses UBE4B or expresses a UBE4B with no ligase activity. Levels of EGF receptor were analyzed after certain periods of ligand-induced receptor internalization. I observed that higher expression levels of UBE4B correspond to increased degradation of EGF receptor. In an in vitro ubiquitination assay, I also determined that UBE4B mediates the ubiquitination of EGF receptor. These data suggest that UBE4B is required for EGFR degradation specifically because it ubiquitinates the receptor allowing it to be sorted into the internal vesicles of MVBs and subsequently degraded in lysosomes.

Evolutionarily conserved role of calcineurin in phosphodegron-dependent degradation of phosphodiesterase 4D.

Calcineurin is a widely expressed and highly conserved Ser/Thr phosphatase. Calcineurin is inhibited by the immunosuppressant drug cyclosporine A (CsA) or tacrolimus (FK506). The critical role of CsA/FK506 as an immunosuppressant following transplantation surgery provides a strong incentive to understand the phosphatase calcineurin. Here we uncover a novel regulatory pathway for cyclic AMP (cAMP) signaling by the phosphatase calcineurin which is also evolutionarily conserved in Caenorhabditis elegans. We found that calcineurin binds directly to and inhibits the proteosomal degradation of cAMP-hydrolyzing phosphodiesterase 4D (PDE4D). We show that ubiquitin conjugation and proteosomal degradation of PDE4D are controlled by a cullin 1-containing E(3) ubiquitin ligase complex upon dual phosphorylation by casein kinase 1 (CK1) and glycogen synthase kinase 3beta (GSK3beta) in a phosphodegron motif. Our findings identify a novel signaling process governing G-protein-coupled cAMP signal transduction-opposing actions of the phosphatase calcineurin and the CK1/GSK3beta protein kinases on the phosphodegron-dependent degradation of PDE4D. This novel signaling system also provides unique functional insights into the complications elicited by CsA in transplant patients.

Mutations affecting beta-tubulin folding and degradation.

Revertants of a colcemid-resistant Chinese hamster ovary cell line with an altered (D45Y) beta-tubulin have allowed the identification of four cis-acting mutations (L187R, Y398C, a 12-amino acid in-frame deletion, and a C-terminal truncation) that act by destabilizing the mutant tubulin and preventing it from incorporating into microtubules. These unstable beta-tubulins fail to form heterodimers and are predominantly found in association with the chaperonin CCT, suggesting that they cannot undergo productive folding. In agreement with these in vivo observations, we show that the defective beta-tubulins do not stably interact with cofactors involved in the tubulin folding pathway and, hence, fail to exchange with beta-tubulin in purified alphabeta heterodimers. Treatment of cells with MG132 causes an accumulation of the aberrant tubulins, indicating that improperly folded beta-tubulin is degraded by the proteasome. Rapid degradation of the mutant tubulin does not elicit compensatory changes in wild-type tubulin synthesis or assembly. Instead, loss of beta-tubulin from the mutant allele causes a 30-40% decrease in cellular tubulin content with no obvious effect on cell growth or survival.

Microbial formation and degradation of oxygen-containing polycyclic aromatic hydrocarbons (OPAHs) in soil during short-term incubation

We tested whether OPAHs were formed during 19-wk incubation of a fertile soil at optimum moisture in the dark. The soil had initial mean (±s.e., n = 3) concentrations of 22 ± 1.7 (Σ28PAHs) and 4.2 ± 0.34 μg g−1 (Σ14OPAHs). After 19 wk, individual PAH and OPAH concentrations had decreased by up to 14 and 37%, respectively. Decreases in % of initial concentrations were positively correlated with their KOW values for PAHs (r = 0.48, p = 0.022) and 9 OPAHs (r = 0.78, p = 0.013) but negatively, albeit not significantly, for 5 OPAHs (r = −0.75, p = 0.145) suggesting net formation of some OPAHs. The latter was supported by significantly increasing 1-indanone/fluorene ratios while the other OPAH to parent-PAH ratios remained constant or tended to increase. We conclude that OPAHs are formed in soils during microbial turnover of PAHs in a short time.

SMG6 mediated degradation of nonsense mRNA requires phosphorylation-independent interaction with the helicase domain of UPF1

Eukaryotic mRNAs with premature translation-termination codons (PTCs) are recognized and eliminated by nonsense-mediated mRNA decay (NMD). NMD targeted mRNAs can be degraded by different routes that all involve phosphorylated UPF1 (P-UPF1) as a starting point. The endonuclease SMG6, which cleaves mRNA near the PTC, is one of three known NMD factors thought to be recruited to nonsense mRNAs by interaction with P-UPF1, leading to eventual mRNA degradation. By MS2-mediated tethering of SMG6 and mutants thereof to a reporter RNA combined with knockdowns of various NMD factors, we demonstrate that besides its endonucleolytic activity, SMG6 also requires UPF1 and SMG1 for inducing RNA decay. Our experiments revealed a phosphorylation-independent interaction between SMG6 and UPF1 that is important for SMG6-mediated mRNA decay and using yeast two hybrid assays, we mapped this interaction to the unique stalk region of the UPF1 helicase domain. This region of UPF1 is essential for SMG6-mediated reporter RNA decay and also for NMD. Our results postulate that besides recruiting SMG6 to its RNA substrates, UPF1 is also required to activate its endonuclease activity.

SMG6 mediated degradation of nonsense mRNA requires phosphorylation-independent interaction with the helicase domain of UPF1

Eukaryotic mRNAs with premature translation-termination codons (PTCs) are recognized and eliminated by nonsense-mediated mRNA decay (NMD). NMD targeted mRNAs can be degraded by different routes that all involve phosphorylated UPF1 (P-UPF1) as a starting point. The endonuclease SMG6, which cleaves mRNA near the PTC, is one of three known NMD factors thought to be recruited to nonsense mRNAs by interaction with P-UPF1, leading to eventual mRNA degradation. By MS2-mediated tethering of SMG6 and mutants thereof to a reporter RNA combined with knockdowns of various NMD factors, we demonstrate that besides its endonucleolytic activity, SMG6 also requires UPF1 and SMG1 for inducing RNA decay. Our experiments revealed a phosphorylation-independent interaction between SMG6 and UPF1 that is important for SMG6-mediated mRNA decay and using yeast two hybrid assays, we mapped this interaction to the unique stalk region of the UPF1 helicase domain. This region of UPF1 is essential for SMG6-mediated reporter RNA decay and also for NMD. Our results postulate that besides recruiting SMG6 to its RNA substrates, UPF1 is also required to activate its endonuclease activity.

Size-dependent accumulation of particles in lysosomes modulates dendritic cell function through impaired antigen degradation.

INTRODUCTION Nanosized particles may enable therapeutic modulation of immune responses by targeting dendritic cell (DC) networks in accessible organs such as the lung. To date, however, the effects of nanoparticles on DC function and downstream immune responses remain poorly understood. METHODS Bone marrow-derived DCs (BMDCs) were exposed in vitro to 20 or 1,000 nm polystyrene (PS) particles. Particle uptake kinetics, cell surface marker expression, soluble protein antigen uptake and degradation, as well as in vitro CD4(+) T-cell proliferation and cytokine production were analyzed by flow cytometry. In addition, co-localization of particles within the lysosomal compartment, lysosomal permeability, and endoplasmic reticulum stress were analyzed. RESULTS The frequency of PS particle-positive CD11c(+)/CD11b(+) BMDCs reached an early plateau after 20 minutes and was significantly higher for 20 nm than for 1,000 nm PS particles at all time-points analyzed. PS particles did not alter cell viability or modify expression of the surface markers CD11b, CD11c, MHC class II, CD40, and CD86. Although particle exposure did not modulate antigen uptake, 20 nm PS particles decreased the capacity of BMDCs to degrade soluble antigen, without affecting their ability to induce antigen-specific CD4(+) T-cell proliferation. Co-localization studies between PS particles and lysosomes using laser scanning confocal microscopy detected a significantly higher frequency of co-localized 20 nm particles as compared with their 1,000 nm counterparts. Neither size of PS particle caused lysosomal leakage, expression of endoplasmic reticulum stress gene markers, or changes in cytokines profiles. CONCLUSION These data indicate that although supposedly inert PS nanoparticles did not induce DC activation or alteration in CD4(+) T-cell stimulating capacity, 20 nm (but not 1,000 nm) PS particles may reduce antigen degradation through interference in the lysosomal compartment. These findings emphasize the importance of performing in-depth analysis of DC function when developing novel approaches for immune modulation with nanoparticles.

Impaired DNase1-mediated degradation of neutrophil extracellular traps is associated with acute thrombotic microangiopathies.

BACKGROUND Acute thrombotic microangiopathies (TMAs) are characterized by excessive microvascular thrombosis and are associated with markers of neutrophil extracellular traps (NETs) in plasma. NETs are composed of DNA fibers and promote thrombus formation through the activation of platelets and clotting factors. OBJECTIVE The efficient removal of NETs may be required to prevent excessive thrombosis such as in TMAs. To test this hypothesis, we investigated whether TMAs are associated with a defect in the degradation of NETs. APPROACH AND RESULTS We show that NETs generated in vitro were efficiently degraded by plasma from healthy donors. However, NETs remained stable after exposure to plasma from TMA patients. The inability to degrade NETs was linked to a reduced DNase activity in TMA plasma. Plasma DNase1 was required for efficient NET-degradation and TMA plasma showed decreased levels of this enzyme. Supplementation of TMA plasma with recombinant human DNase1 restored NET-degradation activity. CONCLUSIONS Our data indicates that DNase1-mediated degradation of NETs is impaired in patients with TMAs. The role of plasma DNases in thrombosis is, as of yet, poorly understood. Reduced plasma DNase1 activity may cause the persistence of pro-thrombotic NETs and thus promote microvascular thrombosis in TMA patients. This article is protected by copyright. All rights reserved.