Structural, biochemical, and in vivo characterization of the first virally encoded cyclophilin from the Mimivirus

Although multiple viruses utilize host cell cyclophilins, including severe acute respiratory syndrome (SARS) and human immunodeficiency virus type-1(HIV-1), their role in infection is poorly understood. To help elucidate these roles, we have characterized the first virally encoded cyclophilin (mimicyp) derived from the largest virus discovered to date (the Mimivirus) that is also a causative agent of pneumonia in humans. Mimicyp adopts a typical cyclophilin-fold, yet it also forms trimers unlike any previously characterized homologue. Strikingly, immunofluorescence assays reveal that mimicyp localizes to the surface of the mature virion, as recently proposed for several viruses that recruit host cell cyclophilins such as SARS and HIV-1. Additionally mimicyp lacks peptidyl-prolyl isomerase activity in contrast to human cyclophilins. Thus, this study suggests that cyclophilins, whether recruited from host cells (i.e. HIV-1 and SARS) or virally encoded (i.e. Mimivirus), are localized on viral surfaces for at least a subset of viruses.     

New Middle Miocene Caviomorph Rodents from Quebrada Honda,Bolivia

The rodents of the middle Miocene fauna of Quebrada Honda Bolivia are described. The most abundant rodent is the chinchillid Prolagostomus sp. More precise identification of this species will require revision of early to middle Miocene lagostomines, taking into account variation in modern populations. The next most common rodents are the tiny octodontoid Acarechimys, sp. nov.?, and the caviid Guiomys unica. The Acarechimys species may be unique to Quebrada Honda, but verification awaits revision of this geographically and temporally widespread genus. Guiomys unica is a recently described species otherwise known only from two Patagonian localities, El Petiso and Río Chico. Two rodents are unique to Quebrada Honda. Mesoprocta hypsodus, gen. et sp. nov., is a dasyproctid distinguished by its very hypsodont, cement-covered cheek teeth. Quebradahondomys potosiensis, gen. et sp. nov., is an adelphomyine echimyid distinguished by the less oblique lophids of its trilophodont cheek teeth, among other features. The rodents of Quebrada Honda are more similar to those of Patagonia than those of northern South America, paralleling patterns seen in other mammal groups from this fauna.     

Testing the extreme value domain of attraction for distributions of beneficial fitness effects

In modeling evolutionary genetics, it is often assumed that mutational effects are assigned according to a continuous probability distribution, and multiple distributions have been used with varying degrees of justification. For mutations with beneficial effects, the distribution currently favored is the exponential distribution, in part because it can be justified in terms of extreme value theory, since beneficial mutations should have fitnesses in the extreme right tail of the fitness distribution. While the appeal to extreme value theory seems justified, the exponential distribution is but one of three possible limiting forms for tail distributions, with the other two loosely corresponding to distributions with right-truncated tails and those with heavy tails. We describe a likelihood-ratio framework for analyzing the fitness effects of beneficial mutations, focusing on testing the null hypothesis that the distribution is exponential. We also describe how to account for missing the smallest-effect mutations, which are often difficult to identify experimentally. This technique makes it possible to apply the test to gain-of-function mutations, where the ancestral genotype is unable to grow under the selective conditions. We also describe how to pool data across experiments, since we expect few possible beneficial mutations in any particular experiment.     

Ubiquitination of BST-2 protein by HIV-1 Vpu protein does not require lysine, serine, or threonine residues within the BST-2 cytoplasmic domain

The cellular protein BST-2/CD317/Tetherin has been shown to inhibit the release of HIV-1 and other enveloped viruses from infected cells. The HIV-1 accessory protein Vpu binds to both BST-2 and βTrCP, a substrate-recognition subunit for the SCF (Skip1-Cullin1-F-box protein) E3 ubiquitin ligase complex. This interaction leads to both the degradation of BST-2 and the enhancement of viral egress. Recently BST-2 was shown to be ubiquitinated in this process. Here we have confirmed the Vpu- and βTrCP-dependent multi/polyubiquitination of BST-2. Ubiquitinated BST-2 accumulated in cells treated with a lysosomal inhibitor but not a proteasomal inhibitor. Additionally, we observed that a BST-2 mutant deleted for its cytosolically exposed lysine residues is also ubiquitinated. Subsequent experiments suggested that Vpu promotes BST-2 ubiquitination upon amino acid residues bearing hydroxyl- but not thiol-bearing side chains. However, a BST-2 mutant bearing substitutions for its cytoplasmically exposed Ser, Thr, and Lys residues was still down-regulated, ubiquitinated, and degraded in a Vpu-dependent manner. Our results suggest that Vpu may target either the BST-2 cytoplasmic Tyr residues or the NH(2) terminus itself for ubiquitination.     

Life cycle assessment of cheese and whey production in the USA

Purpose

A life cycle assessment was conducted to determine a baseline for environmental impacts of cheddar and mozzarella cheese consumption. Product loss/waste, as well as consumer transport and storage, is included. The study scope was from cradle-to-grave with particular emphasis on unit operations under the control of typical cheese-processing plants.

Methods

SimaPro© 7.3 (PRé Consultants, The Netherlands, 2013) was used as the primary modeling software. The ecoinvent life cycle inventory database was used for background unit processes (Frischknecht and Rebitzer, J Cleaner Prod 13(13–14):1337–1343, 2005), modified to incorporate US electricity (EarthShift 2012). Operational data was collected from 17 cheese-manufacturing plants representing 24 % of mozzarella production and 38 % of cheddar production in the USA. Incoming raw milk, cream, or dry milk solids were allocated to coproducts by mass of milk solids. Plant-level engineering assessments of allocation fractions were adopted for major inputs such as electricity, natural gas, and chemicals. Revenue-based allocation was applied for the remaining in-plant processes.

Results and discussion

Greenhouse gas (GHG) emissions are of significant interest. For cheddar, as sold at retail (63.2 % milk solids), the carbon footprint using the IPCC 2007 factors is 8.60 kg CO₂e/kg cheese consumed with a 95 % confidence interval (CI) of 5.86–12.2 kg CO₂e/kg. For mozzarella, as sold at retail (51.4 % milk solids), the carbon footprint is 7.28 kg CO₂e/kg mozzarella consumed, with a 95 % CI of 5.13–9.89 kg CO₂e/kg. Normalization of the results based on the IMPACT 2002+ life cycle impact assessment (LCIA) framework suggests that nutrient emissions from both the farm and manufacturing facility wastewater treatment represent the most significant relative impacts across multiple environmental midpoint indicators. Raw milk is the major contributor to most impact categories; thus, efforts to reduce milk/cheese loss across the supply chain are important.

Conclusions

On-farm mitigation efforts around enteric methane, manure management, phosphorus and nitrogen runoff, and pesticides used on crops and livestock can also significantly reduce impacts. Water-related impacts such as depletion and eutrophication can be considered resource management issues—specifically of water quantity and nutrients. Thus, all opportunities for water conservation should be evaluated, and cheese manufacturers, while not having direct control over crop irrigation, the largest water consumption activity, can investigate the water use efficiency of the milk they procure. The regionalized normalization, based on annual US per capita cheese consumption, showed that eutrophication represents the largest relative impact driven by phosphorus runoff from agricultural fields and emissions associated with whey-processing wastewater. Therefore, incorporating best practices around phosphorous and nitrogen management could yield improvements.     

Lung Epithelial Cells Coordinate Innate Lymphocytes and Immunity against Pulmonary Fungal Infection

1. Download high-res image (212KB)
2. Download full-size image

     

The CDK4/6 Inhibitor Abemaciclib Induces a T Cell Inflamed Tumor Microenvironment and Enhances the Efficacy of PD-L1 Checkpoint Blockade

1. Download high-res image (224KB)
2. Download full-size image

     

Influence of age and breed on the binding of oxygen to red blood cells of bovine calves

Gustin, P., B. Detry, A. Robert, M. L. Cao, F. Lessire, C. Cambier, V. Katz, M. Ansay, A. Frans, and T. Clerbaux.Influence of age and breed on the binding of oxygen to red bloodcells of bovine calves. J. Appl.Physiol. 82(3): 784-790, 1997.The influence ofsomatic growth and genetic selection on the whole blood oxygen equilibrium curve (OEC) was measured under standard conditions indouble-muscled and dairy calves during their first 3 mo of life.Crossbreed animals were also investigated. Hemoglobin,2,3-diphosphoglycerate (DPG), Cl, andP_i concentrations were alsomeasured. The percentage of fetal hemoglobin (HbF) was determined. Theinfluence of exogenous Cl, P_i, andpH on the OEC was also assessed. ThePO₂ at 50% hemoglobin saturation(P₅₀) increased during somaticgrowth, probably because of the increase in DPG recorded indouble-muscled neonates and to the progressive disappearance of HbF inboth breeds. The oxygen exchange fraction (OEF%) was used to assessthe combined influence of the OEC shift and OEC shape changes on bloodoxygen desaturation under standard conditions, when thePO₂ decreases within a physiologicalrange. The OEF% showed an increase during the first month, then astabilization. The effects of Cl, P_i, and pH in Friesian calves weresimilar as in adult cattle. Double-muscled neonates had alower P₅₀, OEF% values, and DPG concentrations and higher hemoglobin and Cl concentrations than Friesian neonates. The P_iconcentration and the percentage of HbF were similar in both breeds.The pH and the Cl concentration had significantly less effect on theOEC in double-muscled than in Friesian calves. Crossbreed animalsexhibited intermediate parameter values, between those recorded fordouble-muscled and Friesian calves. All differences between breedsprogressively disappeared during the first month. These data show thatblood function changes markedly in calves during the first month of life and that genetic selection can alter blood function.

     

Water transport and the distribution of aquaporin-1 in pulmonary air spaces

Effros, R. M., C. Darin, E. R. Jacobs, R. A. Rogers, G. Krenz, and E. E. Schneeberger. Water transport and thedistribution of aquaporin-1 in pulmonary air spaces.J. Appl. Physiol. 83(3): 1002-1016, 1997.Recent evidence suggests that water transport between the pulmonary vasculature and air spaces can be inhibited byHgCl₂, an agent that inhibitswater channels (aquaporin-1 and -5) of cell membranes. In the presentstudy of isolated rat lungs, clearances of labeled(³HOH) and unlabeled water werecompared after instillation of hypotonic or hypertonic solutions intothe air spaces or injection of a hypotonic bolus into the pulmonaryartery. The clearance of ³HOHbetween the air spaces and perfusate after intratracheal instillation and from the vasculature to the tissues after pulmonary arterial injections was invariably greater than that of unlabeled water, indicating that osmotically driven transport of water is limited bypermeability of the tissue barriers rather than the rate of perfusion.Exposure to 0.5 mM HgCl₂ in theperfusate and air-space solution reduced the product of the filtrationcoefficient and surface area(P_fS)of water from the air spaces to the perfusate by 28% afterinstillation of water into the trachea. In contrast, perfusion of 0.5 mM HgCl₂ in air-filled lungs reducedP_fSof the endothelium by 86% after injections into the pulmonary artery, suggesting that much of the action of this inhibitor is on the endothelial surfaces. Confocal laser scanning microscopy demonstrated that aquaporin-1 is on mouse pulmonary endothelium. No aquaporin-1 wasfound on alveolar type I cells with immunogold transmission electronmicroscopy, but small amounts were present on some type II cells.