Using dynamic relative climate impact curves to quantify the climate impact of bioenergy production systems over time

The climate impact of bioenergy is commonly quantified in terms of CO₂ equivalents, using a fixed 100‐year global warming potential as an equivalency metric. This method has been criticized for the inability to appropriately address emissions timing and the focus on a single impact metric, which may lead to inaccurate or incomplete quantification of the climate impact of bioenergy production. In this study, we introduce Dynamic Relative Climate Impact (DRCI) curves, a novel approach to visualize and quantify the climate impact of bioenergy systems over time. The DRCI approach offers the flexibility to analyze system performance for different value judgments regarding the impact category (e.g., emissions, radiative forcing, and temperature change), equivalency metric, and analytical time horizon. The DRCI curves constructed for fourteen bioenergy systems illustrate how value judgments affect the merit order of bioenergy systems, because they alter the importance of one‐time (associated with land use change emissions) versus sustained (associated with carbon debt or foregone sequestration) emission fluxes and short‐ versus long‐lived climate forcers. Best practices for bioenergy production (irrespective of value judgments) include high feedstock yields, high conversion efficiencies, and the application of carbon capture and storage. Furthermore, this study provides examples of production contexts in which the risk of land use change emissions, carbon debt, or foregone sequestration can be mitigated. For example, the risk of indirect land use change emissions can be mitigated by accompanying bioenergy production with increasing agricultural yields. Moreover, production contexts in which the counterfactual scenario yields immediate or additional climate impacts can provide significant climate benefits. This paper is accompanied by an Excel‐based calculation tool to reproduce the calculation steps outlined in this paper and construct DRCI curves for bioenergy systems of choice.     

Persistent replication of hepatitis C virus replicons expressing the beta-lactamase reporter in subpopulations of highly permissive Huh7 cells

Progress toward development of better therapies for the treatment of hepatitis C virus (HCV) infection has been hampered by poor understanding of HCV biology and the lack of biological assays suitable for drug screening. Here we describe a powerful HCV replication system that employs HCV replicons expressing the beta-lactamase reporter (bla replicons) and subpopulations of Huh7 cells that are more permissive (or "enhanced") to HCV replication than na?ve Huh7 cells. Enhanced cells represent a small fraction of permissive cells present among na?ve Huh7 cells that is enriched during selection with replicons expressing the neomycin phosphotransferase gene (neo replicons). The level of permissiveness of cell lines harboring neo replicons can vary greatly, and the enhanced phenotype is usually revealed upon removal of the neo replicon with inhibitors of HCV replication. Replicon removal is responsible for increased permissiveness, since this effect could be reproduced either with alpha interferon or with an HCV NS5B inhibitor. Moreover, adaptive mutations present in the replicon genome used during selection do not influence the permissiveness of the resulting enhanced-cell population, suggesting that the mechanisms governing the permissiveness of enhanced cells are independent from viral adaptation. Because the beta-lactamase reporter allows simultaneous quantitation of replicon-harboring cells and reporter activity, it was possible to investigate the relationship between genome replication activity and the frequency with which transfected genomes can establish persistent replication. Our study demonstrates that differences in the replication potential of the viral genome are manifested primarily in the frequency with which persistent replication is established but modestly affect the number of replicons observed per replicon-harboring cell. Replicon copy number was found to vary over a narrow range that may be defined by a minimal number required for persistent maintenance and a maximum that is limited by the availability of essential host factors.     

Identification of a key determinant of hepatitis C virus cell culture adaptation in domain II of NS3 helicase

Efficient replication of hepatitis C virus (HCV) replicons in cell culture is associated with specific sequences not generally observed in vivo. These cell culture adaptive mutations dramatically increase the frequency with which replication is established in vitro. However, replicons derived from HCV isolates that have been shown to replicate in chimpanzees do not replicate in cell culture even when these adaptive mutations are introduced. To better understand this apparent paradox, we performed a gain-of-function screen to identify sequences that could confer cell culture replication competence to replicons derived from chimpanzee infectious HCV isolates. We found that residue 470 in domain II of the NS3 helicase is a critical determinant in cell culture adaptation. Substitutions in residue 470 when combined with the NS5A-S232I adaptive mutation are both necessary and sufficient to confer cell culture replication to otherwise inactive replicons, including those derived from genotype 1b HCV-BK and genotype 1a HCV-H77 isolates. The specific substitution at residue 470 required for replication is context-dependent, with R470M and P470L being optimal for the activity of HCV-BK and HCV-H77 replicons, respectively. Together these data indicate that mutations in the NS3 helicase domain II act in concert with previously identified adaptive mutations and predict that introduction of compatible residues at these positions can confer cell culture replication activity to diverse HCV isolates.     

Anesthesia of boma-captured Lichtenstein's hartebeest (Sigmoceros lichtensteinii) with a combination of thiafentanil,medetomidine, and ketamine

A dose range was determined for anesthesia of recently boma-captured Lichtenstein's hartebeest (Sigmoceros lichtensteinii) (n = 13) with the synthetic opiate thiafentanil (THIA) (formerly called A3080) combined with medetomidine (MED) and ketamine (KET) in the Kasungu National Park, Malawi on 4 to 5 September 1999. The dose range of 11-29 micrograms/kg THIA (mean +/- SD = 21 +/- 4 micrograms/kg) combined with 5-10 mg/kg MED (8 +/- 1 micrograms/kg) plus 0.7-1.4 mg/kg KET (1.1 +/- 0.2 mg/kg) was found to be safe and effective for the field conditions associated with this study. The anesthesia produced by this drug combination was very predictable and characterized by a short induction time (3:34 +/- 1:20 min:sec), good muscle relaxation, and acceptable physiologic parameters for anesthesia periods ranging from 22:30-35:00 min:sec (31:14 +/- 2:50). Within the range of doses used in this study, times to onset of initial effects and recumbency were not dependent on THAI, MED, or KET doses. Anesthesia was rapidly and completely reversed by intravenous injections of naltrexone at 30 times the THAI dosage (0.69 +/- 0.19 mg/kg) and atipamezole at about four times the MED dosage (38 +/- 14 micrograms/kg). There was no residual effect from ketamine noted following reversal of THIA and MED and no mortality or morbidity was associated with this anesthetic regimen.     

Exercise and CaMK activation both increase the binding of MEF2A to the Glut4 promoter in skeletal muscle in vivo

In vitro binding assays have indicated that the exercise-induced increase in muscle GLUT4 is preceded by increased binding of myocyte enhancer factor 2A (MEF2A) to its cis-element on the Glut4 promoter. Because in vivo binding conditions are often not adequately recreated in vitro, we measured the amount of MEF2A that was bound to the Glut4 promoter in rat triceps after an acute swimming exercise in vivo, using chromatin immunoprecipitation (ChIP) assays. Bound MEF2A was undetectable in nonexercised controls or at 24 h postexercise but was significantly elevated approximately 6 h postexercise. Interestingly, the increase in bound MEF2A was preceded by an increase in autonomous activity of calcium/calmodulin-dependent protein kinase (CaMK) II in the same muscle. To determine if CaMK signaling mediates MEF2A/DNA associations in vivo, we performed ChIP assays on C(2)C(12) myotubes expressing constitutively active (CA) or dominant negative (DN) CaMK IV proteins. We found that approximately 75% more MEF2A was bound to the Glut4 promoter in CA compared with DN CaMK IV-expressing cells. GLUT4 protein increased approximately 70% 24 h after exercise but was unchanged by overexpression of CA CaMK IV in myotubes. These results confirm that exercise increases the binding of MEF2A to the Glut4 promoter in vivo and provides evidence that CaMK signaling is involved in this interaction.     

Serum concentrations of amino acids,fatty acids,lipoproteins, vitamins A and E,and minerals in apparently healthy,free‐ranging southern giraffe (Giraffa camelopardalis giraffe)

This pilot project began establishing a nutritional profile for free‐ranging giraffe. The results will be used as a tool to begin assessing the nutritional status of captive giraffe. In October 2004 serum samples were collected opportunistically from seven adult and 17 sub‐adult giraffe being anesthetized for different studies. Seventeen animals were from Double Drift Game Reserve and seven animals were from Kariega Private Game Reserve. The serum samples were analyzed for circulating concentrations of amino acids, fatty acids, lipoproteins, vitamins, and minerals. Information from 15 serum samples collected from anesthetized giraffe in Kruger National Park during April and August 2003 was included in the calcium and phosphorus concentration data. No significant differences were identified between genders. Significant differences between locations were identified for concentrations of certain amino acids, fatty acids, and lipoproteins. Differences between locations are likely due to different nutrient concentrations of foods and possibly the result of different animal densities forcing different food choices among locations. This pilot project may expand to include changes in circulating nutrient concentrations for free‐ranging giraffe as is influenced by other locations, seasonal food availability, and different giraffe subspecies. Zoo Biol 0:1–13, 2007. © 2006 Wiley‐Liss, Inc.     

The static allometry of sexual and nonsexual traits in vervet monkeys

Sexual traits vary tremendously in static allometry. This variation may be explained in part by body size‐related differences in the strength of selection. We tested this hypothesis in two populations of vervet monkeys, using estimates of the level of condition dependence for different morphological traits as a proxy for body size‐related variation in the strength of selection. In support of the hypothesis, we found that the steepness of allometric slopes increased with the level of condition dependence. One trait of particular interest, the penis, had shallow allometric slopes and low levels of condition dependence, in agreement with one of the most consistent patterns yet detected in the study of allometry, namely that of genitalia exhibiting shallow allometries. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 527–537.     

Two new records of Oribatula (Zygoribatula) species (Acari: Oribatida) from Turkey, with redescriptions

The oribatid mite fauna of Turkey is still relatively poorly known. The present paper adds two species of oribatid mites to the known Turkish fauna viz., Oribatula (Zygoribatula) debilitranslamellata (Kulijev, 1962) and O. (Z.) exilis (Nicolet, 1855). Both species are characterised by large, prominent lamellar cusps, with the lamellar setae inserted apically on the cusps, and by the presence of distinct translamellae. They can be distinguished, however, by the smaller lamellae, absence of cuspidal teeth, narrowly fusiform sensilli and, 13 pairs of thin, smooth, apically almost flagellate notogastral setae, in O. (Z.) debilitranslamellata, and by the wider lamellae, presence of cuspidal teeth, widely fusiform sensilli, and 14 pairs of thin, smooth notogastral setae, with seta c (1) slightly thicker and minutely barbed in O. (Z.) exilis. The following species have been previously reported from Turkey: O. (Z.) cognata (Oudemans, 1902), O. (Z.) undulata (Berlese, 1917), O. (Z.) terricola Van der Hammen, 1952, and O. (Z.) lanceolata Grobler, Bayram & Cobanoglu, 2004.     

Assessing introgressive hybridization between blue wildebeest (<Emphasis Type="Italic">Connochaetes taurinus</Emphasis>) and black wildebeest (<Emphasis Type="Italic">Connochaetes gnou</Emphasis>) from South Africa

Introgressive hybridization poses a threat to the genetic integrity of black wildebeest (Connochaetes gnou) and blue wildebeest (Connochaetes taurinus) populations in South Africa. Black wildebeest is endemic to South Africa and was driven to near extinction in the early 1900s due to habitat destruction, hunting pressure and disease outbreaks. Blue wildebeest on the other hand are widely distributed in southern and east Africa. In South Africa the natural distribution ranges of both species overlap, however, extensive translocation of black wildebeest outside of its normal distribution range in South Africa have led to potential hybridization between the two species. The molecular identification of pure and admixed populations is necessary to design viable and sustainable conservation strategies, since phenotypic evidence of hybridization is inconclusive after successive generations of backcrossing. The aim of this study was to assess levels of hybridization in wildebeest using both species-specific and cross-species microsatellite markers. Black wildebeest (157) and blue wildebeest (122) from provincial and national parks and private localities were included as reference material, with 180 putative hybrid animals also screened. A molecular marker panel consisting of 13 cross-species and 11 species-specific microsatellite markers was developed. We used a Bayesian clustering model to confirm the uniqueness of blue- and black wildebeest reference groups, assign individuals to each of the two clusters, and determine levels of admixture. Results indicated a clear partition between black wildebeest and blue wildebeest (the average proportions of membership to black wildebeest and blue wildebeest clusters were QI?=?0.994 and QI?=?0.955 respectively). From the putative hybrid samples, only five hybrid individuals were confirmed. However, high levels of linkage disequilibrium were observed in the putative hybrid populations which may indicate historical hybridization. Measures of genetic diversity in the black wildebeest populations were found to be lower than that of the blue wildebeest. The observed lower level of genetic diversity was expected due to the demographic history of the specie. This study will make a significant contribution to inform a national conservation strategy to conserve the genetic integrity of both species.