Category Archives: Generic Inhibitor

Green turtles are exposed to a

Green turtles are exposed to a number of threats including ingestion of marine debris, degradation, urbanisation and pollution of nesting habitats and foraging areas, nest and hatchling depredation by wild, feral and domestic animals, boat strike, traditional hunting and egg harvest, the impacts of climate change on the marine and terrestrial environment, and entanglement in fishing nets and lines (Bjorndal, 1995; Herbst and Klein, 1995a; Lutz, 2002; Van Houtan et al., 2010). Conservation efforts which aim to abate many of these threats have assisted in the recovery of some of the major Green turtle populations (Chaloupka et al., 2008a). However, outbreaks of disease are also contributing to morbidity and mortality in this already vulnerable species (Foley et al., 2005; Chaloupka et al., 2008b; Flint et al., 2010b).
Fibropapillomatosis (FP) is a disease that has now been reported in every species of marine turtle: Green (Smith and Coates, 1938), Loggerhead (Caretta caretta) (Harshbarger, 1991), Kemp\’s Ridley (Lepidochelys kempii) (Barragan and Sarti, 1994), Hawksbill (Eretmochelys imbricata) (D\’Amato and Moraes-Neto, 2000), Olive Ridley (Lepidochelys olivacea) (Aguirre et al., 1999), Flatback (Natator depressus) (Limpus et al., 1993), and Leatherback (Dermochelys coriacea) (Huerta et al., 2002) turtles. FP is of greatest concern in Green turtles as it has only reached a panzootic status in this species (Williams et al., 1994).
FP is a neoplastic condition which may lead to the growth of lesions on the skin, oral cavity, shell, eyes and internal Tenovin-6 of the affected turtle, which in severe cases reduces the probability of survival (Herbst, 1995; Work et al., 2004; Flint et al., 2010a). The disease was first identified in a Green turtle with multiple wart-like lesions on display at the New York Aquarium, although originally from Key West, Florida (Smith and Coates, 1938). Despite being described in 1938 (Lucke, 1938; Smith and Coates, 1938), FP did not reach epizootic proportions until the 1980s (Herbst, 1994; Herbst et al., 2004) and has now been reported from every major ocean basin that Green turtles inhabit (Herbst, 1994).

Disease presentation
FP can be identified in marine turtles by the presence of single or multiple benign fibroepithelial lesions. The characteristic lesions are easily noticed and are pathognomonic for FP, often limiting or obstructing the vision, feeding and locomotive ability of the affected turtle (Herbst, 1994, 1995; Work et al., 2004; Flint et al., 2010a). Cutaneous lesions are typically present on the external soft tissue of the turtle, but may grow on the carapace, plastron (Smith and Coates, 1938; Jacobson et al., 1989; Balazs and Pooley, 1991; Brooks et al., 1994; Herbst, 1994) and cornea of affected turtles (Brooks et al., 1994; Flint et al., 2010a). The lesions can be observed on all visceral organs (Herbst, 1994; Work et al., 2004; Foley et al., 2005) and are thought to develop during later stages of the disease (Herbst et al., 1999; Wyneken et al., 2006). However, as most visceral lesions are observed during post mortem investigations, the data available on the prevalence of this type of lesion are skewed. Individual lesions can range from 0.1 to 30 cm in diameter and can be sessile or pedunculated. The appearance of these lesions can vary from smooth to verrucous and the colour is dependent on the pigment at the site of origin (Herbst, 1994) (Fig. 2).
Myxofibromas, fibrosarcomas, papillomas, fibromas and fibropapillomas have all been found to be associated with FP (Norton et al., 1990; Work et al., 2004). Three of these lesions are thought to be linked with different stages of lesion development (Herbst, 1994; Kang et al., 2008). The early development phase is associated with papilloma lesions, proliferation of epidermal cells, with little or no involvement of the dermal layer. The chronic phase of lesion development is marked by the presence of fibromas, with proliferation of the dermal layer, while the epidermal layer remains normal. Fibropapillomas represent the intermediate phase of lesion development and consist of characteristics of both the papillomas and fibromas (Herbst, 1994; Kang et al., 2008).

nociceptin receptor br Avian pathogenic APEC are responsible for

Avian pathogenic (APEC) are responsible for significant economic losses in the poultry industry (). APEC strains exhibit distinct profiles of virulence-associated nociceptin receptor (VAGs) according to their geographic location (). The aim of the present study was to determine the molecular characteristics of pathogenic and avian faecal (AFEC) isolated from Brazil and to correlate these characteristics with the pathogenicity levels of the isolates.
Avian isolates ( = 120) from four Brazilian states (Pernambuco, PE; Paraná, PR; São Paulo, SP; Rio Grande do Sul, RS) comprised 91 APEC strains from broilers and laying hens with colisepticaemia () and 29 AFEC strains from the faeces of healthy birds. DNA was extracted using a thermal lysis procedure and subjected to PCR for 38 VAGs (; see : ).
Isolates were assigned to phylogenetic groups according to (see : ). Six 1-day-old Cobb chicks were inoculated with each isolate to classify them into high, medium or low pathogenicity strains (). All experiments were approved by the Committee of Ethics on Animal Experimentation (number 2449-1; date of approval 26 March 2012) of the Institute of Biology, University of Campinas, São Paulo, Brazil.
Cluster analysis was based on the presence and absence of VAGs. A binary matrix was used to determine similarities using the Euclidean distance and complete linkage, and strains were grouped using Gene Cluster 3.0 (). Dendrograms were constructed using Java TreeView 1.1.6r2. The frequencies of VAGs were compared with Fisher\’s exact test using Prism for Windows version 6.01 (GraphPad Software). Statistical significance was declared at <0.05. The VAGs with the highest frequencies (≥50%) in both populations were , , , and . The highest frequencies of VAGs in APEC strains were , , , , , and ; no APEC contained , or . In AFEC strains, the VAGs with frequencies >50% were , and ; no AFEC was positive for , , , , or .
Pathogenicities among APEC strains were 46/91 (50.5%) high (HP), 13/91 (14.3%) medium (MP) and 32/91 (35.2%) low (LP) pathogenicity strains. Amongst AFEC strains, 7/29 (24.1%) were HP, 8/29 (27.5%) were MP and 14/29 (48.2%) were LP. shows the VAG frequencies amongst HP, MP and LP strains; 14/38 (36.8%) VAGs were positively associated with HP and MP strains. The nociceptin receptor VAGs with higher discriminatory power were those related to iron acquisition systems (6/8 VAGs). No VAG was negatively correlated with HP and MP strains.
Phylogenetic typing demonstrated that HP and MP strains were mainly classified as B1 or D, whereas LP strains were mainly classified as A or B1 (; see : ). On cluster analysis, strains were distributed into four groups (I, IIa, IIb and IIc; ). represents the cluster analysis only with VAGs showing highly significant statistical differences (<0.001); there were three large clusters (III, IV and V). Groups III and IV presented most of the HP and MP strains, whilst group V contained most of the LP strains. Most of the AFEC strains were in cluster V, with the exception of HP and MP AFEC strains, which were included in groups III and IV.
Canine monocytic ehrlichiosis (CME), caused by infection with , can have multisystemic effects (). Increased risk for myocardial injury in naturally infected dogs has been demonstrated, based on serum cardiac troponin I (cTnI) concentrations and echocardiographic, electrocardiographic (ECG), and histopathological findings (). Myocardial hemorrhage, vasculitis, myocarditis, anaemia, and a systemic inflammatory response most likely account for cardiac damage ().
Gross and histopathological evidence of myocardial hemorrhage has been documented in one study of experimentally infected dogs (), but the evaluation of cardiac function in experimental CME remains uninvestigated. Therefore, we evaluated serum cTnI concentrations and echocardiographic and ECG parameters in experimentally induced acute, subclinical CME. Twelve purpose-bred Beagle dogs (six intact males and six intact females), with a median age of 12.9 months (range 5–49 months), were experimentally infected with the Israeli strain 611 (Gen Bank accession number U26740) and were prospectively examined. All dogs had participated in a previous study that evaluated the efficacy of rifampicin in the treatment of experimental acute CME (); both study protocols were approved by the Faculty\’s Research and Ethical Committee (SVM-AUTh, 458 23 June 2009). By 21 days post-inoculation (DPI), all dogs developed clinical and hematological abnormalities compatible with CME, tested positive for antibodies, became PCR positive for DNA, and remained PCR-positive through 20 DPI ( = 12 dogs) and 90 DPI ( = 8, including three dogs that had failed to eradicate the infection following treatment with rifampicin from 21–42 DPI). From 42 DPI and onwards, all 12 dogs remained clinically healthy. In the current study, one examiner (CKK) performed all the cardiological evaluations, ECGs, and echocardiography using standard protocols on day (prior to inoculation;  = 12 dogs), 20 DPI ( = 12; acute ehrlichiosis) and 90 DPI ( = 8; subclinical ehrlichiosis). Blood samples were obtained at each evaluation to determine serum cTnI concentration.

This study constitutes the first report of IVM and

This study constitutes the first report of IVM and multiple drug resistant T. circumcincta isolates from Irish sheep farms. The nematodes were isolated by treatment with IVM and were subsequently found to be resistant to both BZ and LEV. Resistance to BZ and LEV treatment in the ROI is considered widespread (Good et al., 2012; Keane et al., 2014). As a result, it is possible that ML resistance would arise in nematodes that are already BZ and LEV resistant. It has also been suggested that IVM resistance could confer side resistance to different anthelmintic groups with drug efflux pumps implicated as a potential resistance mechanism (Bartley et al., 2004). Considering the increasing reports of multi-drug resistance in Europe (Geurden et al., 2014; Sargison et al., 2007; Taylor et al., 2009; Voigt et al., 2012), practices that delay its further development in Ireland should be undertaken in order to prolong the efficacy of the currently available anthelmintics, such as the promotion of improved biosecurity measures and strategic use of the new anthelmintic TL32711 on the market namely, the amino acetonitrile derivatives and spiriondoles.

Conflict of interest

Acknowledgements

Introduction
Anthelmintics are still the most widely used method for treatment and control of gastrointestinal nematodes (GIN) in sheep throughout the world. However, after decades of intensive use of dewormers, anthelmintic resistance (AR) is now widespread in veterinary practise and sometimes threatens the possibilities to control GIN infections. Within the macrocyclic lactones (ML), during recent decades AR to ivermectin (IVM) has become a common global problem in the highly pathogenic species Haemonchus contortus, especially in the southern hemisphere (e.g. Echevarria et al., 1996; Van Wyk et al., 1999; Besier and Love, 2003; Chandrawathani et al., 2003; Sutherland et al., 2008).
In Europe, AR in GIN of sheep was mainly associated with benzimidazoles (BZ) until the 1990s (for a review see Papadopoulos et al., 2012). However, some years after the introduction of ML in the 1980s reports began to emerge of IVM resistance in European sheep flocks, although these sometimes involved GIN other than H. contortus (e.g. Sargison et al., 2001; Álvarez-Sanchez et al., 2006; Bartley et al., 2006; Cernanská et al., 2006; Borgsteede et al., 2007; Domke et al., 2012; Geurden et al., 2014; Keane et al., 2014; Peña-Espinoza et al., 2014). Until recently, the resistance situation was different in Sweden. In a nationwide faecal egg count reduction test (FECRT) survey based on data from 90 sheep flocks on 45 farms conducted in 2006 and 2007, there was only evidence of BZ resistance in two flocks (Höglund et al., 2009). Unlike in some other European countries, this resistance was exclusively associated with H. contortus.
In contrast to BZ anthelmintics, ML exert their effect by binding to glutamate-gated chloride (Glu-Cl) channels expressed on nematode neurones and pharyngeal muscle cells. In the model nematode Caenorhabditis elegans, it has been shown that genes affecting parallel genetic pathways mediating drug uptake and sensitivity, as defined by the family of GluCl genes, are involved in IVM resistance (Dent et al., 2000). The precise mechanism causing IVM resistance in H. contortus is only partly understood, but in one study intensive treatment with IVM resulted in selection of the gene for the alpha-subunit of the glutamate channel in H. contortus (Blackhall et al., 1998). It was also demonstrated recently that IVM-resistant H. contortus is enriched in a dyf-7 haplotype gene which is involved in the development of amphid sensory neurons, which in turn affects permeability to the drug (Urdaneta-Marquez et al., 2014). Furthermore, IVM resistance in H. contortus is conferred by overexpression of permeability-glycoproteins (P-gp), which have the ability to transport the drug from the cytosol across cell membranes of the worms. In a study by Xu et al. (1998), the levels of P-gp mRNA were higher in IVM-treated H. contortus than in an unselected isolate. Despite this progress, validated molecular markers for IVM-resistance are currently lacking for nematodes of veterinary interest. However, clinical resistance can be detected more easily by a faecal egg count reduction test (FECRT), where AR is commonly declared when a mean percentage faecal egg reduction of less than 95% is observed 7–10days after anthelmintic treatment (McKenna, 1994).

The structure of the following content in this paper

The structure of the following content in this Bafilomycin A1 paper is as follows. The related work on SRC, CRC is introduced in Section 2. In Section 3, we describe our proposed method to integrate absolute distances in collaborative representation based classification (AbsCRC). In the next Section 4, we analyze the selection of fusion factors a and b, as well as some classification examples in the experiments. Section 5 conducts our experiments on a couple of popular benchmark datasets, and Section 6 concludes the paper.

Related work

Our method
Based on nearest feature line (NFL) and nearest feature plane (NFP) [30,31], we can calculate the sum of representation coefficients from all samples in one class and use them to represent to weight of one class. Then the test sample is classified into one class with maximal weight value. The greater the sum value is, the more contribution is produced from that class.
From the procedures of SRC and CRC, We can infer that l2-norm sparse coefficient contains some crucial discrimination clue for classification. In order to generate a more promising result, this is probably a candidate part where we should pay more efforts to. Here comes our proposed method: firstly using absolute value of coefficient instead of original value to obtain the distance between the test sample and each class, and then integrating the distance vector with the one from CRC for classification. Hereafter the schema of proposed AbsCRC is demonstrated.

Analysis
The absolute distance vector may help stabilize the representation coefficients by CRC. This is the most crucial contribution in our AbsCRC method. On the other hand, the fusion process is affected by the selection of weighted factors b. So our second effort is to find out optimized weighted factors for robust image classification or face recognition.
Fig. 1 shows the CRC residuals, absolute distances and fusion residuals in one experiment case, which was run on ORL face database with first 6 images as training samples and the rest as test samples (See subsection 5.3). And this group of residuals are for a test sample at number 113 position, which is the first test sample of twenty-ninth class (number 4 * 28 + 1 = 113 sample). We can see from the Fig. 1 that the fusion residuals (green) are affected by the absolute distance vector and slightly flatter than the original residuals by conventional CRC (yellow).
In this experiment case, with factor of b = 0.1 (See Table 3), both CRC and ABS were failed to classify the number 113 test sample into a right class, while only AbsCRC produced a right answer, as shown in Fig. 2.
Consequently, our experiments have taken into account the weighted factor b for different classification cases. And in a glut of benchmark datasets, we are managed to choose a group of parameters that help AbsCRC generate an optimized result. The next Section 5 will demonstrate all the experimental results.

Experimental results
In this section, we will demonstrate our experimental results on some popular visual benchmark datasets. Extensive experiments were conducted on these datasets to evaluate the classification accuracy of conventional CRC, absolute distance only (ABS) and our AbsCRC method, as well as the selections of fusion factors a and b. The chosen benchmark datasets include Caltech Faces [32], Caltech Leaves [32], ORL [33], FERET [34], CMU Faces [35], and Senthil IRTT Face Database [36].
On each benchmark database, we respectively run experiments with different number of training samples, as well as different integration factors a and b. For simplicity, we keep a = 1 and use different value of b to reflect the weights of two coefficients. In our experiments, we found that when CRC outperforms ABS, it\’s better to assign a value less than one to b, that is b < 1; on the contrary, usually b > 1 usually produces more pleasuring result when ABS outperforms CRC. However, there are still some exceptional experiments cases. So our experiments also paid efforts to seek a optimal fusion factor b. The following subsections will demonstrate the samples, steps, factors and results in every experimental case, as well as our discussion on the results. The experimental results indicate that in most cases the AbsCRC is managed to produce higher accuracy of classification than CRC.

Another unexpected finding in this cohort was the absence

Another unexpected finding in this cohort was the absence of an association between the level of HIV RNA or CD4 count and NAb breadth and potency. The literature is inconclusive with regards to the relationship between NAb breadth and CD4 counts, with some studies showing a relationship (Carotenuto et al., 1998), and others not (Piantadosi et al., 2009a; Doria-Rose et al., 2010). The absence of an association between early viral load and later NAb breadth was unexpected, as several studies have documented such a relationship (Piantadosi et al., 2009a; Doria-Rose et al., 2010; Sather et al., 2009). Interestingly, one study demonstrated the emergence of broad NAb in patients on ART with suppressed viremia, suggesting that high antigenic stimulus may not be the only driving force behind NAb breadth development (Medina-Ramirez et al., 2011). Our findings suggest that while it is certainly possible that high antigenic exposure can contribute to the development of NAb breadth in some individuals, NAb selective pressure is likewise a potent modulator of viral genetic diversity.

Introduction
Initially known as the non-A, non-B hepatitis (NANBH) virus (Alter et al., 1975), the hepatitis C virus (HCV), which was identified in 1989 (Choo et al., 1989; Houghton, 2009), is a single-stranded positive-sense RNA virus (Choo et al., 1991) classified as a member within the Hepacivirus genus in the Flaviviridae family (Drexler et al., 2013; Lindenbach et al., 2007). With high divergence in sequence due to the error-prone nature of the viral RNA-dependent RNA polymerase, HCV is classified into 7 phylogenetic clades designated from genotype 1 through 7, with more than 30% divergence based on nucleotide sequences and over 70 subtypes within an individual genotype (Simmonds, 2013; Simmonds et al., 2005). Chronic HCV infection is estimated to affect about 170 million people worldwide or ~3% of the world’s population (Lavanchy, 2009). In addition, there are 3 to 4 million new yearly infected cases coupled with 350,000 patients dying from HCV-related diseases (Shepard et al., 2005; WHO, 2012). Despite the fact that HCV was identified over two decades ago, there is still no therapeutic vaccine for HCV infection and treatment regimen for chronic infections are limited with various serious side effects as well as high treatment cost (EASL, 2011; Hayashi and Takehara, 2006). Thus, identification and discovery of new, innovative, and effective treatment is highly desirable in order to curb the spread of HCV.
HCV has a 9.6kb LY2584702 size with an open reading frame (ORF) flanked by two regulatory un-translated regions (UTR), the 5′UTR and 3′UTR, respectively (Bostan and Mahmood, 2010). The ORF is translated into a precursor polyprotein of approximately 3000 residues which is then co- and post-translationally processed by viral and cellular proteases into at least three structural proteins (core, E1, and E2), a small ion channel protein (p7), and six non-structural proteins (NS2, NS3, NS4A, NS4B, NS5A, and NS5B) (Lin et al., 1994; Lindenbach et al., 2007).
Although ample studies suggest a strong tie between chronic HCV infection and liver damage, the mechanisms involved are still not well established. A combination of viral cytopathic effects (CPE) and host immune responses are believed to contribute to the liver injury observed in HCV infection (Guicciardi and Gores, 2005; Park et al., 2012). While HCV is not a cytolytic virus, studies have demonstrated that hepatocyte apoptosis plays a major part in the host anti-viral defense mechanism against HCV as it prevents viral replication as well as aids in the elimination of virus-infected hepatocytes (Lim et al., 2012). Similarly, a number of recent studies using the HCV cell culture (HCVcc) system (Lindenbach et al., 2005) have shown that HCV can have direct CPE and induce cell death in the form of apoptosis in hepatocytes (Deng et al., 2008; Mateu et al., 2008; Mohd-Ismail et al., 2009; Walters et al., 2009; Zhu et al., 2007). It is believed that HCV modulates host apoptosis by interacting with a couple of host factors. Ectopic expression of the individual viral proteins in cell culture as well as using the subgenomic replicon system, have shed more light on the contributions of the individual viral genes to host apoptosis (see review (Aweya and Tan, 2011)). For instance, using a NS3-5B subgenomic replicon, Lan et al. (2008) showed that the HCV non-structural proteins are key modulators which sensitize human hepatoma cells to TRAIL-induced apoptosis. Similarly, data from our laboratory have previously demonstrated that the HCV core protein is pro-apoptotic and a novel BH3-only viral homologue (Mohd-Ismail et al., 2009) while more recent data demonstrated that the small ion channel protein, p7, induces apoptosis in Huh7.5 cells in a caspase-dependent manner involving both the extrinsic and intrinsic pathways (Aweya et al., 2013). As the various HCV-encoded proteins play a different role in modulating host apoptosis by interacting and interfering with different host factors and/or cellular events, understanding how this intricate host-viral interaction is regulated so as to prevent premature death of infected cells and to establish persistent infection would be essential in understanding the disease pathogenesis and for instituting an effective treatment regimen.

Nevertheless for nearly all ecologically studied arenaviruses

Nevertheless, for nearly all ecologically studied arenaviruses (both New-World: Junin Mills et al., 1994, Oliveros Mills et al., 2007 and Old-World: Lassa Demby et al., 2001, Morogoro Borremans et al., 2011) the probability to carry anti-arenavirus buy LY2228820 increases with the age of the host individuals, and we found this also for GAIV (Table 2). In other words, the older an animal becomes, the higher chance it has to have acquired an arenavirus infection at some point in its life. While not excluding sexual or vertical transmission, this observation suggests that horizontal transmission is important for most arenaviruses. It also implies that relatively higher proportions of animals in younger age categories are still susceptible; and indeed we found a significant negative relationship between GAIV RT-PCR positivity and age. This was previously also observed in M. natalensis populations with Lassa (Fichet-Calvet et al., 2008) and Morogoro viruses (Borremans et al., 2011).
In conclusion, the discovery of GAIV in M. natalensis highlights the great arenavirus diversity a single rodent species can harbor. This is clearly buy LY2228820 not solely due to the wide, near pan-African distribution of the rodent, as we detected GAIV in M. natalensis populations just 90km from the locality where previously Morogoro virus, an outlier strain of Mopeia virus from Mozambique, was described. M. natalensis’ arenavirus diversity is also markedly distinct from that of the house mouse, Mus musculus, from which only one arenavirus species (Lymphocytic choriomeningitis virus—LCMV) has been described across its cosmopolitan range. A more detailed sampling across the transition zone between two divergent arenaviruses of M. natalensis should allow a better understanding of the ecological processes that keep the occurrence of its arenaviruses limited to distinct geographical regions.

Material and methods

Acknowledgments
The authors thank Shabani Lutea, Khalid Kibwana and Clement Pangapanga from the SUA Pest Management Centre, Natalie Van Houtte from the University of Antwerp, and Stephanie Wurr and Beate Becker-Ziaja from the Bernard-Nocht Institute for Tropical Medicine for excellent technical assistance. This work was supported by the Fund for Scientific Research—Flanders (FWO grant 1.5.264.12 and 1167112N); the University of Antwerp (GOA BOF FFB3567); the Czech Science Foundation (GACR grant P502/11/J07g0 and CZ.1.07/2.3./20.0303); and the German Research Foundation (DFG grant GU 883/2-1 GU 883/4-1 and LE 3111/1-1—AOBJ: 600977). S. Gryseels, B.B. and BC are PhD fellows with FWO during part of the work and J.G.B. is a postdoctoral fellow with FWO.

Introduction
The Potyviridae family is a major group of plant viruses, with 177 assigned species distributed in seven genera containing viruses with monopartite genomes, and one genus with bipartite genome members (Adams et al., 2012). In the Potyvirus and Ipomovirus genera, both containing viruses with monopartite genomes, translation of viral genomic RNA gives rise to a polyprotein that is cleaved into at least 10 different products (López-Moya et al., 2009). A frameshift in the P3 cistron originates an additional polyprotein product, P3N-PIPO (Chung et al., 2008). The polyprotein is processed by leader self-cleaving proteases such as P1 or HCPro, and by the protease domain of NIa, a protein with self- and trans-cleaving proteolytic activity found in all Potyviridae (Adams et al., 2005). HCPro has protease activity which is independent of host factors (Carrington et al., 1989), and acts as a suppressor of host antiviral RNA silencing defenses, among other functions (Brigneti et al., 1998; Kasschau and Carrington, 1998; Ivanov et al., 2014). Full-length P1 protein needs a still unidentified host factor for its proteolytic activity and has been linked to viral host specificity (Verchot et al., 1992; Salvador et al., 2008; Maliogka et al., 2012b; Rodamilans et al., 2013; Pasin et al., 2014b). Defects in P1 protease activity impair the HCPro silencing suppressor activity and preclude viral infectivity (Pasin et al., 2014b). Infectivity is restored in RNA silencing-defective hosts, as well as when an NIa target site or a 2A “self-cleaving” peptide are inserted between a cleavage-deficient P1 and HCPro (Verchot and Carrington, 1995a; Pasin et al., 2014b).

br Discussion The survey demonstrated that poultry is widely exposed

Discussion
The survey demonstrated that poultry is widely exposed to T. gondii in Israel (Fig. 1).
Importantly, and as has been mentioned in the results section, this MAT assay demonstrated high specificity as no cross-reaction was observed with sera obtained from Eimeria tenella-infected chickens used as controls.
The results of the survey present evidence that housing conditions which prevent oocyst-shedding cats to access premises have a significant impact on T. gondii seroprevalence of poultry (Fig. 1). Battery-raised egg layers (Group 2) had the highest cumulative seroprevalence of all 6 survey groups with 35.4% of angiotensin receptor blocker infected (Fig. 3.1). Housing egg-laying chickens in batteries above the ground did not change the level of T. gondii seroprevalence since they were initially housed on the ground until the age of 105days. A varying lack of strict biosecurity conditions in this group, which was personally observed, with rodents and cats occasionally gaining access to the housing facilities might be a possible explanation. It might also be related to differences in the age composition of these groups. Conditions of high bird concentrations in limited spaces where cats readily frequent may allow for easier T. gondii oocyst exposure allowing for these high seroprevalence rates to be achieved. Broilers in Israel are often raised on cement pens and on the ground under conditions of relatively high biosecurity with regard to access to cats and rodents. Broiler raising pens are thoroughly cleaned and disinfected with aldehydes after each batch of broilers is removed and before reintroduction of a new flock. This is probably also the reason why birds in Group 3 were seronegative. Even the relatively much older 2-year-old breeders (Group 4) were found to be seronegative and this can only be explained by an effective housing system where biosecurity is strictly enforced and feed/litter is not contaminated with oocysts. Zhu et al. (2008), Yan et al. (2009) and Maksimov et al. (2011) have reported similar findings amongst biosecurity-enforced, caged and free-range poultry in North East China and enclosed and free-range geese and ducks in Saxony, Germany. Both reports relate high T. gondii seroprevalence in free-range birds due to their exposure to feral cats. Unfortunately, these surveys compared only two types of housed poultry and did not include the possibility of housing birds above the ground exclusively in their investigations.
Although relatively few turkeys were sampled in the survey, close to 10% of those birds sampled (4/45) were seropositive for T. gondii anntibodies. In fact, three of 4 birds had antibody titers that were ≥50 (Results not shown). This finding should signal a warning to stakeholders in the poultry industry and officials involved in public health. Further surveys should be conducted in turkeys using larger sample groups in order to confirm the high seroprevalence of T. gondii in this poultry species since turkey meat is consumed extensively by the Israeli public (http://www.thepoultrysite.com/).
Housing conditions as a modifying mechanism for T. gondii prevalence in poultry is crucial, especially in a day and age whereby animal production systems that offer outdoor access to animals have become increasingly popular in the Western world, including Israel, due to the growing general discontent of consumers with conventional bio-industrial farming practices. These open production systems offer improved animal welfare but may create new problems for animal health, resulting in increased food safety risks from parasitic infections, like toxoplasmosis. In current organic husbandry systems, the animals are kept at lower stocking densities and have outdoor access. The design of new animal production systems with outdoor access requires both a thorough analysis of possible risks and optimal communication of these risks throughout the food chain and appropriate partitioning of responsibility concerning these risks. Some risks are inherent to the choice of keeping animals in a more natural environment and could be judged as an inherent responsibility of the consumer, whereas other risks may be mitigated by further refinement or adjustment of the housing or farm management system used.

Our results show that Alpha

Our results show that Alpha- and Betacoronavirus S proteins interact with the charge-rich region of their cytoplasmic domains with tubulin beta chains. An interaction with microtubules facilitates TGEV replication and infection efficiency but the depolymerization of microtubules did not inhibit it completely. Thus, an interaction of S with tubulin supports an efficient generation of infectious virus progeny.

Competing interests

Acknowledgements
Financial support was provided by a Grant to CSW (SCHW 1408/1.1) from the German Research Foundation (DFG) and by the “Bundesministerium fuer Bildung und Forschung” of the German Government (Zoonosis Network, Consortium on ecology and pathogenesis of SARS, project code 01KI1005A,F to AvB).
CSW is funded by the Emmy Noether Programme from the DFG. ATR is a recipient of a Georg Christoph Lichtenberg Ph.D. fellowship from the Ministry for Science and Culture of Lower Saxony.

Introduction
Oncolytic or replication-competent adenovirus (Ad) vectors are considered promising virotherapy vehicles of high utility because they can be easily constructed, are produced at high titers, and can efficiently transduce various types of cells. Most commonly, the Ad vectors that are used for clinical purposes are based on adenovirus serotype 5 (Ad5), which belongs to subgroup C. In recent years, however, it has become apparent that Ad5 vectors have some drawbacks, such as the high seroprevalence of anti-Ad5 PX-478 2HCl in adult humans and the low transduction efficiency of Ad5 vectors in cells lacking the primary receptor for Ad5, the coxsackievirus and adenovirus receptor (CAR), which is the case for numerous types of metastatic solid tumors and leukemia cells. This critical roadblock could be overcome by using an alternative serotype of the virus to bypass the presence of pre-existing antibodies that have been elicited by previous natural Ad infections. The replication competent Ad11 vector could be used to overcome the disadvantages associated with Ad5 vectors, as species B Ad11 also uses DSG-2 and CD46 as receptors (Wang et al., 2011), which are ubiquitously expressed on metastatic tumor cells, and Ad11 shows a low seroprevalence in humans. Indeed, only approximately 10–31% of the population is seropositive for Ad11, whereas up to 90% of the population is seropositive for Ad5. Notably, there is no serum cross reactivity between Ad11 and Ad5 (Holterman et al., 2004; Stone et al., 2005).
A number of species B Ads, such as Ad3, Ad7, Ad11 and Ad35, have been developed as gene therapy or vaccine vectors. Such vectors have primarily been designed according to conventional methodology: they incorporate an E1 deletion followed by substitution with an expression cassette. Such vectors display characteristics common to Ad, showing low production and heat lability, and they satisfy the requirements needed to produce virus in packaging cell lines. Replication-competent Ad11 vectors have also been reported by Wong et al. (2012). To create these vectors, the promoter-enhancer and promoter sequence from 195 nt to 358 nt of Ad5 were replaced with a sequence fragment from 249 nt to 392 nt of Ad11p, resulting in Ad11p-Ad5-EP vectors that could replicate in a greater variety of cancer cell lines than the parent viruses.
Ad E1A, a multifunctional protein expressed early after infection, interferes with numerous important regulatory processes by interacting with host cell proteins or directly transcriptionally activating target genes. Although E1A was initially identified as an adenoviral component that can cause the malignant conversion of rodent cells, this protein has also been shown to possess remarkable tumor suppressive effects on various types of human cancer cells (Frisch, 1991; Frisch and Mymryk, 2002). For instance, E1A downregulated HER2/neu expression in addition to participating in other antitumor mechanisms unrelated to Her-2 (Chang et al., 1997). E1A also negatively regulates cellular proteins that are important for gene transcription, such as p300/CBP, TATA-binding protein, TBP-associated factors, NF-kB, ATF-4 and c-Jun (Brockmann et al., 1995; Chen and Hung, 1997; Liang and Hai, 1997). The E1A protein has also been shown to induce sensitization to anticancer drug-induced apoptosis, as well as to reduce tumor metastasis and promote apoptosis under conditions of serum deprivation caused by the application of tumor necrosis factor a (TNF-a), irradiation or anticancer agents such as Taxol, etoposide, and Adriamycin. For these reasons, E1A-based viral gene therapies have been extensively exploited in both pre-clinical and clinical settings. Thus, there is a need to keep the E1 gene intact, and recent studies have focused on creating Ad vectors that include a therapeutic gene insertion in the E3 region as opposed to in the E1 region. The E3 region of the Ad genome has been previously shown as unnecessary for virus replication and can therefore be deleted to introduce a large expression cassette for therapeutic purposes. However, this concept has been challenged by recent reports indicating that the re-introduction of full-length E3 back into the virus genome increases its therapeutic efficacy (Danielsson et al., 2008). Thus, the deletion of E3 may affect viral function.

We have also recently elucidated the

We have also recently elucidated the pathway by which IL-7 regulates cell surface expression of CD127 on CD8 T glucose assay (Faller et al., 2015; Ghazawi et al., 2013). IL-7 binding to CD127 triggers receptor internalization through clathrin coated pits resulting in receptor accumulation in early endosomes. IL-7 binding also activates JAK3 which phosphorylates tyrosine 449 (Y449) in the cytoplasmic tail of CD127 as well as STAT5 which in turn translocates to the cell nucleus where it up regulates expression SOCS proteins SOCS2 and Cytokine-inducible SH2 containing (CIS) protein. CIS and SOCS2 then associate with CD127 phosphorylated at Y449 via their SH2 domains and traffic with the receptor to the proteasome. This CIS-dependent degradation of CD127 in response to IL-7 is dependent on cellular E3 ubiquitin ligase strongly implicating ubiquitination in this process.

Results

Discussion
We have previously shown that soluble Tat protein is taken up by CD8 T cells, binds to the cytosolic tail of CD127 and induces receptor internalization and proteasomal degradation (Faller et al., 2010). Tat interacts with CD127 through its N-terminal region (Sugden and MacPherson, 2015) and as we show here recruits CIS via its basic domain resulting in receptor ubiquitination.
We have also shown recently that IL-7 binding to its receptor induces phosphorylation of CD127 at Y449 and also through the JAK/STAT5 signaling pathway up regulates production of the SOCS protein CIS (Ghazawi et al., 2016). CIS then interacts with phosphorylated CD127 via its SH2 domain and targets the receptor for degradation through association with E3 ligases. CIS is well known to be up regulated in response to numerous cytokines (Matsumoto et al., 1997; Yoshimura et al., 1995), and another SOCS family member, SOCS1, has been shown to attenuate JAK/STAT signaling in response to IL-7 in differentiating murine CD8 T cells (Chong et al., 2003). The SOCS family of proteins negatively regulates cytokine signaling by blocking STAT recruitment to the cytokine receptor, by interacting with JAK kinases to inhibit their enzymatic activity, and by binding directly to the phosphorylated cytokine receptor and targeting the receptor complex to the proteasome through recruitment of an E3 ubiquitin ligase. CIS itself has been shown to interact with the cullin5-elonginB/C-Rbx2 E3 ubiquitin ligase complex (Piessevaux et al., 2008).
This is not the first example where Tat has been shown to exploit host cell ubiquitination machinery to induce the removal of a receptor from the cell membrane. Tat has been shown to down regulate the Recepteur d′origine nantais (RON) receptor in monocytes (Kalantari et al., 2008). Interestingly, this mechanism is strongly reminiscent of what we find here. Although Tat and RON were not shown to associate physically, Tat induces the ubiquitination of RON resulting in surface down regulation and proteasomal degradation (Kalantari et al., 2008). Similar to the effect of Tat on CD127, the effect of Tat on RON is specific for the receptor as well as independent of transcription and de novo protein synthesis. Notably, a Tat mutant containing a glycine and a phenylalanine substitution in the N-terminal region between aa 18 and 19 prevented Tat-induced RON degradation. Together, these data suggest a possible common mechanism whereby the N-terminus of Tat interacts with surface receptors and then recruits additional cellular factors and E3 ligases to induce receptor degradation.
Tat recruitment of CIS to CD127 may explain our previous observation that Tat is able to act synergistically with IL-7 to down regulate CD127 surface expression (Faller et al., 2009). Since we have shown IL-7 binding to its receptor results in an increase in de novo CIS production, and it is shown here that Tat increases the recruitment of CIS to CD127, Tat/IL-7 synergy may be explained by convergence of both mechanisms. IL-7 increases the pool of CIS protein while Tat recruits CIS to CD127 when IL-7 concentrations are not saturating. This synergistic effect may play an important role in vivo, particularly in lymphoid micro-environments such as GALT and other secondary lymphoid tissues where there are higher densities of HIV+ CD4 T cells and thus likely increased Tat concentrations as well as IL-7 producing epithelial and follicular dendritic cells (Sportes et al., 2008; Teeuwsen et al., 1990).

The anti V glycan class of antibodies primarily target the

The anti-V3/glycan class of melatonin receptor agonist primarily target the conserved (Gao et al., 1996; Louwagie et al., 1995; Travers, 2012) glycans at positions 301, 332 and 334 (HXB2 numbering), around the base of the V3 loop (Julien et al., 2013b; Mouquet et al., 2012; Pejchal et al., 2011; Sok et al., 2014; Walker et al., 2011; Ward and Wilson, 2015). Some moderately broad neutralizing anti-V3/glycan antibodies, such as early antibodies in the PGT121–123 lineages, require both the 301 glycan and the 332 glycan to neutralize viral variants but as the antibodies mature and gain breadth they lose their dependence on the 301 glycan, presumably due to higher affinity binding to the 332 glycan (Sok et al., 2013). This indicates that the dependence of epitopes on the presence of particular glycans can change over time with the evolution of the antibodies. In aggregate, the primary targets of the anti-V3/glycan class of antibodies are the glycans at 301 and melatonin receptor agonist 332 (Walker et al., 2011), although other glycans or arrays of glycans (including 334 to a lesser extent) are recognized in some viruses (Doores et al., 2015; Sok et al., 2014). These secondary targets are not restricted to glycans on the V3 loop but may include glycans in the V1/V2 loops, such as at position 137 (Sok et al., 2014).
Narrowly-neutralizing antibodies which recognize underlying epitopes may select for viruses expressing glycans to protect their V3 loops while glycan-recognizing bnAbs may select for loss of their target glycans (Moore et al., 2012; Wei et al., 2003). Illustratively, HIV-1 populations in two individuals first evolved to exhibit a PNG at position 332 to escape early neutralizing antibodies, and then induced anti-V3/glycan broadly neutralizing antibodies. Subsequently, the virus populations lost the PNG at 332, likely to evade neutralization by those anti-glycan antibodies (Moore et al., 2012). Little is known about how the construction of the glycan shield may affect such concurrent antibody-mediated selection for or against the V3/glycans.
Therefore, in this study, we investigated the role of key glycans around the base of the V3 loop, at positions 301, 332 and 334, to understand the balance between their role in blocking antibody responses (glycan shield) and being a target of bnAbs. Using in vitro neutralization assays and energy minimization models of fully glycosylated Env timers, we show that dependence on the glycan at 301 for maintenance of the “glycan shield” differs in two subtype C viruses, Du156.12 and CAP45.G3 that share approximately 90% sequence identity. In particular, we used monoclonal antibodies (mAbs) to help elucidate exposure of new epitopes and a large set (n=64) of sera from chronically HIV-infected individuals in order to study antibodies that are commonly found in natural infection.
We show that Du156.12 requires the glycan at position 301 for effective blocking of commonly neutralizing antibodies, similar to previous work with other viral isolates (Binley et al., 2010; Koch et al., 2003; Li et al., 2008; McCaffrey et al., 2004; Townsley et al., 2016; Zolla-Pazner et al., 2016). In contrast, CAP45.G3 depends very little on the presence of this glycan for resistance to neutralizing antibodies commonly found in immune sera. Our data therefore indicate that the contribution of the glycan at 301 to resistance to common neutralizing antibodies varies between viruses. The PNG at position 301 is highly conserved (Gao et al., 1996; Louwagie et al., 1995; Travers, 2012) and is found across all subtypes, although it is less common in subtypes D (Gao et al., 1996; Louwagie et al., 1995; Travers, 2012) and CRF01_AE (Travers, 2012). This suggests that, with sufficient pressure, certain viruses with the properties of CAP45.G3 may more easily simultaneously evade both anti-V3/glycan antibody responses and antibody responses normally blocked by the same glycans. The ability to simultaneously evade broadly neutralizing anti-V3/glycan antibodies and antibodies blocked by V3/glycans may impair the efficacy of anti-V3/glycan antibodies passively infused as therapy or those induced by a future vaccine.