Assisted evolution enables HIV-1 to overcome a high trim5α-imposed genetic barrier to rhesus macaque tropism

Diversification of antiretroviral factors during host evolution has erected formidable barriers to cross-species retrovirus transmission. This phenomenon likely protects humans from infection by many modern retroviruses, but it has also impaired the development of primate models of HIV-1 infection. Indeed, rhesus macaques are resistant to HIV-1, in part due to restriction imposed by the TRIM5α protein (rhTRIM5α). Initially, we attempted to derive rhTRIM5α-resistant HIV-1 strains using two strategies. First, HIV-1 was passaged in engineered human cells expressing rhTRIM5α. Second, a library of randomly mutagenized capsid protein (CA) sequences was screened for mutations that reduced rhTRIM5α sensitivity. Both approaches identified several individual mutations in CA that reduced rhTRIM5α sensitivity. However, neither approach yielded mutants that were fully resistant, perhaps because the locations of the mutations suggested that TRIM5α recognizes multiple determinants on the capsid surface. Moreover, even though additive effects of various CA mutations on HIV-1 resistance to rhTRIM5α were observed, combinations that gave full resistance were highly detrimental to fitness. Therefore, we employed an 'assisted evolution' approach in which individual CA mutations that reduced rhTRIM5α sensitivity without fitness penalties were randomly assorted in a library of viral clones containing synthetic CA sequences. Subsequent passage of the viral library in rhTRIM5α-expressing cells resulted in the selection of individual viral species that were fully fit and resistant to rhTRIM5α. These viruses encoded combinations of five mutations in CA that conferred complete or near complete resistance to the disruptive effects of rhTRIM5α on incoming viral cores, by abolishing recognition of the viral capsid. Importantly, HIV-1 variants encoding these CA substitutions and SIVmac239 Vif replicated efficiently in primary rhesus macaque lymphocytes. These findings demonstrate that rhTRIM5α is difficult to but not impossible to evade, and doing so should facilitate the development of primate models of HIV-1 infection

Channel Assignment with Separation for Interference Avoidance in Wireless Networks

Given an integer $\sigma > 1$, a vector $(\delta_1, \delta_2, \ldots, \delta_{\sigma-1})$ of nonnegative integers, and an undirected graph $G=(V,E)$, an $L(\delta_1, \delta_2, \ldots,\delta_{\sigma-1})$-coloring of $G$ is a function $f$ from the vertex set $V$ to a set of nonnegative integers such that $| f(u) -f(v) | \ge \delta_i$, if $d(u,v) = i, \ 1 \le i \le \sigma-1, \$ where $d(u,v)$ is the distance (i.e. the minimum number of edges) between the vertices $u$ and $v$. An optimal $L(\delta_1, \delta_2, \ldots,\delta_{\sigma-1})$-coloring for $G$ is one using the smallest range $\lambda$ of integers over all such colorings. This problem has relevant application in channel assignment for interference avoidance in wireless networks, where channels (i.e. colors) assigned to interfering stations (i.e. vertices) at distance $i$ must be at least $\delta_i$ apart, while the same channel can be reused in vertices whose distance is at least $\sigma$. In particular, two versions of the coloring problem -- $L(2,1,1)$, and $L(\delta_1, 1, \ldots,1)$ -- are considered. Since these versions of the problem are $NP$-hard for general graphs, efficient algorithms for finding optimal colorings are provided for specific graphs modeling realistic wireless networks including rings, bidimensional grids, and cellular grids

Evidence for Restriction of Ancient Primate Gammaretroviruses by APOBEC3 but Not TRIM5α Proteins

Because of evolutionary pressures imposed through episodic colonization by retroviruses, many mammals express factors, such as TRIM5α and APOBEC3 proteins, that directly restrict retroviral replication. TRIM5 and APOBEC restriction factors are most often studied in the context of modern primate lentiviruses, but it is likely that ancient retroviruses imposed the selective pressure that is evident in primate TRIM5 and APOBEC3 genes. Moreover, these antiretroviral factors have been shown to act against a variety of retroviruses, including gammaretroviruses. Endogenous retroviruses can provide a ‘fossil record’ of extinct retroviruses and perhaps evidence of ancient TRIM5 and APOBEC3 antiviral activity. Here, we investigate whether TRIM5 and APOBEC3 proteins restricted the replication of two groups of gammaretroviruses that were endogenized in the past few million years. These endogenous retroviruses appear quite widespread in the genomes of old world primates but failed to colonize the human germline. Our analyses suggest that TRIM5α proteins did not pose a major barrier to the cross-species transmission of these two families of gammaretroviruses, and did not contribute to their extinction. However, we uncovered extensive evidence for inactivation of ancient gammaretroviruses through the action of APOBEC3 cytidine deaminases. Interestingly, the identities of the cytidine deaminases responsible for inactivation appear to have varied in both a virus and host species–dependent manner. Overall, sequence analyses and reconstitution of ancient retroviruses from remnants that have been preserved in the genomes of modern organisms offer the opportunity to probe and potentially explain the evolutionary history of host defenses against retroviruses

Adding corticosteroids to the pudendal nerve block for pudendal neuralgia: a randomised, double-blind, controlled trial

International audienceOBJECTIVE:To compare the effect of corticosteroids combined with local anaesthetic versus local anaesthetic alone during infiltrations of the pudendal nerve for pudendal nerve entrapment.DESIGN:Randomised, double-blind, controlled trial.SETTING:Multicentre study.POPULATION:201 patients were included in the study, with a subgroup of 122 women.METHODS:CT-guided pudendal nerve infiltrations were performed in the sacrospinous ligament and Alcock's canal. There were three study arms: patients in Arm A (n = 68) had local anaesthetic alone, those in Arm B (n = 66) had local anaesthetic plus corticosteroid and those in Arm C (n = 67) local anaesthetic plus corticosteroid with a large volume of normal saline.MAIN OUTCOME MEASURES:The primary end-point was the pain intensity score at 3 months. Patients were regarded as responders (at least a 30-point improvement on a 100-point visual analogue scale of mean maximum pain over a 2-week period) or nonresponders.RESULTS:Three months' postinfiltration, 11.8% of patients in the local anaesthetic only arm (Arm A) were responders versus 14.3% in the local anaesthetic plus corticosteroid arms (Arms B and C). This difference was not statistically significant (P = 0.62). No statistically significant difference was observed in the female subgroup between Arm A and Arms B and C (P = 0.09). No significant difference was detected for the various pain assessment procedures, functional criteria or quality-of-life criteria.CONCLUSIONS:Corticosteroids provide no additional therapeutic benefits compared with local anaesthetic and should therefore no longer be used

Mercapto-phosphonate compounds as broad-spectrum inhibitors of the metallo-beta-lactamases

peer reviewedObjectives: One of the emergent factors for the b-lactam antibiotic resistance of pathogenic bacteria is the production of metallob- lactamases (MBLs), which are able to hydrolyse the b-lactam ring in a broad spectrum of substrates, particularly the carbapenems. MBLs have been divided into three different sub-classes B1, B2 and B3 based on sequence similarities [1]. In this report, we investigated the inhibitory effect of mercapto-phosphonate derivatives against MBLs. Methods: The laboratory of P Metzner (University of Caen, France) synthesized 12 different mercapto-phosphonate compounds with the ability to inhibit the subclass B1 VIM-4, the subclass B2 CphA and the subclass B3 L1 MBLs respectively. Consequently, we determined the competitive inhibition constant (Ki) as described by DeMester et al. [2]. We also measured the minimal inhibition concentration (MIC) for Escherichia coli recombinant strains producing VIM-4, CphA or L1, for ampicillin or imipenem in the presence or absence of mercaptophosphonate compounds. Results: In the present study, we show that all the mercaptophosphonates, with the exception of compound 1a, behaved as good competitive inhibitors (Ki<15 mM) for CphA. Their activities against the sub-classes B1 and B3 enzymes were more contrasted. In addition, the presence of free Zn++ abolished the inhibitory activity of compound 2b. The compound behaving as zinc chelator could explain this phenomenon. Nevertheless, the (2-sulfanylphenyl) phosphonic acid, the (4-bromophenyl)(sulfanyl)methyl phosphonic acid and the [(2,4-dichlorophenyl)(sulfanyl)methyl] phosphonic acid were good inhibitors (Ki<15 mM) against the different studied enzymes and can be used as leads to the synthesis of new MBL inhibitors. Our tests indicated that the presence of compounds 2b, 4a and mgfg decreased the MIC value for imipenem. Conclusion: In this study, we show that members of the phosphonates group are able to enhance the inhibition of Zn b-lactamases. This is the first report of new inhibitors possessing a strong activity against the different sub-classes of MBLs. Reference(s) [1] Galleni M, Lamotte-Brasseur J, Rossolini GM, Spencer J, Dideberg O, Frere JM. Antimicrob Agents Chemother 2001; 45(3): 660−3. [2] De Meester F, Joris B, Reckinger G, Bellefroid-Bourguignon C, Frere JM, Waley SG. Biochem Pharmacol 1987 Jul 15; 36(14): 2393–403

Slednice, soslednice, padnice, preseki in prebodi splošne ravnine v večpoglednih projekcijah

Type IV pili are surface-exposed filaments and bacterial virulence factors, represented by the Tfpa and Tfpb types, which assemble via specific machineries. The Tfpb group is further divided into seven variants, linked to heterogeneity in the assembly machineries. Here we focus on PilO2(Bp), a protein component of the Tfpb R64 thin pilus variant assembly machinery from the pathogen Burkholderia pseudomallei. PilO2(Bp) belongs to the PF06864 Pfam family, for which an improved definition is presented based on newly derived Hidden Markov Model (HMM) profiles. The 3D structure of the N-terminal domain of PilO2(Bp) (N-PilO2(Bp)), here reported, is the first structural representative of the PF06864 family. N-PilO2(Bp) presents an actin-like ATPase fold that is shown to be present in BfpC, a different variant assembly protein; the new HMM profiles classify BfpC as a PF06864 member. Our results provide structural insight into the PF06864 family and on the Type IV pili assembly machinery