Functional central polypurine tract provides downstream protection of the human immunodeficiency virus type 1 genome from editing by APOBEC3G and APOBEC3B

Lentiviruses utilize two polypurine tracts for initiation of plus-strand viral DNA synthesis. We have examined to what extent human immunodeficiency virus type 1 plus-strand initiation at the central polypurine tract (cPPT) could protect the viral genome from DNA editing by APOBEC3G and APOBEC3B. The presence of a functional cPPT, but not of a mutated cPPT, extensively reduced editing by both APOBEC3G and APOBEC3B of sequences downstream, but not upstream, of the cPPT, with significant protection observed as far as 400 bp downstream. Thus, in addition to other potential functions, the cPPT could help protect lentiviruses from editing by cytidine deaminases of the APOBEC family.     

Genetic diversity and quinolone resistance in Campylobacter jejuni isolates from poultry in Senegal

We used the multilocus sequence typing (MLST) method to evaluate the genetic diversity of 46 Campylobacter jejuni isolates from chickens and to determine the link between quinolone resistance and sequence type (ST). There were a total of 16 ST genotypes, and the majority of them belonged to seven clonal complexes previously identified by using isolates from human disease. The ST-353 complex was the most common complex, whereas the ST-21, ST-42, ST-52, and ST-257 complexes were less well represented. The resistance phenotype varied for each ST, and the Thr-86-Ile substitution in the GyrA protein was the predominant mechanism of resistance to quinolone. Nine of the 14 isolates having the Thr-86-Ile substitution belonged to the ST-353 complex. MLST showed that the emergence of quinolone resistance is not related to the diffusion of a unique clone and that there is no link between ST genotype and quinolone resistance. Based on silent mutations, different variants of the gyrA gene were shown to exist for the same ST. These data provide useful information for understanding the epidemiology of C. jejuni in Senegal.     

Clinical and molecular genetic features of ARC syndrome

Arthrogryposis, renal dysfunction and cholestasis (ARC) syndrome (MIM 208085) is an autosomal recessive multisystem disorder that may be associated with germline VPS33B mutations. VPS33B is involved in regulation of vesicular membrane fusion by interacting with SNARE proteins, and evidence of abnormal polarised membrane protein trafficking has been reported in ARC patients. We characterised clinical and molecular features of ARC syndrome in order to identify potential genotype-phenotype correlations. The clinical phenotype of 62 ARC syndrome patients was analysed. In addition to classical features described previously, all patients had severe failure to thrive, which was not adequately explained by the degree of liver disease and 10% had structural cardiac defects. Almost half of the patients who underwent diagnostic organ biopsy (7/16) developed life-threatening haemorrhage. We found that most patients (9/11) who suffered severe haemorrhage (7 post biopsy and 4 spontaneous) had normal platelet count and morphology. Germline VPS33B mutations were detected in 28/35 families (48/62 individuals) with ARC syndrome. Several mutations were restricted to specific ethnic groups. Thus p.Arg438X mutation was common in the UK Pakistani families and haplotyping was consistent with a founder mutation with the most recent common ancestor 900–1,000 years ago. Heterozygosity was found in the VPS33B locus in some cases of ARC providing the first evidence of a possible second ARC syndrome gene. In conclusion we state that molecular diagnosis is possible for most children in whom ARC syndrome is suspected and VPS33B mutation analysis should replace organ biopsy as a first line diagnostic test for ARC syndrome.     

Mechanically induced helix-coil transition in biopolymer networks

The quasi-equilibrium evolution of the helical fraction occurring in a biopolymer network (gelatin gel) under an applied stress has been investigated by observing modulation in its optical activity. Its variation with the imposed chain extension is distinctly nonmonotonic and corresponds to the transition of initially coiled strands to induced left-handed helices. The experimental results are in qualitative agreement with theoretical predictions of helices induced on chain extension. This new effect of mechanically stimulated helix-coil transition has been studied further as a function of the elastic properties of the polymer network: crosslink density and network aging.     

Characterization of Ni-tolerant methylobacteria associated with the hyperaccumulating plant Thlaspi goesingense and description of Methylobacterium goesingense sp. nov

Various pink-pigmented facultative methylotrophic (PPFM) bacteria (strains iEII3, iEIV1, iEI6, iEII1, iEIII3 iEIII4, iEIII5, iRII1, iRII2, iRIII1, iRIV1 and iRIV2) were obtained from the rhizosphere and endosphere of hyperaccumulating plant Thlaspi goesingense grown in Redschlag, Austria [R. Idris, R. Trifonova, M. Puschenreiter, W.W. Wenzel, A. Sessitsch, Bacterial communities associated with flowering plants of the Ni hyperaccumulator Thlaspi goesingense, Appl. Environ. Microbiol. 70 (2004) 2667–2677]. Due to their unexpected diversity, abundance and nickel tolerance they were further characterized by detailed 16S rRNA gene analysis, DNA–DNA hybridization, fatty acid analysis, heavy metal tolerance, screening for known Ni resistance genes and phenotypic analysis. These strains were found to exhibit different multiple heavy metal resistance characteristics to Ni, Cd, Co, Zn and Cr. On the basis of their physiological and genotypic properties, strains could be grouped with Methylobacterium extorquens and M. mesophilicum. One endophyte, strain iEII3, was found to belong to a novel species for which the name M. goesingense is proposed.     

PROXIMO--a new docking algorithm to model protein complexes using data from radical probe mass spectrometry (RP-MS)

The design and implementation of a new algorithm, known as PROXIMO for protein oxidation interface modeller, is described to predict the structure of protein complexes using data generated in radical probe mass spectrometry (RP-MS) experiments. Photochemical radiolysis and discharge sources can be used to effect RP-MS in which hydroxyl radicals are formed directly from the bulk solvent on millisecond timescales and react with surface accessible residues in footprinting-like experiments. The algorithm utilizes a geometric surface fitting routine to predict likely structures for protein complexes. These structures are scored based on a correlation between the measured solvent accessibility of oxidizable residue side chains and oxidation shielding data obtained by RP-MS. The algorithm has been implemented to predict structures for the ribonuclease S-protein-peptide and calmodulin-melittin complexes using RP-MS data generated in this laboratory. The former is in close agreement with the high-resolution experimental structure available.     

An integrated strategy for analyzing the unique developmental programs of different myoblast subtypes

An important but largely unmet challenge in understanding the mechanisms that govern the formation of specific organs is to decipher the complex and dynamic genetic programs exhibited by the diversity of cell types within the tissue of interest. Here, we use an integrated genetic, genomic, and computational strategy to comprehensively determine the molecular identities of distinct myoblast subpopulations within the Drosophila embryonic mesoderm at the time that cell fates are initially specified. A compendium of gene expression profiles was generated for primary mesodermal cells purified by flow cytometry from appropriately staged wild-type embryos and from 12 genotypes in which myogenesis was selectively and predictably perturbed. A statistical meta-analysis of these pooled datasets—based on expected trends in gene expression and on the relative contribution of each genotype to the detection of known muscle genes—provisionally assigned hundreds of differentially expressed genes to particular myoblast subtypes. Whole embryo in situ hybridizations were then used to validate the majority of these predictions, thereby enabling true-positive detection rates to be estimated for the microarray data. This combined analysis reveals that myoblasts exhibit much greater gene expression heterogeneity and overall complexity than was previously appreciated. Moreover, it implicates the involvement of large numbers of uncharacterized, differentially expressed genes in myogenic specification and subsequent morphogenesis. These findings also underscore a requirement for considerable regulatory specificity for generating diverse myoblast identities. Finally, to illustrate how the developmental functions of newly identified myoblast genes can be efficiently surveyed, a rapid RNA interference assay that can be scored in living embryos was developed and applied to selected genes. This integrated strategy for examining embryonic gene expression and function provides a substantially expanded framework for further studies of this model developmental system.     

d-Maurocalcine,a Pharmacologically Inert Efficient Cell-penetrating Peptide Analogue

Maurocalcine has been the first demonstrated animal toxin acting as a cell-penetrating peptide. Although it possesses competitive advantages, its use as a cell-penetrating peptide (CPP) requires that analogues be developed that lack its characteristic pharmacological activity on ryanodine-sensitive calcium channels without affecting its cell-penetrating and vector efficiencies. Here, we present the synthesis, three-dimensional ¹H NMR structure, and activity of d-maurocalcine. We demonstrate that it possesses all of the desired features for an excellent CPP: preserved structure, lack of pharmacological action, conserved vector properties, and absence of cell toxicity. This is the first report of a folded/oxidized animal toxin in its d-diastereomer conformation for use as a CPP. The protease resistance of this new peptide analogue, combined with its efficient cell penetration at concentrations devoid of cell toxicity, suggests that d-maurocalcine should be an excellent vector for in vivo applications.     

The Insulin-like Growth Factor-1 Binding Protein Acid-labile Subunit Alters Mesenchymal Stromal Cell Fate

Age-related osteoporosis is accompanied by an increase in marrow adiposity and a reduction in serum insulin-like growth factor-1 (IGF-1) and the binding proteins that stabilize IGF-1. To determine the relationship between these proteins and bone marrow adiposity, we evaluated the adipogenic potential of marrow-derived mesenchymal stromal cells (MSCs) from mice with decreased serum IGF-1 due to knockdown of IGF-1 production by the liver or knock-out of the binding proteins. We employed 10–16-week-old, liver-specific IGF-1-deficient, IGFBP-3 knock-out (BP3KO) and acid-labile subunit knock-out (ALSKO) mice. We found that expression of the late adipocyte differentiation marker peroxisome proliferator-activated receptor γ was increased in marrow isolated from ALSKO mice. When induced with adipogenic media, MSC cultures from ALSKO mice revealed a significantly greater number of differentiated adipocytes compared with controls. MSCs from ALSKO mice also exhibited decreased alkaline-phosphatase positive colony size in cultures that were stimulated with osteoblast differentiation media. These osteoblast-like cells from ALSKO mice failed to induce osteoclastogenesis of control cells in co-culture assays, indicating that impairment of IGF-1 complex formation with ALS in bone marrow alters cell fate, leading to increased adipogenesis.     

High Prevalence,Coinfection Rate,and Genetic Diversity of Retroviruses in Wild Red Colobus Monkeys (Piliocolobus badius badius) in Ta? National Park,C?te d'Ivoire

Simian retroviruses are precursors of all human retroviral pathogens. However, little is known about the prevalence and coinfection rates or the genetic diversity of major retroviruses—simian immunodeficiency virus (SIV), simian T-cell lymphotropic virus type 1 (STLV-1), and simian foamy virus (SFV)—in wild populations of nonhuman primates. Such information would contribute to the understanding of the natural history of retroviruses in various host species. Here, we estimate these parameters for wild West African red colobus monkeys (Piliocolobus badius badius) in the Taï National Park, Côte d''Ivoire. We collected samples from a total of 54 red colobus monkeys; samples consisted of blood and/or internal organs from 22 monkeys and additionally muscle and other tissue samples from another 32 monkeys. PCR analyses revealed a high prevalence of SIV, STLV-1, and SFV in this population, with rates of 82%, 50%, and 86%, respectively. Forty-five percent of the monkeys were coinfected with all three viruses while another 32% were coinfected with SIV in combination with either STLV or SFV. As expected, phylogenetic analyses showed a host-specific pattern for SIV and SFV strains. In contrast, STLV-1 strains appeared to be distributed in genetically distinct and distant clades, which are unique to the Taï forest and include strains previously described from wild chimpanzees in the same area. The high prevalence of all three retroviral infections in P. b. badius represents a source of infection to chimpanzees and possibly to humans, who hunt them.Lentiviruses and deltaretroviruses that infect African nonhuman primates have received considerable attention as they are the precursors of all pathogenic human retroviruses: human immunodeficiency virus types 1 and 2 (HIV-1/HIV-2) and human T-cell lymphotropic virus type 1 (HTLV-1). These human infections are the results of past zoonotic transfers of simian immunodeficiency virus (SIV) and simian T-cell lymphotropic viruses type 1 (STLV-1) from wild monkeys and apes into local human populations, presumably through primate hunting and handling of primate bushmeat (13, 19, 43, 46, 55, 58, 59). Via the same route, zoonotic transmission of simian foamy virus (SFV), a spumaretrovirus whose exact pathogenicity in human hosts is still unknown, has also been shown (64). The increasing contact between humans and wild primates implies that further zoonotic transmission of retroviruses is likely to happen (42, 63). Studying the occurrence and circulation of simian retroviruses such as SIV, STLV-1, and SFV in wild primate populations enables us to better understand retrovirus evolution in primates and also provides tools for monitoring possible future retroviral zoonotic events.Systematic studies of SIV, STLV-1, and SFV in wild primates are relatively rare. Many use bushmeat samples, which can vary in their quality and are prone to cross-contamination from butchering and storage with other carcasses. Confiscated primates are also not representative of the situation in the wild since the animals are caught at a young age when the occurrence of different retroviruses may be extremely low (24). The technical possibilities for the detection of various pathogens in noninvasive samples such as urine and feces have greatly improved and are frequently used; however, in general, the sensitivity of detection methods is higher when blood and tissue samples are used (25, 32, 47). Such samples can be collected if fresh carcasses are found, or they can be collected by anesthetizing live primates for sampling purpose, animal translocation, or medical intervention, such as snare removal. The practical and ethical issues of each of the sampling methods have been discussed elsewhere (12, 14).Red colobus monkeys [Procolobus (Piliocolobus)] are interesting subjects for retroviral infection studies for a number of reasons. First, they are widely distributed (yet in a fragmented manner) from East to West Africa, which suggests that red colobus species and subspecies, or more likely ancestor(s) of these, could have been key hosts in transmitting retroviruses across tropical Africa (4, 54). Second, as they are herbivore primates, the hunting of other primates can be excluded as a route of infection. Finally, these monkeys are frequently hunted by humans and chimpanzees and represent a possibly large reservoir for retroviruses and other pathogens that ought to be investigated further (2, 45).Very little information is available about the prevalence and coinfection of SIV, STLV-1, and SFV in wild red colobus monkeys across Africa. In other colobine monkeys only SIV has been documented: in olive colobus (Procolobus verus) in Côte d''Ivoire and in black and white colobus (Colobus guereza) in Cameroon (7, 8). Based on fecal samples from habituated adult individuals, the prevalence of SIV in West African red colobus monkeys (SIVwrc; local subspecies, Piliocolobus badius badius) has been estimated to a minimum of 26% in the Taï National Park, Côte d''Ivoire, but the authors recognized the low sensitivity of viral RNA detection in fecal samples (34). Another study conducted on the same population revealed that 5 out of 10 blood samples were SIV positive (7). These results highlight that the most reliable prevalence data are based on analyses of blood/tissue samples although such sampling is not always feasible for reasons discussed above. Published prevalence information concerning STLV-1 and SFV in wild red colobus monkeys (STLV-1wrc and SFVwrc) in the same area is restricted to results obtained from analyses of a limited number of blood and necropsy samples collected as a part of studies whose focus was on cross-species transmission of these two viruses to chimpanzees (27, 28). However, these samples indicated a high prevalence of STLV-1wrc and SFVwrc in the red colobus monkey population (56% and 90%, respectively). A recent study from Uganda, East Africa, estimated the prevalence of SIV, STLV-1, and SFV in another red colobus species (Piliocolobus rufomitratus tephrosceles) to be 22.6%, 6.4%, and 97%, respectively (15). The study was performed using blood samples collected from anesthetized wild red colobus monkeys living in their natural habitat, which allowed reliable assessment of the prevalence and genetic diversity of these three retroviruses.The preliminary data from the Taï National Park indicate that there might be great variation in the prevalence of retroviruses across the African continent, even in closely related species of wild primates. Here, we aimed at generating reliable prevalence and coinfection data for SIVwrc, STLV-1wrc, and SFVwrc based on the analysis of blood and tissue samples from wild Western red colobus monkeys. We expected that this would allow for proper comparison of retroviral prevalence in the allied species P. b. badius and P. r. tephrosceles.