A ribosome-related signature in peripheral blood CLL B cells is linked to reduced survival following treatment.

We have used polysome profiling coupled to microarray analysis to examine the translatome of a panel of peripheral blood (PB) B cells isolated from 34 chronic lymphocytic leukaemia (CLL) patients. We have identified a 'ribosome-related' signature in CLL patients with mRNAs encoding for ribosomal proteins and factors that modify ribosomal RNA, e.g. DKC1 (which encodes dyskerin, a pseudouridine synthase), showing reduced polysomal association and decreased expression of the corresponding proteins. Our data suggest a general impact of dyskerin dysregulation on the translational apparatus in CLL and importantly patients with low dyskerin levels have a significantly shorter period of overall survival following treatment. Thus, translational dysregulation of dyskerin could constitute a mechanism by which the CLL PB B cells acquire an aggressive phenotype and thus have a major role in oncogenesis.

Remodelling of a polypyrimidine tract-binding protein complex during apoptosis activates cellular IRESs.

Post-transcriptional control of gene expression is mediated by the interaction of RNA-binding proteins with their cognate mRNAs that specifically regulate their stability, localization and translation. mRNA-binding proteins are multifunctional and it has been proposed therefore that a combinatorial RNA-binding protein code exists that allows specific protein sub-complexes to control cytoplasmic gene expression under a range of pathophysiological conditions. We show that polypyrimidine tract-binding protein (PTB) is central to one such complex that forms in apoptotic cells. Thus, during apoptosis initiated by TNF-related apoptosis inducing ligand there is a change in the repertoire of RNA-binding proteins with which PTB interacts. We show that altering the cellular levels of PTB and its binding partners, either singly or in combination, is sufficient to directly change the rates of apoptosis with increased expression of PTB, YBX1, PSF and NONO/p54(nrb) accelerating this process. Mechanistically, we show that these proteins post-transcriptionally regulate gene expression, and therefore apoptotic rates, by interacting with and stimulating the activity of RNA elements (internal ribosome entry segments) found in mRNAs that are translated during apoptosis. Taken together, our data show that PTB function is controlled by a set of co-recruited proteins and importantly provide further evidence that it is possible to dictate cell fate by modulating cytoplasmic gene expression pathways alone.

Rhinovirus RNA in the maxillary sinus epithelium of adult patients with acute sinusitis.

We used in situ hybridization for the detection of rhinovirus in maxillary sinus biopsy specimens obtained from 14 adult patients with acute sinusitis. In 7 specimens, rhinovirus RNA could be demonstrated in the maxillary sinus epithelium, thereby confirming the etiology of rhinovirus and the clinical suspicion of acute sinusitis.

Construction of regulatable picornavirus IRESes as a test of current models of the mechanism of internal translation initiation.

Picornavirus internal ribosome entry sites (IRESs) are approximately 450 nt. RNA elements that direct internal initiation of translation, such that when placed between the two cistrons of a dicistronic construct, they drive independent translation of the downstream cistron. Consequently they have been widely used for coordinated expression of two or more proteins. All picornavirus IRESs have an AUG triplet at the very 3' end, which is thought to be the actual site of internal ribosome entry. However with some IRESs, such as foot-and-mouth disease virus, and especially poliovirus, the majority of ribosomes do not initiate translation at this putative entry site AUG, but at the next AUG further downstream, which is thought to be accessed by a process of linear ribosome scanning from the entry site. If this is so, then it should be possible to regulate IRES-dependent translation by inserting an iron responsive element (IRE) between the putative entry site AUG and the main functional initiation site. This should make IRES-dependent translation sensitive to the concentration of iron regulatory protein (IRP), the protein that specifically binds to the IRE. This has been attempted with both the foot-and-mouth disease virus and poliovirus IRESs, and was successful in so far as an inhibition specifically of IRES-dependent translation was observed that was strictly dependent on both the presence of IRP and of a functional IRE motif inserted in the sense orientation. However, the range over which expression could be varied was rather limited (three- to fourfold maximum), because some IRES-dependent translation remained completely refractory to inhibition by even very high IRP concentrations. In contrast, with a cap-proximal IRE in the 5' untranslated region of an mRNA translated by the scanning mechanism, addition of sufficient IRP results in complete inhibition. These results support the model of IRES-promoted ribosome entry at an upstream site followed by strictly linear scanning to the main functional initiation site for the majority of internal initiation events, but imply that some ribosomes must access the functional initiation site by another route, possibly a nonlinear shunting-like mechanism.

Antigenic properties of human parechovirus 1.

Human parechoviruses 1 and 2 (HPEV1 and HPEV2, respectively), formerly known as echoviruses 22 and 23, have been assigned to a novel picornavirus genus on the basis of their distinct molecular and biological properties. To study the immunological characteristics of HPEV1 capsid proteins, antigenic analysis was carried out by a peptide scanning technique, which can be used to identify the immunogenic peptide sequences of a protein. Partially overlapping peptides, representing the capsid of HPEV1, were synthesized using a 12 aa window in a three residue shift and reactivity of rabbit and murine HPEV1 antisera against these peptides were tested. Using this method, an antigenic site in the VP0 polypeptide, recognized by both rabbit and murine antisera, was identified. The sequence of this region was conserved among HPEV1 clinical isolates obtained from Finland and the United States. Antiserum against this peptide region showed neutralizing activity against HPEV1 in cell culture. Because the C-terminal region of HPEV1 VP1 contains a functional RGD motif, the antigenicity of this region was also tested. By using the corresponding peptide antiserum, neutralization of HPEV1 was observed. Cross-neutralization between HPEV1 and coxsackievirus A9, an enterovirus with a similar RGD motif in VP1, was also detected.

Molecular typing of enteroviruses: current status and future requirements. The European Union Concerted Action on Virus Meningitis and Encephalitis.

Human enteroviruses have traditionally been typed according to neutralization serotype. This procedure is limited by the difficulty in culturing some enteroviruses, the availability of antisera for serotyping, and the cost and technical complexity of serotyping procedures. Furthermore, the impact of information derived from enterovirus serotyping is generally perceived to be low. Enteroviruses are now increasingly being detected by PCR rather than by culture. Classical typing methods will therefore no longer be possible in most instances. An alternative means of enterovirus typing, employing PCR in conjunction with molecular genetic techniques such as nucleotide sequencing or nucleic acid hybridization, would complement molecular diagnosis, may overcome some of the problems associated with serotyping, and would provide additional information regarding the epidemiology and biological properties of enteroviruses. We argue the case for developing a molecular typing system, discuss the genetic basis of such a system, review the literature describing attempts to identify or classify enteroviruses by molecular methods, and suggest ways in which the goal of molecular typing may be realized.

Genetic and phylogenetic clustering of enteroviruses.

Genetic and phylogenetic analysis of enteroviruses showed that in the 5'NCR enteroviruses formed three clusters: polioviruses (PVs), coxsackievirus A type 21 (CAV21), CAV24 and enterovirus type 70 (ENV70) formed one cluster; coxsackievirus B isolates (CBVs), CAV9, CAV16, ENV71, echovirus type 11 (EV11), EV12 and all partially sequenced echoviruses and swine vesicular disease virus (SVDV) belonged to another cluster and bovine enteroviruses (BEVs) formed the third cluster. In the capsid coding region five clusters were seen: PVs, CAV21 and CAV24 formed one cluster (PV-like); ENV70 formed a cluster of its own; all CBVs, CAV9, EV11, EV12 and SVDV formed the third cluster (CBV-like); CAV16, CAV2 and ENV71 belonged to the fourth cluster (CAV16-like) and BEVs formed their own cluster (BEV-like). In the 3'NCR the same clusters were seen as in the coding region suggesting a close association of the 3'NCR with viral proteins while the cellular environment may be more important in the evolution of the 5'NCR. Secondary structures were predicted in the 3'NCR, which showed two different patterns among the five clusters. A potential pseudoknot region common in all five clusters was identified. Although the BEV-like viruses formed a separate cluster in all genomic regions, in the coding region they seem to be phylogenetically related to the CAV16-like viruses.

Genetic divergence of poliovirus strains isolated in the Karachi region of Pakistan.

Seventy-seven wild poliovirus strains isolated from poliomyelitis cases in the Civil Hospital of Karachi in Pakistan in 1989-1993 were selected for partial sequence analysis covering the VP1/2A junction region of the viral genome to study the genetic relationships and epidemiological links between strains. Viral RNA was partially amplified by RT-PCR and sequenced by a solid phase method. Computer analysis revealed genetic divergence of the strains within each serotype. Most of the nucleotide differences between strains were silent: only a few specific amino acid substitutions were seen in the sequenced region. Three genotypes of poliovirus type 1 and two of poliovirus type 3 were co-circulating, while type 2 strains were represented by a single genotype. Representatives of all the genotypes present have been found among previously or concurrently characterized stains isolated elsewhere, but direct epidemiological links were found only in the case of serotype 1. Many of the epidemics caused by poliovirus type 1 in other countries were genetically linked to Pakistan. This study clearly shows the endemic circulation and wide variation of all three poliovirus serotypes in southern Pakistan and indicates the need for more effective vaccination programmes to prevent the further spread of these wild viruses.

Molecular analysis of coxsackievirus A16 reveals a new genetic group of enteroviruses.

Coxsackievirus A16 (CAV16) a member of the Enterovirus genus of Picornaviridae, is associated with hand-foot-and-mouth disease, a febrile papulovesicular rash of childhood. We have determined the complete nucleotide sequence of the genome of the prototype strain of CAV16 which consists of 7413 nucleotides plus the poly(A) tail. Alignment of the sequence with the previously studied enteroviruses showed that the genome organization is typical for a member of this virus genus. However, the predicted amino acid sequence of individual CAV16 proteins differed from those of all previously sequenced enteroviruses by 25-62%. The genomic sequence of CAV2 in the capsid and 2A polypeptide regions was also determined. It was found to differ from that of CAV16 by no more than 5-43%. The partial nucleotide sequence of enterovirus 71 in the VP1-2A region suggested that it is also closely related to CAV16. The results indicate that CAV16, CAV2, and enterovirus 71 represent a distinct genetic group of enteroviruses.

Poliovirus type 3/Saukett: antigenic and structural correlates of sequence variation in the capsid proteins.

The Saukett/USA/50 strain is the type 3 component of the inactivated poliovirus vaccine. The capsid-coding region of genomic RNA of Saukett strains from five different sources was sequenced and the sequence differences were correlated with antigenic differences measurable with poliovirus type 3-specific neutralizing monoclonal antibodies. All strains appeared to have capsid protein genes identical in size to those of the entirely sequenced type 3 poliovirus strains. The nucleotide sequence identity between the strains was 91% on the average and the strains could be divided into three groups. Amino acid differences were seen in 30 positions located throughout the capsid region both within and outside the known antigenic sites. Substitutions at the known antigenic sites explained most of the observed antigenic differences. Use of the atomic coordinates of the crystal structure model of the Sabin 3 virus and prior data based on escape mutants and peptide scanning revealed that most of the exposed substitutions located outside the known antigenic sites are spatially associated with regions found to be antigenic by either or both of these methods.

Genetic variation in vivo and proposed functional domains of the 5' noncoding region of poliovirus RNA.

Poliovirus has a single-stranded RNA genome of about 7,440 nucleotides (nt) with an unusually long 750-nt noncoding region in the 5' end (5'NCR). Several regulatory functions have been assigned to the 5'NCR. We sequenced the 5'NCRs of 33 wild-type 3 poliovirus strains to study the range and distribution of naturally occurring sequence variations. In this regard, the 5'NCR can be divided into a conserved part (nt 1 to 650) and a hypervariable part (nt 651 to 750). In the conserved part, altogether 234 unevenly distributed nucleotide positions (36%) showed variation. When these positions were plotted against the predicted secondary-structure models, it was found that the existence of most of the proposed stem-loop structures was supported by extensive structure-conserving substitutions in the stems. Regions with conserved sequences, as well as mutational hot spots, were observed. The hypervariable part of the 5'NCR varied up to 56% between the strains studied. The A + U percentage was significantly higher than in the conserved part. The number of AUG codons varied between 5 and 15 in the conserved part of the 5'NCR, while none was found in the hypervariable part. These results provide information that can be used in site-directed mutagenesis and other approaches targeted to reveal the functional domains of the 5'NCR.

Evolution of influenza B/Victoria/2/87-like viruses: occurrence of a genetically conserved virus under conditions of low epidemic activity.

Nucleotide sequence analysis of the gene region coding for the HA1 domain of the influenza B virus haemagglutinin was performed on seven field strains isolated during the 1989 to 1990 season and two field strains isolated in 1985 and 1988 in Finland. All isolates were antigenically and genetically related to B/Victoria/2/87 virus and distinct from B/Yamagata/16/88 virus. The three strains isolated at the beginning of the 1989 1990 season in Turku were almost identical to an American variant (B/Texas/37/88-B/Ohio/10/88) of the previous season, whereas the four strains isolated later in the 1989 to 1990 season in Helsinki formed a new group of heterogeneous viruses. The phylogenetic tree compiled suggests that the two branches had evolved from a common origin, probably in 1987.

Evolution of influenza A(H1N1) viruses during a period of low antigenic drift in 1986-91: sequence of the HA1 domain of influenza A/Finland/158/91.

This study used the nucleotide sequence coding for the HA1 domain of virus haemagglutinin to show that influenza A/Finland/158/91, which represents the H1N1 subtype viruses prevalent in Finland in 1990/91, was a direct descendant of a virus (A/NN/1605/88) isolated during the 1988/89 epidemic season in Japan. The elevated rate of 7.4 x 10(-3) nucleotide substitutions per site per year is discussed. The new branch of H1N1 subtype viruses is characterized by loss of a glycosylation site, which may affect subsequent antigenic drift.

Generation of virus genetic lineages during an outbreak of poliomyelitis.

Wild poliovirus type 3 isolates collected during the Finnish outbreak (1984 to 1985) in different geographical locations were compared by partial RNA sequencing. The entire 5' non-coding end and a discontinuous part of the capsid coding region were sequenced from 15 isolates. Combining the present sequence data with previously published data and analysing these by the maximum parsimony method showed that the epidemic strains had diverged in cocirculating lineages. Genetic comparison of strains isolated from a single person often revealed a branched structure in the phylogenetic tree indicating high potential for diversification. The extent of variation generated under immunological pressure during an infection lasting for weeks in one person was high as compared with the observed geographical variation.

Type 3 poliovirus/Finland/1984 is genetically related to common Mediterranean strains.

Strains of poliovirus type 3 isolated in Finland in 1984 and 1985 (P3/Fin/84) are known to differ considerably from the type 3 vaccine strains in both nucleotide sequence and antigenic properties. In the search for the origin of the outbreak we first tested 80 type 3 strains that had been isolated elsewhere in the world during the years 1953 to 1986. An oligonucleotide probe complementary to a highly variable 17 nucleotide interval in the 5' non-coding region of the genomic RNA of P3/Fin/84 reacted with five strains. Also it was revealed that two of the latter five strains were related to the P3/Fin/84 strains in two separate genomic regions compared after partial RNA sequencing. One of them was isolated in Switzerland in 1980 and the other in Turkey in 1981. The Swiss strain was from a patient who had recently returned from a journey to various Mediterranean countries. Consequently, 16 other strains isolated in the late 1970s and early 1980s in Europe or in the Mediterranean countries were studied in detail by partial genomic sequencing and with neutralizing monoclonal antibodies. Two separate regions of the genome were compared by sequencing and corresponding dendrograms were constructed. The Switzerland and Turkey strains were found to be the strains most closely related to the viruses of the 1984 Finland epidemic. These results indicate that type 3 poliovirus strains related to P3/Fin/84 had been circulating in Mediterranean countries since the late 1970s.

Rapid molecular evolution of wild type 3 poliovirus during infection in individual hosts.

A panel of nine neutralizing monoclonal antibodies was used to analyse the antigenic properties of 188 plaque-purified type 3 poliovirus strains from 17 faecal specimens, derived from eight people during a 2 month observation period. Most poliovirus specimens consisted of a mixture of antigenically distinct variants and the composition of the mixture was found to change between sequential specimens in many individuals, indicating antigenic evolution. Thirty-five strains representing different antigenic patterns were selected for partial sequencing of genomic RNA. Mutations leading to amino acid substitutions, as well as silent mutations, were seen at and close to the known antigenic sites. The frequency of silent mutations was used to estimate the evolutionary potential of the virus. The largest difference in silent changes between strains isolated from one person was 0.8%, which corresponds to a minimum of about 60 mutations per genome within a period of 3 weeks. The observed incidence of silent mutations between isolates from different persons was usually between 0.8 and 2%. These figures agree with the previously reported overall mutation rates of poliovirus, determined by other methods.

Ultrastructure of a Bacillus sp. strain KL8 isolated from indoor dust.

A motile Gram-positive bacterial strain (KL8) was isolated from indoor dust. It was identified by API-test50 CHB as a species of Bacillus. This Bacillus sp. strain KL8 was described using different electron microscopic techniques: negative staining, thin sectioning, metal shadowing and freeze-etching. An additional surface layer (S-layer) was the outermost layer of the cell wall of this flagellated bacterium. The hexagonally arranged protein lattice covering the cells had a lattice constant about 9-10 nm, which falls in the same range as that of Bacillus anthracis.

Restricted variability of a 17 nucleotide stretch within the 5'-noncoding region of poliovirus genome.

The outbreak of poliomyelitis in Finland in 1984 was caused by a wild strain of poliovirus 3 with uncommon molecular and antigenic properties. We prepared a synthetic oligonucleotide probe complementary to nucleotides 494-510 in the 5'-noncoding part of the genome of a representative strain of the outbreak. This short nucleotide stretch was found to be relatively well conserved within the outbreak and uncommon among 82 independent poliovirus isolates. It may thus be a useful marker for screening isolates to identify those requiring more detailed genetic comparison. The sequences of the corresponding region of the genome are known for 32 separate poliovirus strains and 3 coxsackie B virus strains and show 6 fully conserved nucleotides that could assume a constant hairpin-loop position in a hypothetical secondary structure of the RNA. This could explain the persistence of a particular 17 nucleotide sequence for 40 years in nature in this highly variable region of the poliovirus genome.

Viruses in sewage waters during and after a poliomyelitis outbreak and subsequent nationwide oral poliovirus vaccination campaign in Finland.

During an outbreak of paralytic poliomyelitis in Finland in 1984 and 1985 the widespread circulation of the causative wild-type serotype 3 poliovirus in the population was documented by demonstrating the virus in sewage water specimens in 13 different locations in the greater Helsinki district and in 13 other cities or towns all over the country. After the nationwide campaign with oral poliovirus vaccine in 1985, poliovirus serotypes 2 and 3 were readily isolated from sewage waters for up to 2 months, whereas type 1 poliovirus seemed to disappear from the sewage more rapidly. All of these isolates were temperature sensitive and therefore most likely vaccine related. The efficacy of the vaccination campaign in regard to elimination of the epidemic type 3 strain was evaluated by a follow-up study on viruses in sewage waters continued for 12 months through the subsequent expected season of poliomyelitis. Several types of enteroviruses, including five vaccine-related poliovirus strains, were identified in the 72 virus-positive specimens out of 93 studied. No wild-type polioviruses were found, indicating the success of the campaign.