L1 Sequences Research Articles

Virological and molecular characterization of a mammalian orthoreovirus type 3 strain isolated from a dog in Italy.

A mammalian orthoreovirus (MRV) strain was isolated from a pup with fatal diarrhea, which had a concurrent infection by canine parvovirus type 2. The reovirus isolate showed an atypical hemagglutination pattern and a retarded electrophoretic mobility of the S1 segment, which is characteristic of MRV type 3 (MRV-3). Assignment of the isolated virus to MRV-3 was confirmed by type-specific RT-PCR assays, targeting the S1 gene, and by subsequent sequence analysis of the PCR product. By phylogeny based on the S1 gene of several MRVs, the isolate fell into lineage E, along with the murine strain T3C9/61 and the bovine strains T3C18/61 and T3C31/59. Conversely, L1 sequences were found to segregate regardless of the viral type. A total of 110 fecal samples, 56 nasal and 31 ocular swabs from dogs with diarrhea or nasal/ocular discharge were tested by a nested-PCR assay specific for reoviruses, and no sample was found to contain MRV RNA, a finding that is apparently in contrast with the seroprevalence (25.77%) observed in dogs.

Chromosomal aberrations induced by double strand DNA breaks

It has been suggested that introduction of double strand DNA breaks (DSBs) into mammalian chromosomes can lead to gross chromosomal rearrangements through improper DNA repair. To study this phenomenon, we employed a model system in which a double strand DNA break can be produced in human cells in vivo at a predetermined location. The ensuing chromosomal changes flanking the breakage site can then be cloned and characterized. In this system, the recognition site for the I- SceI endonuclease, whose 18 bp recognition sequence is not normally found in the human genome, is placed between a strong constitutive promoter and the Herpes simplex virus thymidine kinase ( HSV-tk) gene, which serves as a negative selectable marker. We found that the most common mutation following aberrant DSB repair was an interstitial deletion; these deletions typically showed features of non-homologous end joining (NHEJ), such as microhomologies and insertions of direct or inverted repeat sequences. We also detected more complex rearrangements, including large insertions from adjacent or distant genomic regions. The insertion events that involved distant genomic regions typically represented transcribed sequences, and included both L1 LINE elements and sequences known to be involved in genomic rearrangements. This type of aberrant repair could potentially lead to gene inactivation via deletion of coding or regulatory sequences, or production of oncogenic fusion genes via insertion of coding sequences.

L1 sequence of a new human papillomavirus type-58 variant associated with cervical intraepithelial neoplasia

The present study on molecular characterization of a human papillomavirus (HPV) isolated in Central Brazil describes the L1 gene sequence from a new variant of HPV-58, the isolate Bsb-02. The sample was from a smear obtained from a woman with cervical intraepithelial neoplasia grade II. The whole L1 gene from isolate Bsb-02 was sequenced automatically, showing 99.1% nucleotide identity with the gene from the HPV-58 reference. The clustering between Bsb-02 and HPV-58 reference sequence was also supported by phylogenetic analysis. Fourteen nucleotide substitutions were observed: eight were synonymous and six were associated with amino acid substitutions. A10V and V144I have not been previously described. At GenBank, the only complete L1 sequence from HPV-58 in addition to the HPV-58 reference one is that of Bsb-02. These data provide information that may be relevant to HPV diagnosis and to rational vaccine strategies. HPV variants may also be associated with host immune responses and with the risk of cervical neoplasia.

Cervical Cancer-causing Human Papillomaviruses have an Alternative Initiation Site for the L1 Protein

All known sequences of the DNA encoding the major cervical cancer-causing human papillomavirus type 16 (HPV16) L1 capsid protein contain initiation codons which would allow translation to begin at either nucleotide 5559 or 5637. However the formation of virus-like particles (VLPs) only occurs efficiently when the initiation codon at nucleotide 5637 is used for in vitro expression studies. This knowledge, in concert with the fact that virions have not been observed in HPV16-infected epithelium, raises the notion that the major L1 translation product in this HPV type may be largely confined to initiation at nucleotide 5559. Sequence analysis of various HPV types associated with particular clinical outcomes has revealed that L1 sequences of the major cervical cancer-associated viruses generally possess the ability to encode a longer translation product whilst the non-cancer-causing viruses do not. Equally intriguing, the upstream initiation codon is always separated by 78 nucleotides from the initiation codon that produces L1 protein which efficiently assembles into VLPs. We speculate that the longer L1 protein could play a role in the development of cervical carcinoma and that HPVs with the potential to cause cervical cancer may be identified by the presence of an in-frame ATG situated 78 nucleotides upstream.

Mutations on the FG surface loop of human papillomavirus type 16 major capsid protein affect recognition by both type-specific neutralizing antibodies and cross-reactive antibodies

The aim of this study was to further characterize the conformational neutralizing epitopes present on the surface-exposed FG loop of human papillomavirus (HPV) type 16 L1 major capsid protein. We have generated previously two chimeric L1 proteins by insertion of a foreign peptide encoding an epitope of the hepatitis B core (HBc) antigen within the FG loop. In addition, three other chimeric L1 proteins were obtained by replacing three different FG loop sequences by the HBc motif and three others by point mutations. All these chimeric L1 proteins retained the ability to self-assemble into virus-like particles (VLPs), with the exception of the mutant with substitution of the L1 sequence 274-279 by the HBc motif. The eight chimeric VLPs were then analyzed for differential reactivity with a set of six HPV-16 and HPV-31 monoclonal antibodies that bound to conformational and linear epitopes. The binding patterns of these monoclonal antibodies confirmed that the FG loop contained or contributed to neutralizing conformational epitopes. The results obtained suggested that the H31.F7 antibody, an anti-HPV-31 cross-reacting and neutralizing antibody, recognized a conformational epitope situated before the 266-271 sequence. In addition, H16.E70 neutralizing antibody reactivity was reduced with L1 VLPs with an Asn to Ala point mutation at position 270, suggesting that Asn is a part of the epitope recognized by this antibody. This study contributes to the understanding of the antigenic structure of HPV-16 and -31 L1 proteins by confirming that the FG loop contributes to neutralizing epitopes and suggesting the existence of both type-specific and cross-reactive conformational epitopes within the FG loop.

Limits of integrals involving almost periodic functions

Let Sp ⊂ R+ be a discrete countable set, let {αλ}λ∈Sp be a sequence in l1(Sp) and f(x) ≔ ∑λ∈Spαλsin(λx). f is an almost periodic odd function with {λ: ±λ ∈ Sp} as spectrum. We give some conditions about the set S so that \(\int _1^{+\infty}\ f(x){\rm sin}(Rx){dx\over x}\rightarrow 0\) whenever R → +∞, R ∈ S.

Identity by descent and DNA sequence variation of human SINE and LINE elements

To test the hypothesis that Alu and L1 elements are genetic characters that are essentially homoplasy-free, we sequenced a total of five human L1 elements and eleven recently integrated Alu elements from 160 chromosomes (80 individuals representing four diverse human populations). Analysis of worldwide samples at L1 loci revealed 292 segregating sites and a nucleotide diversity of 0.0050. For Ya5 Alu loci, there were 129 segregating sites and nucleotide diversity was estimated at 0.0045. The Alu and L1 sequence diversity varied element to element. No completely or partially deleted Alu or L1 alleles were identified during the analysis. These data suggest that mobile element insertions are identical by descent characters for the study of human population genetics.

Timing of establishment of paternal methylation imprints in the mouse

Imprinted genes are characterized by predominant expression from one parental allele and differential DNA methylation. Few imprinted genes have been found to acquire a methylation mark in the male germ line, however, and only one of these, H19, has been studied in detail. We examined methylation of the Rasgrf1 and Gtl2 differentially methylated regions (DMR) to determine whether methylation is erased in male germ cells at e12.5 and when the paternal allele acquires methylation. We also compared their methylation dynamics with those of H19 and the maternally methylated gene Snrpn. Our results show that methylation is erased on Rasgrf1, H19, and Snrpn at e12.5, but that Gtl2 retains substantial methylation at this stage. Erasure of methylation marks on Gtl2 appears to occur later in female germ cells to give the unmethylated profile seen in mature MII oocytes. In the male germ line, de novo methylation of Rasgrf1, Gtl2, and H19 occurs in parallel between e12.5 and e17.5, but the DMR are not completely methylated until the mature sperm stage, suggesting a methylation dynamic different from that of IAP, L1, and minor satellite sequences, which have been shown to become fully methylated by e17.5 in male germ cells. This study also indicates important differences between different imprinted DMR in timing and extent of methylation in the germ cells.

Teleost Fish Genomes Contain a Diverse Array of L1 RetrotransposonLineages That Exhibit a Low Copy Number and High Rate of Turnover

Retrotransposable elements exhibit a wide range of variation in population dynamics, abundance, and lineage diversity among host genomes across taxa. This range of diversity is illustrated by a single well-defined constituent monophyletic clade of L1 non-LTR retrotransposons that is shared between mammalian and teleost fish genomes. Despite the clear phylogenetic relationships that exist between mammalian and teleost L1 sequences, these elements exhibit markedly different dynamics within their respective taxa. While mammalian genomes typically contain a single, abundant lineage of L1 elements that traces millions of years of evolution, the zebraflsh genome was recently shown to exhibit a high diversity of ancient lineages coexisting at a very low copy number and apparently exhibiting a high rate of turnover. In the present study, a combination of degenerate PCR, lineage-specific PCR, and genomic Southern blot analysis is utilized to demonstrate high L1 lineage diversity, low copy number, and a high proportion of polymorphic inserts in the genomes of the killifish species, Fundulus heteroclitus. Additional species surveyed by degenerate PCR include Cyprinodon variegatus, Rivulus marmoratus, and Menidia beryllina. These results further support the generality of the differences that exist in host-element dynamics between teleost fish and mammalian genomes with regard to L1 retrotransposons.

Mixed valence aspects of diruthenium complexes [((L)ClRu)2(mu-tppz)]n+ incorporating 2-(2-pyridyl)azoles (L) as ancillary functions and 2,3,5,6-tetrakis(2-pyridyl)pyrazine (Tppz) as bis-tridentate bridging ligand.

Tppz [2,3,5,6-tetrakis(2-pyridyl)pyrazine]-bridged complexes [((L)ClRu)(2)(mu-tppz)]n+ with structurally similar but electronically different ancillary ligands, 2-(2-pyridyl)azoles (L), were synthesized as diruthenium(II) species. Cyclic voltammetry, EPR of paramagnetic states, and UV-vis-NIR spectroelectrochemistry show that the first two reduction processes occur at the tppz bridge and that oxidation involves mainly the metal centers. The mixed valent intermediates from one-electron oxidation exhibit moderate comproportionation constants 10(4) < K(c) < 10(5) but appear to be valence-averaged according to the Hush criterion. Redox potentials, EPR, and UV-vis-NIR results show the effect of increasing donor strength of the ancillary ligands along the sequence L(1) < L(2) < L(4) << L(3), L(1) = 2-(2-pyridyl)benzoxazole, L(2) = 2-(2-pyridyl)benzthiazole, L(3) = 2-(2-pyridyl)benzimidazolate, L(4) = 1-methyl-2-(2-pyridyl)-1H-benzimidazole. Whereas the mixed valent complexes with L(1) and L(2) remain EPR silent at 4 K, the analogues with L(4) and L(3) exhibit typical ruthenium(III) EPR signals, albeit with some noticeable ligand contribution in the case of the L(3)-containing complex. Intervalence charge transfer (IVCT) bands were found in the visible spectrum for the complex with L(3) but in the near-infrared range (at ca. 1500 nm) for the other systems.

Mutations of human papillomavirus (HPV) 16 type L1 genes from cervical carcinoma biopsies in southern Xinjiang Uygur women

To study the mutations of Human Papillomavirus (HPV) 16 type L1 genes of cervical carcinoma biopsies from Uygur women in Southern Xinjiang, and analyze changes of L1 protein function. The tissue DNA was extracted from cervical carcinoma biopsies. HPV16 L1 genes were amplified by PCR from the DNA HPV16 type L1 genes were sequenced and analyzed. The result of PCR showed that the positive rate of HPV16 L1 was 84.21% (16/19). These DNA were sequenced, and we found some mutations in comparison with the previously published sequence of prototype HPV16 L1. Some of the mutations changed the triplet codes, subsequently led to changes of amino acids. The mutations of all thirteen HPV16 L1 fragments formed six patterns (XJL1-1 approximately XJL1-6) at nucleic acid level. Compare to HPV16 prototype, their homology were 99.69% to 99.87%. There were four mutations in nucleic acid sequences of XJL1-1, which occurred also in XJL1-2 approximately XJL1-6. Moreover, there are other mutations in XJL1-2 approximately XJL1-6 besides the four mutations in XJ L1-1. The mutations of all thirteen HPV16 L1 fragments formed four patterns at amino acid level, among the mutations XJL1-1/2/3 was by 76.92% (8/13). HPV16 type L1 genes from cervical carcinoma biopsies occurred some mutations in Uygur women from southern Xinjiang, and formed several patterns as well as mainstream pattern. The mutations of L1 proteins changed its hydrophobicity and antigenicity. The research suggested that the mutations of HPV16 type L1 genes associated with HPV16 phylogenesis and escape from immune recognition.

African Haplogroup L mtDNA sequences show violations of clock-like evolution.

A set of 96 complete mtDNA sequences that belong to the three major African haplogroups (L1, L2, and L3) was analyzed to determine if mtDNA has evolved as a molecular clock. Likelihood ratio tests (LRTs) were carried out with each of the haplogroups and with combined haplogroup sequence sets. Evolution has not been clock-like, neither for the coding region nor for the control region, in combined sets of African haplogroup L mtDNA sequences. In tests of individual haplogroups, L2 mtDNAs showed violations of a molecular clock under all conditions and in both the control and coding regions. In contrast, haplogroup L1 and L3 sequences, both for the coding and control regions, show clock-like evolution. In clock tests of individual L2 subclades, the L2a sequences showed a marked violation of clock-like evolution within the coding region. In addition, the L2a and L2c branch lengths of both the coding and control regions were shorter relative to those of the L2b and L2d sequences, a result that indicates lower levels of sequence divergence. Reduced median network analyses of the L2a sequences indicated the occurrence of marked homoplasy at multiple sites in the control region. After exclusion of the L2a and L2c sequences, African mtDNA coding region evolution has not significantly departed from a molecular clock, despite the results of neutrality tests that indicate the mitochondrial coding region has evolved under nonneutral conditions. In contrast, control region evolution is clock-like only at the haplogroup level, and it thus appears to have evolved essentially independently from the coding region. The results of the clock tests, the network analyses, and the branch length comparisons all caution against the use of simple mtDNA clocks.

Human papillomavirus genomes in squamous cell carcinomas of the uterine cervix

The association between invasive cervical carcinoma and human papillomavirus (HPV) has now been established beyond doubt, but this is not necessarily a direct-and-effect association. To assess the causality of HPV, we analyzed HPV genomes in squamous cell carcinomas (SCCS) of the uterine cervix by both blot hybridization and PCR. Genital HPV sequences were found in 231 (79%) of 294 SCCs by blot hybridization with more than five copies of entire HPV genomes identified in some cases including HPV 16 (92 cases), HPV 58 (32 cases), and HPV 52 (24 cases). By PCR-direct sequence analysis in 250 of 294 SCCs, genital HPV sequences were found in 240 samples (96%). The partial L1 sequences of HPV 16 were identified in 123 cases, and those of HPVs 18 and 31 were found in 24 and 20 cases, respectively. In addition, multiple HPV types were identified in 29 (12%) of 250 SCCs, and the HPV copy number, detected by PCR only, was less than 0.05. Marked discrepancies were therefore evident between the two analytical techniques. In this report, we discuss the causality of HPV for SCC with regard to the length of the viral genome, the amount of viral DNA, and multiple HPVs in single SCCs.

Existence and Conditional Energetic Stability of Capillary-Gravity Solitary Water Waves by Minimisation

Firstly, the two-dimensional stationary water-wave problem is considered. Existence of capillary-gravity solitary waves is proved by minimising a functional related to Smale’s amended potential. We first establish the existence of periodic solutions of arbitrarily large periods, leading to a minimising sequence in L2(ℝ) that stays away from the boundary of the neighbourhood of 0 ∈ W2,2(ℝ) in which the analysis is carried out. With the help of the concentration-compactness principle, we then show that every minimising sequence has a subsequence that, after possible shifts in the propagation direction, converges in L2(ℝ) to a minimiser. Secondly, for the evolutionary problem, we prove that the set of minimal solitary waves as a whole is energetically conditionally stable. “Energetically” means that the distance to the set of all minimisers is defined in terms of the total energy, and “conditionally” means that we consider solutions to the evolutionary problem that do not explode instantaneously but could perhaps explode in finite time (e.g., via the explosion of another norm). We work in some bounded set in W2,2(ℝ) that contains the quiescent state and we are not interested in the fate of solutions that leave this set.

Antinematodal activity and the mechanism of the antimicrobial peptide, HP (2-20), against Caenorhabditis elegans.

The peptide HP (2-20), derived from the N-terminal sequence of Helicobacter pylori ribosomal protein L1 (RPL1), has a nematicidal activity against eggs and worms of Caenorhabditis elegans. Eggs treated with HP (2-20) (69%) has a higher fluorescence intensity with propidium iodide staining, which was similar to that of melittin (82%) but higher than untreated cells (5.7%). Confocal microscopy showed that the peptides were located in the shell of the eggs and the inner and outer surfaces of the worms. HP (2-20) therefore may exert its antinematodal activity by disrupting the structure of the egg's shell and the cell membrane via pore formation or by direct interaction with the lipid bilayers in a detergent-like manner.

The L1 Retroelement-related p40 Protein Induces p38δ MAP Kinase

We characterized a full length L1 mRNA in a rheumatoid arthritis (RA) synovial tissue and determined the degree of methylation of its 5′-UTR. We asked whether not only intact but also altered L1s can exert biological activities by transfecting RA synovial fibroblasts (SF) with either retrotransposition-competent or incompetent L1s and examined their capacity to induce p38δ. Total RNA was isolated from the synovial tissue of a 35-year-old woman with highly destructive RA. A complete L1 sequence was obtained by 3′/5′-RACE. Methylation of the genomic 5′-UTR was determined by the sodium-disulfide/PCR method. RA-SF were transfected by lipofection with either a functional L1 or an ORF2-mutated L1 element. The expression of p38δ was measured by RT-PCR and Western blot. The full length L1 mRNA included a 5′-UTR, an ORF1 and an ORF2. Three of five CpG islands (60%) of the genomic L1 5′-UTR were hypomethylated and the ORF2 was deactivated by the insertion of stop codons. Both, intact and ORF2-mutated L1 vectors, induced the expression of p38δ. Thus, even an ORF2-mutated L1 element, as expressed in RA, is biologically active and both L1 ORF1 and p38δ transcripts may appear as a consequence of genomic hypomethylation. The induction of p38δ appears to be mediated by an ORF1/p40-dependent process. This is the first indication of a p40 mediated transactivation.

Identification of a human papillomavirus type 16-specific epitope on the C-terminal arm of the major capsid protein L1.

To characterize epitopes on human papillomavirus (HPV) virus-like particles (VLPs), a panel of mutated HPV-16 VLPs was created. Each mutated VLP had residues substituted from HPV-31 or HPV-52 L1 sequences to the HPV-16 L1 backbone. Mutations were created on the HPV-31 and -52 L1 proteins to determine if HPV-16 type-specific recognition could be transferred. Correct folding of the mutated proteins was verified by resistance to trypsin digestion and by binding to one or more conformation-dependent monoclonal antibodies. Several of the antibodies tested were found to bind to regions already identified as being important for HPV VLP recognition (loops DE, EF, FG, and HI). Sequences at both ends of the long FG loop (amino acids 260 to 290) were required for both H16.V5 and H16.E70 reactivity. A new antibody-binding site was discovered on the C-terminal arm of L1 between positions 427 and 445. Recognition of these residues by the H16.U4 antibody suggests that this region is surface exposed and supports a recently proposed molecular model of HPV VLPs.

Characterisation of a fourth immunoglobulin light chain isotype in the common carp

Three isotypes of immunoglobulin (Ig) light (L) chain, designated L1A, L1B, and L3, have been characterised in the common carp ( Cyprinus carpio L.) to date. In this paper the molecular cloning of a fourth IgL isotype in carp, designated L2, is described. A reverse transcription–polymerase chain reaction (RT–PCR) method including 5′- and 3′-RACE was used to isolate carp L2 cDNA clones. The VL sequences could be divided into two distinct VL families, designated VL2-1 and VL2-2, most similar to rainbow trout (68% similarity) and zebrafish (78%) VL2 amino acid sequences, respectively. The CL amino acid sequences showed the highest similarity to zebrafish L2 (80%), and contained the characteristic cysteines necessary for intradomain or interchain disulphide bridges as did the VL sequences. Neither the VL nor CL sequences demonstrated such a high similarity to the other carp IgL isotypes, L1A, L1B, and L3. For JL segments, sequence variations appeared to be confined to a few positions. In the course of 5′- and 3′-RACE, cDNA clones containing recombination signal sequence (RSS), representatives of IgL sterile transcripts, were obtained. Southern blot analyses suggested that the locus of carp L2 has a cluster-like organisation. Phylogenetic analyses showed that both carp VL2 and CL2 amino acid sequences highly clustered with other teleost L2 sequences.

Human papillomavirus type 16 and 18 L1 protein peptide binding to VERO and HeLa cells inhibits their VLPs binding.

Human papillomaviruses (HPVs) are the cause of epithelial lesions, HPV type 16 and type 18 being associated with the development of anogenital cancer. The L1 Major Capsid Protein (L1) represents about 90% of total HPV protein and is involved in virus-host cell interaction, but little is known about this binding process. L1 sequences from HPV types 16 and 18 were synthesized in 56 20-mer peptides, covering the entire protein, HPLC-purified, (125)I-radiolabeled and tested in VERO and HeLa cell-binding assays to identify those peptides with high specific binding activity. Peptides 18283 (residues 54-77) and 18294 (274-308) from HPV16 L1, as well as 18312 (59-78) and 18322 (259-278) from HPV18 L1, presented high specific target cell binding activity. Peptide 18283 and 18294 affinity constants were 300 and 600 nM, respectively. Enzyme cell treatment before binding assay indicated that VERO and HeLa cell peptide receptor is a surface-exposed protein. There was a 60% reduction in peptide 18283 binding to heparin lyase-treated cells. Cross-linking assays showed that these proteins molecular weights were around 69 and 54 kDa. Peptides 18283 and 18294 specifically inhibited HPV-16 VLP binding to HeLa cells. According to the L1- and VLP-reported structure, both peptides are close on the VLP-surface, belonging to the outer surface broad pockets suggested as being potential receptor sites. Furthermore, it has been reported that a conserved motif from peptide 18294 is the target for neutralizing antibodies. These results suggest that such binding sequences are used by the virus as cell-binding regions.

Chimeric human papillomavirus type 16 (HPV-16) L1 particles presenting the common neutralizing epitope for the L2 minor capsid protein of HPV-6 and HPV-16.

Both the Human papillomavirus (HPV) major (L1) and minor (L2) capsid proteins have been well investigated as potential vaccine candidates. The L1 protein first oligomerizes into pentamers, and these capsomers assemble into virus-like particles (VLPs) that are highly immunogenic. Here we examine the potential of using HPV type 16 (HPV-16) L1 subunits to display a well-characterized HPV-16 L2 epitope (LVEETSFIDAGAP), which is a common-neutralizing epitope for HPV types 6 and 16, in various regions of the L1 structure. The L2 sequence was introduced by PCR (by replacing 13 codons) into sequences coding for L1 surface loops D-E (chideltaC-L2), E-F (chideltaA-L2), and an internal loop C-D (chideltaH-L2); into the h4 helix (chideltaF-L2); and between h4 and beta-J structural regions (chideltaE-L2). The chimeric protein product was characterized using a panel of monoclonal antibodies (MAbs) that bind to conformational and linear epitopes, as well as a polyclonal antiserum raised to the L2 epitope. All five chimeras reacted with the L2 serum. ChideltaA-L2, chideltaE-L2, and chideltaF-L2 reacted with all the L1 antibodies, chideltaC-L2 did not bind H16:V5 and H16:E70, and chideltaH-L2 did not bind any conformation-dependent MAb. The chimeric particles elicited high-titer anti-L1 immune responses in BALB/c mice. Of the five chimeras tested only chideltaH-L2 did not elicit an L2 response, while chideltaF-L2 elicited the highest L2 response. This study provides support for the use of PV particles as vectors to deliver various epitopes in a number of locations internal to the L1 protein and for the potential of using chimeric PV particles as multivalent vaccines. Moreover, it contributes to knowledge of the structure of HPV-16 L1 VLPs and their derivatives.