Nanoscale lattice dynamics in hexagonal boron nitride moiré superlattices.

Twisted two-dimensional van der Waals (vdW) heterostructures have unlocked a new means for manipulating the properties of quantum materials. The resulting mesoscopic moiré superlattices are accessible to a wide variety of scanning probes. To date, spatially-resolved techniques have prioritized electronic structure visualization, with lattice response experiments only in their infancy. Here, we therefore investigate lattice dynamics in twisted layers of hexagonal boron nitride (hBN), formed by a minute twist angle between two hBN monolayers assembled on a graphite substrate. Nano-infrared (nano-IR) spectroscopy reveals systematic variations of the in-plane optical phonon frequencies amongst the triangular domains and domain walls in the hBN moiré superlattices. Our first-principles calculations unveil a local and stacking-dependent interaction with the underlying graphite, prompting symmetry-breaking between the otherwise identical neighboring moiré domains of twisted hBN.

Sensitivity of the superconducting state in thin films.

For more than two decades, there have been reports on an unexpected metallic state separating the established superconducting and insulating phases of thin-film superconductors. To date, no theoretical explanation has been able to fully capture the existence of such a state for the large variety of superconductors exhibiting it. Here, we show that for two very different thin-film superconductors, amorphous indium oxide and a single crystal of 2H-NbSe2, this metallic state can be eliminated by adequately filtering external radiation. Our results show that the appearance of temperature-independent, metallic-like transport at low temperatures is sufficiently described by the extreme sensitivity of these superconducting films to external perturbations. We relate this sensitivity to the theoretical observation that, in two dimensions, superconductivity is only marginally stable.

Assessment of the genetic causes of recessive childhood non-syndromic deafness in the UK - implications for genetic testing.

Approximately one in 2000 children is born with a genetic hearing impairment, mostly inherited as a non-syndromic, autosomal recessive trait, for which more than 30 different genes have been identified. Previous studies have shown that one of these genes, connexin 26 (GJB2), accounts for 30-60% of such deafness, but the relative contribution of the many other genes is not known, especially in the outbred UK population. This lack of knowledge hampers the development of diagnostic genetic services for deafness. In an effort to determine the molecular aetiology of deafness in the population, 142 sib pairs with early-onset, non-syndromic hearing impairment were recruited. Those in whom deafness could not be attributed to GJB2 mutations were investigated further for other mapped genes. The genetic basis of 55 cases (38.7%) was established, 33.1% being due to mutations in the GJB2 gene and 3.5% due to mutations in SLC26A4. None of the remaining 26 loci investigated made a significant contribution to deafness in a Caucasian population. We suggest that screening the GJB2 and SLC26A4 genes should form the basis of any genetic testing programme for childhood deafness and highlight a number of important issues for consideration and future work.

Complete nucleotide sequence and genome organization of Beet soilborne mosaic virus, a proposed member of the genus Benyvirus.

The complete nucleotide sequences of RNAs 1 to 4 of Beet soilborne mosaic virus (BSBMV) were determined. The genomic organization of BSBMV is identical to Beet necrotic yellow vein virus (BNYVV), the type species of the genus Benyvirus. BSBMV RNA1 encodes a single large open reading frame (ORF) with similar replicase-associated motifs identified for BNYVV. BSBMV RNA2 has six potential ORFs with an organization resembling BNYVV RNA2. RNA3 and RNA4 resemble the analogous BNYVV RNAs, which encode proteins associated with symptom development and fungal transmission, respectively. The predicted ORFs on BNYVV and BSBMV reveal 23% to 83% amino acid identity and the overall nucleotide sequences are 35% to 77% identical. Based on sequence analyses, BSBMV is a new benyvirus that can be distinguished from BNYVV.

Isolation and characterisation of a cDNA encoding the precursor for a novel member of the acyl-CoA dehydrogenase gene family.

A gene encoding the precursor for a novel member of the human acyl-CoA dehydrogenase (ACD) gene family has been isolated which maps to human chromosome 11q25. The cDNA contains an open reading frame of 1248 nucleotides encoding a predicted 415-amino-acid peptide, and shares considerable sequence similarity with other members of the ACD family.

The DNA sequence of equine herpesvirus-4.

The complete DNA sequence of equine herpesvirus-4 (EHV-4) strain NS80567 was determined. The genome is 145597 bp in size and consists of a long unique region (UL, 112398 bp) flanked by a short inverted repeat (TRL/IRL, 27 bp) linked to a short unique region (Us, 12789 bp) flanked by a substantial inverted repeat (TRs/IRs, 10178 bp). EHV-4 is predicted to contain 76 different genes; three of these are present twice in TRs/IRs, giving a total of 79 genes. The closely related virus equine herpesvirus-1 (EHV-1) also possesses 76 different genes corresponding to those of EHV-4, but has a total of 80 genes because four are present twice in TRs/IRs. Interpretations of the coding capacity of the EHV-4 and EHV-1 genomes were refined by comparing the complete DNA sequences.

cDNA cloning, genomic organization, and chromosomal localization of a novel human gene that encodes a kinesin-related protein highly similar to mouse Kif3C.

We report the cloning and characterization of a novel human kinesin-like gene with strong homology to the mouse kinesin Kif3c. The full-length cDNA contains an open reading frame of 2382 nucleotides encoding a predicted 793 amino acid peptide that includes a 389 amino acid motor domain conserved among other kinesins. PCR and DNA sequence analysis of PAC clones containing the human KIF3C sequence revealed that the gene contains 8 exons. All introns have the conserved GT and AG dinucleotides present at their donor and acceptor sites, respectively. We have localized KIF3C to chromosome band 2p23 by fluorescence in situ hybridization.

Characterisation of human patched germ line mutations in naevoid basal cell carcinoma syndrome.

Mutations in the human patched gene have recently been detected in patients with naevoid basal cell carcinoma syndrome. We have characterised a further 5 novel germ line mutations in patients presenting with multiple odontogenic keratocysts. Four mutations cause premature stop codons and one mutation results in an amino-acid substitution towards the carboxyl terminus of the predicted patched protein. No obvious genotype-phenotype correlations could be interpreted, consistent with previous studies.

An EST and STS-based YAC contig map of human chromosome 9q22.3.

We have isolated 48 yeast artificial chromosome (YAC) clones from a 4 cM/27 cR region of human chromosome 9q22.3 encompassed by the markers cen-D9S196-D9S173-tel. Within this region, we have assembled a 4.3-Mb YAC contig across the interval cen-FACC-D9S173-tel containing 42 clones. As a first step toward completing the detailed transcription map of the region, we have mapped 9 gene sequences and 10 expressed sequence tags. Fifteen polymorphic microsatellite repeat markers and 17 novel sequence-tagged sites from the region are also described. The mapping of polymorphic simple tandem repeat markers has permitted the integration of existing genetic and physical maps of the region. Together these maps provide a valuable resource for fine structure mapping and DNA sequencing across the region as well as for the identification of disease gene loci and the isolation of novel coding sequences.

The DNA sequence of equine herpesvirus 2.

The complete DNA sequence of equine herpesvirus 2 (EHV-2) strain 86/67 was determined. The genome is 184,427 bp in size and has a base composition of 57.5% G + C. Unusually for a herpesvirus, about a third of the sequence distributed in several large blocks appears not to encode proteins. The 79 open reading frames that were identified as probably polypeptide-coding are predicted to encode 77 distinct proteins. Amino acid sequence comparisons confirmed that EHV-2 is a gamma-herpesvirus that is genetically collinear with herpesvirus saimiri (HVS; a gamma 2-herpesvirus) and Epstein-Barr virus (EBV; a gamma 1-herpesvirus), with a closer relationship to the former. Moreover, EHV-2 specifies eight proteins that have counterparts in HVS but not in EBV and only a single protein that has a homologue in EBV but not in HVS (EBV BCRF1, which encodes an interleukin 10-like protein). EHV-2 also encodes three potential G protein-coupled receptors, one with a counterpart in HVS that is specific for alpha chemokines, another with a counterpart in human cytomegalovirus (a beta-herpesvirus), which is specific for beta chemokines, and a third that is assigned more tentatively and lacks detectable counterparts in other herpesviruses.

Molecular phylogeny and evolutionary timescale for the family of mammalian herpesviruses.

A detailed phylogenetic analysis for mammalian members of the family Herpesviridae, based on molecular sequences is reported. Sets of encoded amino acid sequences were collected for eight well conserved genes that are common to mammalian herpesviruses. Phylogenetic trees were inferred from alignments of these sequence sets using both maximum parsimony and distance methods, and evaluated by bootstrap analysis. In all cases the three recognised subfamilies (Alpha-, Beta- and Gammaherpesvirinae), and major sublineages in each subfamily, were clearly distinguished, but within sublineages some finer details of branching were incompletely resolved. Multiple-gene sets were assembled to give a broadly based tree. The root position of the tree was estimated by assuming a constant molecular clock and also by analysis of one herpesviral gene set (that encoding uracil-DNA glycosylase) using cellular homologues as outgroups. Both procedures placed the root between the Alphaherpesvirinae and the other two subfamilies. Substitution rates were calculated for the combined gene sets based on a previous estimate for alphaherpesviral UL27 genes, where the time base had been obtained according to the hypothesis of cospeciation of virus and host lineages. Assuming a constant molecular clock, it was then estimated that the three subfamilies arose approximately 180 to 220 million years ago, that major sublineages within subfamilies were probably generated before the mammalian radiation of 80 to 60 million years ago, and that speciations within sublineages took place in the last 80 million years, probably with a major component of cospeciation with host lineages.

Comparative studies of the structural proteins and glycoproteins of equine herpesviruses 2 and 5.

The structural proteins of equine herpesvirus 2 (EHV-2) and EHV-5, recently shown to be gammaherpesviruses, were identified and compared. Labelled proteins and glycoproteins were separated by SDS-PAGE and although EHV-2 and EHV-5 had similar protein profiles, bands in some positions were virus-specific. Six glycoproteins, with distinct profiles, were identified for both EHV-2 and EHV-5. Rabbit antisera to EHV-2 and EHV-5 and horse antiserum to EHV-2 were used in radioimmunoprecipitations, Western blot analysis and ELISA to investigate the immunogenicity and cross-reactivity of virus proteins. These analyses revealed that while EHV-2 and EHV-5 proteins share many common epitopes, they also possess type-specific epitopes. A 0.71 kb region of the EHV-2 glycoprotein B (gB) gene was expressed as a fusion protein in Escherichia coli. Antiserum raised in a rabbit to the EHV-2 fusion protein was used to identify a 64K EHV-2 protein as EHV-2 gB. Antiserum to EHV-2 gB was used to identify a 66K EHV-5 protein as EHV-5 gB. These proteins, which may represent subunits of gB rather than the entire molecule, appear the most immunodominant of the structural virion proteins as identified by Western blot.

The equine herpesvirus type 1 glycoprotein homologous to herpes simplex virus type 1 glycoprotein M is a major constituent of the virus particle.

Glycoprotein 45 is a major envelope glycoprotein of equine herpesvirus type 1. The gene encoding this protein is located between map units 0.615 and 0.636 on the virus genome and evidence has suggested that it is encoded by gene 52, one of four genes within this region. Using PCR we have amplified gene 52 and subsequently cloned it into a mammalian expression vector under the control of the human cytomegalovirus immediate early gene promoter. The gene was expressed in COS-7 cells and its product was detected by immunofluorescence and Western blotting. The results indicate that glycoprotein 45 is encoded by gene 52, and that it is the homologue of herpes simplex virus type 1 glycoprotein M.

Equid herpesviruses 1 and 4 encode functional homologs of the herpes simplex virus type 1 virion transactivator protein, VP16.

The herpes simplex virus type 1 (HSV-1) tegument protein VP16 is a potent transcriptional inducer of immediate-early gene expression, comprising an N-terminal domain involved in binding DNA linked to an acidic transactivating C-terminal domain. The gene encoding the counterpart of this protein in equid herpesvirus 4 (EHV-4) was sequenced. Comparisons with VP16 and the homologous proteins of equine herpesvirus 1 (EHV-1) and varicella-zoster virus (VZV) showed that a region in the N-terminal domain involved in formation of a complex with cellular proteins is partially conserved in all four proteins. In contrast, the C-terminal regions of the EHV proteins, like that of VZV, are not particularly acidic and are not significantly conserved with respect to the C-terminal region of VP16. Nevertheless, transient expression experiments indicated that the EHV-1 and EHV-4 proteins are able to transactivate HSV-1 and EHV-1 immediate-early promoters in a dose-dependent manner, which suggests that this activity is not dependent on an acidic C-terminal domain.

The DNA sequence of adenovirus type 40.

The 34,214 bp DNA sequence of adenovirus type 40 strain Dugan was determined directly from random fragments of virion DNA cloned into a bacteriophage M13 cloning vector. The gene layout is similar to that of other human adenoviruses, and in addition contains two potential protein-coding regions that are conserved, but have not been recognized previously, in other adenovirus genomes. One is oriented rightward, contained within the intron in the protein-coding region for the L4 33K gene, and would encode a protein sharing N-terminal sequence with 33K. The other is a leftward oriented exon located between the E3 and L5 IV (fibre) regions which would specify the N terminus of a novel protein. The region encoding the C terminus of this protein is not apparent from sequence data.

Equine herpesviruses 2 and 5 are gamma-herpesviruses.

Equine herpesviruses 2 and 5 (EHV-2 and EHV-5) have biological properties and genome structures that support their classification as members of the Betaherpesvirinae. In order to investigate whether this is supported by genetic data, we analysed the sequences of random DNA fragments and identified 25 EHV-2 and 28 EHV-5 genes that encode amino acid sequences with significant homology to proteins from other herpesviruses. Greatest similarity was to proteins specified by the gamma-herpesviruses Epstein-Barr virus (a gamma 1-herpesvirus) and herpesvirus saimiri (a gamma 2-herpesvirus), and the level of similarity was marginally greater to the latter. Also, like other gamma-herpesviruses, the EHV-2 and EHV-5 genomes are deficient in the CG dinucleotide, suggesting that latent genomes are methylated. EHV-2 and EHV-5 are related to each other more closely than they are to other herpesviruses, but are clearly distinct gamma-herpesviruses. The data support the establishment of at least one more subdivision of the gamma-herpesviruses (the gamma 3-herpesviruses).

A novel herpes simplex virus gene (UL49A) encodes a putative membrane protein with counterparts in other herpesviruses.

Comparative analysis of DNA sequences located between the coding regions of genes UL49 and UL50 of herpes simplex virus types 1 and 2 (HSV-1 and -2) has revealed a small open reading frame (ORF) of 91 and 87 codons respectively with the characteristics of a genuine protein-coding region. The predicted protein products are clearly related and exhibit features of membrane-inserted proteins, with potential N-proximal signal peptides and C-proximal membrane anchor regions. Counterparts are present in the other sequenced alphaherpesviruses, namely varicella-zoster virus (a previously undescribed gene, 9A) and equine herpesvirus type 1 (gene 10), in the betaherpesvirus human cytomegalovirus (gene UL73) and in the gammaherpesvirus Epstein-Barr virus (gene BLRF1). Therefore, we consider that this ORF represents an additional HSV gene (UL49A) with counterparts in all sequenced alpha-, beta- and gammaherpesviruses.

The DNA sequence of equine herpesvirus-1.

The complete DNA sequence was determined of a pathogenic British isolate of equine herpesvirus-1, a respiratory virus which can cause abortion and neurological disease. The genome is 150,223 bp in size, has a base composition of 56.7% G + C, and contains 80 open reading frames likely to encode protein. Since four open reading frames are duplicated in the major inverted repeat, two are probably expressed as a spliced mRNA, and one may contain an internal transcriptional promoter, the genome is considered to contain 76 distinct genes. The genes are arranged collinearly with those in the genomes of the two previously sequenced alphaherpesviruses, varicella-zoster virus, and herpes simplex virus type-1, and comparisons of predicted amino acid sequences allowed the functions of many equine herpesvirus 1 proteins to be assigned.

Inhibition of equine herpesvirus type 1 subtype 1-induced ribonucleotide reductase by the nonapeptide YAGAVVNDL.

The synthetic nonapeptide YAGAVVNDL [identical to the nine carboxy-terminal amino acids of the small subunit of herpes simplex virus (HSV)-encoded ribonucleotide reductase (RR)] was found to inhibit the RR activity induced by equine herpesvirus type 1 subtype 1 (EHV-1). Parallel experiments with HSV type 1 (HSV-1)-encoded RR established that the concentration of peptide required to inhibit 50% of the RR activity was 28 microM for both enzymes. The optimum pH for the EHV-1 enzyme was found to be between 8.0 and 8.1 which is the same as that of HSV-1 RR. By use of antisera made against peptides corresponding to different regions of the large subunit (RR1) of the HSV-1 enzyme and monoclonal antibodies directed against HSV-1 RR1 we have obtained evidence which suggests that the EHV-1 large subunit has an Mr of approximately 90,000 and lacks the N-terminal domain which is so far unique to HSV.

The unique N-terminal domain of the large subunit of herpes simplex virus ribonucleotide reductase is preferentially sensitive to proteolysis.

Using antisera made against peptides corresponding to different regions of the large subunit of herpes simplex virus type 1 ribonucleotide reductase we have probed proteolytic fragments of this protein and found that at least a part of its unique N-terminal domain is not necessary for enzyme activity. This non-essential region encompasses the domain previously predicted to be composed of beta sheets with a well buried core of hydrophobic residues. Truncated forms of the large subunit are generated in vivo and are located almost exclusively in the nucleus.