Population genetic screening efficiently identifies carriers of autosomal dominant diseases.

Three inherited autosomal dominant conditions-BRCA-related hereditary breast and ovarian cancer (HBOC), Lynch syndrome (LS) and familial hypercholesterolemia (FH)-have been termed the Centers for Disease Control and Prevention Tier 1 (CDCT1) genetic conditions, for which early identification and intervention have a meaningful potential for clinical actionability and a positive impact on public health1. In typical medical practice, genetic testing for these conditions is based on personal or family history, ethnic background or other demographic characteristics2. In this study of a cohort of 26,906 participants in the Healthy Nevada Project (HNP), we first evaluated whether population screening could efficiently identify carriers of these genetic conditions and, second, we evaluated the impact of genetic risk on health outcomes for these participants. We found a 1.33% combined carrier rate for pathogenic and likely pathogenic (P/LP) genetic variants for HBOC, LS and FH. Of these carriers, 21.9% of participants had clinically relevant disease, among whom 70% had been diagnosed with relevant disease before age 65. Moreover, 90% of the risk carriers had not been previously identified, and less than 19.8% of these had documentation in their medical records of inherited genetic disease risk, including family history. In a direct follow-up survey with all carriers, only 25.2% of individuals reported a family history of relevant disease. Our experience with the HNP suggests that genetic screening in patients could identify at-risk carriers, who would not be otherwise identified in routine care.

Structure-Based, Rational Design of T Cell Receptors.

Adoptive cell transfer using engineered T cells is emerging as a promising treatment for metastatic melanoma. Such an approach allows one to introduce T cell receptor (TCR) modifications that, while maintaining the specificity for the targeted antigen, can enhance the binding and kinetic parameters for the interaction with peptides (p) bound to major histocompatibility complexes (MHC). Using the well-characterized 2C TCR/SIYR/H-2K(b) structure as a model system, we demonstrated that a binding free energy decomposition based on the MM-GBSA approach provides a detailed and reliable description of the TCR/pMHC interactions at the structural and thermodynamic levels. Starting from this result, we developed a new structure-based approach, to rationally design new TCR sequences, and applied it to the BC1 TCR targeting the HLA-A2 restricted NY-ESO-1157-165 cancer-testis epitope. Fifty-four percent of the designed sequence replacements exhibited improved pMHC binding as compared to the native TCR, with up to 150-fold increase in affinity, while preserving specificity. Genetically engineered CD8(+) T cells expressing these modified TCRs showed an improved functional activity compared to those expressing BC1 TCR. We measured maximum levels of activities for TCRs within the upper limit of natural affinity, K D = ∼1 - 5 µM. Beyond the affinity threshold at K D < 1 µM we observed an attenuation in cellular function, in line with the "half-life" model of T cell activation. Our computer-aided protein-engineering approach requires the 3D-structure of the TCR-pMHC complex of interest, which can be obtained from X-ray crystallography. We have also developed a homology modeling-based approach, TCRep 3D, to obtain accurate structural models of any TCR-pMHC complexes when experimental data is not available. Since the accuracy of the models depends on the prediction of the TCR orientation over pMHC, we have complemented the approach with a simplified rigid method to predict this orientation and successfully assessed it using all non-redundant TCR-pMHC crystal structures available. These methods potentially extend the use of our TCR engineering method to entire TCR repertoires for which no X-ray structure is available. We have also performed a steered molecular dynamics study of the unbinding of the TCR-pMHC complex to get a better understanding of how TCRs interact with pMHCs. This entire rational TCR design pipeline is now being used to produce rationally optimized TCRs for adoptive cell therapies of stage IV melanoma.

Fulminant Wilson's disease requiring liver transplantation in one monozygotic twin despite identical genetic mutation.

Acute decompensated Wilson's disease (WD) that presents as fulminant hepatic failure carries significant mortality without hepatic replacement. The abnormal gene implicated in WD, ATP7B, has been mapped to chromosome 13, and leads to decreased passage of copper from hepatocytes to bile. Excess copper accumulation exceeds hepatocyte storage capacity resulting in intracellular necrosis, apoptosis and cell death in various organs of the body. The hepatic injury induced by the abnormal accumulation of copper in WD has variable presentation such as acute hepatitis, rapid hepatic deterioration resembling fulminant hepatic failure, or as progressive chronic liver disease in the form of chronic active hepatitis or cirrhosis. There are reports in the literature describing monozygotic (identical) twins with similar hepatic progression requiring liver transplantation, however, with different neurological outcome after transplant. We report a case of one monozygotic twin presenting with acute liver failure requiring emergent liver transplantation while the other twin presented with mild liver disease, when both shared an identical genetic mutation.

Annotation pattern of ESTs from Spodoptera frugiperda Sf9 cells and analysis of the ribosomal protein genes reveal insect-specific features and unexpectedly low codon usage bias.

MOTIVATION: A whole set of Expressed Sequence Tags (ESTs) from the Sf9 cell line of Spodoptera frugiperda is presented here for the first time. By this way we want to identify both conserved and specific genes of this pest species. We also expect from this analysis to find a class of protein sequences providing a tool to explore genomic features and phylogeny of Lepidoptera. RESULTS: The ESTs display both housekeeping as well as developmentally regulated genes, and a high percentage of sequences with unknown function. Among the identified ORFs, almost all ribosomal proteins (RPs) were found with high EST redundancy and hence sequence accuracy. The codon usage found among RP genes is in average surprisingly much less biased in Lepidoptera than in other organisms. Other Spodoptera genes also displayed a low bias, suggesting a general genome expression feature in this Lepidoptera. We also found that the L35A and L36 RP sequences, respectively, display 40 and 10 amino-acid insertions, both being present only in insects. Sequence analysis suggests that they are probably not subjected to a strong selective pressure and may be good phylogenetic markers for Lepidoptera. Most interestingly, the Lepidoptera sequences of 9 RP genes displayed a specific signature different from the canonical one. We conclude that the RP family allows valuable comparative genomics and phylogeny of Lepidoptera. AVAILABILITY: All EST sequence data are available from the private 'Spodo-Base' upon request.

Integrations of the hepatitis B virus (HBV) and human papillomavirus (HPV) into the human telomerase reverse transcriptase (hTERT) gene in liver and cervical cancers.

Chronic infections with the hepatitis B virus (HBV) and high-risk human papillomaviruses (HPVs) are important risk factors for hepatocellular carcinoma (HCC) and cervical cancer (CC), respectively. HBV and HPV are DNA viruses that almost invariably integrate into the host genome in invasive tumors. The viral integration sites occur throughout the genome, leading to the presumption that there are no preferred sites of integration. A number of viral integrations have been shown to occur within the vicinity of important cancer-related genes. In studies of HBV-induced HCC and HPV-induced CC, we have identified two HBV and three HPV integrations into the human telomerase reverse transcriptase (hTERT) gene. Detailed characterization of the integrations revealed that four integrations occurred within the hTERT promoter and upstream region and the fifth integration occurred in intron 3 of the hTERT gene. None of the integrations altered the hTERT coding sequence and all resulted in juxtaposition of viral enhancers near hTERT, with potential activation of hTERT expression. Our work supports the hypothesis that the sites of oncogenic viral integration are nonrandom and that genes at the sites of viral integration may play important roles in carcinogenesis.

Maturation of muscle properties and its hormonal control in an adult insect.

The oviposition of female locusts requires longitudinal muscles to tolerate remarkable lengthening. Whether this ability together with concomitant properties develops during maturation or is present throughout life was investigated. The properties of the locust abdominal muscles involved in oviposition behaviour were investigated with respect to their maturation, segment- and gender-specificity and regulation by juvenile hormone (JH). Muscles from the sixth abdominal segment (an oviposition segment) of mature females (>18 days old) were able to tolerate large extensions (>8 mm). At this length, muscles were still able to generate considerable neurally evoked twitch tension. In contrast, muscle fibres from females less than 5 days old did not tolerate extension of more than 4 mm. At this length, tension generation was negligible. The maximum tension generated at different stimulus frequencies was significantly higher in muscles of females more than 18 days old than in females less than 5 days old. Furthermore, the cross-sectional area of muscle fibres increased significantly during reproductive development. Current-clamp recordings from denervated muscle fibres of females more than 18 days old revealed their ability to generate overshooting action potentials. The potentials were tetrodotoxin (TTX)-insensitive (0.5 micromol l(-1) TTX), but were blocked by Cd(2+) (50 micromol l(-1)) or nifedipine (50 micromol l(-1)), which suggests the involvement of L-type Ca(2+) channels. Action potentials recorded from females less than 5 days old differed considerably in amplitude and shape from those recorded from females more than 18 days old, suggesting their maturation during the first 2 weeks of adult life. Inactivation of the corpora allata (CA) by precocene inhibited the maturation of these muscle properties, whereas injection of JH into precocene-treated females reversed this effect. Homologous muscles from the third abdominal segment (a non-oviposition segment, M169) and muscles from males (M214) revealed no comparable changes, although some minor changes occurred during reproductive development. The results suggest a gender- and segment-specific maturation of muscle properties that is related to reproductive behaviour and controlled by JH.

Diversity, distribution, and mobility of bro gene sequences in Bombyx mori nucleopolyhedrovirus.

Genetic differences between strains of a baculovirus are often limited to some restriction sites, short DNA deletions or absence of some nonessential genes. The recently coined bro gene family, represents a new major source of intraspecific variability. A comparison between two bro gene sets of Bombyx mori nucleopolyhedroviruses (NPV) shows that bro genes are distributed in three regions for the -T3 and -SC7 virus strains. In BmNPV T3, five bro genes are distributed in three genome locations, whereas the BmNPV SC7 strain possess a single bro copy in each region. In addition, each of the BmNPV SC7 bro genes belongs to one of the three subfamilies present in BmNPV T3. Analysis of bro copy sequences and of adjacent sequences suggests an active redistribution of sequences due to intraspecific recombination. The maintenance of one allele of each subfamily suggests that they play different roles in the viral cycle, and that they are essential.

Digger wasp versus cricket: mechanisms underlying the total paralysis caused by the predator's venom.

The data presented here describe neurophysiological experiments addressing the question of cellular mechanisms underlying the total paralysis of locomotor behavior in crickets occurring after being stung by females of the digger wasp species Liris niger. The Liris venom effects have been studied by both in vivo recordings from identified neurons of the well-described giant fiber pathway and in vitro recordings from cultured neurons isolated from the terminal ganglion of crickets. The total paralysis of the prey is characterized by a general block of action potential generation as well as by a block of synaptic transmission. Intracellular recordings from neurons in intact ganglia under single electrode voltage-clamp conditions, as well as whole-cell patch-clamp recordings from cultured cricket neurons consistently show that the block of action potential generation by the Liris venom is due to a block of voltage-gated sodium inward currents in neurons of the stung ganglia. Furthermore, our data provide evidence that the Liris venom also blocks calcium currents in identified neurosecretory neurons. On the other hand, outward currents are not affected by the Liris venom. The in vitro recordings suggest that the Liris venom contains active venom components, which, at least for the observed block of inward currents, do not require a metabolic modification. Because venom application does not affect the ACh-induced EPSPs in giant interneurons, the Liris venom does not seem to influence the postsynaptic ACh receptors. The possible pre- and postsynaptic sites of venom action and the functional consequences on synaptic transmission within the giant fiber system are discussed.

Comparative analysis of the granulin regions of the Phthorimaea operculella and Spodoptera littoralis granuloviruses.

The nucleotide sequence of two cloned restriction fragments encompassing the granulin genes from the granuloviruses of the potato tuber moth, Phthorimaea operculella, PhopGV, and the Egyptian cotton leaf worm, Spodoptera littoralis, SpliGV, have been determined. Although both viruses are able to infect the same Ph. operculella cell line, their granulins do not cluster in the same phylogenetic branches. PhopGV ganulin is closely related to Cydia pomonella GV (CpGV) and Cryptophlebia leucotreta GV (ClGV) (95.2 and 94% identity at the aminoacid level), while SpliGV granulin falls close to Trichoplusia ni GV and Xestia c-nigrum GV (91.6 and 92.0% respectively). The gene organization around the granulins reflects this clustering. Upstream the PhopGV granulin, an ORF belonging to the ME53 gene family (as ORF 124R of CpGV and 909 of ClGV) is present, while no equivalent ORF is found in this region in SpliGV. Downstream the granulin, both viruses present a gene homologous to the Autographa californica nucleopolyhedrovirus (AcMNPV) ORF 9 followed by a Protein Kinase (AcMNPV ORF10). The structure of this region seems thus conserved not only among nucleopolyhedroviruses but also in at least some granuloviruses.

Protein requirements for assembly of virus-like particles of Junonia coenia densovirus in insect cells.

The coding sequences of four overlapping polypeptides starting at four different in-frame AUG codons and co-terminating at the stop codon of the cap gene of Junonia coenia densovirus (JcDNV) were inserted under the control of the p10 promoter of Autographa californica nucleopolyhedrovirus (AcMNPV) to generate AcMNPV-VP1 (four polypeptides), AcMNPV-VP2 (three polypeptides), AcMNPV-VP3 (two polypeptides), and AcMNPV-VP4 (one polypeptide) recombinant viruses. In all cases, infection of Spodoptera frugiperda cells (Sf9) by each of the four recombinant viruses resulted in the production of virus-like particles (VLPs) 22-25 nm in diameter. The VLPs produced by the three recombinants AcMNPV-VP2, AcMNPV-VP3 and AcMNPV-VP4 were abundant and contained three, two and one polypeptides, respectively. VP4, the shortest polypeptide, thus appears to be sufficient for assembly of VLPs morphologically similar to those formed with two to four polypeptides. The ratio of VPs did not appear to be critical for assembly of the particles. The polypeptide starting at the first AUG immediately downstream from the p10 promoter was always the most abundantly expressed in infected cells, regardless of the construct. In contrast, plaque-purified AcMNPV-VP1 recombinants were unstable and produced less than one-twentieth of the VLPs produced by the others. All VP transcripts started at the TAAG late motif of the p10 promoter and had a poly(A) tail 14 nt downstream of a poly(A) addition signal located 98 nucleotides downstream of the common stop codon. No significant transcription initiation inside the cap sequence of AcMNPV-VP2, AcMNPV-VP3 and AcMNPV-PV4 was observed.

Digger wasp versus cricket: immediate actions of the predator's paralytic venom on the CNS of the prey.

The females of the palaearctic digger wasp species Liris niger hunt crickets (e.g., Acheta domesticus) as food for their future brood. The wasps paralyze the prey by injecting their venom directly into each of the three thoracic ganglia and the suboesophageal ganglion. This study describes the effects produced by the Liris venom at the level of the intact prey animal (by chronic electromyogram) and at the level of a dissected preparation (by extra- and intracellular records) during the immediate action. Natural or artificial injections of the Liris venom into various ganglia revealed that: (a) The venom injection induced an about 15- to 35-s long tonical discharge of the neurons located in the stung ganglion. This discharge is usually accompanied by convulsions of the prey's limbs. (b) Subsequently, the generation and propagation of action potentials are blocked for up to 30 min (total paralysis). (c) During total paralysis, the venom blocks synaptic transmission. (d) The effects of the venom are restricted to the stung ganglion. Responses of mechanoreceptors in the legs can be recorded from the peripheral nerves of the stung ganglion during the whole period of total paralysis. (e) The neurons almost completely recover after this period. The venom does not selectively affect leg motoneurons, but affects any neuron (e.g., internerneurons or neurosecretory neurons) in any part of the central nervous system of the prey where it was released.

Combinatorial selection of a small RNA that induces amplification of IncFII plasmids in Escherichia coli.

Cellular RNAs play fundamental roles as genetic messages, structural components and, in some cases, as catalytic agents. The ability to create vast combinatorial libraries of random RNA sequences has previously been exploited in vitro to identify RNA aptamers with desirable binding specificities, and to isolate RNAs with novel catalytic properties. Despite the advantages of in vitro selections from RNA libraries, there is no way to predict if the identified RNAs can function in living cells. We are therefore exploring random RNA expression libraries in Escherichia coli to search for small RNAs with novel functions. Here we describe selections that identified a small RNA (approximately 260 nucleotides) capable of altering the copy-number control circuitry of IncFII plasmids. The novel RNA appears to function by annealing to a region of the mRNA encoding the plasmid replicator protein. The resulting RNA-RNA hybrid permits translation of the replicator protein, but blocks base-pairing with a natural negative regulatory RNA. Implications of this in vivo selection strategy are discussed.

Two key mutations in the host-range specificity domain of the p143 gene of Autographa californica nucleopolyhedrovirus are required to kill Bombyx mori larvae.

Autographa californica nucleopolyhedrovirus (AcMNPV) does not replicate in Bombyx mori cells (Bm5, BmN). We have shown previously that when a short DNA sequence within AcMNPV ORF95, which encodes the viral helicase P143, is replaced with the colinear region of B. mori nucleopolyhedrovirus (BmNPV), AcMNPV gains the ability to replicate in Bm5 cells. To determine the mutational events in the p143 gene required to allow AcMNPV replication in B. mori cells, AcMNPV recombinants produced in Sf9 cells were screened in vivo in B. mori larvae, which are more permissive to baculovirus infection than B. mori cell lines. Eight combinations of mutations were tested and characterization of viral DNA extracted from dead larvae showed that amino acid changes at position 564 and 577 are required to kill B. mori larvae.

Temporal expression of the AcMNPV lef-4 gene and subcellular localization of the protein.

Autographa californica nucleopolyhedrovirus (AcMNPV) lef-4 gene [ORF 90; Ayres et al. (1994) Virology 202, 586-605] is involved in both late and very late gene expression [Passarelli and Miller (1993) Virology 197, 704-714]. The transcriptional properties of this gene have been analyzed. It is transcribed as a single 1.6-kb mRNA and transcripts were first detected 3 h postinfection (pi). The extremities of the transcript have been mapped by primer extension and 3' RACE-PCR to positions -56 from the translation start codon and +96 downstream of the stop codon. A rabbit polyclonal antiserum has been raised against an internal polypeptide of LEF-4. A 55-kDa protein was observed by Western blot analysis from 5 h pi. LEF-4 localizes preferentially in the nucleus of infected cells and is associated with the virogenic stroma.

The pnk/pnl gene (ORF 86) of Autographa californica nucleopolyhedrovirus is a non-essential, immediate early gene.

Autographa californica nucleopolyhedrovirus (AcMNPV) ORF 86, located within the HindIII C fragment, potentially encodes a protein which shares sequence similarity with two T4 bacteriophage gene products, RNA ligase and polynucleotide kinase. This AcMNPV gene has been designated pnk/pnl but has yet to be assigned a function in virus replication. It has been classified as an immediate early virus gene, since the promoter was active in uninfected insect cells and mRNA transcripts were detectable from 4 to 48 h post-infection and in the presence of cycloheximide or aphidicolin in virus-infected cells. The extremities of the transcript have been mapped by primer extension and 3' RACE-PCR to positions -18 from the translational start codon and +15 downstream of the stop codon. The function of pnk/pnl was investigated by producing a recombinant virus (Acdel86lacZ) with the coding region replaced with that of lacZ. This virus replicated normally in Spodoptera frugiperda (Sf 21) cells, indicating that pnk/pnl is not essential for propagation in these cells. Virus protein production in Acdel86lacZ-infected Sf 21 cells also appeared to be unaffected, with normal synthesis of the IE-1, GP64, VP39 and polyhedrin proteins. Shut-down of host protein synthesis was not abolished in recombinant infection. When other baculovirus genomes were examined for the presence of pnk/pnl by restriction enzyme digestion and PCR, a deletion was found in AcMNPV 1.2, Galleria mellonella NPV (GmMNPV) and Bombyx mori NPV (BmNPV), suggesting that in many isolates this gene has either never been acquired or has been lost during genome evolution. This is one of the first baculovirus immediate early genes that appears to be nonessential for virus survival.

Infection of the gonads of the SimES strain of Drosophila simulans by the hereditary reovirus DSV.

The S character of Drosophila simulans SimES-st strain undergoes a non-mendelian transmission. It has been postulated that a virus, Drosophila S virus (DSV), could be the causative agent. Electron microscopy analysis of gonads of flies showing a strong S phenotype revealed the presence of virus in or near the germ cells. The S character transmission rate is greater in females than that in males. Similarly, the level of infection by DSV is higher in ovaries than that in testes. Flies treated at a nonpermissive temperature do not present the S phenotype and appear to be cured from the virus. This information, taken together with previous work, makes the hypothesis that DSV is the causative agent of the S phenotype more than likely.

Quantitating oligonucleotide affinities for duplex DNA: footprinting vs electrophoretic mobility shift assays.

Determining the affinities of oligonucleotides for duplex DNA is an important analytical problem that arises during the design of potential gene repressors based on triple helix recognition. Quantitative DNa-seI footprinting assays (QDFA) offer a rigorous technique for this purpose. Electrophoretic mobility shift assays (EMSA) have proven to be simpler and more rapid. Although EMSA can separate triplex and duplex complexes, there is concern that this technique does not afford as rigorous an equilibrium measurement as is provided by QDFA. We show that QDFA and EMSA techniques provide Kd estimates that agree within one order of magnitude under common experimental conditions. Agreement is best in buffers with low concentrations of monovalent cations. Surprisingly, EMSA appears to slightly overestimate triplex stabilities relative to QDFA in the presence of physiological concentrations of monovalent cations (100 mM). Under these conditions, agreement between the techniques can be improved by quenching EMSA samples with excess unlabeled competitor duplex just prior to gel loading. The data suggest that EMSA can provide results in reasonable agreement with QDFA and offer some insight into sources of deviation between the two methods.

The complete DNA sequence of Autographa californica nuclear polyhedrosis virus.

The complete nucleotide sequence of the genome of clone 6 of the baculovirus Autographa californica nuclear polyhedrosis virus (AcNPV) has been determined. The molecule comprises 133,894 base pairs and has an overall A + T content of 59%. Our analysis suggests that the virus encodes some 154 methionine-initiated, and potentially expressed, open reading frames (ORFs) of 150 nucleotides or greater. These ORFs are distributed evenly throughout the virus genome on either strand. The ORFs are arranged as adjacent, nonoverlapping reading frames separated by short intergenic regions. Based on the primary nucleotide sequence, predictions have been made concerning the functions of certain genes, the sites for initiation of viral DNA replication, the regulation of early and late gene transcription, and factors that may affect the AcNPV gene translational efficiency. The genome sequence data confirm, with minor differences, the information obtained for other AcNPV clones. It is proposed that clone C6 is considered the archetype AcNPV for comparison purposes.

Women's employment and the Social Security system.

The rapid rise in women's labor-force participation and the great increase in diversity of family and household structures raise serious questions about the equity and adequacy of a Social Security system developed primarily to meet the needs of traditional families with male wage earners and female homemakers. This article examines the changes in women's roles in the home and in the labor market, then goes on to consider possible reforms in the Social Security system that might help it to better meet the requirements of this profoundly altered society.