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Quantum bits, or qubits, are an example of coherent circuits envisioned for next-generation computers and detectors. A robust superconducting qubit with a coherent lifetime of O(100 µs) is the transmon: a Josephson junction functioning as a non-linear inductor shunted with a capacitor to form an anharmonic oscillator. In a complex device with many such transmons, precise control over each qubit frequency is often required, and thus variations of the junction area and tunnel barrier thickness must be sufficiently minimized to achieve optimal performance while avoiding spectral overlap between neighboring circuits. Simply transplanting our recipe optimized for single, stand-alone devices to wafer-scale (producing 64, 1x1 cm dies from a 150 mm wafer) initially resulted in global drifts in room-temperature tunneling resistance of 30%. Inferring a critical current ≡σIc≪Ic≫ variation from this resistance distribution, we present an optimized process developed from a systematic 38 wafer study that results in < 3.5% relative standard deviation (RSD) in critical current () for 3000 Josephson junctions (both single-junctions and asymmetric SQUIDs) across an area of 49 cm2. Looking within a 1x1 cm moving window across the substrate gives an estimate of the variation characteristic of a given qubit chip. Our best process, utilizing ultrasonically assisted development, uniform ashing, and dynamic oxidation has shown = 1.8% within 1x1 cm, on average, with a few 1x1 cm areas having < 1.0% (equivalent to < 0.5%). Such stability would drastically improve the yield of multi-junction chips with strict critical current requirements.

Fast, high-fidelity, and quantum nondemolition (QND) qubit readout is an essential element of quantum information processing. For superconducting qubits, state-of-the-art readout is based on a dispersive cross-Kerr coupling between a qubit and its readout resonator. The resulting readout can be high fidelity and QND, but readout times are currently limited to the order of 50 nanoseconds due to the dispersive cross-Kerr of magnitude 10 megahertz. Here, we present a readout scheme that uses the quarton coupler to facilitate a large (greater than 200 megahertz) cross-Kerr between a transmon qubit and its readout resonator. Full master equation simulations of the coupled system show a 5-nanosecond readout time with greater than 99% readout fidelity and greater than 99.9% QND fidelity. The quartonic readout circuit is experimentally feasible and preserves the coherence properties of the qubit. Our work reveals a path for order of magnitude improvements of superconducting qubit readout by engineering nonlinear light-matter couplings in parameter regimes unreachable by existing designs.

The experimental demonstration of a p-type 2D WSe 2 transistor with a ferroelectric perovskite BaTiO 3 gate oxide is presented. The 30 nm thick BaTiO 3 gate stack shows a robust ferroelectric hysteresis with a remanent polarization of 20 μC/cm 2 and further enables a capacitance equivalent thickness of 0.5 nm in the hybrid WSe 2 /BaTiO 3 stack due to its high dielectric constant of 323. We demonstrate one of the best ON currents for perovskite gate 2D transistors in the literature. This is enabled by high-quality epitaxial growth of BaTiO 3 and a single 2D layer transfer based fabrication method that is shown to be amenable to silicon platforms. This demonstration is an important milestone toward the integration of crystalline complex oxides with 2D channel materials for scaled CMOS and low-voltage ferroelectric logic applications.

Tools to effectively demonstrate and quantify functional delivery in cellular communication have been lacking. This study reports the use of a fluorescently labeled split Nanoluc reporter system to demonstrate and quantify functional transfer between cells in vitro and in a subcutaneous tumor mouse model. Our construct allows monitoring of direct, indirect, and specifically extracellular vesicle-mediated functional communication., Competing Interests: The authors declare no competing interests., (© 2023 The Authors.)

Strong nonlinear coupling of superconducting qubits and/or photons is a critical building block for quantum information processing. Because of the perturbative nature of the Josephson nonlinearity, linear coupling is often used in the dispersive regime to approximate nonlinear coupling. However, this dispersive coupling is weak and the underlying linear coupling mixes the local modes, which, for example, distributes unwanted self-Kerr nonlinearity to photon modes. Here, we use the quarton to yield purely nonlinear coupling between two linearly decoupled transmon qubits. The quarton's zero ϕ^{2} potential enables an ultrastrong gigahertz-level cross-Kerr coupling, which is an order of magnitude stronger compared to existing schemes, and the quarton's positive ϕ^{4} potential can cancel the negative self-Kerr nonlinearity of qubits to linearize them into resonators. This ultrastrong cross-Kerr coupling between bare modes of qubit-qubit, qubit-photon, and even photon-photon is ideal for applications such as single microwave photon detection, ultrafast two-qubit gates, and readout.

Extracellular vesicles (EVs) shuttle microRNA (miRNA) throughout the circulation and are believed to represent a fingerprint of the releasing cell. We isolated and characterized serum EVs of breast tumour-bearing animals, breast cancer (BC) patients, and healthy controls. EVs were characterized using transmission electron microscopy (TEM), protein quantification, western blotting, and nanoparticle tracking analysis (NTA). Absolute quantitative (AQ)-PCR was employed to analyse EV-miR-451a expression. Isolated EVs had the appropriate morphology and size. Patient sera contained significantly more EVs than did healthy controls. In tumour-bearing animals, a correlation between serum EV number and tumour burden was observed. There was no significant relationship between EV protein yield and EV quantity determined by NTA, highlighting the requirement for direct quantification. Using AQ-PCR to relate miRNA copy number to EV yield, a significant increase in miRNA-451a copies/EV was detected in BC patient sera, suggesting potential as a novel biomarker of breast cancer., Competing Interests: The authors declare no conflict of interest.

Adult Mesenchymal Stem Cells (MSCs) have a well-established tumor-homing capacity, highlighting potential as tumor-targeted delivery vehicles. MSCs secrete extracellular vesicle (EV)-encapsulated microRNAs, which play a role in intercellular communication. The aim of this study was to characterize a potential tumor suppressor microRNA, miR-379, and engineer MSCs to secrete EVs enriched with miR-379 for in vivo therapy of breast cancer. miR-379 expression was significantly reduced in lymph node metastases compared to primary tumor tissue from the same patients. A significant reduction in the rate of tumor formation and growth in vivo was observed in T47D breast cancer cells stably expressing miR-379. In more aggressive HER2-amplified HCC-1954 cells, HCC-379 and HCC-NTC tumor growth rate in vivo was similar, but increased tumor necrosis was observed in HCC-379 tumors. In response to elevated miR-379, COX-2 mRNA and protein was also significantly reduced in vitro and in vivo. MSCs were successfully engineered to secrete EVs enriched with miR-379, with the majority found to be of the appropriate size and morphology of exosomal EVs. Administration of MSC-379 or MSC-NTC cells, or EVs derived from either cell population, resulted in no adverse effects in vivo. While MSC-379 cells did not impact tumor growth, systemic administration of cell-free EVs enriched with miR-379 was demonstrated to have a therapeutic effect. The data presented support miR-379 as a potent tumor suppressor in breast cancer, mediated in part through regulation of COX-2. Exploiting the tumor-homing capacity of MSCs while engineering the cells to secrete EVs enriched with miR-379 holds exciting potential as an innovative therapy for metastatic breast cancer.

It is believed that microRNAs have potential as circulating biomarkers of disease; however, successful clinical implementation remains a challenge. This chapter highlights broad variations in approaches to microRNA analysis where whole blood, serum and plasma have each been employed as viable sources. Further discrepancies in approaches are seen in endogenous controls and extraction methods utilized. This has resulted in contradictory publications, even when the same microRNA is targeted in the same disease setting.Analysis of blood samples highlighted the impact of both collection method and storage, on the microRNA profile. Analysis of a panel of microRNAs across whole blood, serum, and plasma originating from the same individual emphasized the impact of starting material on microRNA profile. This is a highly topical field of research with immense potential for translation into the clinical setting. Standardization of sample harvesting, processing and analysis will be key to this translation. Methods of sample harvesting, preservation, and analysis are outlined, with important mitigating factors highlighted.

Objectives: Neisseria gonorrhoeae (GC) and Chlamydia trachomatis (CT) can facilitate transmission of HIV. Men who have sex with men (MSM) may harbour infections at genital and extragenital sites. Data regarding extragenital GC and CT infections in military populations are lacking. We examined the prevalence and factors associated with asymptomatic GC and CT infection among this category of HIV-infected military personnel., Design: Cross-sectional cohort study (pilot)., Setting: Infectious diseases clinic at a single military treatment facility in San Diego, CA., Participants: Ninety-nine HIV-positive men were evaluated-79% men who had sex with men, mean age 31 years, 36% black and 33% married., Inclusion Criteria: male, HIV-infected, Department of Defense beneficiary., Exclusion Criteria: any symptom related to the urethra, pharynx or rectum., Primary Outcome Measures: GC and CT screening results., Results: Twenty-four per cent were infected with either GC or CT. Rectal swabs were positive in 18% for CT and 3% for GC; pharynx swabs were positive in 8% for GC and 2% for CT. Only one infection was detected in the urine (GC). Anal sex (p=0.04), male partner (OR 7.02, p=0.04) and sex at least once weekly (OR 3.28, p=0.04) were associated with infection. Associated demographics included age <35 years (OR 6.27, p=0.02), non-Caucasian ethnicity (p=0.03), <3 years since HIV diagnosis (OR 2.75, p=0.04) and previous sexually transmitted infection (STI) (OR 5.10, p=0.001)., Conclusions: We found a high prevalence of extragenital GC/CT infection among HIV-infected military men. Only one infection was detected in the urine, signalling the need for aggressive three-site screening of MSM. Clinicians should be aware of the high prevalence in order to enhance health through comprehensive STI screening practices.

A central goal of green chemistry is to avoid hazard in the design of new chemicals. This objective is best achieved when information about a chemical's potential hazardous effects is obtained as early in the design process as feasible. Endocrine disruption is a type of hazard that to date has been inadequately addressed by both industrial and regulatory science. To aid chemists in avoiding this hazard, we propose an endocrine disruption testing protocol for use by chemists in the design of new chemicals. The Tiered Protocol for Endocrine Disruption (TiPED) has been created under the oversight of a scientific advisory committee composed of leading representatives from both green chemistry and the environmental health sciences. TiPED is conceived as a tool for new chemical design, thus it starts with a chemist theoretically at "the drawing board." It consists of five testing tiers ranging from broad in silico evaluation up through specific cell- and whole organism-based assays. To be effective at detecting endocrine disruption, a testing protocol must be able to measure potential hormone-like or hormone-inhibiting effects of chemicals, as well as the many possible interactions and signaling sequellae such chemicals may have with cell-based receptors. Accordingly, we have designed this protocol to broadly interrogate the endocrine system. The proposed protocol will not detect all possible mechanisms of endocrine disruption, because scientific understanding of these phenomena is advancing rapidly. To ensure that the protocol remains current, we have established a plan for incorporating new assays into the protocol as the science advances. In this paper we present the principles that should guide the science of testing new chemicals for endocrine disruption, as well as principles by which to evaluate individual assays for applicability, and laboratories for reliability. In a 'proof-of-principle' test, we ran 6 endocrine disrupting chemicals (EDCs) that act via different endocrinological mechanisms through the protocol using published literature. Each was identified as endocrine active by one or more tiers. We believe that this voluntary testing protocol will be a dynamic tool to facilitate efficient and early identification of potentially problematic chemicals, while ultimately reducing the risks to public health.

The evolution of electronic structure of graphene nanoribbons (GNRs) as a function of the number of layers stacked together is investigated using ab initio density functional theory (DFT), including interlayer van der Waals interactions. Multilayer armchair GNRs (AGNRs), similar to single-layer AGNRs, exhibit three classes of band gaps depending on their width. In zigzag GNRs (ZGNRs), the geometry relaxation resulting from interlayer interactions plays a crucial role in determining the magnetic polarization and the band structure. The antiferromagnetic (AF) interlayer coupling is more stable compared to the ferromagnetic (FM) interlayer coupling. ZGNRs with the AF in-layer and AF interlayer coupling have a finite band gap, while ZGNRs with the FM in-layer and AF interlayer coupling do not have a band gap. The ground state of the bilayer ZGNR is nonmagnetic with a small but finite band gap. The magnetic ordering is less stable in multilayer ZGNRs compared to that in single-layer ZGNRs. The quasiparticle GW corrections are smaller for bilayer GNRs compared to single-layer GNRs because of the reduced Coulomb effects in bilayer GNRs compared to single-layer GNRs., (© 2011 American Chemical Society)

In this study, we report the development of a microenvironment probe station capable of detecting the effect of small changes to the local environment around a carbon nanotube conduction channel. The microenvironment probe station is highly versatile and is used to characterize alterations in carbon nanotube field effect transistor electrical behavior in response to changes in temperature, gas species, infrared and ultraviolet light. All devices were electrically characterized in atmospheric, ultrahigh vacuum and oxygen-rich environments. The results suggest that devices could be changed from n-type at 1 x 10(-8) torr through an intermediate ambipolar state at 1 x 10(-4) torr to p-type at atmosphere solely by increasing the oxygen concentration. The average resistance of these carbon nanotube field effect transistors after annealing was observed to decrease by approximately 54% from their initial value under ultrahigh vacuum to their final value in the presence of pure oxygen while corresponding threshold voltages shifts were also observed. Illumination with infrared light resulted in a approximately 10% increase in drain current with an estimated response time <1 fs due to photon-induced electron-hole pair generation. Illumination with ultraviolet light resulted in approximately 5-15% reduction in drain current due to photon-induced desorption of oxygen adsorbate.

Growth of vertically aligned carbon nanotube (CNT) carpets on metallic substrates at low temperatures was achieved by controlled thermal treatment of ethylene and hydrogen at a temperature higher than the substrate temperature. High-resolution transmission electron microscopy showed that nanotubes were crystalline for a preheating temperature of 770 degrees C and a substrate temperature of 500 degrees C. Conductive atomic force microscopy measurements indicated electrical contact through the CNT carpet to the metallic substrate with an approximate resistance of 35 kOmega for multiwall carpets taller than two micrometers. An analysis of the activation energies indicated that thermal decomposition of the hydrocarbon/hydrogen gas mixture was the rate-limiting step for low-temperature chemical vapor deposition growth of CNTs. These results represent a significant advance toward the goal of replacing copper interconnects with nanotubes using CMOS-compatible processes.

We directly compared ensemble spectroscopic measurements to a statistically rigorous single molecule electrical characterization of individual SWNT devices using a high throughput electrical probe station and reported, for the first time, a highly accurate extinction coefficient ratio for metallic to semiconducting SWNTs of 0.352 +/- 0.009. The systematic counting of metallic and semiconducting types from solution also allows us to examine the variances associated with device properties and therefore provide the first measure of potential defect generation during processing methods.

The PSORS1 locus in the major histocompatibility complex region on chromosome 6p21.3 contains a major predisposing factor for psoriasis for which several candidate genes have been tested. The analyses are complicated by strong linkage disequilibrium in the region and the complex genetic background of psoriasis. In the search for an alternative to HLA-C we have identified a novel gene, PSORS1C3, and characterized it with regard to psoriasis. PSORS1C3 is located approximately 7 kb centromeric to POU5F1. A putative protein of 58 amino acids was predicted and expression was detected in both normal and psoriasis skin. Sequencing of the coding region revealed a total of 11 single nucleotide polymorphisms. When comparing the frequencies of PSORS1C3 variants in a case-control material in the Swedish population, three single nucleotide polymorphisms displayed significant association with psoriasis. This association appeared to be HLA-Cw*0602-dependent due to linkage disequilibrium, thus HLA-C remains the strongest associating factor in the region.

The Inparanoid eukaryotic ortholog database (http://inparanoid.cgb.ki.se/) is a collection of pairwise ortholog groups between 17 whole genomes; Anopheles gambiae, Caenorhabditis briggsae, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Takifugu rubripes, Gallus gallus, Homo sapiens, Mus musculus, Pan troglodytes, Rattus norvegicus, Oryza sativa, Plasmodium falciparum, Arabidopsis thaliana, Escherichia coli, Saccharomyces cerevisiae and Schizosaccharomyces pombe. Complete proteomes for these genomes were derived from Ensembl and UniProt and compared pairwise using Blast, followed by a clustering step using the Inparanoid program. An Inparanoid cluster is seeded by a reciprocally best-matching ortholog pair, around which inparalogs (should they exist) are gathered independently, while outparalogs are excluded. The ortholog clusters can be searched on the website using Ensembl gene/protein or UniProt identifiers, annotation text or by Blast alignment against our protein datasets. The entire dataset can be downloaded, as can the Inparanoid program itself.

One of the greatest promises of genome sequencing projects is to further the understanding of human diseases and to develop new therapies. Model organism genomes have been sequenced in parallel to human genomes to provide effective tools for the investigation of human gene function. Many of their genes share a common ancestry and function with human genes, and this is particularly true for orthologous genes. Here we present OrthoDisease, a comprehensive database of model organism genes that are orthologous to human disease genes. OrthoDisease was constructed by applying the Inparanoid ortholog detection algorithm to disease genes derived from the Online Mendelian Inheritance in Man database (OMIM). Pairwise whole genome/proteome comparisons between Homo sapiens and six other organisms were performed to identify ortholog clusters. OMIM numbers were extracted from the OMIM Morbid Map and were converted to gene sequences using the Locuslink mim2loc and loc2acc tables. These were mapped to Inparanoid ortholog clusters using Blast. The number of ortholog clusters in OrthoDisease with each respective species is currently: M. musculus, 1,354; D. melanogaster, 724; C. elegans, 533; A. thaliana, 398; S. cerevisiae, 290; and E. coli, 153. The database is accessible online at http://orthodisease.cgb.ki.se, and can be searched with disease or protein names. The web interface presents all ortholog clusters that include a selected disease gene. A capability to download the entire dataset is also provided., (Copyright 2004 Wiley-Liss, Inc.)

Psoriasis is a chronic inflammatory skin disease that is known to have a strong genetic predisposition. Several psoriasis-susceptibility loci have been previously found through genomic scans. Of these, psoriasis-susceptibility region 1 (PSORS1) on chromosome 6p21 remains the most consistently identified region across populations with the highest association with disease. STG is a gene that was previously isolated from rhesus monkey taste buds, and its ortholog in humans was found to be part of the cluster of genes in PSORS1, which is telomeric to HLA-C. Upon characterization of STG, we identified several sequence variants and investigated their association with psoriasis in cases and controls from the Swedish population. None of these STG single-nucleotide polymorphisms were found to be significantly associated with psoriasis. However, HLA-Cw*0602 status was strongly associated with disease. STG expression was investigated in human tissues and found not to be restricted to taste buds, with signals also being detected in skin and tonsils.

Psoriasis is a chronic skin disease that results in red and scaly lesions. Several psoriasis susceptibility loci have been identified across the genome, of which PSORS1 on 6p21.3 is predominant. There is an ongoing debate regarding whether the HLA-C allele, Cw*0602, can be considered the major predisposing factor in this region. Investigation of other genes in the PSORS1 region with regard to psoriasis may provide alternate candidates to HLA-C. We have characterized two overlapping genes, SEEK1 and SPR1. SEEK1 encodes two putative protein isoforms: the first being one of 152 amino acids from the full-length splice-isoform (exon 1-6), and the second being one of 100 amino acids from an alternate splice-isoform (exon 1 and 6). SPR1 encodes a highly conserved protein of 134 amino acids, and in addition to characterization of human SPR1 we report the cloning of its orthologs in mouse and pig. Both SEEK1 and SPR1 are expressed in normal and psoriasis skin. In a case-control study, five of the nine single nucleotide polymorphisms (SNPs) found in SEEK1 were associated with psoriasis, while one of the four SNPs found in SPR1 showed association. Testing the Cw*0602 confounding status revealed that two of the SEEK1 SNPs showed Cw*0602-independent association, while the SPR1 SNP showed Cw*0602-dependent association. The second exon of SEEK1, containing the two Cw*0602-independent SNPs, showed the highest concentration of the psoriasis-associating SNPs, but did not appear to be translated.

Neutrophil gelatinase-associated lipocalin (NGAL) is a 25-kDa protein initially isolated from the specific granules of human neutrophils. It is a member of the highly heterogeneous lipocalin protein family, which shares a common tertiary structure. Its synthesis is induced in gastrointestinal epithelium in association with inflammation and malignancy. To gain insight into its potential role in other epithelia we have investigated the expression of NGAL in human skin embryonic development, in normal adult skin, and in skin associated with inflammation and neoplastic transformation. In the present study we report that the embryonic expression of NGAL appears to be regulated in a spatio-temporal pattern. It was induced in the interfollicular epidermis at 20-24 weeks of gestational age but thereafter progressively receded towards the hair follicles. In normal adult skin, NGAL was detected solely in association with hair follicles. However, strong induction of NGAL in the epidermis was seen in a variety of skin disorders characterized by dysregulated epithelial differentiation such as psoriasis, pityriasis rubra and squamous cell carcinoma. In these tissues production of NGAL was confined to spatially distinct subpopulations of keratinocytes underlying areas of parakeratosis, whereas skin samples lacking parakeratotic epithelium such as lichen ruber planus, acute contact eczema and basal cell carcinoma were negative for NGAL. Consistent with being a marker for disturbed terminal differentiation, NGAL immunoreactivity showed an inverse pattern when compared with that of the differentiation marker filaggrin. The biologic functions of NGAL in epithelia are not fully known, although an immunomodulatory role in host defense has been proposed. In addition, the transient interfollicular NGAL expression during skin embryogenesis along with the induction of NGAL in adult parakeratotic epidermis suggests it play a role in epithelial differentiation pathways.

Dermatofibrosarcoma protuberans (DFSP) and giant cell fibroblastoma (GCF) are recurrent, infiltrative skin tumors that presently are treated with surgery. DFSP and GCF tumors are genetically characterized by chromosomal rearrangements fusing the collagen type Ialpha1 (COLIA1) gene to the platelet-derived growth factor B-chain (PDGFB) gene. It has been shown that the resulting COL1A1/PDGF-B fusion protein is processed to mature PDGF-BB. Autocrine PDGF receptor stimulation has therefore been predicted to contribute to DFSP and GCF tumor development and growth. Here we demonstrate presence of activated PDGF receptors in primary cultures derived from six different DFSP and GCF tumors. Three of the primary cultures were further characterized; their in vitro growth displayed an increased sensitivity to treatment with the PDGF receptor tyrosine kinase inhibitor STI571, as compared with normal fibroblasts. Transplantable tumors, displaying a DFSP-like histology, were established from one of the DFSP primary cultures. Treatment of tumor-bearing severe combined immunodeficient mice with STI571 reduced tumor growth. The growth-inhibitory effects in vitro and in vivo occurred predominantly through induction of tumor cell apoptosis. Our study demonstrates growth-inhibitory effects of PDGF receptor antagonists on human DFSP- and GCF-derived tumor cells and demonstrates that autocrine PDGF receptor stimulation provides antiapoptotic signals contributing to the growth of these cells. These findings suggest targeting of PDGF receptors as a novel treatment strategy for DFSP and GCF.

The PSORS1 locus in the human major histocompatibility complex on 6p21 has been consistently associated with psoriasis in populations of diverse ethnicity. The HLA-C allele Cw*0602, located therein, has been found in up to 67% of psoriasis patients but is no longer considered a candidate gene in itself. The alpha-helix coiled-coil rod homolog gene (HCR, previously Pg8) is located 110 kb from the HLA-C gene, positioned between the CDSN and SC1 genes, within a region thought to harbor a psoriasis gene (PSORS1). We investigated the HCR gene for disease association by direct sequencing of nine polymerase chain reaction products amplified from a series of Swedish psoriasis patients and controls. We found that HCR is a very polymorphic gene with 25 polymorphisms in the open reading frame alone, of which 10 demonstrated disease association; however, the relationship between HCR polymorphisms and HLA-Cw*0602 indicates that HCR cannot truly be considered a likely candidate gene. We investigated Cw*0602 association while stratifying for HCR single nucleotide polymorphisms. We also investigated HCR single nucleotide polymorphism association with the disease while stratifying for the presence of Cw*0602. We found that whichever single nucleotide polymorphism that was stratified for, there was still a strongly significant Cw*0602 association with psoriasis; however, when we stratified for Cw*0602 presence, only one silent polymorphism showed significant association. In a recent similar study this polymorphism was actually found to be decreased in psoriasis individuals. Thus we conclude that HCR polymorphisms display association with psoriasis due to linkage disequilibrium with Cw*0602 and is, therefore, unlikely to be directly involved in the development of psoriasis.

The C7 gene was identified in a project aimed to characterize differential gene expression upon attachment of cells to extracellular matrix proteins in vitro. C7 is the homologue of Drosophila L82, a late puff gene (Stowers et al. (1999) Dev. Biol. 213, 116-130) and human OXR1, a gene, which protects cells against oxidation (Volkert et al. (2000) Proc. Natl. Acad. Sci. USA 97, 14530-14535). All are transcribed into multiple splice forms with a common 3' domain. Additional members of this novel gene family are found in a number of eukaryotic species. In the mouse, the C7 gene is highly and broadly expressed during development in at least 4 splice forms, 3 of which were sequenced. In the adult, the C7 gene is most highly expressed in brain and testis. Antibodies to recombinant C7 protein localized to nucleoli in a variety of cell types, suggesting that C7 may be involved in the formation or function of this important organelle., (Copyright 2001 Academic Press.)

Dermatofibrosarcoma protuberans (DFSP) is a highly recurrent low-grade soft tissue sarcoma, which is usually located on the trunk. Presentation in the vulva is rare, with only 13 cases being reported to date, none of which have been investigated at the cytogenetic or molecular level. Specific cytogenetic abnormalities, involving chromosomes 17 and 22, are characteristic features of DFSP and giant cell fibroblastoma (GCF), a tumor closely related to DFSP. These chromosomal rearrangements result in the fusion of the COL1A1 and PDGFB genes in both lesions and show wide variation in the position of the fusion point in COL1A1. Here, we describe a case of DFSP of the vulva with a typical monotonous storiform pattern, with no foci of multinucleated giant cells. Cytogenetic analysis showed a 47,XX,+r karyotype in 50% of the cells, and molecular investigation disclosed the presence of a transcript fusing COL1A1 exon 37 to PDGFB exon 2. This is the first case of DFSP showing such a fusion point, which is intriguingly identical to that found in a GCF case, indicating that the COL1A1/PDGFB fusion point position does not seem to affect tumor morphology. This finding further underlines the very close relationship between these two morphologically distinct entities.

The redundancy of sequences in dbEST has approached a level where contiguous cDNA sequences of genes can be assembled, without the need to physically handle the clones from which the ESTs are derived. This is termed EST based in silico gene cloning. With the availability of sequence chromatogram files for a subset of ESTs, the quality of EST sequences can be ascertained accurately and used in contig assembly. In this report, we performed a study using this approach and isolated five novel human genes, C11orf1-C11orf5, in the 11q13-q22 region. The full open reading frames of these genes were determined by comparison with their orthologs, of which four mouse orthologs were isolated (c11orf1, c11orf2, c11orf3 and c11orf5). These genes were then analyzed using several proteomics tools. Both C11orf1 and C11orf2 are nuclear proteins with no other distinguishing features. C11orf3 is a cytoplasmic protein containing an ATP/GTP binding site, a signal peptide located in the N-terminus and a similarity to the C. elegans protein "Probable ARP 2/3 complex 20kD subunit." C11orf4 is a peptide which displays four putative transmembrane domains and is predicted to have a cytoplasmic localization. It contains signal peptides at the N- and C-termini. C11orf5 is a putative nuclear protein displaying a central coiled coil domain. Here, we propose that this purely EST-based cloning approach can be used by modestly sized laboratories to rapidly and accurately characterize and map a significant number of human genes without the need of further sequencing., (Copyright 2000 Academic Press.)

Translocation t(11;22)(q23;q11) is the most common constitutional reciprocal translocation in man. Balanced carriers are phenotypically normal, except for decreased fertility, an increased spontaneous abortion rate and a possible predisposition to breast cancer in some families. Here, we report the high resolution mapping of the t(11;22)(q23;q11) breakpoint. We have localised the breakpoint, by using fluorescence in situ hybidisation (FISH) walking, to a region between D11S1340 and WI-8564 on chromosome 11, and D22S134 and D22S264 on chromosome 22. We report the isolation of a bacterial artificial chromosome (BAC) clone spanning the breakpoint in 11q23. We have narrowed down the breakpoint to an 80-kb sequenced region on chromosome 11 and FISH analysis has revealed a variation of the breakpoint position between patients. In 22q11, we have sequenced two BACs (BAC2280L11 and BAC41C4) apparently mapping to the region; these contain low copy repeats (LCRs). Southern blot analysis with probes from BAC2280L11 has revealed different patterns between normal controls and translocation carriers, indicating that sequences similar/identical to these probes flank the translocation breakpoint. The occurrence of LCRs has previously been associated with genomic instability and "unclonable" regions. Hence, the presence of such repeats renders standard translocation breakpoint cloning techniques ineffective. Thus, we have used high resolution fiber-FISH to study this region in normal and translocation cases by using probes from 22q11, LCRs and 11q23. We demonstrate that the LCR containing the gap in 22q11 is probably substantially larger than the previous estimates of 100 kb. Using fiber-FISH, we have localised the breakpoint in 22q11 to approximately 20-40 kb from the centromeric border of the LCR (i.e. the telomeric end of AC006547) and have confirmed the breakpoint position on 11q23.

Knowledge of the complete genomic DNA sequence of an organism allows a systematic approach to defining its genetic components. The genomic sequence provides access to the complete structures of all genes, including those without known function, their control elements, and, by inference, the proteins they encode, as well as all other biologically important sequences. Furthermore, the sequence is a rich and permanent source of information for the design of further biological studies of the organism and for the study of evolution through cross-species sequence comparison. The power of this approach has been amply demonstrated by the determination of the sequences of a number of microbial and model organisms. The next step is to obtain the complete sequence of the entire human genome. Here we report the sequence of the euchromatic part of human chromosome 22. The sequence obtained consists of 12 contiguous segments spanning 33.4 megabases, contains at least 545 genes and 134 pseudogenes, and provides the first view of the complex chromosomal landscapes that will be found in the rest of the genome.

Chromosomal deletions on 3p have been described in a large number of human tumors, suggesting the presence of a tumor suppressor gene(s). Using an experimental system, called the elimination test, we previously identified a 1 Mb segment, the common eliminated region 1 (C3CER1). C3CER1 was also covered by a PAC contig. Using the sequence of two overlapping PACs from C3CER1, we localized the human KIAA0028 cDNA, encoding the precursor of mitochondrial leucyl-tRNA synthetase. We also characterized a novel human LIM domain-containing gene (LIMD1) and its mouse ortholog (Limd1). LIM domains consist of a cysteine-rich consensus sequence containing two distinct zinc-binding subdomains, which mediate protein-protein interactions. The predicted protein sequences of the human and mouse genes reveal three LIM domains located at the C-terminal end, which indicates that they belong to the group 3 of the gene family encoding LIM motifs. We characterized the genomic structure of the human LIMD1 gene and assigned the mouse Limd1 gene to the chromosome 9F subtelomeric region. Both genes are ubiquitously expressed at the mRNA level. The LIM motif has been previously identified in many developmentally important factors from various eukaryotes. These factors have been shown to play a role in intracellular signaling, transcriptional regulation and cellular differentiation during development. The human C3CER1-located LIMD1 gene should therefore be further studied for its possible role in tumor suppression.

Multiple endocrine neoplasia type 1 (MEN1) is an autosomal dominant syndrome predisposing to multiple tumors. The responsible gene, MEN1, has been identified and inactivating mutations reported. It encodes a protein named menin, which lacks homology to any known proteins. Comparative genomics is used to ascertain important functional domains via the identification of evolutionary conserved regions. Here we report the sequencing and characterization of the MEN1 gene in zebrafish (Danio rerio) at the cDNA level. Zebrafish menin is a 617 amino acid protein and, when compared with human and rodent proteins, shows 75% and 76% similarity, respectively. The most conserved region is amino acid residues 41-322 which shows a human/zebrafish similarity of 83%. Amino acids affected by inactivating missense mutations in MEN1 patients in this region are completely conserved between human and zebrafish. Such high correlation between conservation throughout evolution and mutation position strongly emphasizes the importance of this region., (Copyright 1999 Academic Press.)

Dermatofibrosarcoma protuberans (DFSP) displays chromosomal rearrangements involving chromosome 17 and 22, which fuse the collagen type Ialpha1 (COLIA1) gene to the platelet-derived growth factor (PDGF) B-chain (PDGFB) gene. To characterize the functional and structural properties of the COLIA1/PDGFB fusion protein, we generated a stable NIH3T3 cell line that contained a tumor-derived chimeric gene resulting from a COIA1 intron 7-PDGFB intron 1 fusion. Expression of the fusion protein led to morphological transformation and increased growth rate of these cells. The PDGF receptor kinase inhibitor CGP57148B reversed the transformed phenotype and reduced the growth rate of COLIA1/PDGFB-expressing cells but had no effects on control cells. The presence of dimeric COLIA1/PDGFB precursors was demonstrated through PDGFB immunoprecipitations of metabolically labeled cells and also by PDGFB immunoprecipitations followed by immunoblotting with COLIA1 antibodies. Pulse-chase studies demonstrated that the COLIA1/PDGFB precursor was processed to an end product that was indistinguishable from wild-type PDGF-BB. Finally, COLIA1/PDGFB-expressing cells generated tumors after s.c. injection into nude mice, and tumor growth was reduced by treatment with CGP57148B. We conclude that the COLIA1/PDGFB fusion associated with DFSP contributes to tumor development through ectopic production of PDGF-BB and the formation of an autocrine loop. Our findings, thus, suggest that PDGF receptors could be a target for pharmacological treatment of DFSP and giant cell fibroblastoma, e.g., through the use of PDGF receptor kinase inhibitors such as CGP57148B.

Dermatofibrosarcoma protuberans (DFSP) is a cutaneous tumour of borderline malignancy, the cytogenetic features of which include the translocation t(17;22)(q22;q13) or, more commonly, supernumerary ring chromosomes containing material from 17q22 and 22q13. These rearrangements result in the COL1A1/PDGFB fusion gene. Here, we describe a case of DFSP displaying a ring chromosome 5 together with a large marker chromosome composed of chromosome 22 alphoid DNA, material from distal 12q and amplified COL1A1 and PDGFB sequences. This is the first case of DFSP with multiple copies of COL1A1 and PDGFB not confined to ring chromosomes, showing that DFSP is similar to other borderline malignant mesenchymal tumours, where rings and giant markers are alternative vehicles for amplified material.

Dermatofibrosarcoma protuberans (DFSP) and its juvenile form, giant-cell fibroblastoma (GCF), are uncommon infiltrative tumors of the dermis, which present unique cytogenetic features, such as the reciprocal translocation t(17;22) or, more commonly, supernumerary ring chromosomes containing sequences from chromosomes 17 and 22. We have recently shown that these aberrations are cytogenetic manifestations of gene fusions between the platelet-derived growth factor B-chain gene (PDGFB), the cellular equivalent of the v-sis oncogene, and the collagen type 1 alpha 1 gene (COL1A1), the major protein constituent of the extracellular matrix in connective tissue of skin. We now report characterization of COL1A1/PDGFB chimeric genes at the RNA and DNA sequence levels in a series of DFSPs and GCFs. All 16 tumors studied contained the COL1A1/PDGFB gene. The location of breakpoints within COL1A1 varied greatly, but was always limited to the region encoding the alpha-helical domain. The PDGFB segment of the chimeric transcript always starts with exon 2, placing PDGFB under the control of the COL1A1 promoter and removing all known elements negatively controlling PDGFB transcription and translation. Production of these aberrant transcripts in fibroblasts, the suspected cell of origin of DFSP/GCF, likely causes autocrine stimulation and cell proliferation. No specific function has yet been assigned to exon 2 of PDGFB, and this exon does not encode for the mature growth factor. Its retention in all chimeric COL1A1/PDGFB genes suggests that it is important for the normal processing of the PDGFB polypeptide.

Objective and Method: This review examines the scope of forensic psychiatry with particular emphasis on its ethical and social implications. Some comparisons are made between the development of the subspecialty in Australasia and similar developments in the United Kingdom and North America, and the reasons for differences., Results: There has been inadequate debate in Australasia about some of the ethical issues relating to the practice of forensic psychiatry. Furthermore, Australian forensic psychiatry in particular has been slow to develop comprehensive and integrated services compared to other jurisdictions, and remains predominantly an assessment-based activity with primacy of the expert witness., Conclusions: Australasian psychiatry faces significant problems with respect to maldistribution of services. Governments are becoming more radical in their attempts to address this maldistribution and this has ethical implications for the profession itself and the practice of forensic psychiatry. Greater emphasis on the development of integrated and community-based forensic services, with leadership being provided by the profession itself, may deflect some of the present criticism, thereby allowing the subspecialty to more fully mature and develop with the approach of the new millennium.

The quality improvement techniques of managed care are dramatically upgrading the delivery of asthma education and therapy, yielding cost-effective outcomes through a variety of approaches. Guidelines have been available in national and international references, but successful implementation outside of managed care has been poor. The complex components known to produce success in asthma care have not been properly reimbursed in the fee-for-service tradition. Even within managed care settings, attention to cost-effectiveness varies widely, and creative new approaches promise better returns than early asthma programs. Tools that managed care can offer for improved asthma outcomes and cost-effective options are presented.