Increasing sample diversity in psychiatric genetics - Introducing a new cohort of patients with schizophrenia and controls from Vietnam - Results from a pilot study.

OBJECTIVES: Genome-Wide Association Studies (GWAS) of Schizophrenia (SCZ) have provided new biological insights; however, most cohorts are of European ancestry. As a result, derived polygenic risk scores (PRS) show decreased predictive power when applied to populations of different ancestries. We aimed to assess the feasibility of a large-scale data collection in Hanoi, Vietnam, contribute to international efforts to diversify ancestry in SCZ genetic research and examine the transferability of SCZ-PRS to individuals of Vietnamese Kinh ancestry. METHODS: In a pilot study, 368 individuals (including 190 SCZ cases) were recruited at the Hanoi Medical University's associated psychiatric hospitals and outpatient facilities. Data collection included sociodemographic data, baseline clinical data, clinical interviews assessing symptom severity and genome-wide SNP genotyping. SCZ-PRS were generated using different training data sets: (i) European, (ii) East-Asian and (iii) trans-ancestry GWAS summary statistics from the latest SCZ GWAS meta-analysis. RESULTS: SCZ-PRS significantly predicted case status in Vietnamese individuals using mixed-ancestry (R2 liability = 4.9%, p = 6.83 × 10-8), East-Asian (R2 liability = 4.5%, p = 2.73 × 10-7) and European (R2 liability = 3.8%, p = 1.79 × 10-6) discovery samples. DISCUSSION: Our results corroborate previous findings of reduced PRS predictive power across populations, highlighting the importance of ancestral diversity in GWA studies.

A new species of the Simulium (Simulium) crocinum species-group (Diptera: Simuliidae) from Vietnam.

A new black fly species, Simulium yukawai, is described on the basis of one female and its pupal exuviae from Vietnam. This new species is placed in the S. crocinum species-group of Simulium (Simulium) (Diptera: Simuliidae). It is characterized in the female by the paraproct covered with 48-50 distinct hairs on its ventral and lateral surfaces, and in the pupa by the frons and most of the thorax bare, gill with six dark filaments in three pairs closely arising from the base, of which the two outer filaments of the dorsal and middle pairs are much longer than other filaments, abdomen with distinct spine-combs on the dorsal surface of segments 7-9, and cocoon wall-pocket shaped, with a large anterolateral window on each side. Taxonomic notes are given to separate this new species from related species. This species is the fourth member of the S. crocinum species-group known from Vietnam.

A new species of the Simulium (Simulium) crocinum species-group (Diptera: Simuliidae) from Vietnam

@#A new black fly species, Simulium yukawai, is described on the basis of one female and its pupal exuviae from Vietnam. This new species is placed in the S. crocinum species-group of Simulium (Simulium) (Diptera: Simuliidae). It is characterized in the female by the paraproct covered with 48–50 distinct hairs on its ventral and lateral surfaces, and in the pupa by the frons and most of the thorax bare, gill with six dark filaments in three pairs closely arising from the base, of which the two outer filaments of the dorsal and middle pairs are much longer than other filaments, abdomen with distinct spine-combs on the dorsal surface of segments 7–9, and cocoon wall-pocket shaped, with a large anterolateral window on each side. Taxonomic notes are given to separate this new species from related species. This species is the fourth member of the S. crocinum species-group known from Vietnam.

The DPYSL2 gene connects mTOR and schizophrenia.

We previously reported a schizophrenia-associated polymorphic CT di-nucleotide repeat (DNR) at the 5'-untranslated repeat (UTR) of DPYSL2, which responds to mammalian target of Rapamycin (mTOR) signaling with allelic differences in reporter assays. Now using microarray analysis, we show that the DNR alleles interact differentially with specific proteins, including the mTOR-related protein HuD/ELAVL4. We confirm the differential binding to HuD and other known mTOR effectors by electrophoretic mobility shift assays. We edit HEK293 cells by CRISPR/Cas9 to carry the schizophrenia risk variant (13DNR) and observe a significant reduction of the corresponding CRMP2 isoform. These edited cells confirm the response to mTOR inhibitors and show a twofold shortening of the cellular projections. Transcriptome analysis of these modified cells by RNA-seq shows changes in 12.7% of expressed transcripts at a false discovery rate of 0.05. These transcripts are enriched in immunity-related genes, overlap significantly with those modified by the schizophrenia-associated gene, ZNF804A, and have a reverse expression signature from that seen with antipsychotic drugs. Our results support the functional importance of the DPYSL2 DNR and a role for mTOR signaling in schizophrenia.

Kaposi's sarcoma after repeated surgical procedures in an immunocompetent patient: the lymphatic hypothesis.

A 63-year-old Swiss patient developed acquired nodules on his right palm after 3 localized surgeries, called 'needle fasciotomy', for Dupuytren's disease. Kaposi's sarcoma (KS) was diagnosed in a biopsy of a nodule. A positive immunolabeling and serology for human herpesvirus 8 has been found, but human immunodeficiency virus and hepatitis C identification remained negative. The nodules were limited to the surgically traumatized area. This first report of a nonimmunocompromised patient developing a KS after repeated surgeries in a unique peculiar localized area with a dense lymphatic network sustains the hypothesis that tissue alterations involving the lymphatic system could play a central role in the occurrence of KS.

Sacral inflammatory pseudotumor revealed by paraneoplastic syndrome.

There is still debate on whether inflammatory pseudotumor should be considered benign or malignant. This lesion has only been reported twice in bone, apart from cases complicating foreign body reaction to joint replacement arthroplasty. We report here a third case, localized at the sacrum. A 31-year-old man had inflammatory dorsalgia and polyarthralgia without synovitis but with fever, asthenia, and erythema nodosa. Biological tests and X-rays were not informative, but technetium scintigraphy revealed a high level of left sacroiliac tracer binding. Several nonsteroidal anti-inflammatory drugs and sulfasalazine treatment were given over 3 months but ineffective. Pelvic magnetic resonance imaging showed an osteolytic tumor of the sacrum. Biopsy suggested a malignant fibrosarcoma, but complete evaluation after surgical resection demonstrated an inflammatory pseudotumor. All clinical symptoms disappeared within a few days after surgery, which is suggestive of a paraneoplastic syndrome. No relapse has occurred after 4 years.

Detection of Orientia tsutsugamushi (Rickettsiales: rickettsiaceae) in unengorged chiggers (Acari: Trombiculidae) from Oita Prefecture, Japan, by nested polymerase chain reaction.

The current study surveyed the 56-kDa type-specific antigen (TSA) gene DNAs of Orientia tsutsugamushi (Hayashi) in approximately 4.000 unengorged chiggers obtained from the soil or ground surface in an endemic and a nonendemic area of the Tsutsugamushi disease in Oita Prefecture, southwestern Japan, by nested polymerase chain reaction (PCR). Serotypes of O. tsutsugamushi were identified by restriction fragment-length polymorphism (RFLP) analysis. In the endemic area, 242 pools from five species [234 pools of Leptotrombidium scutellare (Nagayo, Miyagawa, Mitamura, Tamiya and Tenjin), two L. pallidum (Nagayo, Miyagawa, Mitamura and Tamiya), four L. kitasatoi (Fukuzumi & Obata), one L. fuji (Kuwata, Berge and Philip), and one Neotrombicula japonica (Tanaka, Kaiwa, Teramura and Kagaya)] were tested, and eight (seven pools of L. scutellare and one N. japonica) were positive for O. tsutsugamushi. Among the seven positive pools of L. scutellare, the distribution of serotypes was as follows: Kuroki (4), Gilliam (1), Karp (1), and Kawasaki (1). The first two serotypes (Kuroki and Gilliam) were identified for the first time in this species. In the nonendemic area, 128 pools from eight species were tested, and 13 were positive for O. tsutsugamushi. The positive rate was as follows: L. pallidum (4/41). L. kitasatoi (1/18), Gahrliepia saduski Womersley (2/10), L. fuji (4/50), L. himizu (Sasa, Kumada, Hayashi, Enomoto, Fukuzumi and Obata) (1/2), and Miyatrombicula kochiensis (Sasa, Kawashima and Egashira) (1/3). The latter three species were shown for the first time to harbor O. tsutsugamushi. All ofthe positive pools were Kuroki, except for two pools (one L. pallidum and one L. fuji), which were Gilliam (this serotype was also detected for the first time in L. pallidum). Further analysis revealed no differences in the nucleotide sequences (125 bp of variable domain 1 of TSA gene) of the same serotypes (i.e., Kuroki and Gilliam) among the positive samples. These data indicate that O. tsutsugamushi was widely distributed in various trombiculid species, even in the nonendemic area. The data are also suggestive of a possible horizontal transmission of O. tsutsugamushi among trombiculid species.

Identification of a genomic island present in the majority of pathogenic isolates of Pseudomonas aeruginosa.

Pseudomonas aeruginosa, a ubiquitous gram-negative bacterium, is capable of colonizing a wide range of environmental niches and can also cause serious infections in humans. In order to understand the genetic makeup of pathogenic P. aeruginosa strains, a method of differential hybridization of arrayed libraries of cloned DNA fragments was developed. An M13 library of DNA from strain X24509, isolated from a patient with a urinary tract infection, was screened using a DNA probe from P. aeruginosa strain PAO1. The genome of PAO1 has been recently sequenced and can be used as a reference for comparisons of genetic organization in different strains. M13 clones that did not react with a DNA probe from PAO1 carried X24509-specific inserts. When a similar array hybridization analysis with DNA probes from different strains was used, a set of M13 clones which carried sequences present in the majority of human P. aeruginosa isolates from a wide range of clinical sources was identified. The inserts of these clones were used to identify cosmids encompassing a contiguous 48.9-kb region of the X24509 chromosome called PAGI-1 (for "P. aeruginosa genomic island 1"). PAGI-1 is incorporated in the X24509 chromosome at a locus that shows a deletion of a 6,729-bp region present in strain PAO1. Survey of the incidence of PAGI-1 revealed that this island is present in 85% of the strains from clinical sources. Approximately half of the PAGI-1-carrying strains show the same deletion as X24509, while the remaining strains contain both the PAGI-1 sequences and the 6,729-bp PAO1 segment. Sequence analysis of PAGI-1 revealed that it contains 51 predicted open reading frames. Several of these genes encoded products with predictable function based on their sequence similarities to known genes, including insertion sequences, determinants of regulatory proteins, a number of dehydrogenase gene homologs, and two for proteins of implicated in detoxification of reactive oxygen species. It is very likely that PAGI-1 was acquired by a large number of P. aeruginosa isolates through horizontal gene transfer. The selection for its maintenance may be the consequence of expression of any one of the genes of unknown function or the genes which allow P. aeruginosa to survive under the conditions that generate reactive oxygen species. Alternatively, one or both of the transcriptional regulators encoded in PAGI-1 may control the expression of genes in the P. aeruginosa chromosome, which provides a selective advantage for strains that have acquired this genomic island.

Distribution of unengorged larvae of Leptotrombidium pallidum and other species in and around the rodent nest holes.

The distribution of unengorged larvae of Leptotrombidium pallidum, L. fuji and L. kitasatoi in and around 12 rodent-nest holes in Oita Prefecture, Japan was studied using the Tullgren funnel apparatus. Soil was taken from each nest hole, and the ground-surface soil and litter from the surrounding area A (an inner quadrate of 20 cm x 20 cm except the nest hole), and also from the outer area B (an outer quadrate of 40 cm x 40 cm excluding A and the nest hole) were sampled, separately. The numbers (% of the total) of L. pallidum collected from soil samples of the nest holes and areas A and B were 38 (19.0), 111 (55.5) and 30 (15.0); those of L. fuji were 171 (58.8), 104 (35.7) and 14 (4.8); those of L. kitasatoi were 35 (77.9), 7 (15.6) and 3 (6.7), and those of G. saduski were 20 (50.0), 17 (42.5) and 3 (7.5). The larvae recovered from litter samples were few, representing 0-8.5% of the total. It is shown that unengorged larvae of these species are distributed not only in the nest holes but also in the nearby areas, and exist mainly on (or in) the soil.

A DNA helicase from Pisum sativum is homologous to translation initiation factor and stimulates topoisomerase I activity.

DNA helicases play an essential role in all aspects of nucleic acid metabolism, by providing a duplex-unwinding function. This is the first report of the isolation of a cDNA (1.6 kb) clone encoding functional DNA helicase from a plant (pea, Pisum sativum). The deduced amino-acid sequence has eight conserved helicase motifs of the DEAD-box protein family. It is a unique member of this family, containing DESD and SRT motifs instead of DEAD/H and SAT. The encoded 45.5 kDa protein has been overexpressed in bacteria and purified to homogeneity. The purified protein contains ATP-dependent DNA and RNA helicase, DNA-dependent ATPase, and ATP-binding activities. The protein sequence contains striking homology with eIF-4A, which has not so far been reported as DNA helicase. The antibodies against pea helicase inhibit in vitro translation. The gene is expressed as 1.6 kb mRNA in different organs of pea. The enzyme is localized in the nucleus and cytosol, and unwinds DNA in the 3' to 5' direction. The pea helicase interacts with pea topoisomerase I protein and stimulates its activity. These results suggest that pea DNA helicase could be an important multifunctional protein involved in protein synthesis, maintaining the basic activities of the cell, and in upregulation of topoisomerase I activity. The discovery of such a protein with intrinsic multiple activity should make an important contribution to our better understanding of DNA and RNA transactions in plants.

High-frequency flp recombinase-mediated inversions of the oriC-containing region of the Pseudomonas aeruginosa genome.

The genomes of the two clonally derived Pseudomonas aeruginosa prototypic strains PAO1 and DSM-1707 differ by the presence of a 2. 19-Mb inversion including oriC. Integration of two Flp recombinase target sites near the rrn operons containing the inversion endpoints in PAO1 led to Flp-catalyzed inversion of the intervening 1.59-Mb fragment, including oriC, at high frequencies (83%), favoring the chromosome configuration found in DSM-1707. The results indicate that the oriC-containing region of the P. aeruginosa chromosome can readily undergo and tolerate large inversions.

Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen.

Pseudomonas aeruginosa is a ubiquitous environmental bacterium that is one of the top three causes of opportunistic human infections. A major factor in its prominence as a pathogen is its intrinsic resistance to antibiotics and disinfectants. Here we report the complete sequence of P. aeruginosa strain PAO1. At 6.3 million base pairs, this is the largest bacterial genome sequenced, and the sequence provides insights into the basis of the versatility and intrinsic drug resistance of P. aeruginosa. Consistent with its larger genome size and environmental adaptability, P. aeruginosa contains the highest proportion of regulatory genes observed for a bacterial genome and a large number of genes involved in the catabolism, transport and efflux of organic compounds as well as four potential chemotaxis systems. We propose that the size and complexity of the P. aeruginosa genome reflect an evolutionary adaptation permitting it to thrive in diverse environments and resist the effects of a variety of antimicrobial substances.

Upper cervical spine surgery in rheumatoid arthritis: retrospective study of 30 patients followed for two years or more after Cotrel-Dubousset instrumentation.

PURPOSE: To evaluate the efficacy of upper cervical spine surgery in symptomatic atlantoaxial instability due to rheumatoid arthritis (RA). MATERIAL AND METHODS: Thirty RA patients (29 women and one man) with a mean age of 56 years were studied retrospectively. Symptomatic forward slippage of the atlas on the axis with a synovial pannus surrounding the odontoid and magnetic resonance imaging evidence of spinal cord compression was present in all 30 patients; 18 patients had vertical translocation of the odontoid and 14 had basilar invagination. Surgery, performed between 1991 and 1997, consisted of occipitocervical fusion in 18 patients and atlantoaxial fusion in 12. Cotrel-Dubousset instrumentation was performed in all 30 patients. RESULTS: Mean follow-up was four and a half years. All patients were satisfied with the procedure and exhibited marked functional gains and objective neurological improvement (by one class in the Ranawat scheme). Stable fusion was documented in all 30 patients. CONCLUSION: Cervical instrumentation and bone grafting seems to provide functional and neurological gains in carefully selected RA patients with atlantoaxial instability and spinal cord compression. Long term follow-up suggests that the benefits are sustained and that morbidity is low.

Role of water mobility on mold spore germination.

A sugar transport defected strain of Aspergillus nidulans (biA-1 sorA-2) was tested for spore germination in nutrient media containing various water activity (a(w)) values and varying amounts of non-nutritive, nontoxic carbohydrates (L-sorbose and cellulose). Freeze-dried media [containing the same nutrient level but different in sorbose/cellulose (s:c) ratio] were adjusted to 0.75-0.97a(w) at 25 degrees C before inoculation. Minimum a(w) for germination varied with s:c ratio. Because both sorbose and cellulose were not metabolizable and unable to be transported into the cells, the results reflected the molecular mobility of water. (2)H NMR T(2) relaxation time correlated well with spore germination time, and it distinguished the difference between water sorbed to cellulose and water in a solution associated with dissolved sorbose. On the other hand, mold germination time correlated poorly with a(w). It was highly dependent on the s:c ratio. Water mobility was found to correlate better with biological activity than a(w) because it differentiated the availability between water in dissolved sorbose and adsorbed water in cellulose.

Magnetic resonance imaging changes in periarticular soft tissues during flares of medial compartment knee osteoarthritis. Preliminary study in 10 patients.

OBJECTIVE: To quantify changes in magnetic resonance imaging signals from the deep and superficial capsulo-ligamentous planes and the medial collateral ligament in flares of knee osteoarthritis. PATIENTS AND METHODS: Preliminary prospective study of ten patients with medial compartment knee osteoarthritis meeting American College of Rheumatology criteria and associated with a Lequesne index of 5 or more. A grid was used to evaluate signal changes as compared to the opposite (asymptomatic) knee. Magnetic resonance images were read independently by two radiologists blinded to clinical data. RESULTS AND DISCUSSION: In all ten patients the capsulo-ligamentous planes and medial collateral ligament generated low signal on T1 images and high signal on T2 images. No significant changes were seen in the asymptomatic knee. The evaluation grid produced satisfactory interobserver agreement. CONCLUSION: Flares of medial compartment knee osteoarthritis are associated with changes in magnetic signal as compared to the contralateral asymptomatic osteoarthritic knee. The grid developed for this study could be used to evaluate the effects of treatment in a larger number of patients.

Cytotoxicity evaluation of multipurpose contact lens solutions using an in vitro test battery.

PURPOSE: Many in vitro alternatives to eye irritation testing are not mechanism-specific and do not employ ocular cell lines. We have developed an effective and reliable test battery that reveals toxicity mechanisms of contact lens solutions on cell metabolism and proliferation. METHODS: Cytotoxicity endpoints were quantified using bovine corneal epithelial cultures in 96-well microplates. A kenacid blue assay provided information on total cell protein, while lactate production and alamarBlue assays served as indicators of aerobic/anaerobic metabolism and redox state of cells grown in serum-free Dulbecco's modified Eagle's/Ham's F12 medium (DMEM/F12). Concentrations (% v/v) causing 10-90% inhibition of the control assay responses were used for correlations with in vivo data. RESULTS: Cytotoxicities of contact lens solutions correlated better with irritant symptoms than with corneal staining, and were ranked as follows: Lens Plus << Opti-Free < or = ContaClair < or = ReNu. Lens Plus was not toxic to cell glycolysis, respiration, and proliferation for up to 20% v/v. However, the multi-purpose solutions inhibited these endpoints in a concentration-dependent manner. Opti-Free and ReNu, containing Dymed and Polyquad (ammonium surfactants), showed non-specific cell inhibition. The lactate production assay had a flatter log concentration-response curve than the other two assays. CONCLUSIONS: The proposed biochemically-based test battery using the target corneal epithelium has the potential to be a simple and effective method for screening and defining toxicity profiles of contact lens care solutions. The model can be applicable to small- or large-scale testing programs and research and development of new ocular products.