Mapping structural variants to rare disease genes using long-read whole genome sequencing and trait-relevant polygenic scores

Recent studies have revealed the pervasive landscape of rare structural variants (rSVs) present in human genomes. rSVs can have extreme effects on the expression of proximal genes and, in a rare disease context, have been implicated in patient cases where no diagnostic single nucleotide variant (SNV) was found. Approaches for integrating rSVs to date have focused on targeted approaches in known Mendelian rare disease genes. This approach is intractable for rare diseases with many causal loci or patients with complex, multi-phenotype syndromes. We hypothesized that integrating trait-relevant polygenic scores (PGS) would provide a substantial reduction in the number of candidate disease genes in which to assess rSV effects. We further implemented a method for ranking PGS genes to define a set of core/key genes where a rSV has the potential to exert relatively larger effects on disease risk. Among a subset of patients enrolled in the Genomic Answers for Kids (GA4K) rare disease program (N=497), we used PacBio HiFi long-read whole genome sequencing (lrWGS) to identify rSVs intersecting genes in trait-relevant PGSs. Illustrating our approach in Autism (N=54 cases), we identified 1,827 deletions, 158 duplications, 619 insertions, and 14 inversions overlapping putative core/key PGS genes. Additionally, by integrating genomic constraint annotations from gnomAD, we observed that rare duplications overlapping putative core/key PGS genes were frequently in higher constraint regions compared to controls (P = 2×10-04). This difference was not observed in the lowest-ranked gene set (P = 0.18). Overall, our study provides a framework for the annotation of long-read rSVs from lrWGS data and prioritization of disease-linked genomic regions for downstream functional validation of rSV impacts. To enable reuse by other researchers, we have made SV allele frequencies and gene associations freely available.

Wuyiencin produced by Streptomyces albulus CK-15 displays biocontrol activities against cucumber powdery mildew

AIMS

Wuyiencin is a nucleoside antibiotic produced by Streptomyces albulus CK-15. The aim of this study was to determine whether wuyiencin can be used, as a suitable alternative to chemical pesticides, to protect cucumbers (Cucumis sativus L.) from powdery mildew caused by Sphaerotheca fuliginea. Further, the mechanisms underlying the control of cucumber powdery mildew by S. albulus CK-15 were preliminarily elucidated.

METHODS AND RESULTS

Wuyiencin solutions of different concentrations were used to treat infected cucumber plants under greenhouse conditions. The results indicated that wuyiencin could significantly reduce powdery mildew disease incidence, with a maximum prevention efficacy of 94·38%. Further, scanning electron micrographs and enzyme assays showed that wuyiencin inhibited S. fuliginea spore growth and elicited the activity of plant systemic resistance-related enzymes. Additionally, real-time quantitative reverse transcription PCR suggested that wuyiencin can activate a salicylic acid-dependent plant defence response.

CONCLUSIONS

Wuyiencin produced by S. albulus CK-15 possessed antifungal effects and was able to mitigate cucumber powdery mildew disease via antagonistic action. Wuyiencin also induced defence responses in the plants.

SIGNIFICANCE AND IMPACT OF THE STUDY

These results reinforce the biotechnological potential of wuyiencin as both an antagonistic agent and an inducer of plant systemic resistance.

Effects of Folic Acid and Vitamin B12 Supplementation on Cognitive Impairment and Inflammation in Patients with Alzheimer's Disease: A Randomized, Single-Blinded, Placebo-Controlled Trial

OBJECTIVES

To evaluate the combined action of folic acid and vitamin B12 supplementation on cognitive performance and inflammation in patients with Alzheimer's disease (AD).

DESIGN

This was a randomized, single-blind, placebo-controlled trial.

PARTICIPANTS

Patients (n=120) diagnosed clinically as probable AD and in stable condition from Tianjin Key Laboratory of Cerebrovascular and Neurodegenerative Diseases.

MEASUREMENTS

Individuals were randomly divided into the intervention group (n=60, folic acid 1.2 mg/d + vitamin B12 50 μg/d) and the placebo group (n=60). Cognitive performance, blood folate, vitamin B12, one carbon cycle metabolite, and inflammatory cytokine levels were measured at baseline and after 6 months. The data were analyzed using linear mixed models for repeated measures.

RESULTS

A total of 101 participants (51 in the intervention group and 50 in the placebo group) completed the trial. Folic acid plus vitamin B12 supplementation had a beneficial effect on the MoCA total scores (P=0.029), naming scores (P=0.013), orientation scores (P=0.004), and ADAS-Cog domain score of attention (P=0.008), as compared to those of the control subjects. Moreover, supplementation significantly increased plasma SAM (P<0.001) and SAM/SAH (P<0.001), and significantly decreased the levels of serum Hcy (P<0.001), plasma SAH (P<0.001), and serum TNFα (P<0.001) compared to in the control subjects.

CONCLUSIONS

Folic acid and vitamin B12 supplementation showed a positive therapeutic effect in AD patients who were not on a folic acid-fortified diet. The findings of this study help to delineate nutrient intervention as far as public health management for the prevention of dementia is concerned.

High-glucose promotes proliferation of human bladder cancer T24 cells by activating Wnt/β-catenin signaling pathway

OBJECTIVE

Bladder cancer is the most prevalent genitourinary malignant disorder worldwide. We aimed to observe effects of high-glucose on bladder cancer proliferation and explore the associated mechanisms.

MATERIALS AND METHODS

Human bladder cancer cell line, T24, was divided into Blank, Control (Ctrl), 10 mmol/l, 20 mmol/l and 30 mmol/l group. T24 cell proliferation was evaluated by using multiple table tournament (MTT) assay and colony formation analysis, respectively. Quantitative Real-time PCR (qRT-PCR) assay was employed to examine mRNA expression of Wnt-5a and β-catenin. Meanwhile, Western blot assay was used to evaluate expression of Wnt-5a and β-catenin protein. The linear regression analysis was utilized to analyze correlation between Wnt-5a/β-catenin expression and T24 cell proliferation.

RESULTS

High-glucose significantly enhanced proliferation of T24 cells compared to that of Blank and Ctrl group (p < 0.05). High-glucose significantly promoted colony formation of T24 cells compared to that of Blank and Ctrl group (p < 0.05). High-glucose significantly up-regulated Wnt-5a mRNA and protein expression compared to that of Blank and Ctrl group (p < 0.01). High-glucose significantly increased β-catenin mRNA and protein expression compared to that of Blank and Ctrl group (p < 0.01). Effects of high-glucose on T24 cell proliferation were increased following with the enhanced glucose concentration. Wnt/β-catenin signaling pathway molecules were correlated with colony formation of T24 cells (p < 0.05).

CONCLUSIONS

High-glucose promoted the proliferation of T24 cells by activating the Wnt/β-catenin signaling pathway. This study would provide the novel targets for bladder cancer therapy.

The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project

The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.

Robustness of Salmonella loop-mediated isothermal amplification assays for food applications

AIMS

Loop-mediated isothermal amplification (LAMP) assays have been developed recently for Salmonella detection. This study aimed at evaluating the robustness of two Salmonella LAMP assays in comparison with PCR and real-time quantitative PCR for food applications.

METHODS AND RESULTS

Performance of the assays was examined under abusive preparation conditions, running temperatures and pH, and with the addition of various inhibitors and food rinses. LAMP achieved robust detection under abusive assay preparation conditions (holding at 22 and 37°C for up to 30 min) and running temperatures (57-68°C). With a hot-start DNA polymerase, PCR obtained comparable results under these temperature ranges. However, PCR performed markedly poorer under abusive pH. LAMP also showed greater tolerance to potential inhibitors than PCR. When food rinses including meat juice, chicken rinse, egg homogenate and produce homogenate were added at 20% of the reaction mix, PCR amplifications were completely inhibited, but LAMP reactions were not.

CONCLUSIONS

Our results demonstrated that LAMP is a robust alternative to PCR in Salmonella detection for food applications.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study filled important knowledge gaps regarding the robustness of Salmonella LAMP assays. The findings will help bring Salmonella LAMP assays closer to wider applications in food testing.

Population genetic structure and historical demography of Oratosquilla oratoria revealed by mitochondrial DNA sequences

Genetic diversity, population genetic structure and molecular phylogeographic pattern of mantis shrimp Oratosquilla oratoria in Bohai Sea and South China Sea were analyzed by mitochondrial DNA sequences. Nucleotide and haplotype diversities were 0.00409-0.00669 and 0.894-0.953 respectively. Neighbor-Joining phylogenetic tree clustered two distinct lineages. Both phylogenetic tree and median-joining network showed the consistent genetic structure corresponding to geographical distribution. Mismatch distributions, negative neutral test and "star-like" network supported a sudden population expansion event. And the time was estimated about 44000 and 50000 years ago.

Recruitment of Grb2 and SHIP1 by the ITT-like motif of TIGIT suppresses granule polarization and cytotoxicity of NK cells

Activating and inhibitory receptors control natural killer (NK) cell activity. T-cell immunoglobulin and ITIM (immunoreceptor tyrosine-based inhibition motif) domain (TIGIT) was recently identified as a new inhibitory receptor on T and NK cells that suppressed their effector functions. TIGIT harbors the immunoreceptor tail tyrosine (ITT)-like and ITIM motifs in its cytoplasmic tail. However, how its ITT-like motif functions in TIGIT-mediated negative signaling is still unclear. Here, we show that TIGIT/PVR (poliovirus receptor) engagement disrupts granule polarization leading to loss of killing activity of NK cells. The ITT-like motif of TIGIT has a major role in its negative signaling. After TIGIT/PVR ligation, the ITT-like motif is phosphorylated at Tyr225 and binds to cytosolic adapter Grb2, which can recruit SHIP1 to prematurely terminate phosphatidylinositol 3-kinase (PI3K) and MAPK signaling, leading to downregulation of NK cell function. In support of this, Tyr225 or Asn227 mutation leads to restoration of TIGIT/PVR-mediated cytotoxicity, and SHIP1 silencing can dramatically abolish TIGIT/PVR-mediated killing inhibition.

Multiplex PCR assays for simultaneous detection and characterization of Vibrio vulnificus strains

AIMS

Vibrio vulnificus is a major cause of seafood-related deaths in the United States. Several biomarkers, e.g. the virulence-correlated gene (vcg), 16S rRNA, and the capsular polysaccharide operon (CPS) have been used to differentiate virulent- from nonvirulent-type V. vulnificus strains. In this study, we combined the use of these biomarkers with a species-specific V. vulnificus cytolysin/haemolysin gene (vvhA) to develop two pairs of multiplex PCR assays that simultaneously detect and characterize V. vulnificus strains.

METHODS AND RESULTS

The first multiplex PCR pair amplified four genes (vvhA, vcg, 16S rRNA, and CPS), with one for virulent-type and the other one for nonvirulent-type V. vulnificus strains, while the second pair targeted three of those genes excluding CPS. Primer concentration and annealing temperature were optimized for the four multiplex PCR assays. When testing ten V. vulnificus reference strains and 80 field oyster isolates, results from each multiplex PCR matched 100% with known strain characteristics for these target genes.

CONCLUSIONS

The optimized multiplex PCR assays were capable of simultaneously detecting and characterizing V. vulnificus with high specificity and speed.

SIGNIFICANCE AND IMPACT OF THE STUDY

Multiplex PCR assays designed in this study are valuable tools for microbial ecology and epidemiology studies. They may facilitate better control of V. vulnificus risks in oysters, thereby reducing the number of illnesses and deaths because of V. vulnificus in the long run.

Weight gain in breast cancer patients: Tamoxifen versus anastrazole

10544

Background: Weight gain is a common complaint among breast cancer patients, especially those taking tamoxifen. Aromatase inhibitors have been increasingly used in postmenopausal breast cancer patients, and are generally thought to have a more tolerable side-effect profile than selective estrogen receptor modulators (SERM’s). This study specifically addresses weight gain in patients on the SERM, tamoxifen, compared to patients on the aromatase inhibitor, anastrazole. Methods: Ninety-six outpatients with primary breast cancer of any stage received standard doses of adjuvant hormonal therapy. Seventy received tamoxifen (Group T) and 26 anastrazole (Group A). The nursing staff in the clinic weighed all patients at the time of diagnosis, at start of chemotherapy (if received), at start of hormone therapy, and at 3 month intervals for 12 months after starting hormone therapy. Data were gathered in a retrospective manner. Results: Demographic variables were compared between the two groups. In all patients, it was noted that increasing age was correlated with greater weight gain at 3 months after starting hormone therapy (p = 0.0257), but not at any other intervals. No other variables were significantly correlated with weight gain. In Group T, mean weight gain was clinically (>1.8 kgs) and statistically significant at 9 and 12 months (p = 0.0137, p = 0.0003). In Group A, mean weight gain was not clinically significant at any point. Using the Wilcoxon two-sample tests to compare groups T and A, it was shown that there was no statistically significant difference in weight gain between the two groups at any interval (see table). Conclusions: These results are consistent with previous studies that show significant weight gain in breast cancer patients on tamoxifen. This study failed to show a statistically significant difference in weight gain between patients on tamoxifen and patients on anastrazole. Group A did not have statistically significant weight gain at any interval after starting hormone therapy.

[Table: see text]

No significant financial relationships to disclose.

BCL3 is induced by IL-6 via Stat3 binding to intronic enhancer HS4 and represses its own transcription

BCL3 is a proto-oncogene affected by chromosomal translocations in some patients with chronic lymphocytic leukemia. It is an IkappaB family protein that is involved in transcriptional regulation of a number of NF-kappaB target genes. In this study, interleukin (IL)-6-induced BCL3 expression and its effect on survival of multiple myeloma (MM) cells were examined. We demonstrate the upregulation of BCL3 by IL-6 in INA-6 and other MM cell lines. Sequence analysis of the BCL3 gene locus revealed four potential signal transducer and activator of transcription (Stat) binding sites within two conserved intronic enhancers regions: one located within enhancer HS3 and three within HS4. Chromatin immunoprecipitation experiments showed increased Stat3 binding to both enhancers upon IL-6 stimulation. Silencing Stat3 expression by small interfering RNA (siRNA) abrogated BCL3 expression by IL-6. Using reporter gene assays, we demonstrate that BCL3 transcription depends on HS4. Mutation of the Stat motifs within HS4 abolished IL-6-dependent BCL3 induction. Furthermore, BCL3 transcription was inhibited by its own gene product. This repressive feedback is mediated by NF-kappaB sites within the promoter and HS3. Finally, we show that overexpression of BCL3 increases apoptosis, whereas BCL3-specific siRNA does not affect the viability of INA-6 cells suggesting that BCL3 is not essential for the survival of these cells.

Genotyping of Campylobacter spp. from retail meats by pulsed-field gel electrophoresis and ribotyping

AIMS

To determine the genetic relatedness of Campylobacter spp. from retail meat products, and compare the discriminatory power of pulsed-field gel electrophoresis (PFGE) and automatic ribotyping.

METHODS AND RESULTS

A total of 378 Campylobacter isolates recovered from 159 raw meats (130 chicken, 25 turkey, three pork and one beef) sampled from 50 retail grocery stores of four supermarket chains in the Maryland suburban area from August 1999 to July 2000 were analysed by PFGE with SmaI, 120 isolates of which were also characterized by ribotyping with PstI using RiboPrinter system. A total of 148 unique PFGE patterns were identified, 91 of which were present in multiple Campylobacter isolates and 24 in multiple meat samples. Nineteen Campylobacter clones with identical PFGE patterns recurred frequently (up to nine times) throughout the sampling period. Comparing ribotyping with PFGE, we identified 44 PFGE patterns and 22 RiboGroups among the 120 isolates tested. Multiple PFGE patterns within one RiboGroup were commonly observed, as well as multiple RiboGroups within one PFGE pattern.

CONCLUSIONS

Although Campylobacter present in retail meats were genetically diverse, certain clones persisted in poultry meats. PFGE had a greater discriminatory power than ribotyping, and the two methods were complementary in genotyping Campylobacter.

SIGNIFICANCE AND IMPACT OF THE STUDY

Genomic DNA fingerprinting of Campylobacter confirmed diverse and recurrent Campylobacter clones in the retail meats, which provides additional data for a better understanding of the epidemiological aspect of Campylobacter infection.

Effect of nebulized albuterol on blood glucose in patients with diabetes mellitus with and without cystic fibrosis

Over 90% of cystic fibrosis (CF) patients are treated with bronchodilators, and 6% have diabetes. Some with asthma also have diabetes, and most are treated with bronchodilators. Systemic administration of adrenergic agents can cause increases in blood glucose, but the effect of inhaled agents is unclear. A double-blind study was performed on 10 patients with type 1 diabetes mellitus (DM) without CF (3 male, 7 female, mean age 25.5 years) and 9 patients with insulin-dependent CF-related diabetes (CFRD) (8 male, 1 female, mean age 21.9 years). On 2 separate days before 9 AM fasting and the morning dose of insulin, 2.5 mg of albuterol or nebulized placebo were given. Blood glucose was measured by finger stick with a glucose reflectance meter before and 15, 30, 45, and 60 min after treatment. No significant changes from baseline or differences between placebo and albuterol occurred in either group. The mean maximum increase from baseline in DM was 20 mg/dl on placebo, and 38 mg/dl on albuterol; in the CFRD, the respective changes were 7 and 7 mg/dl. Two DM patients had a > 50 mg/dl increase on albuterol vs. placebo; no CFRD patients had differences of such magnitude. DM patients had greater increases from baseline than CFRD patients on placebo and albuterol. Differences reached statistical significance at 30 and 45 min on placebo, and 45 min on albuterol. Albuterol 2.5 mg by nebulizer causes no clinically significant increases in blood glucose in DM or CFRD patients. Diabetes patients without CF have a significantly greater increase of glucose with time (placebo or albuterol) than CFRD patients.

Electrochemistry of immobilized CuZnSOD and FeSOD and their interaction with superoxide radicals

Copper, zinc superoxide dismutase (CuZnSOD) from bovine erythrocytes and iron superoxide dismutase from Escherichia coli (FeSOD) were immobilized on 3-mercaptopropionic acid (MPA)-modified gold electrodes, respectively. The characterization of the SOD electrodes showed a quasi-reversible, electrochemical redox behavior with a formal potential of 47+/-4 mV and -154+/-5 mV (vs. Ag/AgCl, 1 M KCl) for surface adsorbed CuZnSOD and FeSOD, respectively. The heterogeneous electron transfer rate constants were determined to be about 65 and 35/s, respectively. Covalent fixation of both SODs was also feasible with only slight changes in the formal potential. The interaction of superoxide radicals (O(2)(-)) with the SOD electrode was investigated. No catalytic current could be observed. However, due to the fast cyclic redox reaction of SOD with superoxide, the communication of the protein with the electrode was strongly influenced. The amperometric detection of superoxide radicals is discussed.

Identification of Escherichia coli O157:H7 and other enterohemorrhagic serotypes by EHEC- hlyA targeting, strand displacement amplification, and fluorescence polarization

Human disease caused by enterohemorrhagic E. coli O157:H7 and other serotypes (EHEC) has been associated with bovine fecal contamination of food and the environment. The range of serotypes, low infectious dose, and numerous transmission vehicles for EHEC render development of detection methods for this pathogen complex. In this study, the hemolysin gene (EHEC- hly A) was targeted with oligonucleotides, and probe-target hybrids were amplified using strand displacement amplification (SDA). Amplicons were resolved in the complete reaction mix through changes in the fluorescence polarization (FP) of a fluorescein-labeled detector probe hybridized to the amplicons during amplification. Results combining EHEC- hly A, SDA, and FP were obtained within 35 min of reaction initiation. The test specificity was determined on EHEC strains representing 13 serotypes (49 isolates); and control uropathogenic, commensal, and other organisms (10 isolates). Statistical analysis of results indicated a sensitivity in the reaction vessel to 4.3 bacteria (95% confidence interval), and a specificity for EHEC (n=59) at 100% (P=5.11E-17; i.e. P<<0.05). Detection based on combining EHEC- hly A, SDA, and FP was compatible with water sources directly associated with human infection (drinking and recreational supplies), and bovine drinking trough water representing an environmental matrix linked to the maintenance of an EHEC animal reservoir.

Amperometric biosensor based on a functionalized gold electrode for the detection of antioxidants

A method for the electrochemical detection of antioxidants has been developed, which is based on a radical measurement with a cytochrome c modified electrode. A controlled enzymatic production system for superoxide radicals based on xanthine oxidase was used. The addition of antioxidants facilitated the decomposition of the radical in addition to the spontaneous dismutation. The steady-state of superoxide generation and decomposition was thus shifted to a new situation due to the higher decomposition rate after antioxidant addition. This resulted in a decreased current level at the electrode. Antioxidant activity could be quantified from the response of the sensor electrode by the percentage of the signal decrease. The 50% inhibition value (IC(50)) for different antioxidants was calculated and the antioxidant activity of numerous substances was compared. Thus, a hierarchy of superoxide radical scavenging abilities of flavonoids was established: flavanols>flavonols>flavones>flavonones>isoflavonones.

SB203580 promotes EGF-stimulated early morphological differentiation in PC12 cell through activating ERK pathway

MAP kinases have important role in PC12 cell differentiation, since the activities of both extracellular regulated protein kinase (ERK) and p38 have been indicated as necessary signal for PC12 cell differentiation. Epidermal growth factor (EGF) and NGF both activate ERK and p38 in PC12 cells, but only NGF trigger differentiation. It has been proposed that the duration of ERK activation determines the switch from proliferation to differentiation, since EGF causes more transient activation of ERK than NGF in PC12 cells. Here we report that treatment of PC12 cells with EGF in the presence of SB203580, a widely used p38 inhibitor, caused differentiation. The pro-differentiation effect of SB203580 in EGF-treated PC12 cells was found to be independent of its function of p38 inhibition but was through an effect on the ERK pathway that has been recently reported (Kalmes et al. [1999] FEBS Lett. 444: 71-74; Hall-Jackson et al. [1999] Onc. 18: 2047-2054). We found that SB203580 by itself did not affect the activity of ERK1/2 but significantly extended EGF-induced ERK activation in PC12 cells, which resulted in early morphological differentiation. Our data indicated that although both ERK and p38 are required for PC12 cell differentiation, activation of p38 is not required when ERK is superactivated. Our data provided further evidence for the threshold theory that differentiation is determined by the duration of ERK activation.

Prevalence of Campylobacter spp., Escherichia coli, and Salmonella serovars in retail chicken, turkey, pork, and beef from the Greater Washington, D.C., area

A total of 825 samples of retail raw meats (chicken, turkey, pork, and beef) were examined for the presence of Escherichia coli and Salmonella serovars, and 719 of these samples were also tested for Campylobacter spp. The samples were randomly obtained from 59 stores of four supermarket chains during 107 sampling visits in the Greater Washington, D.C., area from June 1999 to July 2000. The majority (70.7%) of chicken samples (n = 184) were contaminated with Campylobacter, and a large percentage of the stores visited (91%) had Campylobacter-contaminated chickens. Approximately 14% of the 172 turkey samples yielded Campylobacter, whereas fewer pork (1.7%) and beef (0.5%) samples were positive for this pathogen. A total of 722 Campylobacter isolates were obtained from 159 meat samples; 53.6% of these isolates were Campylobacter jejuni, 41.3% were Campylobacter coli, and 5.1% were other species. Of the 212 chicken samples, 82 (38.7%) yielded E. coli, while 19.0% of the beef samples, 16.3% of the pork samples, and 11.9% of the turkey samples were positive for E. coli. However, only 25 (3.0%) of the retail meat samples tested were positive for Salmonella. Significant differences in the bacterial contamination rates were observed for the four supermarket chains. This study revealed that retail raw meats are often contaminated with food-borne pathogens; however, there are marked differences in the prevalence of such pathogens in different meats. Raw retail meats are potential vehicles for transmitting food-borne diseases, and our findings stress the need for increased implementation of hazard analysis of critical control point (HACCP) and consumer food safety education efforts.

Manganese superoxide dismutase induction by iron is impaired in Friedreich ataxia cells

Iron-mediated oxidative stress has been implicated in the pathology of the neurodegenerative disease Friedreich ataxia (FRDA). Here, we show that normal upregulation of the stress defense protein manganese superoxide dismutase (MnSOD) fails to occur in FRDA fibroblasts exposed to iron. This impaired induction was observed at iron levels in which increased activation of the redox-sensitive factor NF-kappaB was absent. Furthermore, MnSOD induction could only be partially suppressed by antioxidants. We conclude that an NF-kappaB-independent pathway that may not require free radical signaling is responsible for the reduction of MnSOD induction. This impairment could constitute both a novel defense mechanism against iron-mediated oxidative stress in cells with mitochondrial iron overload and conversely, an alternative source of free radicals that could contribute to the disease pathology.

Liposome-C-erbB2 antisense oligodoxynucleotides in human ovarian cancer cells

OBJECTIVE

To explore the effects of liposome-C-erbB2 antisense phosphorothioate oligodeoxynucleotides (S-ODNs) on C-erbB2 proto-oncogene expression and cell proliferation in human ovarian cancer cells.

METHODS

The effects of liposome-C-erbB2 S-ODNs on C-erbB2 protein expression, cell cycle and cell proliferation in human ovarian cancer cells were studied by means of flow cytometry and 3H-thymidine incorporation.

RESULTS

Liposome-C-erbB2 S-ODNs can specifically reduce C-erbB2 protein expression in human ovarian cancer cells, accompanied by a 30% inhibition of cell proliferation. The effectiveness of liposome-C-erbB2 S-ODNs on the expression of C-erbB2 was about 40 times higher than that of C-erbB2 S-ODNs.

CONCLUSIONS

The data suggest that antisense therapy might be a useful method of gene therapy in ovarian cancer. The effectiveness of C-erbB2 S-ODNs could be greatly increased by adsorption of S-ODNs by liposomes.

Identification and characterization of integron-mediated antibiotic resistance among Shiga toxin-producing Escherichia coli isolates

A total of 50 isolates of Shiga toxin-producing Escherichia coli (STEC), including 29 O157:H7 and 21 non-O157 STEC strains, were analyzed for antimicrobial susceptibilities and the presence of class 1 integrons. Seventy-eight (n = 39) percent of the isolates exhibited resistance to two or more antimicrobial classes. Multiple resistance to streptomycin, sulfamethoxazole, and tetracycline was most often observed. Class 1 integrons were identified among nine STEC isolates, including serotypes O157:H7, O111:H11, O111:H8, O111:NM, O103:H2, O45:H2, O26:H11, and O5:NM. The majority of the amplified integron fragments were 1 kb in size with the exception of one E. coli O111:H8 isolate which possessed a 2-kb amplicon. DNA sequence analysis revealed that the integrons identified within the O111:H11, O111:NM, O45:H2, and O26:H11 isolates contained the aadA gene encoding resistance to streptomycin and spectinomycin. Integrons identified among the O157:H7 and O103:H2 isolates also possessed a similar aadA gene. However, DNA sequencing revealed only 86 and 88% homology, respectively. The 2-kb integron of the E. coli O111:H8 isolate contained three genes, dfrXII, aadA2, and a gene of unknown function, orfF, which were 86, 100, and 100% homologous, respectively, to previously reported gene cassettes identified in integrons found in Citrobacter freundii and Klebsiella pneumoniae. Furthermore, integrons identified among the O157:H7 and O111:NM strains were transferable via conjugation to another strain of E. coli O157:H7 and to several strains of Hafnia alvei. To our knowledge, this is the first report of integrons and antibiotic resistance gene cassettes in STEC, in particular E. coli O157:H7.

Novel promoter polymorphism in insulin-like growth factor-binding protein-3: correlation with serum levels and interaction with known regulators

Insulin-like growth factor (IGF)-binding protein-3 (IGFBP-3) is a major determinant of circulating levels of the IGFs and is clinically useful for the evaluation of GH deficiency and for predicting the response to GH treatment. Recent studies provide evidence that the circulating level of IGFBP-3 is inversely related to the risk of several common cancers, and that antiproliferative agents such as antiestrogens and retinoids act in part by up-regulating IGFBP-3 gene (IGFBP3) expression. Although approximately 50% of the substantial interindividual variability in circulating IGFBP-3 levels is known to have a genetic basis, the specific loci involved are unknown. Direct sequencing of genomic DNA specimens from a multiethnic population identified several single nucleotide polymorphisms in the promoter region of IGFBP3. For the most common single nucleotide polymorphism (nucleotide -202) found to be in Hardy-Weinberg equilibrium, genotype was highly correlated to circulating level of IGFBP-3 in 478 men from the Physicians' Health Study. In vitro, we documented significantly higher promoter activity of the A allele at the -202 locus compared with the C allele, consistent with the relationship observed between genotype and circulating IGFBP-3 (AA > AC > CC). A positive correlation was observed between circulating retinol levels and circulating IGFBP-3 levels; subset analysis by genotype showed that this relationship was only present among individuals carrying an A allele at -202 (AA > AC > CC). Tall individuals or individuals with a body mass index of 27 or greater had levels of circulating IGFBP-3 that were significantly higher when they possessed at least one A allele (AA > AC > CC). The IGFBP3 promoter region deserves investigation as a locus where polymorphic variation occurs frequently and may influence GH responsiveness, somatic growth, and possibly cancer risk.

[The expression and clinical significance of pRB and E(2)F(1) in human neuroendocrine lung tumor]

OBJECTIVE

To investigate the role pRB and E(2)F(1) play in the cell cycle and the oncogenesis of human nemoendocrine lung fumor and the correlation between their expression and the invasiveness and prognosis of human neuroendocrine lung tumor.

METHODS

Immunohistochemistry and in situ hybridization were used to detect the expression of pRB and E(2)F(1) mRNA in the paraffin embedded tissues of 78 cases of human neuroendocrine lung tumor. Statistics was used to analyze the data.

RESULTS

The positive expression rate of pRB in both typical and atypical carcinoid was 87.5% (14/16). However, pRB was not expressed in large cell neuroendocrine carcinoma and small cell lung cancer (P < 0.001). The positive rate of E(2)F(1) mRNA expression in human neuroendocrine lung tumor was 87.2% (68/78). The strength of expression of pRB and E(2)F(1) was obviously correlated with the tumor stage, lymph node metastasis and prognosis (P < 0.05).

CONCLUSION

The loss of pRB and E(2)F(1) overexpression may play a key role in the development of human neuroendocrine lung tumors.

Enhanced proliferation and directed migration of oligodendroglial progenitors co-grafted with growth factor-secreting cells

Transplantation repair of demyelinating lesions is restricted because relatively few cells can be introduced at only a limited number of sites. Repair could be enhanced by stimulating division of transplanted cells and by directing migration to multiple or distant lesions. This article demonstrates that transplanted oligodendroglial progenitors proliferate more when co-grafted with growth factor-secreting cells, yet retain the capacity to form myelin. Transplanted glial cells also migrate preferentially toward the growth factor-secreting cells when the two are implanted at separate sites. This opens avenues to examine growth factor actions on glia in vivo and improves the prospects for human remyelination therapies.

[Tracheal carina reconstruction and bronchoplasty in the treatment of 94 central type bronchogenic carcinomas]

BACKGROUND

To analyze the short-term effects and long term survival of patients with lung cancer underwent tracheal carina reconstruction and bronchoplasty.

METHODS

From April 1985 to May 1999, 94 patients with lung cancer underwent tracheal carina reconstruction and bronchoplasty, 14 for carinal resection and reconstruction and 80 for bronchial sleeves.

RESULTS

Postoperative complications were atelectasis ( 19 cases) , arrthymia ( 2 cases) and anastomotic leakage ( 1 case) . There was no operative death in this series. The 1-, 3- and 5-year survival rates were 83. 1%( 74/ 89) , 58. 3%( 35/ 56) and 34. 0%( 18/ 53) respectively for the entire group. The 5-year survival rate was 66. 7%( 6/ 9) in stage Ñ B disease, 40%( 6/ 15) in Ò B disease and 21. 1%( 4/ 19) in Ó A disease. The indication of these procedures and the methods of lymph node dissection, bronchoplasty and pulmonary artery reconstruction, and superior vena cava reconstruction have been discussed.

CONCLUSIONS

Bronchoplasty for lung cancer is a safe and effective therapy. The long term survival depends on the stage of lung cancer , proper selection of surgical indication, clearance of lymph nodes in operation and multiple modality therpay after operation.

Electrochemical treatment of lung cancer

A pilot study of electrochemical treatment (ECT) as a therapy for 386 patients with nonsmall cell lung cancer was undertaken. There were 103 stage II cases, 89 stage IIIa cases, 122 stage IIIb cases, and 72 stage IV cases. Two ECT methods were used: For peripherally located lung cancer, platinum electrodes were inserted transcutaneously into the tumor under x-ray or CT guidance. For central type lung cancer or for those inoperable during thoracotomy, electrodes were inserted intraoperatively directly into the cancer. Voltage was 6-8 V, current was 40-100 mA, and electric charge was 100 coulombs per cm of tumor diameter. The number of electrodes was determined from the size of cancer mass, because the diameter of effective area around each electrode is approximately 3 cm. The short-term (6 months after ECT) results of the 386 lung cancer cases were: complete response (CR), 25.6% (99/386); partial response (PR), 46.4% (179/386); no change (NC), 15.3% (59/386); and progressive disease (PD), 12.7% (49/386). The total effective rate (CR + PR) was 72% (278/386). The 1, 3, and 5 year overall survival rates were 86.3% (333/386), 58.8% (227/386), and 29.5% (114/386), respectively. The main complication was traumatic pneumothorax, with an incidence rate of 14.8% (57/386). These clinical results show that ECT is simple, safe, effective, and minimally traumatic. ECT provides an alternative method for treating lung cancers that are conventionally inoperable, that are not responsive to chemotherapy or radiotherapy, or that cannot be resected after thoracotomy. Long-term survival rates suggest that ECT warrants further investigation.

[Repair of soft tissue defect of the hand with a fascia lata flap by microvascular anastomosis]

OBJECTIVE

This is to report the clinical experience in repair of the soft tissue defects of the hand using a free fascia lata flap and skin graft.

METHODS

Eight cases of soft tissue defects of the hand were repaired with a fascia lata flap by means of microvascular anastomosis. The size of the fascia lata flap ranged from 2.5 cm x 7 cm to 6 cm x 16 cm.

RESULTS

All the fascia lata flaps survived completely with satisfactory results.

CONCLUSION

The flap is nourished by the descending branch of the lateral femoral circumflex artery and seems to have a constant vascular supply and a long pedicle. The dissection of the flap is easy. The flap is thin and very suitable for repair of soft tissue defects of the hand.

Tracing human oligodendroglial development in vitro

Human neural precursor cell cultures (neurospheres) were established from fetal brain tissues of 15-20 gestation weeks and propagated for over a year in the presence of epidermal growth factor, basic fibroblast growth factor and leukemia inhibitory factor. Neurospheres were differentiated without the presence of above growth factors to follow the development of oligodendroglia. Oligodendroglial progenitors, identified by their bipolar morphology and expression of platelet-derived growth factor receptor-alpha (PDGFRalpha), emerged from spheres as early as 1 DIV; O4+ cells with bipolar to multipolar processes were observed at 3 DIV whereas O1+ multiprocess-bearing oligodendroglia did not appear until 5-7 DIV. They further differentiated to myelin basic protein-expressing oligodendrocytes after 2-3 weeks in culture. Thus, human oligodendroglial maturation in vitro follows the same pathway as rat cells but takes twice as long as their rodent counterparts. Bromodeoxyuridine incorporation indicated that PDGFRalpha-expressing cells but not O4+ oligodendroglia proliferated. More oligodendroglial progenitors incorporated BrdU and more O4+ cells survived when they were in contact with neurons and astrocytes than when they developed beyond the astrocyte layer. In addition, oligodendroglia on astrocytes had a complex process branching whereas those growing beyond astrocyte layer often formed membrane sheaths. Thus the survival, proliferation and maturation of oligodendroglia are influenced by other cell types.

ARSACS, a spastic ataxia common in northeastern Québec, is caused by mutations in a new gene encoding an 11.5-kb ORF

Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS or SACS) is an early onset neurodegenerative disease with high prevalence (carrier frequency 1/22) in the Charlevoix-Saguenay-Lac-Saint-Jean (CSLSJ) region of Quebec. We previously mapped the gene responsible for ARSACS to chromosome 13q11 and identified two ancestral haplotypes. Here we report the cloning of this gene, SACS, which encodes the protein sacsin. The ORF of SACS is 11,487 bp and is encoded by a single gigantic exon spanning 12,794 bp. This exon is the largest to be identified in any vertebrate organism. The ORF is conserved in human and mouse. The putative protein contains three large segments with sequence similarity to each other and to the predicted protein of an Arabidopsis thaliana ORF. The presence of heat-shock domains suggests a function for sacsin in chaperone-mediated protein folding. SACS is expressed in a variety of tissues, including the central nervous system. We identified two SACSmutations in ARSACS families that lead to protein truncation, consistent with haplotype analysis.

Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS): high-resolution physical and transcript map of the candidate region in chromosome region 13q11

Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS or SACS) is a neurodegenerative disease frequent in northeastern Québec. In a previous study, we localized the disease gene to chromosome region 13q11 by identifying excess sharing of a marker allele in patients followed by linkage analysis and haplotyping. To create a detailed physical map of this region, we screened CEPH mega-YACs with 41 chromosome 13 sequence-tagged-sites (STSs) known to map to 13q11-q12. The YAC contig, composed of 27 clones, extends on the genetic map from D13S175 to D13S221, an estimated distance of at least 19.3 cM. A high-resolution BAC and PAC map that includes the ARSACS critical region flanked by D13S1275 and D13S292 was constructed. These YAC and BAC/PAC maps allowed the accurate placement of 29 genes and ESTs previously mapped to the proximal region of chromosome 13q. We confirmed the position of two candidate genes within the critical region and mapped the other 27 genes and ESTs to nearby intervals. Six BAC/PAC clones form a contig between D13S232 and D13S787 for sequencing within the ARSACS critical region.

Radiation hybrid map of the mouse genome

Radiation hybrid (RH) maps are a useful tool for genome analysis, providing a direct method for localizing genes and anchoring physical maps and genomic sequence along chromosomes. The construction of a comprehensive RH map for the human genome has resulted in gene maps reflecting the location of more than 30,000 human genes. Here we report the first comprehensive RH map of the mouse genome. The map contains 2,486 loci screened against an RH panel of 93 cell lines. Most loci (93%) are simple sequence length polymorphisms (SSLPs) taken from the mouse genetic map, thereby providing direct integration between these two key maps. We performed RH mapping by a new and efficient approach in which we replaced traditional gel- or hybridization-based assays by a homogeneous 5'-nuclease assays involving a single common probe for all genetic markers. The map provides essentially complete connectivity and coverage across the genome, and good resolution for ordering loci, with 1 centiRay (cR) corresponding to an average of approximately 100 kb. The RH map, together with an accompanying World-Wide Web server, makes it possible for any investigator to rapidly localize sequences in the mouse genome. Together with the previously constructed genetic map and a YAC-based physical map reported in a companion paper, the fundamental maps required for mouse genomics are now available.

[Effect of liposome-C-erbB2 antisense oligodeoxynucleotides on human ovarian cancer cells]

OBJECTIVE

To explore the effects of liposome-C-erbB2 antisense phosphorothioate oligo deoxynucleotides(S-ODNs) on C-erbB2 protooncogene expression and cell proliferation in human ovarian cancer cells.

METHODS

The effects on C-erbB2 protooncogene expression, cell proliferation and cell cycle in human ovarian cancer cells were studied by flow cytometry and 3H-thymidine incorporation.

RESULTS

Liposome-C-erbB2 S-ODNs could reduce C-erbB2 expression and inhibit cell proliferation in human ovarian cancer cells; the effectiveness of liposome-C-erbB2 S-ODNs on the expression of C-erbB2 was much higher than that of C-erbB2 S-ODNs, about 40 times.

CONCLUSIONS

The data in this study suggest that antisense therapy is an useful method of gene therapy in ovarian cancer. The effectiveness of C-erbB2 S-ODNs could be greatly increased by C-erbB2 S-ODNs encapsulated in liposomes.

Fractionation and enrichment of oligodendrocytes from developing human brain

Enriched cultures of human oligodendrocytes were obtained from fetal brain specimens between 16 and 21 gestational weeks. Brain cells were separated over a Percoll density gradient and collected as two fractions with initial relative densities of approximately 1.035 g/ml and 1.102 g/ml, for fractions 1 and 2, respectively. After separation, 58.3 and 67.7% of the cells in fractions 1 and 2, respectively, were labeled by the antibody O4 that recognizes immature oligodendrocytes. A total of 15.5 and 29.4% of the cells in fractions 1 and 2, respectively, were positive for tubulin-beta(III), a marker for neurons but none of the freshly isolated cells were positive for glial fibrillary acidic protein (GFAP), a protein associated with astrocytes in the central nervous system. When the fractionated cells were cultured on poly-ornithine coated coverslips for 3 days and processed for immunocytochemistry, the percentage of O4+ oligodendrocytes decreased to less than 4% whereas GFAP+ cells increased to 1.8 and 12.4% for fractions 1 and 2 respectively. The percentage of tubulin-betaIII+ cells increased to 46 and 61% in cultures from the two Percoll fractions. This increase is probably due to the decrease in the number of oligodendrocytes. To avoid the loss of oligodendrocytes, cells were cultured as free-floating aggregates in the presence of 20 ng/ml of fibroblast growth factor-2 for 2 weeks. The resultant cultures became enriched for oligodendrocytes as demonstrated by cellular morphology and by positive O4 labeling. The method described here provides a means of obtaining enriched cultures of immature human oligodendrocytes for developmental and transplantation studies.

Adult brain retains the potential to generate oligodendroglial progenitors with extensive myelination capacity

Remyelination of focal areas of the central nervous system (CNS) in animals can be achieved by transplantation of glial cells, yet the source of these cells in humans to similarly treat myelin disorders is limited at present to fetal tissue. Multipotent precursor cells are present in the CNS of adult as well as embryonic and neonatal animals and can differentiate into lineage-restricted progenitors such as oligodendroglial progenitors (OPs). The OPs present in adults have a different phenotype from those seen in earlier life, and their potential role in CNS repair remains unknown. To gain insights into the potential to manipulate the myelinating capacity of these precursor and/or progenitor cells, we generated a homogenous culture of OPs from neural precursor cells isolated from adult rat subependymal tissues. Phenotypic characterization indicated that these OPs resembled neonatal rather than adult OPs and produced robust myelin after transplantation. The ability to generate such cells from the adult brain therefore opens an avenue to explore the potential of these cells for repairing myelin disorders in adulthood.

Location score and haplotype analyses of the locus for autosomal recessive spastic ataxia of Charlevoix-Saguenay, in chromosome region 13q11

Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) is a clinically homogeneous form of early-onset familial spastic ataxia with prominent myelinated retinal nerve fibers. More than 300 patients have been identified, and most of their families originated in the Charlevoix-Saguenay region of northeastern Quebec, where the carrier prevalence has been estimated to be 1/22. Consistent with the hypothesis of a founder effect, we observed excess shared homozygosity at 13q11, among patients in a genomewide scan of 12 families. Analysis of 19 pedigrees demonstrated very tight linkage between the ARSACS locus and an intragenic polymorphism of the gamma-sarcoglycan (SGCG) gene, but genomic DNA sequence analysis of all eight exons of SGCG revealed no disease-causing mutation. On the basis of haplotypes composed of seven marker loci that spanned 11.1 cM, the most likely position of the ARSACS locus was 0.42 cM distal to the SGCG polymorphism. Two groups of ARSACS-associated haplotypes were identified: a large group that carries a common SGCG allele and a small group that carries a rare SGCG allele. The haplotype groups do not appear to be closely related. Therefore, although chromosomes within each haplotype group may harbor a single ARSACS mutation identical by descent, the two mutations could have independent origins.

Optimization of Cry3A yields in Bacillus thuringiensis by use of sporulation-dependent promoters in combination with the STAB-SD mRNA sequence

The insecticidal activity of Bacillus thuringiensis strains toxic to coleopterous insects is due to Cry3 proteins assembled into small rectangular crystals. Toxin synthesis in these strains is dependent primarily upon a promoter that is active in the stationary phase and a STAB-SD sequence that stabilizes the cry3 transcript-ribosome complex. Here we show that significantly higher yields of Cry3A can be obtained by using dual sporulation-dependent cyt1Aa promoters to drive the expression of cry3Aa when the STAB-SD sequence is included in the construct. The Cry3A yield per unit of culture medium obtained with this expression system was 12.7-fold greater than that produced by DSM 2803, the wild-type strain of B. thuringiensis from which Cry3Aa was originally described, and 1.4-fold greater than that produced by NB176, a mutant of the same strain containing two or three copies of cry3Aa, which is the active ingredient of the commercial product Novodor, used for control of beetle pests. The toxicities of Cry3A produced with this construct or the wild-type strain were similar when assayed against larvae of the cottonwood leaf beetle, Chrysomela scripta. The volume of Cry3A crystals produced with cyt1Aa promoters and the STAB-SD sequence was 1.3-fold that of typical bipyramidal Cry1 crystals toxic to lepidopterous insects. The dual-promoter/STAB-SD system offers an additional method for potentially improving the efficacy of insecticides based on B. thuringiensis.