Cohesin mediated loop extrusion from active enhancers form chromatin jets in C. elegans

In mammals, cohesin and CTCF organize the 3D genome into topologically associated domains (TADs) to regulate communication between cis-regulatory elements. However, many organisms, including S. cerevisiae , C. elegans , and A. thaliana lack CTCF. Here, we use C. elegans as a model to investigate the function of cohesin in 3D genome organization in an animal without CTCF. We use auxin-inducible degradation to acutely deplete SMC-3 or its negative regulator WAPL-1 from somatic cells. Using Hi-C data, we identify a cohesin-dependent 3D genome organization feature called chromatin jets (aka fountains). These are population average reflections of DNA loops that are ∼20-40 kb in scale and often cover a few transcribed genes. The jets emerge from NIPBL occupied segments, and the trajectory of the jets coincides with cohesin binding. Cohesin translocation from jet origins depends on a fully intact complex and is extended upon WAPL-1 depletion. Hi-C results support the idea that cohesin is preferentially loaded at NIPBL occupied sites and loop extrudes in an effectively two-sided manner. The location of putative loading sites coincide with active enhancers and the strength of chromatin jet pattern correlates with transcription. Hi-C analyses upon WAPL-1 depletion reveal unequal loop extrusion processivity on each side and stalling due to cohesin molecules colliding. Compared to mammalian systems, average processivity of C. elegans cohesin is ∼10-fold shorter and NIPBL binding does not depend on cohesin. We conclude that the processivity of cohesin scales with genome size; and regardless of CTCF presence, preferential loading of cohesin at enhancers is a conserved mechanism of genome organization that regulates the interaction of gene regulatory elements in 3D.

Topoisomerases I and II facilitate condensin DC translocation to organize and repress X chromosomes in C. elegans

Condensins are evolutionarily conserved molecular motors that translocate along DNA and form loops. To address how DNA topology affects condensin translocation, we applied auxin-inducible degradation of topoisomerases I and II and analyzed the binding and function of an interphase condensin that mediates X chromosome dosage compensation in C. elegans. TOP-2 depletion reduced long-range spreading of condensin-DC (dosage compensation) from its recruitment sites and shortened 3D DNA contacts measured by Hi-C. TOP-1 depletion did not affect long-range spreading but resulted in condensin-DC accumulation within expressed gene bodies. Both TOP-1 and TOP-2 depletion resulted in X chromosome derepression, indicating that condensin-DC translocation at both scales is required for its function. Together, the distinct effects of TOP-1 and TOP-2 suggest two distinct modes of condensin-DC association with chromatin: long-range DNA loop extrusion that requires decatenation/unknotting of DNA and short-range translocation across genes that requires resolution of transcription-induced supercoiling.

Increased gene dosage and mRNA expression from chromosomal duplications in Caenorhabditis elegans

Isolation of copy number variations and chromosomal duplications at high frequency in the laboratory suggested that Caenorhabditis elegans tolerates increased gene dosage. Here, we addressed if a general dosage compensation mechanism acts at the level of mRNA expression in C. elegans. We characterized gene dosage and mRNA expression in 3 chromosomal duplications and a fosmid integration strain using DNA-seq and mRNA-seq. Our results show that on average, increased gene dosage leads to increased mRNA expression, pointing to a lack of genome-wide dosage compensation. Different genes within the same chromosomal duplication show variable levels of mRNA increase, suggesting feedback regulation of individual genes. Somatic dosage compensation and germline repression reduce the level of mRNA increase from X chromosomal duplications. Together, our results show a lack of genome-wide dosage compensation mechanism acting at the mRNA level in C. elegans and highlight the role of epigenetic and individual gene regulation contributing to the varied consequences of increased gene dosage.

The H4K20 demethylase DPY-21 regulates the dynamics of condensin DC binding

Condensin is a multi-subunit structural maintenance of chromosomes (SMC) complex that binds to and compacts chromosomes. Here, we addressed the regulation of condensin binding dynamics using Caenorhabditis elegans condensin DC, which represses X chromosomes in hermaphrodites for dosage compensation. We established fluorescence recovery after photobleaching (FRAP) using the SMC4 homolog DPY-27 and showed that a well-characterized ATPase mutation abolishes DPY-27 binding to X chromosomes. Next, we performed FRAP in the background of several chromatin modifier mutants that cause varying degrees of X chromosome derepression. The greatest effect was in a null mutant of the H4K20me2 demethylase DPY-21, where the mobile fraction of condensin DC reduced from ∼30% to 10%. In contrast, a catalytic mutant of dpy-21 did not regulate condensin DC mobility. Hi-C sequencing data from the dpy-21 null mutant showed little change compared to wild-type data, uncoupling Hi-C-measured long-range DNA contacts from transcriptional repression of the X chromosomes. Taken together, our results indicate that DPY-21 has a non-catalytic role in regulating the dynamics of condensin DC binding, which is important for transcription repression.

Summary: The histone demethylase DPY-21 has catalytic and non-catalytic roles in condensin DC-mediated X chromosome repression. The non-catalytic activity regulates dynamics of condensin DC binding to X chromosomes.

Identification and prediction of developmental enhancers in sea urchin embryos

Background

The transcription of developmental regulatory genes is often controlled by multiple cis-regulatory elements. The identification and functional characterization of distal regulatory elements remains challenging, even in tractable model organisms like sea urchins.

Results

We evaluate the use of chromatin accessibility, transcription and RNA Polymerase II for their ability to predict enhancer activity of genomic regions in sea urchin embryos. ATAC-seq, PRO-seq, and Pol II ChIP-seq from early and late blastula embryos are manually contrasted with experimental cis-regulatory analyses available in sea urchin embryos, with particular attention to common developmental regulatory elements known to have enhancer and silencer functions differentially deployed among embryonic territories. Using the three functional genomic data types, machine learning models are trained and tested to classify and quantitatively predict the enhancer activity of several hundred genomic regions previously validated with reporter constructs in vivo.

Conclusions

Overall, chromatin accessibility and transcription have substantial power for predicting enhancer activity. For promoter-overlapping cis-regulatory elements in particular, the distribution of Pol II is the best predictor of enhancer activity in blastula embryos. Furthermore, ATAC- and PRO-seq predictive value is stage dependent for the promoter-overlapping subset. This suggests that the sequence of regulatory mechanisms leading to transcriptional activation have distinct relevance at different levels of the developmental gene regulatory hierarchy deployed during embryogenesis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07936-0.

Pneumonia severity indices predict prognosis in coronavirus disease-2019

Background

Early recognition of the severe illness is critical in coronavirus disease-19 (COVID-19) to provide best care and optimize the use of limited resources.

Objectives

We aimed to determine the predictive properties of common community-acquired pneumonia (CAP) severity scores and COVID-19 specific indices.

Methods

In this retrospective cohort, COVID-19 patients hospitalized in a teaching hospital between 18 March-20 May 2020 were included. Demographic, clinical, and laboratory characteristics related to severity and mortality were measured and CURB-65, PSI, A-DROP, CALL, and COVID-GRAM scores were calculated as defined previously in the literature. Progression to severe disease and in-hospital/overall mortality during the follow-up of the patients were determined from electronic records. Kaplan-Meier, log-rank test, and Cox proportional hazard regression model was used. The discrimination capability of pneumonia severity indices was evaluated by receiver-operating-characteristic (ROC) analysis.

Results

Two hundred ninety-eight patients were included in the study. Sixty-two patients (20.8%) presented with severe COVID-19 while thirty-one (10.4%) developed severe COVID-19 at any time from the admission. In-hospital mortality was 39 (13.1%) while the overall mortality was 44 (14.8%). The mortality in low-risk groups that were identified to manage outside the hospital was 0 in CALL Class A, 1.67% in PSI low risk, and 2.68% in CURB-65 low-risk. However, the AUCs for the mortality prediction in COVID-19 were 0.875, 0.873, 0.859, 0.855, and 0.828 for A-DROP, PSI, CURB-65, COVID-GRAM, and CALL scores respectively. The AUCs for the prediction of progression to severe disease was 0.739, 0.711, 0,697, 0.673, and 0.668 for CURB-65, CALL, PSI, COVID-GRAM, A-DROP respectively. The hazard ratios (HR) for the tested pneumonia severity indices demonstrated that A-DROP and CURB-65 scores had the strongest association with mortality, and PSI, and COVID-GRAM scores predicted mortality independent from age and comorbidity.

Conclusion

Community-acquired pneumonia (CAP) scores can predict in COVID-19. The indices proposed specifically to COVID-19 work less than nonspecific scoring systems surprisingly. The CALL score may be used to decide outpatient management in COVID-19.

THU0621-HPR SARC-F SCALE ON SCREENING SARCOPENIA AND PHYSICAL FUNCTION IN PATIENTS WITH KNEE OSTEOARTRITIS

Background:

Sarcopenia has been defined as a loss of muscle mass and consequently of muscle function. In patients affected by osteoarthritis (OA) a more likely and accelerated development of sarcopenia has been reported. The SARC-F is a simple sarcopenia screening tool includes five assessment items: strength, assistance walking, rising from a chair, climbing stairs, and falls. SARC-F ≥ 4 is defined as sarcopenia.

Objectives:

The present study aimed to examine the utility of SARC-F in the patients with knee osteoarthritis.

Methods:

Patients with radiographic and clinic evidence of tibiofemoral OA (Kellgren-Lawrence score ≥2) were included. Sarcopenia were identified using the SARC-F scale. Patients with a total score 4 and higher than 4 were classified as having sarcopenia. Patients were assessed by The Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC), four-meter walking test, hand grip test, shortened version of the falls efficacy scale-international (the short FES-I) and EuroQol- 5 Dimension (EQ-5D). A multiple linear regression model was used to identify independent predictors of SARC-F.

Results:

A total 76 patients with median age 61 ranged 55 to 78 years old (72.4% female) were screened in this study (Table 1). Of the sample, 38.1% of patients were sarcopenic as a SARC-F (Figure 1). Through multiple regression analyses, SARC-F scores was significantly associated with four-meter walking test, hand grip, WOMAC-Function, EQ-5D and short FES-I describing between 57% and 63% of the variance (adjusted R2) (Table 2). Also, poor physical performance and grip strength were associated with SARC-F ≥ 4 independently (P<0.005).

Table 1.

Summary Table of Characteristics of sarcopenic vs non-sarcopenic patients with knee OA

MeasuresSarcopenic patients with knee OA (n:47)Sarc-F≥4Non-Sarcopenic patients with knee OA (n:29)Sarc-F<4p valueφAge,mean(SD)62.7(6.9)59.3 (6.9)0.294BMI,mean(SD)27.84 (9.56)28.54 (8.38)0.327WOMAC,mean(SD)43.52 (10.83)28.06 (14.9)0.001*GRADE (K-L) med (min-max)3(2-4)2(2-4)0.008*Hand Grip,mean(SD)20 33 (4.89)28.22 (7.13)0.001*4 m Walking Test, mean(SD)11.88 (4.24)9.55 (4.30)0.001*EQ-5D,mean(SD)9.41 (1.52)7. 13 (1.75)0.001*EQ-5D-VAS,mean(SD)44.31 (14.12)66.90 (16.25)0.001*Short FES-I,mean(SD)18. 06 (9.45)9.04 (5.32)0.001*Number of falls the past year,mean(SD)4.01 (1.24)3.14 (2.74)0.674

φMann Whitney U test; *p< 0.05; BMI, Body mass index; WOMAC, Western Ontario and McMaster Universities Osteoarthritis Index EQ-5D, EuroQol-5 Dimension; FES-I, Falls Efficacy Scale-International

Table 2.

Multiple linear regression analysis for SARC-F

βtP value95% Confidence Interval(lower-upper bound)Walking Speed0.111.200.23-0.31/ 0.12Hand Grip-0.35-1.730.04-0.20 / 0.01WOMAC-Function0.262.310.010.00 / 0.05Short FES-I0.181.960.010.04 / 0.01EQ-5D0.222.290.020.02 / 0.39EQ-5D VASR2= 0.61-0.24-2.730.001-0.04 / -0.00

WOMAC, Western Ontario and McMaster Universities Osteoarthritis Index, EQ-5D, EuroQol-5 Dimension; FES-I, Falls Efficacy Scale-International

Figure 1.

Sarcopenic vs non-sarcopenic patients according to sex

Conclusion:

In this study, sarcopenia defined by the SARC-F questionnaire has a predictive value of clinical characteristics of patients to predict sarcopenia parameters and poor physical performance in patients with knee OA.

References:

[1]Papalia, R., Zampogna, B., Torre, G., Lanotte, A., Vasta, S., Albo, E., ... & Denaro, V. (2014). Sarcopenia and its relationship with osteoarthritis: risk factor or direct consequence?.Musculoskeletal surgery,98(1), 9-14.

Disclosure of Interests:

None declared

Binding of an X-Specific Condensin Correlates with a Reduction in Active Histone Modifications at Gene Regulatory Elements

Condensins are evolutionarily conserved protein complexes that are required for chromosome segregation during cell division and genome organization during interphase. In Caenorhabditis elegans, a specialized condensin, which forms the core of the dosage compensation complex (DCC), binds to and represses X chromosome transcription. Here, we analyzed DCC localization and the effect of DCC depletion on histone modifications, transcription factor binding, and gene expression using chromatin immunoprecipitation sequencing and mRNA sequencing. Across the X, the DCC accumulates at accessible gene regulatory sites in active chromatin and not heterochromatin. The DCC is required for reducing the levels of activating histone modifications, including H3K4me3 and H3K27ac, but not repressive modification H3K9me3. In X-to-autosome fusion chromosomes, DCC spreading into the autosomal sequences locally reduces gene expression, thus establishing a direct link between DCC binding and repression. Together, our results indicate that DCC-mediated transcription repression is associated with a reduction in the activity of X chromosomal gene regulatory elements.

Condensin Depletion Causes Genome Decompaction Without Altering the Level of Global Gene Expression in Saccharomyces cerevisiae

Condensins are broadly conserved chromosome organizers that function in chromatin compaction and transcriptional regulation, but to what extent these two functions are linked has remained unclear. Here, we analyzed the effect of condensin inactivation on genome compaction and global gene expression in the yeast Saccharomyces cerevisiae by performing spike-in-controlled genome-wide chromosome conformation capture (3C-seq) and mRNA-sequencing analysis. 3C-seq analysis shows that acute condensin inactivation leads to a global decrease in close-range intrachromosomal interactions as well as more specific losses of interchromosomal tRNA gene clustering. In addition, a condensin-rich interaction domain between the ribosomal DNA and the centromere on chromosome XII is lost upon condensin inactivation. Unexpectedly, these large-scale changes in chromosome architecture are not associated with global changes in mRNA levels. Our data suggest that the global transcriptional program of proliferating S. cerevisiae is resistant to condensin inactivation and the associated profound changes in genome organization.

Caenorhabditis elegans Dosage Compensation: Insights into Condensin-Mediated Gene Regulation

Recent work demonstrating the role of chromosome organization in transcriptional regulation has sparked substantial interest in the molecular mechanisms that control chromosome structure. Condensin, an evolutionarily conserved multisubunit protein complex, is essential for chromosome condensation during cell division and functions in regulating gene expression during interphase. In Caenorhabditis elegans, a specialized condensin forms the core of the dosage compensation complex (DCC), which specifically binds to and represses transcription from the hermaphrodite X chromosomes. DCC serves as a clear paradigm for addressing how condensins target large chromosomal domains and how they function to regulate chromosome structure and transcription. Here, we discuss recent research on C. elegans DCC in the context of canonical condensin mechanisms as have been studied in various organisms.

Role of nicotinic acetylcholine receptor subtypes on nicotine's enhancing effect on electrical field stimulation elicited contractile responses in rabbit urine bladder

OBJECTIVE

This study aims to investigate the contribution of presynaptic nicotinic acetylcholine receptors (nAChRs) sub-types to nicotine-induced enhancement in electrical field stimulation (EFS) EFS-mediated contractile responses in rabbit urine bladder smooth muscle preparations.

MATERIALS AND METHODS

Rabbit urine bladder smooth muscle strips were placed in organ baths containing 20 ml of an aerated Krebs-Henseleit solution, and contractions were recorded using isometric force displacement transducers. Following the acquisition of control EFS (60 V, 8 Hz, 1 ms) responses, nicotine was added to the bath at a 3×10-5 M concentration, and EFS responses were obtained. The effect of nAChR antagonists on nicotine-induced augmentation in EFS-mediated responses was investigated in the presence of hexamethonium, dihydro-β-erythroidine, mecamylamine, and α-bungarotoxin.

RESULTS

Tetrodotoxin (TTX; 10-6 M) completely blocked EFS-induced contractile responses in smooth muscle strips. Similarly, Atropine (10-6 M), when administered with α,β-methylene adenosine triphosphate (α,β-methylene-ATP) (10-5 M), completely blocked EFS responses. Nicotine significantly enhanced EFS-mediated contractile responses (23.67% ± 1.75). Nicotine-induced increases in EFS responses were largely inhibited by hexamethonium, mecamylamine, and dihydro-β-erythroidine, whereas α-bungarotoxin only partly inhibited these enhancements.

CONCLUSIONS

These findings demonstrate that EFS-induced neurogenic contractions in rabbit urine bladder smooth muscle strips are mediated by purinergic and cholinergic transmissions, and the α4β2, α3β4, and α7 sub-types of nAChRs contribute to the enhancement effect of nicotine on EFS-induced contractile responses.

Mechanisms of x chromosome dosage compensation

In many animals, males have one X and females have two X chromosomes. The difference in X chromosome dosage between the two sexes is compensated by mechanisms that regulate X chromosome transcription. Recent advances in genomic techniques have provided new insights into the molecular mechanisms of X chromosome dosage compensation. In this review, I summarize our current understanding of dosage imbalance in general, and then review the molecular mechanisms of X chromosome dosage compensation with an emphasis on the parallels and differences between the three well-studied model systems, M. musculus, D. melanogaster and C. elegans.

Genome-wide analysis of condensin binding in Caenorhabditis elegans

Background

Condensins are multi-subunit protein complexes that are essential for chromosome condensation during mitosis and meiosis, and play key roles in transcription regulation during interphase. Metazoans contain two condensins, I and II, which perform different functions and localize to different chromosomal regions. Caenorhabditis elegans contains a third condensin, I^DC, that is targeted to and represses transcription of the X chromosome for dosage compensation.

Results

To understand condensin binding and function, we performed ChIP-seq analysis of C. elegans condensins in mixed developmental stage embryos, which contain predominantly interphase nuclei. Condensins bind to a subset of active promoters, tRNA genes and putative enhancers. Expression analysis in kle-2-mutant larvae suggests that the primary effect of condensin II on transcription is repression. A DNA sequence motif, GCGC, is enriched at condensin II binding sites. A sequence extension of this core motif, AGGG, creates the condensin I^DC motif. In addition to differences in recruitment that result in X-enrichment of condensin I^DC and condensin II binding to all chromosomes, we provide evidence for a shared recruitment mechanism, as condensin I^DC recruiter SDC-2 also recruits condensin II to the condensin I^DC recruitment sites on the X. In addition, we found that condensin sites overlap extensively with the cohesin loader SCC-2, and that SDC-2 also recruits SCC-2 to the condensin I^DC recruitment sites.

Conclusions

Our results provide the first genome-wide view of metazoan condensin II binding in interphase, define putative recruitment motifs, and illustrate shared loading mechanisms for condensin I^DC and condensin II.

Relationship between coronary in-stent restenosis and plasma urotensin II level

AIM

In-stent restonosis is an important limitation for coronary stenting. The cause of in-stent restenosis is neointimal hyperplasia developed from smooth muscle and matrix. We aimed to investigate the association between urotensin II (U-II) and in-stent restenosis after coronary stenting, which causes endothelial and muscle proliferation and accumulation of collagen.

METHODS

Total 153 patient was enrolled to the study who meet criteria for angiographic indication underwent coronary artery angiography. All patients have history undergone for coronary stent implantation 3 to 9 months ago. In-stent restenosis is identified as ≥50% narrowing inside the stent. In-stent restenosis was observed in 73 and remaining of 80 patients revealed no critical lesion in stent on angiographic evaluation. Plasma level measurement of U-II was performed in all subjects.

RESULTS

Urotensin II levels were found to be significantly higher in Group I compared to Group II (1.44±0.74 ng/mL and 1.21±0.59 ng/mL, respectively, P=0.03). In a subgroup analysis, U-II levels were significantly higher in group I than group II in patients treated with bare metal stent (BMS) (1.50±0.76 ng/mL and 1.18±0.56 ng/mL, P=0.016); however, there was not significant change in patients treated with drug-eluted stent (1.26±0.64 ng/mL and 1.27±0.63 ng/mL, P=0.9). Multivariate statistical significance: negative correlation was found between in-stent restenosis and renin-angiotensin-system (RAS) blocker usage (P=0.040) and right coronary artery (RCA) lesion interventions (P=0.018).

CONCLUSION

This study revealed high plasma U-II level might be accepted as a risk factors for in-stent restenosis with BMS. In-stent restenosis is less developed after RCA interventions and taking drug of RAS blockages. Our study findings need to be confirmed in further studies.

Modern techniques for the analysis of chromatin and nuclear organization in C. elegans

In recent years, Caenorhabditis elegans has emerged as a new model to investigate the relationships between nuclear architecture, cellular differentiation, and organismal development. On one hand, C. elegans with its fixed lineage and transparent body is a great model organism to observe gene functions in vivo in specific cell types using microscopy. On the other hand, two different techniques have been applied in nematodes to identify binding sites for chromatin-associated proteins genome-wide: chromatin immunoprecipitation (ChIP), and Dam-mediated identification (DamID). We summarize here all three techniques together as they are complementary. We also highlight strengths and differences of the individual approaches.

The effect of bevacizumab and 5-Fluorouracil combination on epidural fibrosis in a rat laminectomy model

OBJECTIVE

An animal model of laminectomy in rats was used to study scar tissue formation around the spinal cord. Bevacizumab (BV) [a recombinant, humanized, monoclonal antibody targeting vascular endothelial growth factor], 5-Fluorouracil (5-FU) and BV+5-FU was tested in this system for its ability to decrease fibrous tissue formation.

MATERIALS AND METHODS

Twenty-eight Sprague Dawley rats were used in this sudy. Rats were divided into four groups; a control group, a BV group, a 5-FU group and a BV+5-FU group. L1-2 laminectomies were performed on the rats. The medicated groups were treated with topical drug administration. After 6 weeks, the rats were sacrified and histologic sections prepared from the spines were examined and graded by a pathologist. Epidural fibrosis and fibroblast density were evaluated under light microscope.

RESULTS

BV (Avastin: Genentech, San Francisco, CA, USA) significantly reduced the density of the scar tissue undermining the laminas (p < 0.005). Monotherapy with 5-FU did not change the scar formation in the back (p = 0.317). Combination of 5-FU and BV was more effective on reducing the epidural fibrosis after laminectomy on rats (p < 0.001).

CONCLUSIONS

Bevacizumab reduced the spinal epidural fibrosis significantly that developed in rats after laminectomy and 5-Fluorouracil combination had a synergic effect. Further investigations under the light of these findings may help to reduce epidural fibrosis formation after laminectomy.

Highly stable laccase from repeated-batch culture of Funalia trogii ATCC 200800

The effect of temperature, pH, different inhibitors and additives on activity and stability of crude laccase obtained from repeated-batch culture of white rot fungus Funalia trogii ATCC 200800 was studied. The crude enzyme showed high activity at 55-90 degrees C, which was maximal at 80-95 degrees C. It was highly stable within the temperature intervals 20-50 degrees C. The half life of the enzyme was about 2 h and 5 min at 60 degrees C and 70 degrees C, respectively. pH optimum of fungal laccase activity was revealed at pH 2.5. The enzyme from F. trogii ATCC 200800 was very stable between pH values of 3.0-9.0. NaN3 and KCN were detected as the most effective potent enzyme inhibitors among different compounds tested. The fungal enzyme was highly resistant to the various metal ions, inorganic salts, and organic solvents except propanol, at least for 5 min. Because of its high stability and efficient decolorization activity, the use of the crude F. trogii ATCC 200800 laccase instead of pure enzyme form may be a considerably cheaper solution for biotechnological applications.

Increased epicardial fat thickness is related with body mass index in women with polycystic ovary syndrome

AIM

We aimed to investigate the relationship between PCOS and epicardial fat thickness with transthoracic echocardiography.

PATIENTS AND METHODS

PCOS patients were divided into two groups according to the lean or obesity status: PCOS patients with lean 34 subjects (BMI: 23.3±2.8; mean age: 25.5±4), PCOS patients with obese16 subjects (BMI: 32.3±7.6; mean age: 27.2±3.7) were compared with control healthy lean subjects (BMI: 23.5±1.7; mean age: 25.9±2.2).

RESULTS

There was increased epicardial thickness in obese PCOS subjects compared to lean PCOS subjects (6.3±0.9 mm, 4.7±0.5, respectively, p < 0.001). However, epicardial fat thickness between lean PCOS subjects and lean healthy control groups were not significantly varied (4.7±0.5 mm, 4.5±0.5, respectively, p = 0.6). There was increased epicardial thickness in obese PCOS subjects compared to lean healthy control subjects (6.3±0.9 mm, 4.5±0.5, respectively, p < 0.001). This sudy showed for the first time that increased epicardial fat thickness measured using transthoracic echocardiography is associated with increased BMI in PCOS subjects.

CONCLUSIONS

Epicardial fat thickness between lean PCOS subjects and lean healty control group were similar which indicate the importance of obesity in PCOS subjects.

The prevalence and significance of autoantibodies in patients with non-Hodgkin's lymphoma: are they correlated with clinicopathological features?

PURPOSE

It is well known that an association exists between the pathogenesis of lymphomas and autoimmune diseases. Autoantibodies are detected at higher frequency in lymphoproliferative diseases, but neither the precise role of the immune system nor the cause of this is comprehensively understood. In this study we evaluated the presence and significance of some autoantibodies for patients with non- Hodgkin's lymphoma (NHL).

METHODS

150 patients with NHL who had either newly diagnosed disease, or active disease being under chemotherapy or were disease-free during follow-up, were analyzed. The frequency of autoantibodies and the relationship between autoantibodies and several clinicopathological factors were evaluated.

RESULTS

The majority of the patients (50%) had diffuse large B-cell lymphoma (DLBCL). Thirty-two patients (21.4%) were newly diagnosed, 81 (54%) had active disease and were receiving chemotherapy and 37 (24.6%) were disease-free and followed-up. Fifty-one patients (34%) had stage IV disease. Antinuclear antibodies (ANA) were found in 7 (4.7%) patients, perinuclear anti-neutrophil cytoplasmic antibody (p-ANCA) in 10 (6.7%), anti dsDNA in 1 (0.7%), anti ssDNA in 16 (10.7%), anti Jo-1 in 3 (2%), anti-scleroderma antibody (anti Scl-70) in 4 (2.7%), and rheumatoid factor (RF) in 85 (56.7%) patients. No c7horbar;ANCA positivity was found. The mean levels of anti Jo-1 (p=0.028), anti ssDNA (p=0.014), c-ANCA (p=0.015), ANA (p=0.026) and RF (p=0.046) were significantly higher in cases with DLBCL compared to patients with non-DLBCL. In addition, in patients with newly diagnosed NHL the mean levels of anti Scl- 70 (p=0.023), anti Jo-1 (p7equals;0.017), and RF (p=0.046) were significantly higher than the other patient groups. No significant correlation was detected between the presence of autoantibodies and other clinicopathological factors.

CONCLUSION

Our results show that the frequency of autoantibodies is high in NHL patients, especially in DLBCL and newly diagnosed cases. Autoantibodies may be helpful for the diagnosis of autoimmune diseases, but regular and long follow-up is needed in NHL patients with high levels of autoantibodies.

Perioperative airway management strategy and posttransplant successful tracheal resection and reconstruction in a heart transplant candidate with post-intubation stenosis

Post-intubation tracheal stenosis (PTS) is an important clinical situation. It is estimated to occur in approximately 5% to 20% of intubated or tracheostomized patients. PTS most commonly occurs after prolonged intubation, and the treatment options have been well discussed in the literature. However, in solid organ transplantation, the necessity of administering high doses of corticosteroids as well as immunosuppressive therapies may compromise the healing processes following tracheal resection and reconstruction, requiring different treatment strategies for simultaneous PTS. We present a patient suffering from end-stage heart failure and post-intubation tracheal stenosis along with our treatment strategy.

High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans

We mapped nucleosome occupancy by paired-end Illumina sequencing in C. elegans embryonic cells, adult somatic cells, and a mix of adult somatic and germ cells. In all three samples, the nucleosome occupancy of gene promoters on the X chromosome differed from autosomal promoters. While both X and autosomal promoters exhibit a typical nucleosome-depleted region upstream of transcript start sites and a well-positioned +1 nucleosome, X-linked gene promoters on average exhibit higher nucleosome occupancy relative to autosomal promoters. We show that the difference between X and autosomes does not depend on the somatic dosage compensation machinery. Instead, the chromatin difference at promoters is partly encoded by DNA sequence, because a model trained on nucleosome sequence preferences from S. cerevisiae in vitro data recapitulate nearly completely the experimentally observed difference between X and autosomal promoters. The model predictions also correlate very well with experimentally determined occupancy values genome-wide. The nucleosome occupancy differences observed on X promoters may bear on mechanisms of X chromosome dosage compensation in the soma, and chromosome-wide repression of X in the germline.

CYP2C19 Polymorphisms in Patients with Gastric and Colorectal Carcinoma

BACKGROUND

It has been reported that up to 80% of human cancers arise as a consequence of environmental exposure and host susceptibility factors. Environmental carcinogens are predominantly metabolized by the cytochrome P450 (CYP) superfamily of drug- or xenobiotic-metabolizing enzymes. Genetic variations in these enzymes affect individuals' susceptibility to carcinogens.

AIM OF THE STUDY

The aim of this study was to evaluate the relationship between CYP2C19 polymorphism and susceptibility to these cancers by means of CYP2C19 genotyping among Turkish subjects.

METHODS

DNAof subjects were isolated from leukocytes by high pure template preparation kit (Roche Diagnostics, GmbH, Mannheim, Germany) and genotypes were detected by LightCycler CYP2C19 Mutation Detection Kit by real-time PCR with LightCycler instrument (Roche Diagnostics, cat. no. 3113914).

RESULTS

Being male was associated with a 3.5-fold (OR: 4.27, CI: 2.27-8.05) and 4.27-fold (OR: 3.50, CI: 1.948-6.301) risk for colorectal and gastric carcinoma, respectively. The CYP2C19*3 heterozygote genotype was not found in either gastric or colorectal carcinoma patients. Although the frequency of CYP2C19*2 heterozygote genotype is high in patients with gastric and colorectal carcinoma, it is not significantly associated with cancer (OR: 1.79, CI: 0.829-3.865 and OR: 1.998, CI: 0.961-4.154, respectively).

CONCLUSION

Although the frequency of CYP2C19*2 heterozygote genotype is high in our patients with gastric and colorectal carcinoma, there is no the relationship between CYP2C19 polymorphism and susceptibility to these cancer.

Intra-arterial simultaneous administration of anandamide attenuates endothelin-1 induced vasospasm in rabbit basilar arteries

BACKGROUND

Anandamide induces not only endothelium-dependent vasodilatation through cannabinoid receptors but also some endothelium- independent vasodilator effect by calcitonin gene-related peptide release through vanilloid receptors. Endothelin-1, a powerful vasoconstrictive peptide derived from endothelial cells, has been shown to be converted to its active form after cleaving by a vascular matrix metalloproteinase which is also involved in inactivation of calcitonin gene-related peptide. The purpose of this study was to investigate whether anandamide inhibits the acute vascular and morphological effects of Endothelin-1 applied intra-arterially on rabbit basilar arteries.

METHOD

Fifteen albino rabbits were anaesthetised and underwent placement of a vertebral artery catheter for angiography of the basilar artery. Animals were divided, arbitrarily, into animals in which there was either intra-arterial injection of saline (Group I, n=5), Endothelin-1 (Group II, n=5) and Endothelin-1 and anandamide (Group III, n=5). The diameter of the basilar artery between the pre and post injection angiograms was measured in each of the three groups and transmission electron microscopic investigations on basilar arteries were performed.

FINDINGS

Angiographic studies showed that simultaneous administration of anandamide significantly attenuated Endothelin-1 induced vasoconstriction. Furthermore, it was demonstrated that anandamide reversed the morphological changes induced by Endothelin-1 on the vessel wall.

INTERPRETATION

These results indicated that anandamide overcomes the angiographic and morphological effects of intrarterially administered ET-1 induced vasospasm in rabbit basilar arteries probably by induction of CGRP related vasodilatation through vanilloid receptors and prevents the acute ET-1 induced ultrastructural vessel wall damage.

Reservoir and globe-type antireflux surgical techniques in intrathoracic esophagogastrostomies

Gastroesophageal reflux is a major postoperative problem in esophageal patients with cancer, and the principal cause is resection of the lower esophageal sphincter. Two new antireflux operations to solve this problem were investigated. The number of patients studied was 139, with a male to female ratio of 5. The reservoir technique was applied to the first 50 patients and the globe technique was used in the remaining 89. Hospital mortality was 9.35%. Patient satisfaction from a reflux standpoint was excellent in 91.4%, good to fair in 6.5%, and poor in 2.1%. Postoperative barium swallow at the first, third, and sixth months showed no reflux in 93% of cases. Postoperative preanastomotic mean pressure was 14.2 mmHg. Postoperative mucosal biopsies revealed a remarkable reduction in esophagitis. The radiologic, manometric, and histologic findings as well as the patient satisfaction rate suggest that these antireflux operations are suitable and effective for patients undergoing esophageal resection and intrathoracic esophagogastric anastomosis.

Early mobilization after sliding and Z-lengthening of heel cord: a preliminary experimental study in rabbits

Sliding lengthening and Z-lengthening techniques are widely used in heel cord lengthening. Even though most surgeons performing these procedures apply a short leg cast after surgery, their postoperative immobilization intervals vary from 3 to 7 weeks. Nather et al. showed that there was no need for immobilization after the musculotendinous lengthening of long, deep flexor tendons. In the present study, we aimed to show the healing process of heel cords lengthened by sliding and Z-plasty lengthening in rabbits that did not undergo any postoperative immobilization. We performed sliding lengthening in the right heel cords of the rabbits and Z-lengthening in the left heel cords. We compared these two techniques radiographically, biomechanically, and histopathologically. Even though the biomechanical study showed superior results in the sliding lengthening group on the 7th day, elongation of the tendons at both sites was seen radiographically. There was no statistically significant difference between the sites according to the biomechanical study done on the 28th day. We concluded that the ankle should be immobilized in the early healing phase and that both types of lengthening gain a similar level of strength by the 4th week.

Acetabular dysplasia in normal Turkish adults

The aim of this investigation was to examine normal hip joint morphometry and the acetabular dysplasia rate in Turkish adults. Center-edge angle, acetabular angle, acetabular depth, acetabular roof obliquity, and roof angle were measured in standardized pelvic radiographs of 495 adults without any hip symptoms. The center-edge angle was significantly different in the patients over the age of 70 than all other age groups except those in the 60 to 69 group. Additionally, there were differences between those in the 60 to 69 age group compared to those in the 20 to 29 age group. The acetabular angle showed a significant difference between gender and between the age groups over 60. The acetabular angle was negatively correlated with center-edge angle. Even though no significant differences were observed in the acetabular depth, differences in acetabular roof obliquity and roof angle were related to gender and age, all showed high standard deviations. The rate of acetabular dysplasia was 2.4% in the Turkish adult population aged 20 to 79. It is concluded that the center-edge angle may be a useful parameter in the evaluation of acetabular dysplasia if one is aware of its difference in patients over the age of 60.

Comparison of omentum, pleura and diaphragm for tracheal autograft survival in rats

Pleura, diaphragm, pericardial fat pad, intercostal muscles and omentum can be used to protect and revascularize the bronchial suture line. To compare the efficiency of pleura, diaphragm and omentum, an experimental study was designed. Heterotopic tracheal autotransplantation was performed in 15 rats. Animals were divided into three groups; omentum, diaphragm and pleura. Tracheal Segment Necrosis Scoring System was used for pathologic examinations. Pleural and diaphragmatic groups showed the least necrosis and there was significant statistical difference among these groups and omental group (P < 0.05). Our study showed that pleura and diaphragm could be used as safely as omentum for protection and survival of bronchial suture lines.

Ileal and colonic contractions by endothelin-1 in experimentally induced paralytic ileus in rats

The aim of the present study was to investigate the effect of endothelin-1 on the isolated distal ileum and proximal colon in an experimentally induced ileus in rats. Ileal and colonic contractions by endothelin-1, acetylcholine alone and with endothelin-1 were recorded both in normal and experimentally induced paralytic ileus in rats. In the control group, all the responses to acetylcholine were found to be potentiated significantly when used together with endothelin-1 but in paralytic ileus group, no detectable change was observed in the responses of the amine after administration of acetylcholine together with endothelin-1. This study indicates that endothelin-1 might have an effect on gastrointestinal motility and postoperative paralytic ileus.

Role of endogenous endothelin peptides in intestinal ischemia-reperfusion injury in rats

In this study, the effects of BQ123 (an ET(A) receptor antagonist), bosentan (a nonselective ET(A)-ET(B) antagonist), and phosphoramidon (an endothelin converting enzyme inhibitor) were investigated on intestinal mucosal lesion formation and changes in tissue PGE2 and LTC4 levels due to intestinal ischemia-reperfusion (I/R) injury in rats. Following 30 min of ischemia, the substances were given via the inferior caval vein, and 10 min later the intestine was subjected to reperfusion for 30 min. The intestinal specimens were evaluated both microscopically and the tissue PGE2 and LTC4 levels were obtained for each group. The histopathologic examination revealed a significant reduction in tissue injury in both BQ123 and phosphoramidon pretreated groups compared with the control group. Bosentan, on the contrary, did not decrease the injury. The pharmacologic examination revealed a significant reduction of PGE2-like activity in both BQ123 and phosphoramidon pretreated groups, compared with the control group, while LTC4-like activity remained unchanged except for an increase in the bosentan pretreated group.

Correlation between sizes and intracystic pressures of hydatid cysts

BACKGROUND

A bicentral prospective study was performed to assess the relationship between sizes and intracystic pressures (ICP) of pulmonary hydatid cysts as well as to compare these measurements in different age groups.

METHODS

A total of 20 patients with 22 unperforated pulmonary hydatid cysts underwent surgery between April 1994 and September 1995. There were 12 males and 8 females with a mean age of 25.7 (7-62). Intraoperatively, ICP's were measured in cmH2O by direct cannulation.

RESULTS

Out of a total of 22 cysts, 12 were located in the lower lobes. Mean diameter, volume and ICP of cysts were 9.6 cm (S.D. 4.2), 728.8 cm3 (S.D. 1014.9) and 36.6 cmH2O (S.D. 9.3), respectively. There was no significant correlation between various measurements of hydatid cysts, namely their short and long diameters, volumes and intracystic pressures (P > 0.05). There was no difference regarding the volume, ICP and age of patients, either among pulmonary lobes or between sexes. Patients who were 20 years old and less, presented a mean cystic diameter of 7.2 cm and mean ICP of 35.1 cmH2O, whereas the over 20 age group showed results of 11.9 cm and 38.1 cmH2O, respectively (P values were < 0.0083 for diameter and > 0.05 for ICP).

CONCLUSIONS

Due to the small sample size and a few extreme measurements, the correlation between the sizes and the pressures of hydatid cysts turned out to be insignificant, but it is believed that a positive correlation is most probable with larger sample sizes. On the other hand, while the difference between the mean cystic diameters in age groups of below and over 20 was significant, the pressure difference between them was insignificant. This is why young patients carry the same risk of perforation as adults, although they present with relatively smaller cysts. Therefore, due to the well-known anaphylactic, obstructive and infectious risks of hydatid cyst perforation, urgent surgical removal is always necessary.

The effects of indomethacin, NDGA, allopurinol and superoxide dismutase on prostaglandin E2 and leukotriene C4 levels after mesenteric ischemia-reperfusion injury

In this study, the changes of arachidonic acid metabolites after an ischemia-reperfusion (I/R) period are investigated. The cyclooxygenase and lipoxygenase metabolites were found to be significantly increased after a 45 min period of ischemia followed by 5 min of reperfusion. Prostaglandin E2 (PGE2)- and leukotriene C4 (LTC4)-like activities did not change in the ischemic period, but they both increased after reperfusion. A cyclooxygenase inhibitor indomethacin and lipoxygenase inhibitor nordehydroguaretic acid (NDGA) decreased PGE2- and LTC4-like activities, respectively, while allopurinol and superoxide dismutase (SOD) decreased both activities. According to our results, it can be assumed that free oxygen radicals are responsible for the elevation of PGE2- and LTC4-like activities and both of these arachidonic acid metabolites and free oxygen radicals are the main necrotizing agents in ischemia-reperfusion induced damage.