Detection of 3D Genome Folding at Multiple Scales

Understanding 3D genome structure is crucial to learn how chromatin folds and how genes are regulated through the spatial organization of regulatory elements. Various technologies have been developed to investigate genome architecture. These technologies include ligation-based 3C Methodologies such as Hi-C and Micro-C, ligation-based pull-down methods like Proximity Ligation-Assisted ChIP-seq (PLAC Seq) and Paired-end tag sequencing (ChIA PET), and ligation-free methods like Split-Pool Recognition of Interactions by Tag Extension (SPRITE) and Genome Architecture Mapping (GAM). Although these technologies have provided great insight into chromatin organization, a systematic evaluation of these technologies is lacking. Among these technologies, Hi-C has been one of the most widely used methods to map genome-wide chromatin interactions for over a decade. To understand how the choice of experimental parameters determines the ability to detect and quantify the features of chromosome folding, we have first systematically evaluated two critical parameters in the Hi-C protocol: cross-linking and digestion of chromatin. We found that different protocols capture distinct 3D genome features with different efficiencies depending on the cell type (Chapter 2). Use of the updated Hi-C protocol with new parameters, which we call Hi-C 3.0, was subsequently evaluated and found to provide the best loop detection compared to all previous Hi-C protocols as well as better compartment quantification compared to Micro-C (Chapter 3). Finally, to understand how the aforementioned technologies (Hi-C, Micro-C, PLAC-Seq, ChIA-PET, SPRITE, GAM) that measure 3D organization could provide a comprehensive understanding of the genome structure, we have performed a comparison of these technologies. We found that each of these methods captures different aspects of the chromatin folding (Chapter 4). Collectively, these studies suggest that improving the 3D methodologies and integrative analyses of these methods will reveal unprecedented details of the genome structure and function

Government Supported Export Credit: United States Competitiveness

67-70A biosensor for the specific determination of uric acid in urine was developed using urate oxidase (EC 1.7.3.3) in combination with a dissolved oxygen probe. Urate oxidase was immobilized with gelatin by means of glutaraldehyde and fixed on a pretreated teflon membrane to serve as enzyme electrode. The electrode response was maximum when 50 mM glycine buffer was used at <i style="mso-bidi-font-style: normal">pH 9.2 and 35°C. The enzyme electrode response depends linearly on uric acid concentration between 5- 40 μM with a response time of 5 min. The enzyme electrode is stable for more than 2 weeks and during this period over 35 assays were <span style="font-size:14.0pt; font-family:HiddenHorzOCR;mso-bidi-font-family:HiddenHorzOCR">performed.   </span

Can we predict agitation in patients with suicide attempts in the emergency department?

Background: The agitation in patients presenting to the emergency department (ED) after suicide attempts is common and an important problem.Objective: To establish whether we can predict agitated patients among suicide attempt patients in ED.Methods: This is a cross-sectional observational study of adult suicide attempt events in ED. Information was collected prospectively on a specially designed data-collection form. Patients aged 16 years old and above who presented to the ED for care due to suicide attempts were included in the study. Suicide attempts were grouped as aggressive and non-aggressive attempts.Results: A total of 533 patients were included. Forty-three of these patients had agitation in ED (8%). Non-aggressive suicide attempts were referred to psychiatry services more than aggressive ones (73.6%, n=345 vs 32.8%, n=21, P&lt;0.0001). Agitation in ED and being male increased aggressive suicide attempt risk 3.5 (95% CI:1.6-7.6) and 3.2 times (95% CI:1.8-5.5), respectively. Agitation was statistically more frequent among these patients: those on antidepressant  overdose, with previous suicide attempt; with aggressive suicide attempt; and those with confusion; and unconsciousness (P&lt;0.05).Conclusion: Patients who attempted suicide and whose risk of harm to others included those with: antidepressant overdose, aggressive suicide attempt and the unconscious. Response teams should be prepared for these subgroups.Keywords: Agitation, suicide attempt, deliberate self-harm.Due to errors in the previous PDF especially in the 'Cite as' authors names, the PDF fulltext has been reloaded. This information is now correct

Nanočestice L-glutaminske kiseline-g-polihidroksietilnoga metakrilata – akutna i subakutna toksičnost i bioraspodjela u miševa

The aim of this safety study in mice was to determine in vivo toxicity and biodistribution potential of a single and multiple doses of L-glutamic acid-g-p(HEMA) polymeric nanoparticles as a drug delivery system. The single dose did not cause any lethal effect, and its acute oral LD50 was >2.000 mg/kg body weight (bw). Multiple doses (25, 50, or 100 mg/kg bw) given over 28 days resulted in no significant differences in body and relative organ weights compared to control. These results are supported by biochemical and histological findings. Moreover, nanoparticle exposure did not result in statistically significant differences in micronucleus counts in bone marrow cells compared to control. Nanoparticle distribution was time-dependent, and they reached the organs and even bone marrow by hour 6, as established by ex vivo imaging with the IVIS® spectrum imaging system. In conclusion, L-glutamic acid-g-p(HEMA) polymeric nanoparticles appear biocompatible and have a potential use as a drug delivery system.Cilj je ovoga istraživanja bio utvrditi in vivo toksičnost i raspodjelu jednokratne i višekratnih doza polimernih nanočestica L-glutaminske kiseline-g-p(HEMA) u funkciji isporuke lijekova. Jednokratna oralna doza nije prouzročila smrtnost, a akutni LD50 iznosio je >2,000 mg/kg tjelesne težine. Višekratne oralne dnevne doze od 25 mg, 50 mg i 100 mg/kg tjelesne težine, davane 28 dana, nisu dovele do značajnih razlika u ukupnoj tjelesnoj i relativnoj težini organa u usporedbi s kontrolnom skupinom. Ove rezultate potvrđuju biokemijski i histološki nalazi. Izloženost nanočesticama nije uzrokovala statistički značajne razlike u broju mikronukleusa u stanicama koštane srži miševa u odnosu na kontrolu. Raspodjela nanočestica u tijelu mijenjala se s vremenom, a nanočestice bi doprle u organe, pa i u koštanu srž, unutar prvih šest sati od primitka doze, što je utvrđeno ex vivo snimkama dobivenim pomoću sustava IVIS® Spectrum. Naši rezultati upućuju na to da su polimerne nanočestice L-glutaminske kiseline-g-p(HEMA) biokompatibilne i imaju potencijala za primjenu kao sustav isporuke lijekova

Konwencjonalna i płynna cytologia – badania porównawcze

Objectives: The aim of our study is the comparison of the results of conventional smear (CC) technique and liquidbased cytology (LBC) technique used as cervical cancer screening methods. Material and methods: The results of 47954 patients submitted to smear screening in our gynecology clinic between January 2008 and December 2014 have been studied. The smear results have been divided into two groups CC and LBC according to the technique used. Results: When considering the distribution within CC group, the results were as follows: intraepithelial cell abnormalities 2,0% (n=619), insufficient sample for analysis 2,1% (n=660), Atypical squamous cells of undetermined significance (ASC-US) 1.8% (n=554), Low grade squamous intraepithelial lesion (LGSIL) 0.1% (n=35), High grade squamous intraepithelial lesion (HGSIL) 0.1% (n=16), Atypical squamous cells – cannot exclude HGSIL (ASC-H) 0.029% (n=9), Atypical glandular cells- not other wise specified (AGC-NOS) 0.012% (n=4), squamous carcinoma 0.003% (n=1). When considering the distribution in LBC group, the results were as follows: intraepithelial cell abnormalities2.1% (n=357), insufficient sample for analysis 0.9% (n=144), ASC-US 1.8% (n=296), LGSIL 0.2% (n=38), HGSIL 0.1% (n=8), ASC-H 0.1% (n=10), AGC-NOS 0.017% (n=3), squamous carcinoma 0.011% (n=2). Conclusions: Although the rates of epithelial cell abnormalities are similar for both tests, LSIL results are more frequently observed in LBC technique. In LBC technique, the number of insufficient sample for analysis is quite low compared to CC group and thus constitutes an advantage.  Cel pracy: Celem badania było porównanie wyników konwencjonalnej (CC) i płynnej cytologii (LBC) stosowanej w skriningu raka szyjki macicy. Materiał i metoda: Przeanalizowano wyniki od 47954 pacjentek objętych cytologicznym badaniem skriningowym w naszym oddziale ginekologicznym w okresie od stycznia 2008 do grudnia 2014. Wyniki cytologiczne podzielono na dwie grupy CC i LBC w zależności od techniki pobierania. Wyniki: W grupie CC wyniki przedstawiały się nastepująco: nieprawidłowości komórek śródnabłonkowych 2,0% (n=619), nieodpowiednia próbka do analizy 2,1% (n=660), ASC-US 1.8% (n=554), LGSIL 0.1% (n=35), HGSIL 0.1% (n=16), ASC-H 0.029% (n=9), AGC-NOS 0.012% (n=4), rak płaskonabłonkowy 0.003% (n=1). W grupie LBC wyniki przedstawiały się następująco: nieprawidłowości komórek śródnabłonkowych 2.1% (n=357), nieodpowiednia próbka do analizy 0.9% (n=144), ASC-US 1.8% (n=296), LGSIL 0.2% (n=38), HGSIL 0.1% (n=8), ASC-H 0.1% (n=10), AGC-NOS 0.017% (n=3), rak płaskonabłonkowy 0.011% (n=2). Wnioski: Chociaż odsetek nieprawidłowości komórek śródnabłonkowych jest podobny dla obu testów, wyniki LSIL są częściej obserwowane w technice LBC. W metodzie LBC liczba próbek nieodpowiednich do analizy jest dość niska w porównaniu do grupy CC, stąd jest to jej niewątpliwa zaleta.

Characterization of P(Hema-Gma)-Ida Membrane to Adsorbing Leather Dye

Different chemical substances and too much water are used during leather production. Therefore, the waste water load of the leather industry is harmful to the environment. One of the pollution source is the production of leather coloring process is a further need to focus on the removal of dye waste waters subject. These water-soluble dyes have a small organic molecular size. Besides the environmental hazards that these dyes cannot be underestimated, they also have harmful effects on human health. In this study, poly (hydroxyethyl methacrylate-glycidyl methacrylate) p (HEMA-GMA) hydrogel membranes were synthesized by UV polymerization method. The hydrogel synthesized is modified with imino diacetic acid (IDA) and then chelated with trivalent chromium ions. The chelating capacity of the membranes were determined according to the time, pH and concentration parameters. Dynamic swelling test, elemental analysis, ninhydrin analysis and adsorption, desorption and reusability performances of membranes were also determined. As a result of the analyzes, it was understood that the hydrogel membrane had high adsorption capacity. The adsorption capacity of the p (HEMA-GMA) -IDA-Cr (III) hydrogel membrane did not decrease even after 5 desorption. At the end of the fifth cycle, the membrane was found to have a dye-binding capacity of about 92%. According to these results, the reusable property of the membrane also makes it cost effective as well as effective adsorption

The effect of obesity on the onset of spontaneous labor and scheduled delivery rates in term pregnancies

Objective: To determine the effect of obesity on the onset of spontaneous labor, scheduled delivery rates and perinatal outcomes in term pregnancies. Material and methods: 242 obese and 244 non-obese pregnant women ≥37 gestational weeks were compared in terms of the onset of spontaneous labor, scheduled delivery rates and perinatal outcomes. Results: Obese pregnant women had statistically significantly lower onset of spontaneous labor and higher rates of scheduled delivery. No difference was determined in respect of the type of delivery, 1st and 5th minutes APGAR scores and the need for intensive care. Higher values of birth weight, large for gestational age, macrosomia, gestational diabetes mellitus and preeclampsia were determined in obese women. Conclusion: The onset of spontaneous labor rates in term obese pregnancies were lower and scheduled delivery rates were higher than in the non-obese pregnancies. However, more extensive studies are needed to better understand this relationship. Keywords: Pregnancy, Obesity, Delivery, Labor, Pregnancy outcome

LncRNA RP11-19E11 is an E2F1 target required for proliferation and survival of basal breast cancer

Long non-coding RNAs (lncRNAs) play key roles in the regulation of breast cancer initiation and progression. LncRNAs are differentially expressed in breast cancer subtypes. Basal-like breast cancers are generally poorly differentiated tumors, are enriched in embryonic stem cell signatures, lack expression of estrogen receptor, progesterone receptor, and HER2 (triple-negative breast cancer), and show activation of proliferation-associated factors. We hypothesized that lncRNAs are key regulators of basal breast cancers. Using The Cancer Genome Atlas, we identified lncRNAs that are overexpressed in basal tumors compared to other breast cancer subtypes and expressed in at least 10% of patients. Remarkably, we identified lncRNAs whose expression correlated with patient prognosis. We then evaluated the function of a subset of lncRNA candidates in the oncogenic process in vitro. Here, we report the identification and characterization of the chromatin-associated lncRNA, RP11-19E11.1, which is upregulated in 40% of basal primary breast cancers. Gene set enrichment analysis in primary tumors and in cell lines uncovered a correlation between RP11-19E11.1 expression level and the E2F oncogenic pathway. We show that this lncRNA is chromatin-associated and an E2F1 target, and its expression is necessary for cancer cell proliferation and survival. Finally, we used lncRNA expression levels as a tool for drug discovery in vitro, identifying protein kinase C (PKC) as a potential therapeutic target for a subset of basal-like breast cancers. Our findings suggest that lncRNA overexpression is clinically relevant. Understanding deregulated lncRNA expression in basal-like breast cancer may lead to potential prognostic and therapeutic applications

The relationship between serum albumin levels and 24-h ambulatory blood pressure monitoring recordings in non-diabetic essential hypertensive patients

OBJECTIVES: The goal of this study was to evaluate the relationship between serum albumin levels and 24-hour ambulatory blood pressure monitoring (24-h ABPM) recordings in non-diabetic essential hypertensive patients. METHODS: A total of 354 patients (mean [SD] age: 55.5 [14.3] years, 50% females) with essential hypertension and 24-h ABPM recordings were included. Patient 24-h nighttime and daytime ABPM values, systolic and diastolic dipping status and average nocturnal dipping were recorded. The correlations between serum albumin levels and nocturnal systolic and diastolic dipping were evaluated, and correlates of average nocturnal systolic dipping were determined via a linear regression model. RESULTS: Overall, 73.2% of patients were determined to be non-dippers. The mean (SD) levels of serum albumin (4.2 [0.3] g/dL vs. 4.4 [0.4] g/dL,