Sex-biased mouse liver lincRNAs: validation and impact of mouse knockout models that perturb hepatic growth signaling

Sexual dimorphism has a broad impact on human health and disease, including autoimmune diseases, cardiovascular diseases, and liver diseases, specifically hepatocellular carcinoma. Pituitary growth hormone (GH) secretion has a major impact on sex differences in the liver. Previous studies show that signal transducer and activator transcription factor 5b (STAT5b) impacts male-biased gene expression. Somatostatin (SST) inhibits the release of GH, and this in turn impacts STAT5b activity and GH regulation feedback. Long intergenic noncoding RNAs (lincRNAs), which do not encode proteins, have various roles in diverse biological processes including cell differentiation, chromatin remodeling, and gene regulation. In the present study, we discovered lincRNAs in mouse liver using RNA-seq datasets, and identified male and female-biased lincRNAs. Moreover, we validated the sex-specificity of lincRNAs by performing real time PCR (qPCR) and analyzing UCSC genome browser screen shots by comparing male and female expression patterns. We validated the sex-specificities of 22 lincRNAs. Moreover, we investigated whether pituitary GH secretion impacts the regulation of these sex-biased lincRNAs in the same manner as seen in sex-biased protein coding RefSeq genes. qPCR experiments investigated the impact of GH secretion by using SST and STAT5b knockout mouse models, and hypophysectomized, and intermittent (pulsatile) GH-treated mice. Our results show that pituitary GH secretion impacts the regulation of sex-biased lincRNAs. The last part of this thesis investigates the molecular and functional role of sexbiased lincRNAs by using The Database for Annotation, Visualization, and Integrated Discovery (DAVID)

Effect of celery powder as an alternative nitrite source on some quality properties and nitrosamine formation in sucuk

This study aimed to determine the effects of celery powder (nitrate converted to nitrite) and cooking time on the formation of nitrosamine in sucuk. The microbiological and physicochemical properties were also investigated. Four sucuk batters were prepared: T1 - 100 mg/kg synthetic sodium nitrite, T2 - 150 mg/kg synthetic sodium nitrite, T3 - celery powder equivalent to 100 mg/kg nitrite, T4 - celery powder equivalent to 150 mg/ kg nitrite. After ripening (initial fermentation temperature: 24±1°C, ripening time: 7 days), the samples were subjected to the analyses. Lactic acid bacteria and Micrococcus/ Staphylococcus were not affected by the treatment. T4 treatment showed higher pH values than T1 and T2. The celery powder groups (T3 and T4) showed lower aw values than other groups (T1 and T2). No significant differences were observed between the treatments in terms of thiobarbituric acid reactive substance (TBARS) value, residual nitrite level, N-nitrosodimethylamine (NDMA) and N-nitrosodiethylamine (NDEA) contents. However, N-nitrosopiperidine (NPIP) content was found to have higher in T4 treatment. Cooking time, especially 3 min, caused a significant increase in nitrosamine content. The effect of cooking time on nitrosamines was also revealed in principal component analysis

The effect of the combination of rosemary extract and green tea extract on nitrosamine content, microbiological, physicochemical and sensorial properties of heat-treated sucuk

In this study, it was aimed to determine the effect of using rosemary extract together with green tea extract (RE/GTE) on nitrosamine content and quality characteristics of heat-treated sucuk. In addition, the influence of cooking time on the formation of nitrosamines was also investigated. Four different batters were prepared as follows: control (C), 0.1% RE/GTE (RG1), 0.2% RE/GTE (RG2), and 0.3% RE/GTE (RG3). The use of RE/GTE caused a decrease in lactic acid bacteria and Micrococcus/Staphylococcus counts in the final product. While the use of RE/GTE did not affect the aw value, the lowest pH value (4.80±0.05) was observed in the RG3 treatment. RE/GTE resulted in a reduction in residual nitrite, and the lowest level was determined as 12.60±0.87 mg/kg. The lower mean TBARS values were determined in the RG2 and RG3 treatments. RE/ GTE did not affect the L* and a* values, however, b* value increased in the RG2 and RG3 treatments. The lowest odor, taste, and general acceptability scores were determined in the RG3 group. The use of RE/GTE had no significant effect on nitrosodiethylamine, nitrosodimethylamine, nitrosopiperidine and nitrosopyrrolidine. The levels of nitrosamines increased with cooking, but the interaction of RE/GTE and cooking time was not significant. RE/GTE treatments also caused a decrease in hexanal level and an increase in some terpene compounds

Determination of Immunization Status of Pregnant Women Who Attending The Family Health Center

Amaç: Araştırmanın amacı, aile sağlığı merkezlerine başvuran gebelerin bağışıklama durumlarının belirlenmesidir. Gereç ve Yöntem: Karşılaştırmalı-tanımlayıcı desendeki araştırma, İzmir merkez ilçesinde yer alan 10 aile sağlığı merkezinde görüşülen 1021 gebe ile gerçekleştirilmiştir. Veriler, görüşme formu ile toplanmıştır. Veriler sayı, yüzde, varyans ve ki-kare analizi ile değerlendirilmiştir. Bulgular: Gebelerin yaş ortalaması 27,96±4,89 olup %43,9’u lise mezunudur. Gebelik sayısı medyanı iki ve canlı doğum sayısı birdir. Gebelerin %82,2’si aşılanma ile ilgili bilgi almış olup, bunlardan %75,8’inin bilgi kaynağı sağlık çalışanlarıdır. Gebelerin %37,8’i aşı kartı olmadığını bildirmiştir. Gebelik döneminde gebelerin %63,2’si tetanoz, %10,3’ü hepatit B, %11,9’u grip, %3,4’ü pnömokok, %3,0’ü kuduz aşısı yaptırmıştır. Gebelerin eğitim, gelir düzeyi, çalışma durumu, son bir yılda aile sağlığı merkezine gelme durumu, planlı gebelik durumu ile aşılarla ilgili bilgi alma ve aşı kartı bulunma durumu arasında anlamlı fark olduğu saptanmıştır (p<0,001). Eğitim ve gelir düzeyi yüksek, planlı gebeliği olan ve son bir yıl içinde aile sağlığı merkezine başvuran gebelerin aşıya ilişkin bilgileri artmaktadır (p<0,000). Sonuç: Araştırmaya katılan gebelerden yaklaşık beşte birinin aşı yaptırmamış olması ve gebelik dönemi bağışıklamayla ilgili bilgisinin olmaması ana çocuk sağlığı açısından göz ardı edilmemesi gereken bir durumdur. Birinci basamakta çalışan hemşireler tarafından bağışıklama konusunda planlı ve sürekli eğitimlerin yapılması hem anne hem bebek sağlığı açısından önemlidir.Objective: The aim of this study is to determine the immunization status of pregnant women who attend family health centers. Material and Method: Descriptive- comparative research design was carried out with 1027 pregnant women interviewed in 10 family health centers in the İzmir central district region. The data was collected with the interview form. Number, percentage, variance, and chi-square analysis were used to analyze the results. Results: The pregnant women’s average age was 27.96±4.89, 43.9% of the pregnant women were high school graduates. The median number of pregnancies was two, and the number of live births was one. Of the pregnant women, 82.2% received information about immunization, and 75.8% received information from healthcare workers. Of the pregnant women, 37.8% reported that they did not have an immunization card. During pregnancy, 63.2% of pregnant women were vaccinated against tetanus, 10.3% against hepatitis B, 11.9% against influenza, 3.4% against pneumococcus, and 3.0% against rabies. There was a significant difference in the pregnant women's education, the level of income, and the employment status, as well as the status of last years’ attendance at the family health center, the planning status of the pregnancy, and the status of obtaining information about vaccines and having a vaccination card (p<0.001). Those who have a high level of education and income, have been planned pregnancy, and have been applied at the family health center for the past year are increasing their knowledge (p<0.000). Conclusion: Approximately one fifth of the pregnant women in the sample were not vaccinated, and the lack of awareness about immunization during pregnancy is a situation that should not be overlooked in terms of maternal and child health. Planned and ongoing immunization training by nurses working in primary care is crucial for the health of both the mother and the infan

Utjecaj dodatka praha sluzi chia sjemenki (Salvia hispanica L.) na neka fizikalno-kemijska i reološka svojstva ayrana

In this study, chia seed mucilage powder (MP) was added into ayran drinks at different ratios (0.05, 0.10 and 0.15%, w/v), and its effect on physicochemical, rheological, microbiological and sensory properties of ayran drinks was determined during 10 days of storage at 4±1 °C. MP addition did not influence their major chemical composition significantly (p>0.05). Increasing MP ratio in drinks decreased the colour L* values of drinks while increasing their colour a* and b* values. Addition of 0.05, 0.10 and 0.15% MP reduced serum separation values of drinks by 25, 67 and 83%, respectively. The apparent viscosity value of control samples was 103.20 cP and increased to 134.25, 185.35 and 223.38 cP in ayran drinks with 0.05, 0.10 and 0.15% MP, respectively. The obtained results indicated that chia seed MP up to 0.05% can be used in ayran drink production to reduce serum separation and improve viscosity without any adverse effect on sensory liking scores.U ovom istraživanju, prah sluzi chia sjemenki (MP) dodan je u ayran napitke u različitim omjerima (0,05, 0,10 i 0,15 %, w/v) te je ispitivan njegov učinak na fizikalno-kemijska, reološka, mikrobiološka i senzorska svojstva ayran napitaka tijekom 10 dana skladištenja na 4±1 °C. Dodatak MP nije značajno utjecao na njihov glavni kemijski sastav (p>0,05). Povećanje omjera MP u pićima smanjilo je L* vrijednosti boje pića dok je povećalo njihove a* i b* vrijednosti boje. Dodatak 0,05, 0,10 i 0,15 % MP smanjio je vrijednosti sinereze napitaka za 25, 67 odnosno 83 %. Prividna viskoznost kontrolnih uzoraka bila je 103,20 cP i porasla je na 134,25, 185,35 i 223,38 cP u ayran napicima s 0,05, 0,10 i 0,15 % MP. Rezultati su pokazali da se MP chia sjemenki do 0,05 % može koristiti u proizvodnji ayrana, kako bi se smanjila sinereza i poboljšala viskoznost bez ikakvih negativnih učinaka na senzorska svojstva

Machine-Knitted Seamless Pneumatic Actuators for Soft Robotics: Design, Fabrication, and Characterization

Computerized machine knitting offers an attractive fabrication technology for incorporating wearable assistive devices into garments. In this work, we utilized, for the first time, whole-garment knitting techniques to manufacture a seamless fully knitted pneumatic bending actuator, which represents an advancement to existing cut-and-sew manufacturing techniques. Various machine knitting parameters were investigated to create anisotropic actuator structures, which exhibited a range of bending and extension motions when pressurized with air. The functionality of the actuator was demonstrated through integration into an assistive glove for hand grip action. The achieved curvature range when pressurizing the actuators up to 150 kPa was sufficient to grasp objects down to 3 cm in diameter and up to 125 g in weight. This manufacturing technique is rapid and scalable, paving the way for mass-production of customizable soft robotics wearables

Chemerin as a marker of subclinical cardiac involvement in psoriatic patients

Background: Chemerin has been associated with psoriasis and inflammation, but there are no studies demonstrating an association between chemerin and subclinical cardiac involvement in psoriatic patients. Therefore, the present study aimed to evaluate whether psoriatic patients with increased epicardial fat tissue, impaired flow-mediated dilatation, and diastolic dysfunction have higher serum chemerin levels than a healthy control group. Methods: The study included 60 psoriatic patients and 32 healthy controls. Echocardiographic parameters, epicardial fat tissue, flow-mediated dilatation, and chemerin levels were recorded for both groups. Results: The serum levels of chemerin in the psoriatic patients were significantly higher than in the control group. The diastolic function parameters, including isovolumic contraction and relaxation time, E’/A’ (early diastolic mitral annular velocity/late diastolic mitral annular velocity), and E/E’ (early diastolic peak velocity of mitral inflow/early diastolic mitral annular velocity) values, differed significantly between the groups. Epicardial fat tissue was significantly higher and flow-mediated dilatation was significantly lower in psoriatic patients than in the controls. Chemerin was significantly positively correlated with age, body mass index, systolic and diastolic blood pressures, waist circumference, E/E’, and epicardial fat tissue. Serum chemerin was significantly negatively correlated with E’, E’/A’, and flow-mediated dilatation. A multiple linear regression analysis showed that chemerin was independently correlated with E/E’. Conclusions: Psoriatic patients exhibit early subclinical atherosclerosis and diastolic dysfunction. Chemerin can be used as a marker to screen for patients with subclinical cardiac involvement

High level of complexity and global diversity of the 3q29 locus revealed by optical mapping and long-read sequencing.

BACKGROUND: High sequence identity between segmental duplications (SDs) can facilitate copy number variants (CNVs) via non-allelic homologous recombination (NAHR). These CNVs are one of the fundamental causes of genomic disorders such as the 3q29 deletion syndrome (del3q29S). There are 21 protein-coding genes lost or gained as a result of such recurrent 1.6-Mbp deletions or duplications, respectively, in the 3q29 locus. While NAHR plays a role in CNV occurrence, the factors that increase the risk of NAHR at this particular locus are not well understood. METHODS: We employed an optical genome mapping technique to characterize the 3q29 locus in 161 unaffected individuals, 16 probands with del3q29S and their parents, and 2 probands with the 3q29 duplication syndrome (dup3q29S). Long-read sequencing-based haplotype resolved de novo assemblies from 44 unaffected individuals, and 1 trio was used for orthogonal validation of haplotypes and deletion breakpoints. RESULTS: In total, we discovered 34 haplotypes, of which 19 were novel haplotypes. Among these 19 novel haplotypes, 18 were detected in unaffected individuals, while 1 novel haplotype was detected on the parent-of-origin chromosome of a proband with the del3q29S. Phased assemblies from 44 unaffected individuals enabled the orthogonal validation of 20 haplotypes. In 89% (16/18) of the probands, breakpoints were confined to paralogous copies of a 20-kbp segment within the 3q29 SDs. In one del3q29S proband, the breakpoint was confined to a 374-bp region using long-read sequencing. Furthermore, we categorized del3q29S cases into three classes and dup3q29S cases into two classes based on breakpoints. Finally, we found no evidence of inversions in parent-of-origin chromosomes. CONCLUSIONS: We have generated the most comprehensive haplotype map for the 3q29 locus using unaffected individuals, probands with del3q29S or dup3q29S, and available parents, and also determined the deletion breakpoint to be within a 374-bp region in one proband with del3q29S. These results should provide a better understanding of the underlying genetic architecture that contributes to the etiology of del3q29S and dup3q29S

SvAnna: efficient and accurate pathogenicity prediction of coding and regulatory structural variants in long-read genome sequencing.

Structural variants (SVs) are implicated in the etiology of Mendelian diseases but have been systematically underascertained owing to sequencing technology limitations. Long-read sequencing enables comprehensive detection of SVs, but approaches for prioritization of candidate SVs are needed. Structural variant Annotation and analysis (SvAnna) assesses all classes of SVs and their intersection with transcripts and regulatory sequences, relating predicted effects on gene function with clinical phenotype data. SvAnna places 87% of deleterious SVs in the top ten ranks. The interpretable prioritizations offered by SvAnna will facilitate the widespread adoption of long-read sequencing in diagnostic genomics. SvAnna is available at https://github.com/TheJacksonLaboratory/SvAnn a

Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders.

Unlike copy number variants (CNVs), inversions remain an underexplored genetic variation class. By integrating multiple genomic technologies, we discover 729 inversions in 41 human genomes. Approximately 85% of inversionsretrotransposition; 80% of the larger inversions are balanced and affect twice as many nucleotides as CNVs. Balanced inversions show an excess of common variants, and 72% are flanked by segmental duplications (SDs) or retrotransposons. Since flanking repeats promote non-allelic homologous recombination, we developed complementary approaches to identify recurrent inversion formation. We describe 40 recurrent inversions encompassing 0.6% of the genome, showing inversion rates up to 2.7 × 1