The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber.

Over the last decade, genome-scale metabolic models have been increasingly used to study plant metabolic behaviour at the tissue and multi-tissue level under different environmental conditions. Quercus suber, also known as the cork oak tree, is one of the most important forest communities of the Mediterranean/Iberian region. In this work, we present the genome-scale metabolic model of the Q. suber (iEC7871). The metabolic model comprises 7871 genes, 6231 reactions, and 6481 metabolites across eight compartments. Transcriptomics data was integrated into the model to obtain tissue-specific models for the leaf, inner bark, and phellogen, with specific biomass compositions. The tissue-specific models were merged into a diel multi-tissue metabolic model to predict interactions among the three tissues at the light and dark phases. The metabolic models were also used to analyse the pathways associated with the synthesis of suberin monomers, namely the acyl-lipids, phenylpropanoids, isoprenoids, and flavonoids production. The models developed in this work provide a systematic overview of the metabolism of Q. suber, including its secondary metabolism pathways and cork formation.

Clinical and molecular findings in a Turkish family with an ultra-rare condition, ELP2-related neurodevelopmental disorder.

Elongator is a multi-subunit protein complex bearing six different protein subunits, Elp1 to -6, that are highly conserved among eukaryotes. Elp2 is the second major subunit of Elongator and, together with Elp1 and Elp3, form the catalytic core of this essential complex. Pathogenic variants that affect the structure and function of the Elongator complex may cause neurodevelopmental disorders. Here, we report on a new family with three children affected with a severe form of intellectual disability along with spastic tetraparesis, choreoathetosis, and self injury. Molecular genetic analyses reveal a homozygous missense variant in the ELP2 gene (NM_018255.4 (ELP2): c.1385G > A (p.Arg462Gln)), while in silico studies suggest a loss of electrostatic interactions that may contribute to the overall stability of the encoded protein. We also include a comparison of the patients with ELP2-related neurodevelopmental disorder to those previously reported in the literature. Apart from being affected with intellectual disability, we have extremely limited clinical knowledge about patients harboring ELP2 variants. Besides providing support to the causal role of p.Arg462Gln in ELP2-related neurodevelopmental disorder, we add self-injurious behavior to the clinical phenotypic repertoire of the disease.

The evaluation of intracellular energy metabolism in prediabetic patients and patients newly diagnosed with type 2 diabetes mellitus

Background/aim: Increased susceptibility to infections is a serious problem in diabetics. Impairment in the energy metabolism of the immune system is the main source of the problem. Early diagnosis of the impairment in energy metabolism is crucial. Our study aimed to investigate the energy metabolism in leukocytes in patient groups such as prediabetics and patients newly diagnosed with type 2 diabetes mellitus. Materials and methods: Our study included 21 newly diagnosed type 2 diabetic patients (NDDP), 30 prediabetic patients, and 22 adult volunteers. 75 g oral glucose tolerance test (OGTT) was applied to all patients included in the study. Blood samples were taken after 9-16 h of fasting and fasting blood glucose (FBG), postprandial blood glucose (PBG) levels, total cholesterol (TC), triglyceride (TG), high- density lipoprotein (HDL), fasting serum insulin, and hemoglobin A1c (HbA1c) levels were evaluated. After the cells were completely lysed, citrate levels from the released mononuclear leukocyte cells (MNC) content were manually studied, and lactate levels were applied to the autoanalyzer with the lactate kit. Lactate and citrate results were calculated as µg/mL. Statistical comparisons were done using Chi-square test, Mann-Whitney U test and student's t test, and P < 0.05 values were accepted as significant. Results: A significant difference was found between the controls and the other groups (newly diagnosed diabetic patients (NDDP), impaired fasting glucose (IFG), and impaired glucose tolerance (IGT)) in terms of FBG levels (P < 0.001, P < 0.001 and P < 0.001, respectively). IFG and IGT patients had significantly higher PBG levels compared to the control group (P = 0.009 and P < 0.001, respectively). There was a significant difference between the IFG and IGT patients in terms of insulin levels (P = 0.019). There was a significant relationship between FBG levels and lactate production only in the NDDP group (r = 0.610, P = 0.003) Conclusion: The metabolic effects of hyperglycemia on leukocytes is in direction of anaerobic glycolysis. The increased anaerobic pathway is closely related to blood glucose levels and insulin resistance.

Myophosphorylase (PYGM) mutations determined by next generation sequencing in a cohort from Turkey with McArdle disease.

This study aimed to identify PYGM mutations in patients with McArdle disease from Turkey by next generation sequencing (NGS). Genomic DNA was extracted from the blood of the McArdle patients (n = 67) and unrelated healthy volunteers (n = 53). The PYGM gene was sequenced with NGS and the observed mutations were validated by direct Sanger sequencing. A diagnostic algorithm was developed for patients with suspected McArdle disease. A total of 16 deleterious PYGM mutations were identified, of which 5 were novel, including 1 splice-site donor, 1 frame-shift, and 3 non-synonymous variants. The p.Met1Val (27-patients/11-families) was the most common PYGM mutation, followed by p.Arg576* (6/4), c.1827+7A>G (5/4), c.772+2_3delTG (5/3), p.Phe710del (4/2), p.Lys754Asnfs (2/1), and p.Arg50* (1/1). A molecular diagnostic flowchart is proposed for the McArdle patients in Turkey, covering the 6 most common PYGM mutations found in Turkey as well as the most common mutation in Europe. The diagnostic algorithm may alleviate the need for muscle biopsies in 77.6% of future patients. A prevalence of any of the mutations to a geographical region in Turkey was not identified. Furthermore, the NGS approach to sequence the entire PYGM gene was successful in detecting a common missense mutation and discovering novel mutations in this population study.

VCF-Explorer: filtering and analysing whole genome VCF files.

SUMMARY: The decreasing cost in high-throughput technologies led to a number of sequencing projects consisting of thousands of whole genomes. The paradigm shift from exome to whole genome brings a significant increase in the size of output files. Most of the existing tools which are developed to analyse exome files are not adequate for larger VCF files produced by whole genome studies. In this work we present VCF-Explorer, a variant analysis software capable of handling large files. Memory efficiency and avoiding computationally costly pre-processing step enable to carry out the analysis to be performed with ordinary computers. VCF-Explorer provides an easy to use environment where users can define various types of queries based on variant and sample genotype level annotations. VCF-Explorer can be run in different environments and computational platforms ranging from a standard laptop to a high performance server. AVAILABILITY AND IMPLEMENTATION: VCF-Explorer is freely available at: http://vcfexplorer.sourceforge.net/. CONTACT: mete.akgun@tubitak.gov.tr. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A patient with mitochondrial disorder due to a novel mutation in MRPS22.

MRPS22 gene defect is a very rare newly discovered mitochondrial disorder. We report a 4-month-old severely affected male infant with MRPS22 mutation. Whole exome sequencing revealed a novel homozygous splicing mutation c.339 + 5 G > A in MRPS22 gene. He has mild dysmorphism, hypotonia, developmental delay but not hypertrophic cardiomyopathy and tubulopathy which differ from other majority of reported patients. Therefore, hypertrophic cardiomyopathy and tubulopathy may not be considered as constant features of MRPS22. With this case report, we also present first symmetrical bilateral brainstem and medial thalamic lesions, and cerebellar and cerebral atrophy on a brain MR imaging follow-up of ten months.

Exome sequencing identifies a novel homozygous CLN8 mutation in a Turkish family with Northern epilepsy.

Neuronal ceroid lipofuscinosis (NCL), one of the most common neurodegenerative childhood-onset disorders, is characterized by autosomal-recessive inheritance, epileptic seizures, progressive psychomotor deterioration, visual impairment, and premature death. Based on the country of origin of the patients, the clinical features/courses, and the molecular genetics background of the disorder, 14 distinct NCL subtypes have been described to date. CLN8 mutation was first identified in Finnish patients, and the condition was named Northern Epilepsy (NE); however, the severe phenotype of the CLN8 gene was subsequently found outside Finland and named 'variant late-infantile' NCL. In this study, five patients and their six healthy relatives from a large Turkish consanguineous family were enrolled. The study involved detailed clinical, radiological and molecular genetic evaluations. Whole-exome sequencing and homozygosity mapping revealed a novel homozygous CLN8 mutation, c.677T>C (p.Leu226Pro). We defined NE cases in Turkey, caused by a novel mutation in CLN8. WES can be an important diagnostic method in rare cases with atypical courses.

Coffin-Siris syndrome with café-au-lait spots, obesity and hyperinsulinism caused by a mutation in the ARID1B gene.

Coffin-Siris syndrome (CSS) (MIM 135900) is characterized by developmental delay, severe speech impairment, distinctive facial features, hypertrichosis, aplasia or hypoplasia of the distal phalanx or nail of the fifth digit and agenesis of the corpus callosum. Recently, it was shown that mutations in the ARID1B gene are the main cause of CSS, accounting for 76% of identified mutations. Here, we report a 15 year-old female patient who was admitted to our clinic with seizures, speech problems, dysmorphic features, bilaterally big, large thumb, café-au-lait (CAL) spots, obesity and hyperinsulinism. First, the patient was thought to have an association of neurofibromatosis and Rubinstein Taybi syndrome. Because of the large size of the NF1 gene for neurofibromatosis and CREBBP gene for Rubinstein Taybi syndrome, whole exome sequence analysis (WES) was conducted and a novel ARID1B mutation was identified. The proband WES test identified a novel heterozygous frameshift mutation c.3394_3395insTA in exon 13 of ARID1B (NM_017519.2) predicting a premature stop codon p.(Tyr1132Leufs*67). Sanger sequencing confirmed the heterozygous c.3394_3395insTA mutation in the proband and that it was not present in her parents indicating de novo mutation. Further investigation and new cases will help to understand this phenomenon better.

FMFilter: A fast model based variant filtering tool.

The availability of whole exome and genome sequencing has completely changed the structure of genetic disease studies. It is now possible to solve the disease causing mechanisms within shorter time and budgets. For this reason, mining out the valuable information from the huge amount of data produced by next generation techniques becomes a challenging task. Current tools analyze sequencing data in various methods. However, there is still need for fast, easy to use and efficacious tools. Considering genetic disease studies, there is a lack of publicly available tools which support compound heterozygous and de novo models. Also, existing tools either require advanced IT expertise or are inefficient for handling large variant files. In this work, we provide FMFilter, an efficient sieving tool for next generation sequencing data produced by genetic disease studies. We develop a software which allows to choose the inheritance model (recessive, dominant, compound heterozygous and de novo), the affected and control individuals. The program provides a user friendly Graphical User Interface which eliminates the requirement of advanced computer techniques. It has various filtering options which enable to eliminate the majority of the false alarms. FMFilter requires negligible memory, therefore it can easily handle very large variant files like multiple whole genomes with ordinary computers. We demonstrate the variant reduction capability and effectiveness of the proposed tool with public and in-house data for different inheritance models. We also compare FMFilter with the existing filtering software. We conclude that FMFilter provides an effective and easy to use environment for analyzing next generation sequencing data from Mendelian diseases.

Lower plasma pantoprazole level predicts Helicobacter pylori treatment failure in patients with type 2 diabetes mellitus.

OBJECTIVE: We aimed to compare the plasma pantoprazole level (PPL) between patients with type 2 diabetes mellitus and non-diabetic patients during Helicobacter pylori (H. pylori) eradication treatment and to explore the role of PPL in predicting the treatment success rates. METHODS: This study included 40 diabetic and 40 non-diabetic treatment-naive H. pylori-infected patients. Bismuth-based standard quadruple treatment for H. pylori eradication was used for 14 days in both groups. PPL was measured using the square-wave voltammetry method. RESULTS: H. pylori eradication rate (60.0% vs 87.5%, P = 0.005) and PPL (0.25 ± 0.03 µg/mL vs 0.34 ± 0.03 µg/mL, P < 0.001) was significantly lower in the diabetic group compared with the controls. Patients with treatment failure had lower PPL than those with successful treatment (P < 0.001). The receiver operating characteristics curve demonstrated that PPL had a significant predictive value for the outcome of H. pylori eradication. CONCLUSION: Type 2 diabetic patients had lower PPL than the non-diabetic controls, which led to their lower H. pylori eradication rates.

GeneCOST: a novel scoring-based prioritization framework for identifying disease causing genes.

UNLABELLED: Due to the big data produced by next-generation sequencing studies, there is an evident need for methods to extract the valuable information gathered from these experiments. In this work, we propose GeneCOST, a novel scoring-based method to evaluate every gene for their disease association. Without any prior filtering and any prior knowledge, we assign a disease likelihood score to each gene in correspondence with their variations. Then, we rank all genes based on frequency, conservation, pedigree and detailed variation information to find out the causative reason of the disease state. We demonstrate the usage of GeneCOST with public and real life Mendelian disease cases including recessive, dominant, compound heterozygous and sporadic models. As a result, we were able to identify causative reason behind the disease state in top rankings of our list, proving that this novel prioritization framework provides a powerful environment for the analysis in genetic disease studies alternative to filtering-based approaches. AVAILABILITY AND IMPLEMENTATION: GeneCOST software is freely available at www.igbam.bilgem.tubitak.gov.tr/en/softwares/genecost-en/index.html. CONTACT: buozer@gmail.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Atypical diabetic ketoacidosis: case report.

BACKGROUND: Diabetic ketoacidosis (DKA) is a potentially life-threatening complication of diabetes mellitus and can lead to death if untreated. It is a complex metabolic state characterised by hyperglycaemia, acidosis and ketonuria. Bonsai is one of the herbal incense products that contains synthetic cannabinoid and can be easily accessible via the internet in many countries. It cannot be detected in blood and urine studies using conventional methods. Synthetic cannabinoid abuse is associated with severe side effects, including tachycardia, high blood pressure, acidosis, excess sedation and coma. CASE REPORT: A 17-year-old male patient was brought to the emergency department with sudden onset of dyspnoea. Laboratory investigations revealed hyperglycaemia, acidosis and ketonuria. He was admitted to the intensive care unit with a diagnosis of diabetic ketoacidosis. He was not considered a typical case of diabetic ketoacidosis because of the tendency to hypokalaemia, persistent tachycardia and bronchoscopic findings. We learned from his friends that he had used cannabis for a week and used bonzai on the day that he was brought to the emergency service. CONCLUSION: Diabetic ketoacidosis with prolonged acidosis and tendency to hypokalaemia are investigated for the consumption of synthetic cannabinoids.

Association of the angiotensinogen M235T and APO E gene polymorphisms in Turkish type 2 diabetic patients with and without nephropathy.

BACKGROUND: Diabetic nephropathy (DN) is a leading cause of diabetes-related morbidity and mortality. The aim of this study was to evaluate the relationship of AGT M235T and apoprotein E (APO E) gene polymorphism with DN in Turkish patients of Type 2 diabetes, and to compare genotype and allele distributions among DN patients, non-DN patients, and healthy controls. METHODS: AGT M235T and APO E genotype and allele analysis were performed in 111 DN patients, 108 non-DN patients, 106 healthy control subjects for APO E genotype, and 100 for AGT M235T genotype polymorphism. APO E and AGT M235T genotype were determined by RFLP-PCR. RESULTS: The frequencies of APO E ε2/3, ε 3/3, ε 3/4 genotypes were 22.7%, 60%, 60%, respectively, among DN patients and 6.6%, 80%, 10.4%, respectively (p < 0.001), in the non-DN patients. The frequencies of AGT M235T MM, MT, TT genotypes among the same groups were 17%, 46%, 37% and 21%, 63%, 16%, respectively (p < 0.02). Having the ε2/3 genotype and TT genotype increased the risk for DN nephropathy [4.8-fold (95% CI: 1.94-11.67), 2.9-fold (95% CI: 1.27-6.69), respectively]. CONCLUSION: Our study has shown that AGT M235T TT genotype and APO E ε 2/3 genotype may be linked to a risk for DN among Turkish population.

PON1 55 and 192 gene polymorphisms in type 2 diabetes mellitus patients in a Turkish population.

Diabetes mellitus is a multifactorial metabolic disease, caused by the complete or relative absence of insulin hormone, which results in the deterioration of carbohydrate, protein, and lipid metabolism. The PON1 55 and 192 polymorphisms have been reported to be associated with type 2 diabetes and its complications. In this study, the involvement of the PON1 55 and 192 polymorphisms and paraoxonase enzyme activity in diabetic complications was assessed. The MM and QQ genotypes were the most frequent in complications of type 2 diabetes in both of the polymorphisms. PON enzyme activity was lower in the type 2 diabetes group with respect to the control group. Regarding both genotypes and enzyme activity, correlations were found between the PON1 55 and 192 genotypes and diabetic complications. This study thus helps to outline a genotype-phenotype relation for the PON1 gene in a Turkish population.

Frequency of adiponectin gene polymorphisms in polycystic ovary syndrome and the association with serum adiponectin, androgen levels, insulin resistance and clinical parameters.

AIM: Although the association between adiponectin gene polymorphisms and insulin resistance has been investigated in many studies, there are only a few studies, which have investigated adiponectin gene polymorphisms in patients with polycystic ovary syndrome (PCOS). The objectives of this study were to determine the frequency of T45G polymorphisms localised in exon 2 of the adiponectin gene in a Turkish population with PCOS and to determine the association of T45G polymorphisms with insulin resistance and serum adiponectin levels in PCOS. MATERIALS AND METHODS: Ninety-six patients with PCOS and 93 healthy control subjects were included in the study. Insulin resistance was estimated via HOMA-IR. Serum adiponectin levels were measured by ELISA. For determination of adiponectin gene polymorphisms, PCR was performed with appropriate primers after genomic DNA was obtained from the peripheral blood of the patients and control subjects. RESULTS: Adiponectin levels were low in patients with PCOS than control subjects. There was no significant statistical difference between the PCOS and control groups with respect to the frequency of polymorphisms and the genotype distribution. Adiponectin gene polymorphisms were not associated with the anthropometric parameters, hyperandrogenism and adiponectin levels in PCOS. However, the fasting insulin level and insulin resistance were significantly higher and more frequent, respectively, in the polymorphic group compared to the other genotypes among patients with PCOS. CONCLUSION: The risk of PCOS, hyperandrogenism in patients with PCOS and low serum adiponectin levels cannot be directly attributed to T45G adiponectin gene polymorphisms in exon 2, rather these polymorphisms may be associated with insulin resistance and hyperinsulinemia in PCOS.

Increased lipid peroxidation and impaired enzymatic antioxidant defense mechanism in thyroid tissue with multinodular goiter and papillary carcinoma.

OBJECTIVES: We aimed to evaluate the oxidant/antioxidant status of thyroid tissue in patients with multinodular goiter, papillary carcinoma and to compare with their nonpathologic tissues. METHODS: We studied 41 patients with multinodular goiter who underwent surgical treatment. The patients were divided into three groups according to clinical diagnosis. Malondialdehyde, selenium, total superoxide dismutase and glutathione peroxidase of thyroid tissue samples were determined in 14 toxic multinodular goiters, 18 non-toxic multinodular goiters, and 9 papillary carcinomas. RESULT: Superoxide dismutase and glutathione peroxidase and selenium were found lower but malondialdehyde was higher in both nodule and cancerous tissues compared with those of control ones. The level of malondialdehyde in non-toxic multinodular goiters group was higher than toxic multinodular goiters group in nodule tissues. CONCLUSIONS: It can be stated that the lipid peroxidation is increased and enzymatic free radical defense system was significantly impaired in patients with both multinodular goiters and papillary carcinomas.

Serum resistin and adiponectin levels in women with polycystic ovary syndrome.

AIM: This study was performed to compare the serum levels of resistin and adiponectin in women with polycystic ovary syndrome (PCOS) and normal controls. MATERIALS AND METHODS: Seventy-six patients (36 obese, 40 non-obese) with PCOS and 42 healthy subjects were included in the study. Serum levels of resistin, adiponectin, follicle-stimulating hormone, luteinising hormone, dehydroepiandrosterone sulfate (DHEA-S), 17-hydroxy progesterone, free testosterone, androstenedione, glucose, insulin and lipid parameters were measured. Insulin resistance and carbohydrate metabolism were evaluated by using the homeostasis model (HOMA) and the area under the insulin curve (AUCI). RESULTS: Plasma resistin levels, HOMA-IR and AUCI were significantly higher and adiponectin level was lower in women with PCOS than those in healthy women. Plasma resistin levels were similar among obese and non-obese women with PCOS. No correlation was observed between resistin, body mass index (BMI), HOMA-IR, AUCI, insulin, lipid parameters and serum androgen levels. In obese PCOS patients, adiponectin levels were lower than in the lean PCOS patients. A negative correlation was observed among adiponectin, HOMA-IR, AUCI, BMI, testosterone, DHEAS, total-cholesterol, LDL-cholesterol and lipoprotein (a) levels. CONCLUSION: These results suggest that the serum adiponectin level may be involved in the pathogenesis of PCOS. But resistin levels were independently associated with insulin resistance and BMI in PCOS patients. Nevertheless, wider-scale trials are required to be performed on this subject.

The effect of hypothyroidism, hyperthyroidism, and their treatment on parameters of oxidative stress and antioxidant status.

BACKGROUND: Free radical-mediated oxidative stress has been implicated in the etiopathogenesis of several autoimmune disorders. Also, there is growing evidence supporting the role of reactive oxygen species in the pathogenesis of thyroid disorders. The aim of this study was to investigate the influence of hypothyroidism, hyperthyroidism, and their treatments on the metabolic state of oxidative stress, and antioxidant status markers. METHODS: A total of 20 newly diagnosed patients with overt hypothyroidism due to Hashimoto's thyroiditis, 20 patients with overt hyperthyroidism due to Graves' disease, and 20 healthy subjects as the control group were enrolled in the study. Fasting blood samples (12 h), taken at the initiation, after the 30th and 60th day of therapy were analyzed for malondialdehyde, nitrite, vitamin E, vitamin A, beta-carotene, ascorbate, and myeloperoxidase and superoxide dismutase activity. No patient presented additional risk factors for increased reactive oxygen species levels. RESULTS: Malondialdehyde, nitrite, vitamin E, and myeloperoxidase activity increased in patients with hypothyroidism. After 2 months, the levels of nitrite and vitamin E were reduced to control levels by treatment. The patients with hyperthyroidism had increased levels of malondialdehyde and myeloperoxidase activity in comparison with the controls. Treatment with propylthiouracil attenuated these increments after 1 month. CONCLUSIONS: Our results reveal an increased generation of reactive oxygen species and impairment of the antioxidant system in patients with hyperthyroidism, and particularly in patients with hypothyroidism. These findings indicate that thyroid hormones have a strong impact on oxidative stress and the antioxidant system.

Calpain 10 SNP-44 gene polymorphism affects susceptibility to type 2 diabetes mellitus and diabetic-related conditions.

The association of the gene encoding calpain 10 with type 2 diabetes mellitus (T2DM) has been reported. In this study we aimed to evaluate the association of SNP-19,-44, and -63 polymorphisms of calpain 10 with type 2 diabetes and diabetic-related conditions, such as diabetic retinopathy, nephropathy, and neuropathy in a Turkish population. The study group included 202 patients (133 female and 69 male) with T2DM, while the control group included 80 nondiabetic people (44 female and 36 male). Genotyping was done by the polymerase chain reaction and restriction fragment length polymorphism method. Calpain 10 SNP-44 TC genotype was found to be significantly frequent in type 2 diabetic patients with respect to the control group (p < 0.01). Body mass index (BMI) was found to be significantly high in TC genotype with type 2 diabetic patients (p < 0.05). SNP-44 T allele frequency was found to be lower in type 2 diabetic patients compared with the controls (p < 0.01). We conclude that the calpain 10 SNP-44 gene polymorphism may be accepted as a risk factor in the development of T2DM and elevated BMI in type 2 diabetic patients in a Turkish population.