Patient classification and attribute assessment based on machine learning techniques in the qualification process for surgical treatment of adrenal tumours.

Adrenal gland incidentaloma is frequently identified through computed tomography and poses a common clinical challenge. Only selected cases require surgical intervention. The primary aim of this study was to compare the effectiveness of selected machine learning (ML) techniques in proper qualifying patients for adrenalectomy and to identify the most accurate algorithm, providing a valuable tool for doctors to simplify their therapeutic decisions. The secondary aim was to assess the significance of attributes for classification accuracy. In total, clinical data were collected from 33 patients who underwent adrenalectomy. Histopathological assessments confirmed the proper selection of 21 patients for surgical intervention according to the guidelines, with accuracy reaching 64%. Statistical analysis showed that Supported Vector Machines (linear) were significantly better than the baseline (p < 0.05), with accuracy reaching 91%, and imaging features of the tumour were found to be the most crucial attributes. In summarise, ML methods may be helpful in qualifying patients for adrenalectomy.

Elevated Serum Concentration of Adipocyte Fatty Acid-Binding Protein Correlates with the Markers of Abdominal Obesity Independently of Thyroid Hormones in Non-Obese Women with Polycystic Ovary Syndrome.

Adipocyte fatty acid-binding protein (A-FABP) is mainly expressed in adipocytes. The risk of abdominal obesity and autoimmune thyroid disease is increased in women with polycystic ovary syndrome (PCOS). The objective of this study was to explore the relationship of serum concentration of A-FABP with parameters of obesity, e.g., waist to hip ratio (WHR) and the amount of adipose tissue assessed by bioelectrical impedance analysis (BIA), and thyroid hormone homeostasis in women with PCOS. We examined 66 women with PCOS and 67 healthy women. Serum concentrations of A-FABP and thyroid hormones were measured; the FT3/FT4 ratio, thyroid-stimulating hormone index (TSHI), thyrotrope thyroxine resistance index (TT4RI) and thyroid feedback quantile-based index (TFQI) were calculated. In the PCOS group, serum concentrations of A-FABP, FT3 and the FT3/FT4 ratio were significantly higher in comparison to the control group (all p < 0.05). A correlation of A-FABP with WHR (r = 0.26, p = 0.04) and the percentage of adipose tissue (r = 0.33, p = 0.01) has been found only in women with PCOS. We observed no correlation between serum levels of A-FABP and TSHI, TT4RI or TFQI in women with PCOS (all p > 0.05). Our results indicate that A-FABP is an adipokine that may be connected with abdominal obesity independently of thyroid hormone homeostasis in PCOS patients.

Cardiovascular risk factors in mild adrenal autonomous cortisol secretion in a Caucasian population.

Cardiovascular risk factors could be present in mild adrenal autonomous cortisol secretion (MACS). However, the most frequent cardiovascular risk factors in MACS have not been established. The aim of the presseent study was to analyse the difference in cardiovascular risk factors in patients with MACS in comparison to those with non-functioning adrenal tumour (NFAT). A total of 295 patients with adrenal incidentaloma were included in this retrospective study. We divided our group into those who showed suppression in 1 mg overnight dexamethasone suppression test (DST) (NFAT) (serum cortisol level ≤1.8 µg/dL) and those who did not show suppression in the DST (MACS) (serum concentration of cortisol > 1.8 µg/dL and ≤5 µg/dL). In the studied groups, we analysed the presence of cardiovascular risk factors, such as obesity, prediabetes, type 2 diabetes mellitus (T2DM), hypertension, hyperlipidaemia, chronic kidney disease and cardiovascular events. In our study, 18.9% of patients were defined as MACS. Importantly, T2DM was diagnosed in 41% of MACS vs 23% of NFAT (P < 0.01) and higher frequency of occurrence of hyperlipidaemia in NFAT (72.4%) vs MACS (53.6%) (P = 0.01) was observed. We did not observed differences in the frequency of obesity, hypertension, chronic kidney disease, prediabetes, atrial fibrillation, stroke, ST and non-ST elevation myocardial infarction and coronary angioplasty between patients with MACS and NFAT (all P > 0.05; respectively). In MACS, T2DM is more prevalent than in NFAT; hyperlipidaemia is more prevalent in NFAT. Accordingly, no differences were found in the incidence of obesity, hypertension, prediabetes, chronic kidney disease between studied groups as well as cardiovascular events.

Body Composition and Serum Concentration of Thyroid Hormones in Euthyroid Men and Women from General Population.

Body composition, especially an increased amount of fat mass and decreased lean body mass, is connected with metabolic complications. Thyroid hormones can influence body composition pattern. To date, scarce data defining the relationships between thyroid hormones and parameters of body composition using dual-energy X-ray absorptiometry (DXA), especially in cohort studies, are available. Therefore, the aim of the present study was to investigate the relationships among serum concentrations of (thyroid-stimulating hormone (TSH), thyroid hormones, and distribution of fat tissue assessed using the DXA method in a euthyroid cohort from the Bialystok PLUS study. We examined 582 euthyroid subjects who were divided into lean (body mass index (BMI) < 25 kg/m2) and overweight/obese (BMI ≥ 25 kg/m2) (84 lean men, 182 overweight/obese men, 160 lean women, and 156 overweight/obese women). Serum concentrations of TSH, free T3 (fT3), and free T4 (fT4) were assessed, and DXA was performed. We observed lower serum levels of fT4 (p = 0.03) and higher serum levels of fT3 (p = 0.04) in overweight/obese vs. lean men, whereas serum levels of TSH did not differ between these groups (p = 0.38). In lean men, we only observed a relationship between serum levels of TSH and visceral adipose tissue (VAT) (r = −0.24, p = 0.02). In overweight/obese men, we found that serum levels of fT3 were positively connected with total fat mass (r = 0.16, p = 0.02), android fat mass (r = 0.15, p = 0.03), and gynoid fat mass (r = 0.17, p = 0.01), but not with VAT (r = 0.03, p = 0.63). We did not observe differences in serum levels of TSH, fT3, and fT4 between lean and overweight/obese women. Additionally, we did not notice relationships between serum levels of thyroid hormones and fat in different regions estimated by DXA in lean and overweight/obese women (all p > 0.05). We concluded that the serum concentration of TSH is connected with VAT in lean men, whereas, in overweight/obese men, higher fT3 is connected with an increased fat amount. These associations are absent in women.

P2RY8 variants in lupus patients uncover a role for the receptor in immunological tolerance.

B cell self-tolerance is maintained through multiple checkpoints, including restraints on intracellular signaling and cell trafficking. P2RY8 is a receptor with established roles in germinal center (GC) B cell migration inhibition and growth regulation. Somatic P2RY8 variants are common in GC-derived B cell lymphomas. Here, we identify germline novel or rare P2RY8 missense variants in lupus kindreds or the related antiphospholipid syndrome, including a "de novo" variant in a child with severe nephritis. All variants decreased protein expression, F-actin abundance, and GPCR-RhoA signaling, and those with stronger effects increased AKT and ERK activity and cell migration. Remarkably, P2RY8 was reduced in B cell subsets from some SLE patients lacking P2RY8 gene variants. Low P2RY8 correlated with lupus nephritis and increased age-associated B cells and plasma cells. By contrast, P2RY8 overexpression in cells and mice restrained plasma cell development and reinforced negative selection of DNA-reactive developing B cells. These findings uncover a role of P2RY8 in immunological tolerance and lupus pathogenesis.

Expanding the clinical spectrum of pathogenic variation in NR2F2: Asplenia.

We present a case with congenital syndromic asplenia associated with immune deficiency, glandular hypospadias and cryptorchidism. Genetic analysis identified a likely pathogenic de novo variant in NR2F2. Pathogenic NR2F2 variants have been associated with other congenital anomalies affecting the central axis, such as congenital heart disease and diaphragmatic hernia, which were not part of our patient's clinical features. The association between NR2F2 and asplenia (including glandular hypospadias and cryptorchidism) has been described in animal models and our report is the first expanding the NR2F2 clinical spectrum in humans to include asplenia.

Assessment of different markers of ovarian reserve in women with papillary thyroid cancer treated with radioactive iodine.

Treatment with radioactive iodine (RAI) in women with differentiated thyroid cancer is associated with decreased serum concentrations of anti-Müllerian hormone (AMH); however, other markers have not been investigated. Therefore, this study aimed to evaluate the effect of RAI treatment on antral follicle count (AFC) and the serum concentration of inhibin B, follicle-stimulating hormone (FSH), and AMH in women with papillary thyroid cancer (PTC) treated with RAI. We examined 25 women at a median age of 33 years treated with a single dose of RAI. We divided the participants into women over (n = 11) and under 35 years of age (n = 14). Serum concentrations of inhibin B, FSH, AMH, and AFC were assessed at baseline and 1 year after RAI treatment. We found decreased AFC (P = 0.03), serum levels of AMH (P < 0.01), inhibin B (P = 0.03), but not FSH (P = 0.23), 1 year after RAI treatment in comparison to baseline in the whole group. When we compared serum levels of AMH in younger vs older women separately, we observed a significant reduction of this hormone's serum level after RAI treatment in both groups (P < 0.01; P = 0.04, respectively). We concluded that RAI treatment significantly impacts the functional ovarian reserve in premenopausal women with PTC.

Infanticide vs. inherited cardiac arrhythmias.

AIMS: In 2003, an Australian woman was convicted by a jury of smothering and killing her four children over a 10-year period. Each child died suddenly and unexpectedly during a sleep period, at ages ranging from 19 days to 18 months. In 2019 we were asked to investigate if a genetic cause could explain the children's deaths as part of an inquiry into the mother's convictions. METHODS AND RESULTS: Whole genomes or exomes of the mother and her four children were sequenced. Functional analysis of a novel CALM2 variant was performed by measuring Ca2+-binding affinity, interaction with calcium channels and channel function. We found two children had a novel calmodulin variant (CALM2 G114R) that was inherited maternally. Three genes (CALM1-3) encode identical calmodulin proteins. A variant in the corresponding residue of CALM3 (G114W) was recently reported in a child who died suddenly at age 4 and a sibling who suffered a cardiac arrest at age 5. We show that CALM2 G114R impairs calmodulin's ability to bind calcium and regulate two pivotal calcium channels (CaV1.2 and RyR2) involved in cardiac excitation contraction coupling. The deleterious effects of G114R are similar to those produced by G114W and N98S, which are considered arrhythmogenic and cause sudden cardiac death in children. CONCLUSION: A novel functional calmodulin variant (G114R) predicted to cause idiopathic ventricular fibrillation, catecholaminergic polymorphic ventricular tachycardia, or mild long QT syndrome was present in two children. A fatal arrhythmic event may have been triggered by their intercurrent infections. Thus, calmodulinopathy emerges as a reasonable explanation for a natural cause of their deaths.

The Association of Serum Levels of Leptin and Ghrelin with the Dietary Fat Content in Non-Obese Women with Polycystic Ovary Syndrome.

Women with polycystic ovary syndrome (PCOS) are at an increased risk of developing insulin resistance and abdominal obesity in the state of an improper diet balance. Leptin is a peptide considered to be a satiety hormone that plays an important role in the long-term energy balance, whereas ghrelin is a hormone that controls short-term appetite regulation and is considered a hunger hormone. The aim of the present study was to assess the relationship between serum leptin and ghrelin concentrations and the dietary macronutrient content in PCOS women. We examined 73 subjects: 39 women diagnosed with PCOS by the Rotterdam criteria and 34 healthy controls, matched by the body mass index. The subjects completed a consecutive three-day dietary diary to identify the macronutrient and micronutrient intake. Serum concentrations of leptin and total ghrelin were measured and homeostasis model assessment of insulin resistance (HOMA-IR) was calculated. The studied groups did not differ significantly in terms of the intake of macronutrients (proteins, fats, and carbohydrates) and serum concentrations of ghrelin and leptin (all p > 0.05). In the PCOS group, the serum leptin concentration positively correlated with the intake of total fat (r = 0.36, p = 0.02), total cholesterol (r = -0.36, p = 0.02), saturated fatty acids (r = 0.43, p < 0.01), and monounsaturated fatty acids (MUFA) (r = 0.37, p = 0.02), whereas the serum ghrelin concentration correlated in an inverse manner with the intake of total fat (r = -0.37, p = 0.02), MUFA (r = -0.37, p = 0.02), polyunsaturated fatty acids (r = -0.34, p = 0.03), and long chain polyunsaturated fatty acids (r = -0.38, p = 0.02). In this group, we also found a negative association of HOMA-IR with serum ghrelin levels (r = -0.4, p = 0.03) and a positive relationship with the serum leptin concentration (r = 0.5, p < 0.01) and relationships between HOMA-IR and total dietary fat (r = 0.38, p = 0.03) and MUFA (r = 0.35, p = 0.04) intake. In PCOS women, dietary components such as the total fat and type of dietary fat and HOMA-IR are positively connected to serum leptin concentrations and negatively connected to serum ghrelin concentrations, which may influence the energy balance.

Ovarian Reserve and Serum Concentration of Thyroid Peroxidase Antibodies in Euthyroid Women With Different Polycystic Ovary Syndrome Phenotypes.

Objective: It has been shown that women with polycystic ovary syndrome (PCOS), as well as Hashimoto's thyroiditis (HT), are characterized by increased incidence of infertility. Serum anti-Müllerian hormone (AMH), which reflects ovarian reserve, is elevated in PCOS women and is decreased in women with HT. The Rotterdam criteria recognize four clinical PCOS phenotypes, i.e., phenotypes A, B, C, and D. The aim of the present study was to investigate the relation between serum concentrations of thyroid peroxidase antibodies (TPOAbs) and ovarian reserve in different PCOS phenotypes. Patients and methods: We examined 141 women with PCOS [phenotype A was diagnosed in 67 (47.5%) women, phenotype B in 30 (21.3%), phenotype C in 28 (19.9%), and phenotype D in 16 (11.3%)] and 88 control subjects of similar age; all women were euthyroid. Serum concentrations of AMH, thyroid-stimulating hormone (TSH), thyroid hormones, and TPOAbs were assessed. Results: We observed positive serum TPOAbs in 21.9% women with PCOS and in 23.9% controls (p = 0.07). We did not find differences in the frequency of detection of positive serum TPOAbs between phenotypes A, B, and C and the control group (p > 0.05). We did not observe a difference in AMH levels between TPOAbs-positive and TPOAbs-negative women, both in the control group and the PCOS women (all p > 0.05). However, serum AMH concentration was markedly higher in the whole PCOS group (p < 0.01) and in phenotype A (p < 0.01) vs. controls when the serum concentration of TPOAbs was negative. In the groups with positive serum levels of TPOAbs, serum concentration of AMH did not differ between PCOS phenotypes and controls (p = 0.23). Additionally, we observed that serum AMH concentration was related to the level of TPOAbs in the PCOS group (r = -0.4, p = 0.02). Conclusions: The frequency of serum detection of positive TPOAbs did not differ between PCOS phenotypes with clinical/biochemical hyperandrogenism and the control group. The observation of the difference in serum AMH between the PCOS and control groups only in TPOAbs negative women together with the inverse relation of TPOAbs with serum AMH only in the PCOS group might suggest that ovarian reserve is influenced by TPOAbs in PCOS.

Body Composition, Serum Concentrations of Androgens and Insulin Resistance in Different Polycystic Ovary Syndrome Phenotypes.

Insulin resistance and hyperandrogenemia observed in polycystic ovary syndrome (PCOS) are associated with metabolic disturbances and could be connected with body composition pattern. To date, several studies defining the parameters of body composition using dual energy X-ray absorptiometry (DXA) method in the group of PCOS patients have been published, however, without the analysis in different phenotypes. The aim of the present study was to investigate the relationships between serum androgens concentration, insulin resistance and distribution of fat mass using DXA method in various PCOS phenotypes according to the Rotterdam criteria. We examined 146 women: 34 (38%) had PCOS phenotype A, 20 (23%) phenotype B, 20 (23%) phenotype C and 15 (16%) phenotype D (with mean age of each phenotype 25 years), and 57 control subjects (mean age of 25.5 years). Homeostasis model assessment of insulin resistance (HOMA-IR) was calculated. Serum concentrations of testosterone, androstenedione and dehydroepiandrosterone sulfate (DHEA-S) were assessed and free androgen index (FAI) was calculated. In phenotypes A, B and C, we observed higher FAI in comparison to the control group (all p < 0.01). Serum concentrations of androstenedione and DHEA-S were higher in phenotypes A and C in comparison to the control group (all p < 0.01). However, only in phenotype A we found higher visceral adipose tissue (VAT) mass and android/gynoid ratio (A/G ratio) in comparison to the control group (all p < 0.01). In phenotype A, we observed connection of VAT with FAI (r = 0.58, p < 0.01). Accordingly, A/G ratio was related with FAI in all phenotypes (all p < 0.05). Additionally, in phenotype C, A/G ratio was related to serum concentrations of DHEA-S and androstenedione (r = 0.46, p = 0.03; r = 0.53, p = 0.01, respectively). We also found connections of HOMA-IR with VAT and A/G ratio in all phenotypes (all p < 0.05). Women with phenotype A had higher amount of VAT and A/G ratio in comparison to the control group. Serum concentration of androgens and insulin resistance are connected with VAT and A/G ratio in normoandrogenic and hyperandrogenic PCOS phenotypes.

Transcriptional response of Caenorhabditis elegans when exposed to Shigella flexneri.

In recent years, researchers have begun to use Caenorhabditis elegans as a potential animal model to study Shigella pathogenesis. This study aims to further develop this model using RNA-sequencing to understand which pathways/cellular characteristics are affected and potentially cause death in Shigella-exposed worms. We identified 1631 differentially expressed genes in Shigella-exposed worms (6 h exposure). A number of these genes encode proteins involved in fatty-acid ß-oxidation (FAO), antioxidant defense and autophagy. The down-regulation of acyl-CoA dehydrogenases would impede FAO, reducing the overall energy to combat Shigella in the worm's intestinal tract. This is potentially coupled with the production of reactive oxygen species (ROS) that may not be fully quenched by antioxidant defense proteins, leading to damaged cellular organelles in the worm's intestinal cells. These cells may undergo autophagy to remove the mounting damage, but may eventually undergo cell death.

Genomic impact of severe population decline in a nomadic songbird.

Uncovering the population genetic histories of non-model organisms is increasingly possible through advances in next generation sequencing and DNA sampling of museum specimens. This new information can inform conservation of threatened species, particularly those for which historical and contemporary population data are unavailable or challenging to obtain. The critically endangered, nomadic regent honeyeater Anthochaera phrygia was abundant and widespread throughout south-eastern Australia prior to a rapid population decline and range contraction since the 1970s. A current estimated population of 250-400 individuals is distributed sparsely across 600,000 km2 from northern Victoria to southern Queensland. Using hybridization RAD (hyRAD) techniques, we obtained a SNP dataset from 64 museum specimens (date 1879-1960), 102 'recent' (1989-2012) and 52 'current' (2015-2016) wild birds sampled throughout the historical and contemporary range. We aimed to estimate population genetic structure, genetic diversity and population size of the regent honeyeater prior to its rapid decline. We then assessed the impact of the decline on recent and current population size, structure and genetic diversity. Museum sampling showed population structure in regent honeyeaters was historically low, which remains the case despite a severe fragmentation of the breeding range. Population decline has led to minimal loss of genetic diversity since the 1980's. Capacity to quantify the overall magnitude of both genetic diversity loss and population decline was limited by the poorer quality of genomic data derived from museum specimens. A rapid population decline, coupled with the regent honeyeater's high mobility, means a detectable genomic impact of this decline has not yet manifested. Extinction may occur in this nomadic species before a detectable genomic impact of small population size is realised. We discuss the implications for genetic management of endangered mobile species and enhancing the value of museum specimens in population genomic studies.

Decreased deiodinase activity after glucose load could lead to atherosclerosis in euthyroid women with polycystic ovary syndrome.

OBJECTIVE: Glucose and lipid disturbances, as well as higher tendency to atherosclerosis, are observed in women with polycystic ovary syndrome (PCOS). Thyroid hormones action has long been recognized as an important determinant of glucose and lipid homeostasis. Some studies suggest that even in euthyroid subjects, thyroid function may affect atherosclerosis risk factors. The aim of this study was to evaluate the relationships between thyroid hormonal status and glucose and lipid profile before and after oral glucose tolerance test (OGTT) in PCOS women in comparison to the control group. PATIENTS AND METHODS: The study group included 98 women-60 women with PCOS and 38 women matched for age and BMI as a control group. OGTT with estimation of plasma glucose and lipids, as well as serum insulin and thyroid hormones (TH) concentrations was performed. Activity of peripheral deiodinases at baseline (SPINA-GD1) and at the 120 min of OGTT (SPINA-GD2) was calculated according to the formula by Dietrich et al. as a measure of T4-T3 conversion efficiency. Delta GD was estimated as SPINA-GD1-SPINA-GD2, and delta fT3 was calculated as a difference between fT3 before and after OGTT. RESULTS: We did not find differences in TH, SPINA-GDs, and plasma lipid concentrations between PCOS and control group before and after OGTT. Glucose load resulted in a decrease of level TSH, TC, TG, HDL-C, and LDL-C concentrations in women with PCOS, as well as in the control group (all p < 0.05). We found that GD (p = 0.01) and serum fT3 concentration (p = 0.0008) decreased during glucose load only in the PCOS group. We observed a positive relationship between delta fT3 and plasma TG concentration (r = 0.36, p = 0.004), delta GD and plasma TG concentration after glucose load (r = 0.34, p = 0.007), only in the PCOS group. We also found negative relationship between SPINA-GD2 and plasma TC concentration (r = -0.29, p = 0.02) after glucose load and positive relationship between delta GD and insulin at the 60 min of OGTT (r = 0.29, p = 0.02), only in the PCOS women. CONCLUSIONS: These data showed insufficient conversion of fT4 to fT3, as well as a relationship of SPINA-GDs with insulin, TC and TG in PCOS women after glucose load. It may suggest that disturbances in deiodinase activity after glucose load might promote atherosclerosis in PCOS women.

The Role of Homology and Orthology in the Phylogenomic Analysis of Metazoan Gene Content.

Resolving the relationships of animals (Metazoa) is crucial to our understanding of the origin of key traits such as muscles, guts, and nerves. However, a broadly accepted metazoan consensus phylogeny has yet to emerge. In part, this is because the genomes of deeply diverging and fast-evolving lineages may undergo significant gene turnover, reducing the number of orthologs shared with related phyla. This can limit the usefulness of traditional phylogenetic methods that rely on alignments of orthologous sequences. Phylogenetic analysis of gene content has the potential to circumvent this orthology requirement, with binary presence/absence of homologous gene families representing a source of phylogenetically informative characters. Applying binary substitution models to the gene content of 26 complete animal genomes, we demonstrate that patterns of gene conservation differ markedly depending on whether gene families are defined by orthology or homology, that is, whether paralogs are excluded or included. We conclude that the placement of some deeply diverging lineages may exceed the limit of resolution afforded by the current methods based on comparisons of orthologous protein sequences, and novel approaches are required to fully capture the evolutionary signal from genes within genomes.

The Association Between Serum Ferritin Concentration and Visceral Adiposity Estimated by Whole-Body DXA Scan in Women With Polycystic Ovary Syndrome.

Objective: Women with polycystic ovary syndrome (PCOS) are characterized by insulin resistance and higher prevalence of obesity. Serum ferritin is increased in obesity and is associated with insulin resistance. The aim of the present study was to evaluate the relationships between serum ferritin concentration with insulin resistance and body composition estimated by dual-energy X-ray absorptiometry (DXA) in PCOS women in comparison to the control group. Patients and Methods: One hundred four women were enrolled to the study-65 women with PCOS and 39 women matched for age and BMI as a control group. Serum ferritin concentration and oral glucose tolerance test (OGTT) were performed. Homeostasis model assessment of insulin resistance (HOMA-IR) was calculated. DXA was performed to estimate fat, fat-free mass, and visceral adipose tissue (VAT). Results: Women with PCOS have higher serum concentration of ferritin (p = 0.002), insulin at baseline (p = 0.03), at 60 min of OGTT (p = 0.01), at 120 min of OGTT (p = 0.004), HOMA-IR (p = 0.03), and VAT (p = 0.0001) in comparison to the control group. We observed a relationship of serum ferritin with insulin concentration at baseline (r = 0.25, p = 0.04) and at 120 min of OGTT (r = 0.31, p = 0.01) and with HOMA-IR (r = 0.30, p = 0.01) in the PCOS group. We noticed an association between serum ferritin concentration and VAT (r = 0.42, p = 0.001), trunk fat mass (r = 0.25, p = 0.04), and android fat mass (r = 0.25, p = 0.04) in the PCOS group. Multiple regression analysis revealed that ferritin (p = 0.02, ß = 0.17), insulin at baseline (p = 0.001, ß = 0.30), glucose at the 120 min of OGTT (p = 0.007, ß = 0.26), and triglycerides (p = 0.001, ß = 0.33) were independent predictors of VAT amount in PCOS women. Conclusions: Elevated serum ferritin concentration is connected with insulin resistance as well as with DXA-estimated VAT, android, and trunk fat mass in PCOS women, and could be a marker of metabolic dysfunction.

Bacteriophages are the major drivers of Shigella flexneri serotype 1c genome plasticity: a complete genome analysis.

BACKGROUND: Shigella flexneri is the primary cause of bacillary dysentery in the developing countries. S. flexneri serotype 1c is a novel serotype, which is found to be endemic in many developing countries, but little is known about its genomic architecture and virulence signatures. We have sequenced for the first time, the complete genome of S. flexneri serotype 1c strain Y394, to provide insights into its diversity and evolution. RESULTS: We generated a high-quality reference genome of S. flexneri serotype 1c using the hybrid methods of long-read single-molecule real-time (SMRT) sequencing technology and short-read MiSeq (Illumina) sequencing technology. The Y394 chromosome is 4.58 Mb in size and shares the basic genomic features with other S. flexneri complete genomes. However, it possesses unique and highly modified O-antigen structure comprising of three distinct O-antigen modifying gene clusters that potentially came from three different bacteriophages. It also possesses a large number of hypothetical unique genes compared to other S. flexneri genomes. CONCLUSIONS: Despite a high level of structural and functional similarities of Y394 genome with other S. flexneri genomes, there are marked differences in the pathogenic islands. The diversity in the pathogenic islands suggests that these bacterial pathogens are well adapted to respond to the selection pressures during their evolution, which might contribute to the differences in their virulence potential.

Spicule formation in calcareous sponges: Coordinated expression of biomineralization genes and spicule-type specific genes.

The ability to form mineral structures under biological control is widespread among animals. In several species, specific proteins have been shown to be involved in biomineralization, but it is uncertain how they influence the shape of the growing biomineral and the resulting skeleton. Calcareous sponges are the only sponges that form calcitic spicules, which, based on the number of rays (actines) are distinguished in diactines, triactines and tetractines. Each actine is formed by only two cells, called sclerocytes. Little is known about biomineralization proteins in calcareous sponges, other than that specific carbonic anhydrases (CAs) have been identified, and that uncharacterized Asx-rich proteins have been isolated from calcitic spicules. By RNA-Seq and RNA in situ hybridization (ISH), we identified five additional biomineralization genes in Sycon ciliatum: two bicarbonate transporters (BCTs) and three Asx-rich extracellular matrix proteins (ARPs). We show that these biomineralization genes are expressed in a coordinated pattern during spicule formation. Furthermore, two of the ARPs are spicule-type specific for triactines and tetractines (ARP1 or SciTriactinin) or diactines (ARP2 or SciDiactinin). Our results suggest that spicule formation is controlled by defined temporal and spatial expression of spicule-type specific sets of biomineralization genes.

Conservation and divergence of bHLH genes in the calcisponge Sycon ciliatum.

BACKGROUND: Basic Helix-Loop-Helix (bHLH) genes encode a large family of eukaryotic transcription factors, categorized into six high-order groups: pan-eukaryotic group B involved in regulation of cell cycle, metabolism, and development; holozoan-specific groups C and F involved in development and maintenance of homeostasis; and metazoan-specific groups A, D and E including well-studied genes, such as Atonal, Twist and Hairy, with diverse developmental roles including control of morphogenesis and specification of neurons. Current scenarios of bHLH evolution in animals are mainly based on the bHLH gene set found in the genome of demosponge Amphimedon queenslandica. In this species, the majority of the 21 identified bHLH genes belong to group B, and the single group A gene is orthologous to several neurogenic bilaterian subfamilies, including atonal and neurogenin. RESULTS: Given recently discovered differences in developmental toolkit components between siliceous and calcareous sponges, we have carried out genome-wide analysis of bHLH genes in Sycon ciliatum, an emerging calcisponge model. We identified 30 bHLH genes in this species, representing 12 individual families, including four group A families not found in Amphimedon, and two larger family groupings. Notably, the families represented in Sycon are only partially overlapping with those represented in Amphimedon. Developmental expression analysis of a subset of the identified genes revealed patterns consistent with deeply conserved roles, such as specification of sensory cells by Atona-related and stem cells by Myc genes. CONCLUSIONS: Our results demonstrate independent gene loss events in demosponges and calcisponges, implying a complex bHLH toolkit in the last common metazoan ancestor.

Surprisingly rich repertoire of Wnt genes in the demosponge Halisarca dujardini.

BACKGROUND: Wnt proteins are secreted signalling molecules found in all animal phyla. In bilaterian animals, including humans, Wnt proteins play key roles in development, maintenance of homeostasis and regeneration. While Wnt gene repertoires and roles are strongly conserved between cnidarians and bilaterians, Wnt genes from basal metazoans (sponges, ctenophores, placozoans) are difficult or impossible to assign to the bilaterian + cnidarian orthologous groups. Moreover, dramatic differences in Wnt numbers among basal metazoan exist, with only three present in the genome of Amphimedon queenslandica, a demosponge, and 21 in the genome of Sycon ciliatum, a calcisponge. To gain insight into the ancestral Wnt repertoire and function, we have chosen to investigate Wnt genes in Halisarca dujardini, a demosponge with relatively well described development and regeneration, and a very distant phylogenetic relationship to Amphimedon. RESULTS: Here we describe generation of a eukaryotic contamination-free transcriptome of Halisarca dujardini, and analysis of Wnt genes repertoire and expression in this species. We have identified ten Wnt genes, with only one orthologous to Amphimedon Wnt, and six appearing to be a result of a lineage specific expansion. Expression analysis carried out by in situ hybridization of adults and larvae revealed that two Halisarca Wnts are expressed in nested domains in the posterior half of the larvae, and six along the adult body axis, with two specific to the osculum. Strikingly, expression of one of the Wnt genes was elevated in the region undergoing regeneration. CONCLUSIONS: Our results demonstrated that the three Poriferan lineages (Demospongiae, Calcarea and Homoloscleromorpha) are characterized by highly diverse Wnt gene repertoires which do not display higher similarity to each other than they do to the non-sponge (i.e. ctenophore, cnidarian and bilaterian) repertoires. This is in striking contrast to the uniform Wnt repertoires in Cnidarians and Bilaterians, suggesting that the Wnt family composition became "fixed" only in the last common ancestor of Cnidarians and Bilaterians. In contrast, expression of Wnt genes in the apical region of sponge adults and the posterior region of sponge larvae suggests conservation of the Wnt role in axial patterning across the animal kingdom.