Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts

Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s, respectively, and in part owing to their flavors and health-promoting benefits are now cultivated and consumed worldwide. The industry continues to face a wide variety of production challenges (e.g. disease pressures), as well as a demand for higher-yielding cultivars with improved fruit quality characteristics. Unfortunately, molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value crops. Here, we describe the construction and analysis of the first pangenome for both blueberry and cranberry. Our analysis of these pangenomes revealed both crops exhibit great genetic diversity, including the presence-absence variation of 48.4% genes in highbush blueberry and 47.0% genes in cranberry. Auxiliary genes, those not shared by all cultivars, are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites, including compounds previously associated with improving fruit quality traits. The discovery of thousands of genes, not present in the previous reference genomes for blueberry and cranberry, will serve as the basis of future research and as potential targets for future breeding efforts. The pangenome, as a multiple-sequence alignment, as well as individual annotated genomes, are publicly available for analysis on the Genome Database for Vaccinium-a curated and integrated web-based relational database. Lastly, the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.

Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts

Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s, respectively, and in part owing to their flavors and health-promoting benefits are now cultivated and consumed worldwide. The industry continues to face a wide variety of production challenges (e.g. disease pressures) as well as a demand for higher-yielding cultivars with improved fruit quality characteristics. Unfortunately, molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value crops. Here, we describe the construction and analysis of the first pangenome for both blueberry and cranberry. Our analysis of these pangenomes revealed both crops exhibit great genetic diversity, including the presence-absence variation of 48.4% genes in highbush blueberry and 47.0% genes in cranberry. Auxiliary genes, those not shared by all cultivars, are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites, including compounds previously associated with improving fruit quality traits. The discovery of thousands of genes, not present in the previous reference genomes for blueberry and cranberry, will serve as the basis of future research and as potential targets for future breeding efforts. The pangenome, as a multiple-sequence alignment, as well as individual annotated genomes, are publicly available for analysis on the Genome Database for Vaccinium - a curated and integrated web-based relational database. Lastly, the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.

IgA anti-actin antibodies ELISA in coeliac disease: a multicentre study

BACKGROUND

Previous studies have demonstrated that serum anti-actin antibodies are a reliable marker of intestinal damage severity in coeliac disease.

AIMS

To validate in a multicentre study the clinical usefulness of serum IgA anti-actin antibody ELISA and its possible use in monitoring intestinal mucosa lesions during gluten-free diet.

PATIENTS AND METHODS

Four centres recruited 205 newly diagnosed coeliac disease patients with villous atrophy, 80 healthy controls and 81 "disease" controls. Twelve coeliac disease patients on gluten-free diet but with persistent symptoms underwent serum IgA anti-actin antibody assay and intestinal histology evaluation. IgA anti-actin antibody ELISA was performed with a commercial kit. All coeliac disease patients underwent intestinal histology study.

RESULTS

IgA anti-actin antibodies showed a sensitivity of 80% and a specificity of 85% in the diagnosis of coeliac disease patients with villous atrophy. The area under the receiving operator curve for anti-actin antibodies was 0.873 [95% C.I. 0.805-0.899]. Serum anti-actin antibodies values were significantly higher in coeliac disease patients than in healthy or "disease" controls (P<0.0001). Serum anti-actin antibodies were positive in 41 of the 60 coeliac disease patients with mild intestinal histology lesions (69%) and in 123 of the 145 with severe lesions (85.3%) (P<0.05). There was a significant inverse correlation between anti-actin antibody values and the villi/crypts ratio (r=-0.423; P<0.0001). In the 12 coeliac disease patients on gluten-free diet who underwent re-evaluation as they were persistently symptomatic, intestinal histology showed three cases with persistent villous atrophy: all of these were positive for serum anti-actin antibodies ELISA, whereas both serum anti-tTG and EmAs were negative. The other nine patients showed normal intestinal villi and were negative for serum anti-actin antibodies.

CONCLUSIONS

Anti-actin antibodies are a reliable marker of severe intestinal mucosa damage in coeliac disease patients and a simple ELISA technique offers an accurate method for their determination. These antibodies seem to be a very reliable marker of persistent intestinal damage in coeliac disease patients.

Gluten-free diet impact on leptin levels in asymptomatic coeliac adolescents: one year of follow-up

Coeliac disease, daily more frequently diagnosed in our population, involves many organs also in oligosymptomatic patients and with an adequate nutritional regime. Possible endocrine implications include failure to thrive, pubertal delay and reproduction diseases due to deregulation of GH, FSH and LH secretion. Leptin, an adipose tissue hormone, can be decreased as well and its deficiency could be related to growth and puberty anomalies. We studied 14 asymptomatic coeliac patients in peripubertal age (7.5-13.8 years) and tested their leptin levels in order to correlate them with endocrine and anthropometric data. Before the diet was started leptinaemia (M+/-DS) was: 4.94+/-5.53 ng/ml. In 10/14 patients (71%) leptinaemia was<or=2 DS for gender and age. In all the patients, after a period of 6-12 months of gluten-free diet, Leptin levels appreciably raised to 10.8+/-7.9 ng/ml, with a significant correlation to the time of the diet. Leptinaemia was actually lower in patients with a severe mucosal atrophy, and in these patients it increased more significantly after the diet was started. The removal of gluten itself may reduce immunological hit to adipose tissue and the 'malnutrition' of adipocytes: leptin can hence increase despite no significant increase of body mass index occurs. This study could partially explain the correlation between body mass index, Coeliac disease and the deregulation of puberty and fertility, mainly in patients who started the diet late. It could also explain the reversibility of this alteration if the cause is removed.

Hormonal, auxological and clinical follow-up in children with connatal HIV infection. Personal records

AIM

HIV infection and antiretroviral drugs have relevant endocrine implications, affecting growth and pubertal development. Moreover stature impairment cannot depend only on decreased hormonal secretion.

METHODS

We studied for 7 years growth, puberty, bone maturation, hormonal secretion [Growth Hormone (GH) basal and after stimulation with Clonidin and Insulin, Insulin-like Growth Factor 1 (IGF-1), Insulin-like Growth Factor Binding Protein 3 (IGFBP-3), FSH, LH- gonadic hormones axis, ACTH, Cortisol, TSH, fT4, T4, T3, anti-thyroid antibodies, Leptin] of 10 HIV-infected children.

RESULTS

In 3 patients stature was <-2 SDS in the first 2 years and in prepubertal age, with intervals of improved growth. The weight was >2 SDS in 6 children, <-2 SDS in 1 girl, while the other 3 patients had a weight <-2SDS only in the first 2 years of life. Height growth velocity was >10 degrees Centile all over the years of follow-up in 9 patients, while weight growth velocity was pathological in 5. Leptinemia showed higher levels at the beginning of follow up: 0.82-11.68 ng/L (M+/-DS: 3.29+/-4.15) than at the end of the study: 0.2-3 ng/L (M+/-DS: 1.65+/-1.01). Leptin levels showed a statistically significant correlation with CD4/CD8 count (P: 0.010; r: 0.916) and with the CDC stage (P: 0.006; r: 0.937), meaning a strong link to the severity of the disease.

CONCLUSIONS

A good clinical control of HIV infection can guarantee growth within physiological centile in most of HIV-infected children. Over all IGFBP-3 and IGF-1 are good markers of growth, more usable than GH.

The role of calprotectin in predicting endoscopic post-surgical recurrence in asymptomatic Crohn's disease: a comparison with ultrasound

BACKGROUND AND OBJECTIVES

Faecal calprotectin is predictive of clinical relapse in inflammatory bowel disease and ultrasound is sensitive in detecting its post-surgical recurrence. However, no data regarding the role of calprotectin in predicting post-surgical recurrence in asymptomatic Crohn's disease are available. The aim of this study was to prospectively evaluate the role of calprotectin as a predictive marker for one year post-surgical endoscopic recurrence in comparison with ultrasound in patients with asymptomatic Crohn's disease.

MATERIAL AND METHODS

We consecutively enlisted 50 patients who had undergone a resection for Crohn's disease. Faecal calprotectin was analysed and ultrasound were performed at the third month, and a colonoscopy after one year. The sensitivity and specificity of these two techniques were evaluated using endoscopic findings as a golden standard. A Receiver Operator Curve (ROC) curve was plotted, in order to identify the best-cut off value for calprotectin.

RESULTS

39 out of 50 patients were evaluated by performing a colonoscopy after one year; 19 patients had an endoscopic recurrence after one year. Calprotectin sensitivity and specificity were calculated for 5 different cut-off values; the best cut-off value for calprotectin sensitivity (63%) and specificity (75%) was > 200 mg/L. The US sensitivity and specificity at the third month were 26% and 90% respectively.

CONCLUSIONS

When performed three months after surgery ultrasound is more specific than calprotectin in predicting endoscopic recurrence. Faecal calprotectin at a dosage > 200 mg/L seems to have a better sensitivity than ultrasound. Values of calprotectin > 200 mg can be an indication to colonoscopy in the group of patients with negative ultrasound in order to detect early recurrence.

Serum leptin and interleukin-6 levels in pediatric patients with HIV

Recent therapeutic approaches have improved the prognosis of children with HIV. Many new efforts could be involved in their quality of life and therefore could need additional diagnostic strategies. Leptin regulates pubertal development; furthermore a continuous immune stimulus, as in chronic infectious diseases, can enhance leptin's secretion by the action of cytokines such as interleukin (IL)-6. To clarify this role in patients infected with HIV, we assayed leptin and IL-6 and evaluated the influence of HIV severity on its secretion. IL-6 (380.5 +/- 257.6 pg/ml; range: 22-900 pg/ml) showed a significant correlation with leptinemia, HIV-1 RNA, and viremia related to the stage of HIV disease. The difference in leptinemia from a control group (3 +/- 3.2 ng/ml; range: 1-12 ng/ml in HIV patients; 6.72 +/- 8 ng/ml in the controls) did not reach statistical significance, nor did it correlate with pubertal stage, BMI, viremia, CD4 or anti-retroviral therapy. There was a statistically significant correlation between leptinemia and the stage of the HIV disease, and with IL-6 level. We want to stress the role of immunological factors in enhancing leptin secretion.

Production of anti-endomysial antibodies in cultured duodenal mucosa: usefulness in coeliac disease diagnosis

BACKGROUND

Although anti-endomysial antibodies (EmA) have been found in the supernatants of cultured intestinal mucosa from patients with coeliac disease (CD), in no study has the clinical reliability of this new diagnostic tool been investigated. Our aims were to evaluate the clinical usefulness of the in vitro production of EmA in CD diagnosis in consecutive patients with suspected CD, and to evaluate the reliability of the in vitro challenge in CD patients on a gluten-free diet (GFD).

METHODS

For the former aim, consecutive patients who were due to undergo intestinal biopsy for suspected diagnosis of CD were enrolled: according to the final diagnosis, these patients were divided into two groups: Group 1 comprised 91 newly diagnosed CD patients (40 males; age range 7 months to 84 years), Group 2 included 100 subjects with diseases other than CD (44 males; age range 9 months to 76 years). For the latter aim, we also studied 21 CD patients on a gluten-free diet after 16-123 months (8 males; age range 3-51 years), with normal intestinal architecture (Group 3) and 22 patients who served as controls (12 males; age range 4-60 years) with gastroesophageal reflux disease-like symptoms (Group 4). All patients underwent determination of serum anti-gliadin (AGA) and EmA antibodies, histology evaluation of the intestinal biopsies and EmA assay in the supernatants of in vitro gliadin-challenged duodenal mucosa.

RESULTS

EmA assay in the supernatants showed a sensitivity and specificity of 96% and 100%, respectively; these were not significantly different from those observed for serum EmA (88% and 99%, respectively). However, EmA assay in the supernatants was useful in CD patients with mild intestinal histology lesions (infiltrative/hyperplastic type): in this subgroup it was positive in 9/12 of cases, but serum EmA was positive in only 2/12. As regards the reliability of the in vitro gliadin challenge, EmA production in supernatants was recorded only in 10/21 CD patients on a gluten-free diet. The patients with a positive in vitro challenge had a higher number of intra-epithelial lymphocytes than patients with a negative challenge.

CONCLUSIONS

1) EmA assay in the medium of cultured intestinal biopsy can detect gluten-sensitive enteropathy, characterized by an infiltrative/hyperplastic histological pattern, which is often associated with negative serum EmA. 2) The in vitro challenge in CD patients on a gluten-free diet detects EmA production in the culture medium only in half of the cases and other studies must be performed to evaluate whether EmA production after in vitro challenge can be considered a reliable test for confirming CD diagnosis.

[Evaluation of IGF1 and IGFBP3 during diet therapy in patients with food allergy with complex nutritional risk]

The seric levels of IGF1 and IGFBP3 and their molar ratio, together with clinical and auxological parameters, have been evaluated in 16 patients (8 males and 8 females), of average age of 11.6 +/- 8.66 months, who were suffering from complex food allergy and were subjected to a balanced diet will excluded the "offending" food. The results, compared with those of a control population of same age and body surface, have shown a significative reduction of IGF1 and an increase of the molar ratio IGFBP3/IGF1. These observations suggest that, in spite of no significative variation of growth in height and weight, an exclusion diet for a food allergy can reduce the biological activity of some hormonal factors of growth.

Effect of calcitonin gene-related peptide and vasoactive intestinal peptide on murine CD4 and CD8 T cell proliferation

The effects of alpha calcitonin gene-related peptide (alpha CGRP) and vasoactive intestinal peptide (VIP) on the proliferation of CD4 and CD8 T-murine lymphocytes were investigated. When stimulated by a combination of phorbol 12-myristate-13-acetate (PMA) and calcium ionophore (A23187), both neuropeptides in a range of 10(-7)-10(-10) M had an inhibitory effect on the proliferative response of unfractionated splenocytes as well as of purified CD4 and CD8 T lymphocytes. The inhibitory effect of these two neuropeptides was completely or partially blocked by the antagonists of CGRP and VIP receptors. CGRP8-37 and (p-Cl-D-Phe6, Leu17VIP, respectively. The inhibitory effects of each neuropeptide on purified T cells were observed within 4 h after PMA/A23187 activation and their inhibitory actions were correlated with a decrease of IL-2 production. In addition, the two neuropeptides in a range of 10(-7)-10(-10) M induced a rapid and dose-dependent increase in intracellular cAMP in CD4 and CD8 T cells. This suggests the involvement of this second messenger in the inhibitory effects of these two neuropeptides. Taken together these results show that CD4 and CD8 spleen cells represent at least two of the cellular targets for CGRP and VIP inhibition of proliferation mediated by the same type of mechanism.

A cryptic peptide of TRH prohormone inhibits TRH-induced GH release

The effects of two cryptic peptides from pro-TRH: Ps4 (160-169) and Ps5 (178-199) were investigated on basal and secretagogue (GRH and TRH)-induced releases of GH from perifused fragments of rat adenohypophysis. Validation of the perifusion system was done by measuring: (1) the dose-dependent effect of GRH and TRH on GH release; and (2) the stimulation of that release by forskolin (to mimic the adenylate cyclase pathway) or by phorbol ester (to mimic the protein kinase C pathway). We show that: (1) Ps4 and Ps5 (1 microM) do not modify basal GH release; (2) Ps4 (1 microM) changes neither GRH (10 nM)- nor TRH (100 nM)-induced release of GH; (3) Ps5 (100 nM and 1 microM) significantly decreases the release of GH induced by equimolar concentrations of TRH but not that induced by GRH.

[Vaginal infections in a population of diabetic children and adolescents]

The prevalence of vaginal infections has been evaluated in 51 patient affected by insulin-dependent diabetes (IDDM) and in a control group of girls matched for age. Most frequent infectious agents were Candida Albicans (42.8%) and Streptococcus B (28.5%). No statistical significant relationship was observed between infection and duration of diabetes nor metabolic control, while the relationship was positive between infection and puberty. The peculiarity of this infection during IDDM is stressed and the difficulties in the infection when caused by Streptococcus B are discussed.