Analysis of the relationship between grapevine cultivars, sports and clones via DNA fingerprinting

DNA fingerprinting utilizing RAPD polymorphisms was employed to investigate the relationship among 16 grapevine cultivars and sports thought to have arisen from these cultivars. From 53 primers, a total of 464 bands were generated, of which 29 % were common to all genotypes tested. Cluster analysis classified all tested cultivars into two main groups (Vitis vinifera L. and V. x Labruscana Bailey) as expected. No polymorphism was detected among known clones of Chardonnay (Ch. clone 7, Ch. clone 78 and Ch. Geneva clone) or Pinot noir (P. n. clone 29, P. n. Geneva clone and P. n. Pernand). Pinot Meunier, Pinot gris, and Gamay Beaujolais displayed patterns indistinguishable from Pinot noir. Auxerrois and Melon showed unique patterns and may be classified as distinct cultivars. Chardonnay clone 7 shared 84 % of its bands with Pinot noir. There was more than 97 % RAPD amplicon homology between Niagara and two supposed sports, and between Concord and a red-fruited sport. Taking into account the error rate in scoring RAPD bands, the evidence is against the hypothesis that the three sports are distinct cultivars. While RAPD banding patterns could not distinguish between known clones, they were useful for distinguishing between phenotypically similar cultivars and for assessing the origins of cultivars thought to have originated as sports

Multicentric validation of proteomic biomarkers in urine specific for diabetic nephropathy

Background: Urine proteome analysis is rapidly emerging as a tool for diagnosis and prognosis in disease states. For diagnosis of diabetic nephropathy (DN), urinary proteome analysis was successfully applied in a pilot study. The validity of the previously established proteomic biomarkers with respect to the diagnostic and prognostic potential was assessed on a separate set of patients recruited at three different European centers. In this case-control study of 148 Caucasian patients with diabetes mellitus type 2 and duration >= 5 years, cases of DN were defined as albuminuria >300 mg/d and diabetic retinopathy (n = 66). Controls were matched for gender and diabetes duration (n = 82). Methodology/Principal Findings: Proteome analysis was performed blinded using high-resolution capillary electrophoresis coupled with mass spectrometry (CE-MS). Data were evaluated employing the previously developed model for DN. Upon unblinding, the model for DN showed 93.8% sensitivity and 91.4% specificity, with an AUC of 0.948 (95% CI 0.898-0.978). Of 65 previously identified peptides, 60 were significantly different between cases and controls of this study. In <10% of cases and controls classification by proteome analysis not entirely resulted in the expected clinical outcome. Analysis of patient's subsequent clinical course revealed later progression to DN in some of the false positive classified DN control patients. Conclusions: These data provide the first independent confirmation that profiling of the urinary proteome by CE-MS can adequately identify subjects with DN, supporting the generalizability of this approach. The data further establish urinary collagen fragments as biomarkers for diabetes-induced renal damage that may serve as earlier and more specific biomarkers than the currently used urinary albumin

Decreased renal function in overweight and obese prepubertal children

BACKGROUND: Obesity is a potentially modifiable risk factor for the development and progression of kidney disease, both in adults and children. We aim to study the association of obesity and renal function in children, by comparing estimated glomerular filtration rate (eGFR) in nonoverweight and overweight/obese children. Secondarily, we aim to evaluate the accuracy of equations on eGFR estimation when compared to 24-h urinary creatinine clearance (CrCl). METHODS: Cross-sectional study of 313 children aged 8-9 y, followed in the birth cohort Generation XXI (Portugal). Creatinine and cystatin C, GFR estimated by several formulas and CrCl were compared in 163 nonoverweight and 150 overweight/obese, according to World Health Organization growth reference. RESULTS: Overweight/obese children had significantly lower eGFR, estimated by all methods, except for CrCl and revised Schwartz formula. Despite all children having renal function in the normal range, eGFR decreased significantly with BMI z-score (differences ranging from -4.3 to -1.1 ml/min/1.73 m(2) per standard deviation of BMI). The Zappitelli combined formula presented the closest performance to CrCl, with higher correlation coefficients and higher accuracy values. CONCLUSION: Young prepubertal children with overweight/obesity already present significantly lower GFR estimations that likely represent some degree of renal impairment associated with the complex deleterious effects of adiposity

Machine Learning for Nuclear Mechano-Morphometric Biomarkers in Cancer Diagnosis

Current cancer diagnosis employs various nuclear morphometric measures. While these have allowed accurate late-stage prognosis, early diagnosis is still a major challenge. Recent evidence highlights the importance of alterations in mechanical properties of single cells and their nuclei as critical drivers for the onset of cancer. We here present a method to detect subtle changes in nuclear morphometrics at single-cell resolution by combining fluorescence imaging and deep learning. This assay includes a convolutional neural net pipeline and allows us to discriminate between normal and human breast cancer cell lines (fibrocystic and metastatic states) as well as normal and cancer cells in tissue slices with high accuracy. Further, we establish the sensitivity of our pipeline by detecting subtle alterations in normal cells when subjected to small mechano-chemical perturbations that mimic tumor microenvironments. In addition, our assay provides interpretable features that could aid pathological inspections. This pipeline opens new avenues for early disease diagnostics and drug discovery.National Science Foundation (U.S.) (1651995)United States. Defense Advanced Research Projects Agency (W911NF-16-1-0551)United States. Office of Naval Research (N00014-17-1-2147

Serum sialic acid and gamma-glutamyltransferase levels in alcohol-dependent individuals

Alcohol abuse is a very common problem all over the world. Identification of alcoholism is crucial in preventing some adverse health effects, economical and social consequences of excessive alcohol consumption. The aim of this study was to determine sialic acid (SA) and gamma-glutamyltransferase (GGT) levels in serum samples of alcoholics and to compare the diagnostic accuracy of SA with the conventional marker, GGT

Occurrence and identification of grapevine phytoplasmas in main viticultural regions of Turkey.

Intensive surveys were conducted in the main viticultural areas of Turkey in 2009-2010. Two hundred eighty nine symptomatic and 20 non-symptomatic plant samples were collected and subjected to nucleic acid extraction followed by PCR, nested PCR and RFLP analyses to detect phytoplasma presence and for their identification. The incidence rate of phytoplasma infections 18.33% and the majority of the symptomatic grapevines were infected with grapevine yellows phytoplasmas belonging to 16SrXII-A subgroup (“bois noir”). Phytoplasmas of 16SrV group, aster yellows (16SrI-B) and pigeon pea witches’ broom (16SrIX) groups were also detected in the surveyed vineyards. Phytoplasma-associated infections were present more on wine grapevine cultivars (73.6%), such as Alphonse Lavallée, Alicante Bouschet, Chardonnay, Shiraz, Cabernet Sauvignon, Merlot, Sauvignon Blanc and Pinot Noir, compared to table grapes (26.4%), such as Bogazkere, Sirfani, Tahannebi and Emir

Urinary and serum type II collagen: markers of renal fibrosis

Background. The progression of chronic renal failure is characterized by the progressive fibrosis of the kidneys. Such fibrosis reflects the increased deposition of collagens (I, III, and IV) as well as fibronectin within scarred kidneys. In this study, we determined whether changes in renal extracellular matrix (ECM) components are reflected by parallel changes in their circulating or urinary levels. Patients and methods. We studied 40 patients with a range of subacute and chronic nephropathies who underwent a renal biopsy. At the time of the biopsy, their serum and urinary levels of collagens III (amino terminal peptide of procollagen III; PIIINP) and IV, as well as fibronectin were measured. Clinical, biochemical and histological parameters were correlated. Multiple regression analysis was applied to determine the predictive value of circulating and urinary ECM components for the severity of renal fibrosis. Results. We noted an increase in circulating and urinary levels of collagens III and IV but not fibronectin in patients with nephropathies compared to healthy volunteers. Increased immunoreactivity for these ECM components was also detected in kidney biopsies when compared to normal kidneys. A strong positive correlation was detected between circulating and urinary procollagen III (PIIINP) and the severity of renal interstitial fibrosis (serum PIINP: r=0.49,