Non-random retention of protein-coding overlapping genes in Metazoa

<p>Abstract</p> <p>Background</p> <p>Although the overlap of transcriptional units occurs frequently in eukaryotic genomes, its evolutionary and biological significance remains largely unclear. Here we report a comparative analysis of overlaps between genes coding for well-annotated proteins in five metazoan genomes (human, mouse, zebrafish, fruit fly and worm).</p> <p>Results</p> <p>For all analyzed species the observed number of overlapping genes is always lower than expected assuming functional neutrality, suggesting that gene overlap is negatively selected. The comparison to the random distribution also shows that retained overlaps do not exhibit random features: antiparallel overlaps are significantly enriched, while overlaps lying on the same strand and those involving coding sequences are highly underrepresented. We confirm that overlap is mostly species-specific and provide evidence that it frequently originates through the acquisition of terminal, non-coding exons. Finally, we show that overlapping genes tend to be significantly co-expressed in a breast cancer cDNA library obtained by 454 deep sequencing, and that different overlap types display different patterns of reciprocal expression.</p> <p>Conclusion</p> <p>Our data suggest that overlap between protein-coding genes is selected against in Metazoa. However, when retained it may be used as a species-specific mechanism for the reciprocal regulation of neighboring genes. The tendency of overlaps to involve non-coding regions of the genes leads to the speculation that the advantages achieved by an overlapping arrangement may be optimized by evolving regulatory non-coding transcripts.</p

Ionized jet deposition of silver nanostructured coatings: Assessment of chemico-physical and biological behavior for application in orthopedics

Infection is one of the main issues connected to implantation of biomedical devices and represents a very difficult issue to tackle, for clinicians and for patients. This study aimed at tackling infection through antibacterial nanostructured silver coatings manufactured by Ionized Jet Deposition (IJD) for application as new and advanced coating systems for medical devices. Films composition and morphology depending on deposition parameters were investigated and their performances evaluated by correlating these properties with the antibacterial and antibiofilm efficacy of the coatings, against Escherichia coli and Staphylococcus aureus strains and with their cytotoxicity towards human cell line fibroblasts. The biocompatibility of the coatings, the nanotoxicity, and the safety of the proposed approach were evaluated, for the first time, in vitro and in vivo by rat subcutaneous implant models. Different deposition times, corresponding to different thicknesses, were selected and compared. All silver coatings exhibited a highly homogeneous surface composed of nanosized spherical aggregates. All coatings having a thickness of 50 nm and above showed high antibacterial efficacy, while none of the tested options caused cytotoxicity when tested in vitro. Indeed, silver films impacted on bacterial strains viability and capability to adhere to the substrate, in a thickness-dependent manner. The nanostructure obtained by IJD permitted to mitigate the toxicity of silver, conferring strong antibacterial and anti-adhesive features, without affecting the coatings biocompatibility. At the explant, the coatings were still present although they showed signs of progressive dissolution, compatible with the release of silver, but no cracking, delamination or in vivo toxicity was observed

Haplotype affinities resolve a major component of goat (<i>Capra hircus</i>) MtDNA D-loop diversity and reveal specific features of the Sardinian stock

Goat mtDNA haplogroup A is a poorly resolved lineage absorbing most of the overall diversity and is found in locations as distant as Eastern Asia and Southern Africa. Its phylogenetic dissection would cast light on an important portion of the spread of goat breeding. The aims of this work were 1) to provide an operational definition of meaningful mtDNA units within haplogroup A, 2) to investigate the mechanisms underlying the maintenance of diversity by considering the modes of selection operated by breeders and 3) to identify the peculiarities of Sardinian mtDNA types. We sequenced the mtDNA D-loop in a large sample of animals (1,591) which represents a non-trivial quota of the entire goat population of Sardinia. We found that Sardinia mirrors a large quota of mtDNA diversity of Western Eurasia in the number of variable sites, their mutational pattern and allele frequency. By using Bayesian analysis, a distance-based tree and a network analysis, we recognized demographically coherent groups of sequences identified by particular subsets of the variable positions. The results showed that this assignment system could be reproduced in other studies, capturing the greatest part of haplotype diversity. We identified haplotype groups overrepresented in Sardinian goats as a result of founder effects. We found that breeders maintain diversity of matrilines most likely through equalization of the reproductive potential. Moreover, the relevant amount of inter-farm mtDNA diversity found does not increase proportionally with distance. Our results illustrate the effects of breeding practices on the composition of maternal gene pool and identify mtDNA types that may be considered in projects aimed at retrieving the maternal component of the oldest breeds of Sardinia.</br

Modeling Parkinson's Disease Neuropathology and Symptoms by Intranigral Inoculation of Preformed Human α-Synuclein Oligomers.

The accumulation of aggregated α-synuclein (αSyn) is a hallmark of Parkinson's disease (PD). Current evidence indicates that small soluble αSyn oligomers (αSynOs) are the most toxic species among the forms of αSyn aggregates, and that size and topological structural properties are crucial factors for αSynOs-mediated toxicity, involving the interaction with either neurons or glial cells. We previously characterized a human αSynO (H-αSynO) with specific structural properties promoting toxicity against neuronal membranes. Here, we tested the neurotoxic potential of these H-αSynOs in vivo, in relation to the neuropathological and symptomatic features of PD. The H-αSynOs were unilaterally infused into the rat substantia nigra pars compacta (SNpc). Phosphorylated αSyn (p129-αSyn), reactive microglia, and cytokine levels were measured at progressive time points. Additionally, a phagocytosis assay in vitro was performed after microglia pre-exposure to αsynOs. Dopaminergic loss, motor, and cognitive performances were assessed. H-αSynOs triggered p129-αSyn deposition in SNpc neurons and microglia and spread to the striatum. Early and persistent neuroinflammatory responses were induced in the SNpc. In vitro, H-αSynOs inhibited the phagocytic function of microglia. H-αsynOs-infused rats displayed early mitochondrial loss and abnormalities in SNpc neurons, followed by a gradual nigrostriatal dopaminergic loss, associated with motor and cognitive impairment. The intracerebral inoculation of structurally characterized H-αSynOs provides a model of progressive PD neuropathology in rats, which will be helpful for testing neuroprotective therapies

Haplotype Affinities Resolve a Major Component of Goat (Capra hircus) MtDNA D-Loop Diversity and Reveal Specific Features of the Sardinian Stock

Goat mtDNA haplogroup A is a poorly resolved lineage absorbing most of the overall diversity and is found in locations as distant as Eastern Asia and Southern Africa. Its phylogenetic dissection would cast light on an important portion of the spread of goat breeding. The aims of this work were 1) to provide an operational definition of meaningful mtDNA units within haplogroup A, 2) to investigate the mechanisms underlying the maintenance of diversity by considering the modes of selection operated by breeders and 3) to identify the peculiarities of Sardinian mtDNA types. We sequenced the mtDNA D-loop in a large sample of animals (1,591) which represents a non-trivial quota of the entire goat population of Sardinia. We found that Sardinia mirrors a large quota of mtDNA diversity of Western Eurasia in the number of variable sites, their mutational pattern and allele frequency. By using Bayesian analysis, a distance-based tree and a network analysis, we recognized demographically coherent groups of sequences identified by particular subsets of the variable positions. The results showed that this assignment system could be reproduced in other studies, capturing the greatest part of haplotype diversity

Design and baseline characteristics of the finerenone in reducing cardiovascular mortality and morbidity in diabetic kidney disease trial

Background: Among people with diabetes, those with kidney disease have exceptionally high rates of cardiovascular (CV) morbidity and mortality and progression of their underlying kidney disease. Finerenone is a novel, nonsteroidal, selective mineralocorticoid receptor antagonist that has shown to reduce albuminuria in type 2 diabetes (T2D) patients with chronic kidney disease (CKD) while revealing only a low risk of hyperkalemia. However, the effect of finerenone on CV and renal outcomes has not yet been investigated in long-term trials. Patients and Methods: The Finerenone in Reducing CV Mortality and Morbidity in Diabetic Kidney Disease (FIGARO-DKD) trial aims to assess the efficacy and safety of finerenone compared to placebo at reducing clinically important CV and renal outcomes in T2D patients with CKD. FIGARO-DKD is a randomized, double-blind, placebo-controlled, parallel-group, event-driven trial running in 47 countries with an expected duration of approximately 6 years. FIGARO-DKD randomized 7,437 patients with an estimated glomerular filtration rate >= 25 mL/min/1.73 m(2) and albuminuria (urinary albumin-to-creatinine ratio >= 30 to <= 5,000 mg/g). The study has at least 90% power to detect a 20% reduction in the risk of the primary outcome (overall two-sided significance level alpha = 0.05), the composite of time to first occurrence of CV death, nonfatal myocardial infarction, nonfatal stroke, or hospitalization for heart failure. Conclusions: FIGARO-DKD will determine whether an optimally treated cohort of T2D patients with CKD at high risk of CV and renal events will experience cardiorenal benefits with the addition of finerenone to their treatment regimen. Trial Registration: EudraCT number: 2015-000950-39; ClinicalTrials.gov identifier: NCT02545049

Modelling human choices: MADeM and decision‑making

Research supported by FAPESP 2015/50122-0 and DFG-GRTK 1740/2. RP and AR are also part of the Research, Innovation and Dissemination Center for Neuromathematics FAPESP grant (2013/07699-0). RP is supported by a FAPESP scholarship (2013/25667-8). ACR is partially supported by a CNPq fellowship (grant 306251/2014-0)

Cannabinoid CB1/CB2 receptor agonists attenuate hyperactivity and body weight loss in a rat model of activity-based anorexia

BACKGROUND AND PURPOSE: Anorexia nervosa (AN) is a serious psychiatric condition characterized by excessive body weight loss and disturbed perceptions of body shape and size, often associated with excessive physical activity. There is currently no effective drug-related therapy of this disease and this leads to high relapse rate. Clinical data suggest that a promising therapy to treat and reduce reoccurrence of AN may be based on the use of drugs that target the endocannabinoid (EC) system, which appears dysregulated in AN patients. EXPERIMENTAL APPROACH: The activity-based anorexia (ABA) rodent model mimics severe body weight loss and increased physical activity, as well as neuroendocrine disturbances (i.e., hypoleptinemia and hypercortisolemia) in AN. This study investigated whether cannabinoid agonists can effectively modify anorexic-like behaviors and neuroendocrine changes in rats subjected to a repeated ABA regime in order to mimic the human condition in which patients repeatedly undergo recovery and illness cycle. KEY RESULTS: Our data show that subchronic treatment with both the CB1/CB2 receptor natural agonist Δ9-tetrahydrocannabinol and the synthetic CB1/CB2 receptor agonist CP-55,940 significantly reduced body weight loss and running wheel activity in ABA rats. These behavioral effects were accompanied by an increase in leptin signaling and a decrease in plasma levels of corticosterone. CONCLUSION AND IMPLICATIONS: Taken together, our results further demonstrate EC system involvement in AN pathophysiology and that strategies which modulate EC signaling are useful to treat this disorder, specifically in patients where physical hyperactivity plays a central role in its progression and maintenanc

The usefulness of parathyroid hormone and calcitonin detection from needle aspirates (FNAB) in patients with mutinodular goitre.

Objective: To evaluate the usefulness of parathyroid hormone (PTH) and calcitonin (CT) assay in FNAB (PTHn and CTn) in the pre-surgical localization of parathyroid neoplasia (PN) or medullary thyroid carcinoma (MTC). Patients and Methods: Twenty patients [17 with multinodular goiter (MNG)] with suspect primary hyperparathyroidism (PHP) and 11 with high serum CT (7 with MNG) were submitted to neck ultrasound (US) and US-guided FNAB of suspicious lesions for cytology and PTHn or CTn; sesta-MIBI parathyroid scintigraphy (MIBI) and pentagastrin (PG) test were also performed in patients with PHP and high CT, respectively. Results: In PHP, 17/20 patients showed high (366 - >5000 pg/ml) PTHn and a PN at histology; the remaining 3 cases had a thyroid neoplasia (TN) associated to secondary hyperparathyroidism. The sensitivity and the specificity of PTHn was therefore 100%. MIBI was positive in 15 (13 PN and 2 TN) and negative in 5 (4 PN and 1 TN) reaching 76% sensitivity and 33% specificity. Cytology was diagnostic in 10 (all PN) and not-diagnostic in 10 cases (7 PN and 3 TN: 58% sensitivity and 100% specificity). Among the 11 patients with high serum CT, 8 had high (68 - >2000 pg/ml) CTn, positive PG test and a MTC at histology. Three cases showed undetectable CTn: 2 of them, with negative cytology and borderline PG test, were not operated; in the remaining patient with positive PG test and dubious cytology (with suspicious neck MTC recurrence after thyroidectomy) histology showed an inflammatory process. Thus, CTn reached 100% sensitivity and specificity. Cytology correctly identified 3 and was not-diagnostic in 5 patients with histologically proven MTC, (37% of sensitivity and 66% specificity). Conclusions: PTHn and CTn represent the most sensitive and specific available tool to plan a correct pre-surgical localization of PN and MTC even in the presence of multinodular goiter

The usefulness of calcitonin assay in fine needle aspiration biopsy (FNAB) fluid of neck masses of patients with primitive and metastatic medullary thyroid carcinoma.

OBJECTIVE: To evaluate the usefulness of calcitonin (CT) assay in FNAB wash-out fluid (CT-FNAB) alone or combined to cytology in the pre-surgical study of MTC patients with multinodular goiter (MNG) and of suspicious neck MTC recurrences/metastases. PATIENTS AND METHODS: Thirthy-six ultrasound (US)-guided FNAB were performed in neck masses from 23 patients with borderline or high basal and pentagastrin (PG) stimulated serum CT. A total of 18 nodules and 3 neck lymph nodes (these latter present in the same subject) were from 12 MNG patients and 15 suspiciuos neck masses (6 local recurrences and 9 neck lymph nodes) were from 9 totally thyroidectomized MTC patients. Conventional cytology and CT-FNAB were always associated to PG stimulating test. On the basis of CT-FNAB values found in 15 non-MTC lesions, CT-FNAB>24 pg/ml (twice of the highest observed value) was considered as indicative of MTC. Thyroid 99mTc-pertechnetate scintiscan were also performed in patients with MNG. RESULTS: As displayed in the Table, all the 21 positive CT-FNAB neck lesions (10 nodules, 6 neck lymph nodes and 5 local recurrences), 13/21 with positive cytology, were confirmed as MTC at histology. Among the 15 negative CT-FNAB neck masses (8 nodules, 6 suspicious neck lymph nodes and 1 suspicious local recurrences) 5 underwent to surgery and a benign lesion was confirmed at histology. The remaining 10 cases (all with benign cytology) were not operated and no evidence of MTC has been detected so far at follow-up of 2.5 years. CT-FNAB+ n= 21 CT-FNAB– n= 15 Cyto+ n=13 Cyto- n=8 Cyto+ n=1 Cyto- n=14 Histo+ n=13 Histo+ n=8 Histo- n=1 Histo- n=4* * 10 lesions not operated displayed benign clinical features at follow-up Taken together, CT-FNAB reached 100% of sensitivity and specificity for MTC, while cytology displayed only 61.9% of sensitivity and 93.3% of specificity. CONCLUSIONS: US-guided CT-FNAB provided to be a very useful tool to localize primitive MTC in MNG patients and recurrences or lymph node metastases in MTC operated subjects, with much more sensitivity and specificity than cytology. This may have important implications in planning the adequate surgical approach