A Fast and Accurate Heuristic for the Single Individual SNP Haplotyping Problem with Many Gaps, High Reading Error Rate and Low Coverage

Single nucleotide polymorphism (SNP) is the most frequent form of DNA variation. The set of SNPs present in a chromosome (called the haplotype) is of interest in a wide area of applications in molecular biology and biomedicine, including diagnostic and medical therapy. In this paper we propose a new heuristic method for the problem of haplotype reconstruction for (portions of) a pair of homologous human chromosomes from a single individual (SIH). The problem is well known in literature and exact algorithms have been proposed for the case when no (or few) gaps are allowed in the input fragments. These algorithms, though exact and of polynomial complexity, are slow in practice. Therefore fast heuristics have been proposed.In this paper we describe a new heuristic method that is able to tackle the case of many gapped fragments and retains its effectiveness even when the input fragments have high rate of reading errors (up to 20%) and low coverage (as low as 3). We test our method on real data from the HapMap Project

Effects of the administration of Elovl5-dependent fatty acids on a spino-cerebellar ataxia 38 mouse model

BACKGROUND: Spinocerebellar ataxia 38 (SCA38) is a rare autosomal neurological disorder characterized by ataxia and cerebellar atrophy. SCA38 is caused by mutations of ELOVL5 gene. ELOVL5 gene encodes a protein, which elongates long chain polyunsaturated fatty acids (PUFAs). Knockout mice lacking Elovl5 recapitulate SCA38 symptoms, including motor coordination impairment and disruption of cerebellar architecture. We asked whether, in Elovl5 knockout mice (Elovl5(−/−)), a diet with both ω3 and ω6 PUFAs downstream Elovl5 can prevent the development of SCA38 symptoms, and at which age such treatment is more effective. Elovl5(−/−) mice were fed either with a diet without or containing PUFAs downstream the Elovl5 enzyme, starting at different ages. Motor behavior was assessed by the balance beam test and cerebellar structure by morphometric analysis. RESULTS: The administration from birth of the diet containing PUFAs downstream Elovl5 led to a significant amelioration of the motor performance in the beam test of Elovl5(−/−) mice, with a reduction of foot slip errors at 6 months from 2.2 ± 0.3 to 1.3 ± 0.2 and at 8 months from 3.1 ± 0.5 to 1.9 ± 0.3. On the contrary, administration at 1 month of age or later had no effect on the motor impairment. The cerebellar Purkinje cell layer and the white matter area of Elovl5(−/ −)mice were not rescued even by the administration of diet from birth, suggesting that the improvement of motor performance in the beam test was due to a functional recovery of the cerebellar circuitry. CONCLUSIONS: These results suggest that the dietary intervention in SCA38, whenever possible, should be started from birth or as early as possible

Identification and Characterization of New Proteins in Podocyte Dysfunction of Membranous Nephropathy by Proteomic Analysis of Renal Biopsy

Interstitial fluid, obtained by gentle centrifugation of the renal biopsy specimen, is highly enriched in elements directly secreted by the kidney tissue and is suitable for proteomic analysis. Here we describe the first clinical application of renal interstitial fluid analysis in a subset of samples obtained from patients affected by idiopathic membranous nephropathy. We included in the study fifty-one patients with different pathologic diagnoses. We identified the proteomic pattern of idiopathic membranous nephropathy with mass spectrometry analysis by comparing these samples with two controls: normal kidney and IgA nephropathy. Proteomic results were validated by immunofluorescence analysis of renal tissues and Western blot of serum, urines and podocyte cell cultures. We observed an increased expression of PDZ and LIM domain protein 5 (PDLI5) and LIM domain binding protein 3 (LDB3) providing first evidence of the differential expression of these LIM domain-related proteins in kidney and urines of patients with idiopathic membranous nephropathy. Interstitial fluid can be considered a valuable biological fluid in the discovery phase of biomarkers. In order to validate its clinical use, it is pivotal to assess the availability of the biomarkers in ‘usual’ samples: blood and/or urine. PDLI5 and LDB3 share a common LIM domain suggesting a possible role in the cytoskeleton organization and they appear upregulated in glomeruli of patients affected by idiopathic membranous nephropathy. Furthermore the two proteins become highly abundant in the urine of patients affected by idiopathic membranous nephropathy. In conclusion, our approach may be considered a novel method for identifying candidate biomarkers for patients suffering from membranous nephropathy and other glomerulonephrite

An autoregulatory loop controls the expression of the transcription factor NF-Y

The heterotrimeric NF-Y complex is a pioneer factor that binds to CCAAT-genes and regulates their transcription. NF-Y cooperates with multiple transcription factors and co-regulators in order to positively or negatively influence gene transcription. The recruitment of NF-Y to CCAAT box is significantly enriched in cancer-associated gene promoters loci and positively correlates with malignancy. NF-Y subunits, in particular the DNA-binding subunit NF-YA and the histone-fold subunit NF-YC, appear overexpressed in specific types of cancer. Here we demonstrate that NF-Y subunits expression is finely regulated through transcriptional and post-translational mechanisms thus allowing control over basal expression levels. NF-Y negatively regulates the transcription of the genes encoding for its subunits. DNA pull-down/affinity purification assay coupled with Mass Spectrometry identified putative co-regulators, such as Lamin A, involved in NF-YA gene transcription level. We also evidentiate how the stability of the complex is severely affected by the absence of one subunit. Our results identified for the first time one of the mechanisms responsible for NF-Y expression, which may be involved in the aberrant expression and activity observed in tumor cells and other pathological conditions

Oxytetracycline-Protein Complex: The Dark Side of Pet Food

Background: Worldwide antibiotic abuse represents a huge burden, which can have a deep impact on pet and human health through nutrition and medicalization representing another way of antibiotic resistance transmission. Objective: We aimed our research to determine a possible complex formation between biological bone substrates, such as proteins, and Oxytetracycline (OTC), an approved antibiotic for use in zootechny, which might determine a toxic effect on K562 cells. Method: Cell viability and HPLC-ESI/QqToF assays were used to assess potential toxicity of bone extract derived from OTC-treated chickens according to standard withdrawal times and from untreated chickens at 24, 48 and 72h of incubation. Results: Cell culture medium with ground bone from chickens reared in the presence of OTC (OTC-CCM) resulted significantly cytotoxic at every incubation time regardless of the bone concentration while cell culture medium with ground bone from chickens reared without OTC (BIO-CCM) resulted significantly cytotoxic only after 72h of incubation. HPLC-ESI/QqToF assay ruled out the possible presence of OTC main derivatives possibly released by bone within culture medium until 1 \u3bcg/mL. Conclusion: The presence of a protein complex with OTC is able to exert a cytotoxic effect once released in the medium after 24-48h of incubation

Quantitative comparison of the protein corona of nanoparticles with different matrices

: Nanoparticles (NPs) are paving the way for improved treatments for difficult to treat diseases diseases; however, much is unknown about their fate in the body. One important factor is the interaction between NPs and blood proteins leading to the formation known as the "protein corona" (PC). The PC, consisting of the Hard (HC) and Soft Corona (SC), varies greatly based on the NP composition, size, and surface properties. This highlights the need for specific studies to differentiate the PC formation for each individual NP system. This work focused on comparing the HC and SC of three NPs with different matrix compositions: a) polymeric NPs based on poly(lactic-co-glycolic) acid (PLGA), b) hybrid NPs consisting of PLGA and Cholesterol, and c) lipidic NPs made only of Cholesterol. NPs were formulated and characterized for their physico-chemical characteristics and composition, and then were incubated in human plasma. In-depth purification, identification, and statistical analysis were then performed to identify the HC and SC components. Finally, similar investigations demonstrated whether the presence of a targeting ligand on the NP surface would affect the PC makeup. These results highlighted the different PC fingerprints of these NPs, which will be critical to better understand the biological influences of the PC and improve future NP designs

Label-Free Mass Spectrometry Proteomics Reveals Different Pathways Modulated in THP-1 Cells Infected with Therapeutic Failure and Drug Resistance Leishmania infantum Clinical Isolates

As the world is facing increasing difficulties to treat leishmaniasis with current therapies, deeper investigation into the molecular mechanisms responsible for both drug resistance and treatment failure (TF) is essential in drug discovery and development. So far, few available drugs cause severe side effects and have developed several resistance mechanisms. Drug resistance and TF parasite strains from clinical isolates may have acquired altered expression of proteins that characterize specific mechanisms leading to therapy inefficacy. This work aims to identify the biochemical pathways of THP-1 human monocytes infected by different Leishmania infantum clinical isolates from patients with either resistance or with TF outcome, using whole cell differential Mass Spectrometry proteomics. We have adopted network enrichment analysis to integrate the transcriptomics and the proteomic results of infected cells studies. Transferrin receptor C (TFRC) and nucleoside diphosphate kinase 3 (NDK3) were discovered as overexpressed proteins in THP-1 cells infected with paromomycin, antimony, and miltefosine resistant L. infantum lines. The overall achievements represent founding concepts to confirm new targets involved in the parasitic drug resistance and TF mechanisms, and to consider in perspective the importance of a dual host-guest pharmacological approach to treat the acute stage of the disease.We thank Dr. F. Javier Moreno from the WHO Collaborating Center for Leishmaniasis, Instituto de Salud Carlos III (ISCIII), for providing L. infantum lines LLM2070, LLM2165, LLM2255, and LLM2221, isolated from HIV-positive patients with visceral leishmaniasis and TF, and the paromomycin-resistant L. infantum line LEM2126 (L2126) used in this study. Also, we thank Dra. Laurence Lachaud from the Centre National de Référence des Leishmanioses, Université Montpellier (Montpellier, France), for providing the drug-resistant L. infantum lines used in this work: LEM3323 (L3323) and LEM5159 (L5159), which are SbIII- and Mil-resistant lines, respectively. The authors thank Dr. Stefania Ferrari for compiling the Leishmania database for protein search. L. infantum db was obtained from SwissProt (L. infantum entry, exported in FASTA format, updated January 2016, updates are ongoing). This work was supported in part by Grant RTI2018-097210-B-100 (to F.G.), funded by MCIN/AEI/10.13039/501100011033 and by “ERDF A Way of Making Europe” and by Grant FP7-HEALTH-2013-INNOVATION “New Medicine for Trypanosomatidic Infections” (Grant 603240). The authors acknowledge the “Fondazione Cassa di Risparmio di Modena” for funding the UHPLC-ESI-HRMS Q-Exactive system at the Centro Interdipartimentale Grandi Strumenti (CIGS) of the University of Modena and Reggio Emilia. The authors thank the COST Action “OneHealthdrugs” CA21111 for inspiring the research development