Cristian Piras

Farm animal milk proteomics

Milk is one of the most important nutrients for humans during lifetime. Farm animal milk in all its products like cheese and other fermentation and transformation products is a widespread nutrient for the entire life of humans. Proteins are key molecules of the milk functional component repertoire and their investigation represents a major challenge. Proteins in milk, such as caseins, contribute to the formation of micelles that are different from species to species in dimension and casein-type composition; they are an integral part of the MFGM (Milk Fat Globule Membrane) that has being exhaustively studied in recent years. Milk proteins can act as enzymes or have an antimicrobial activity; they could act as hormones and, last but not least, they have a latent physiological activity encoded in their primary structure that turns active when the protein is cleaved by fermentation or digestion processes. In this review we report the last progress in proteomics, peptidomics and bioinformatics. These new approaches allow us to better characterize the milk proteome of farm animal species, to highlight specific PTMs, the peptidomic profile and even to predict the potential nutraceutical properties of the analyzed proteins.

Mechanisms of antibiotic resistance to enrofloxacin in uropathogenic Escherichia coli in dog

Escherichia coli (E. coli) urinary tract infections (UTIs) are becoming a serious problem both for pets and humans (zoonosis) due to the close contact and to the increasing resistance to antibiotics. This study has been performed in order to unravel the mechanism of induced enrofloxacin resistance in canine E. coli isolates that represent a good tool to study this pathology. The isolated E. coli has been induced with enrofloxacin and studied through 2D DIGE and shotgun MS. Discovered differentially expressed proteins are principally involved in antibiotic resistance and linked to oxidative stress response, to DNA protection and to membrane permeability. Moreover, since enrofloxacin is an inhibitor of DNA gyrase, the overexpression of DNA starvation/stationary phase protection protein (Dsp) could be a central point to discover the mechanism of this clone to counteract the effects of enrofloxacin. In parallel, the dramatic decrease of the synthesis of the outer membrane protein W, which represents one of the main gates for enrofloxacin entrance, could explain additional mechanism of E. coli defense against this antibiotic. All 2D DIGE and MS data have been deposited into the ProteomeXchange Consortium with identifier PXD002000 and DOI http://dx.doi.org/10.6019/PXD002000. This article is part of a Special Issue entitled: HUPO 2014.

Differential protein profile in sexed bovine semen: shotgun proteomics investigation

The preparation of sexed semen is based on the differential DNA content between the X and Y chromosome bearing sperm cells determined by fluorescence-activated cell sorting. In spite of its intrinsic limitations this represents the only effective method. However, the employment of sexed sperm for breeding food producing animals on a large scale requires additional knowledge in the protein repertoire for the development of improved methods to differentiate X and Y sperm cells maintaining high vitality. In order to address this issue, we performed a comparative shotgun proteomic investigation by nUPLC-MS/MS to characterize sexed bovine semen. The protein profiles of these two types of sperm cells have shown differential expression of proteins that may be directly associated with the main components of cytoskeletal structures of flagellum, as the axoneme, outer dense fibers and fibrous sheath, as well as glycolytic enzymes and calmodulin, involved in the energetic metabolism regulation. Overall these results may provide a base to a better comprehension of the biological features of sperm cells and may be useful to the development of alternative methods of separation.

Proteomics in food: Quality, safety, microbes, and allergens.

Food safety and quality and their associated risks pose a major concern worldwide regarding not only the relative economical losses but also the potential danger to consumers health. Customers confidence in the integrity of the food supply could be hampered by inappropriate food safety measures. A lack of measures and reliable assays to evaluate and maintain a good control of food characteristics may affect the food industry economy and shatter consumer confidence. It is imperative to create and to establish fast and reliable analytical methods that allow a good and rapid analysis of food products during the whole food chain. Proteomics can represent a powerful tool to address this issue, due to its proven excellent quantitative and qualitative drawbacks in protein analysis. This review illustrates the applications of proteomics in the past few years in food science focusing on food of animal origin with some brief hints on other types. Aim of this review is to highlight the importance of this science as a valuable tool to assess food quality and safety. Emphasis is also posed in food processing, allergies, and possible contaminants like bacteria, fungi, and other pathogens.

Differential effect of lithium on spermidine/spermine N1-acetyltransferase expression in suicidal behaviour

An altered polyamine system has been suggested to play a key role in mood disorders and suicide, a hypothesis corroborated by the evidence that lithium inhibits the polyamine mediated stress response in the rat brain. Recent post-mortem studies have shown that spermidine/spermine N1-acetyltransferase (SAT1), the key regulator of cellular polyamine content, is under-expressed in brains from suicide victims compared to controls. In our study we tested the effect of in vitro lithium treatment on SAT1 gene and protein expression in B lymphoblastoid cell lines (BLCLs) from bipolar disorder (BD) patients who committed suicide (and for which BLCLs were collected prior to their death), BD patients with high and low risk of suicide and a sample of non-psychiatric controls. Baseline mRNA levels were similar in the four groups of subjects (p > 0.05). Lithium had no effect in suicide completers (p > 0.05) while it significantly increased SAT1 expression in the high risk (p < 0.001) and low risk (p < 0.01) groups as well as in controls (p < 0.001). Protein and mRNA levels were not correlated; lithium significantly reduced protein levels only in the control sample (p < 0.05). Our findings suggest that SAT1 transcription is influenced by lithium and that this effect is altered in BD patients who completed suicide, further supporting a role for polyamines in suicide.

Direct analytical sample quality assessment for biomarker investigation: qualifying cerebrospinal fluid samples.

Measurement of biochemical markers represents an important aid to clinicians in the early diagnosis and prognosis of neurological diseases. Many factors can contribute to increase the chances that a biomarker study becomes successful. In a cerebrospinal fluid analysis (CSF), more than 84% of laboratory errors can be attributed to several preanalytical variables that include CSF collection, storage, and freeze thawing cycles. In this concept paper, we focus on some critical issues arising from basic proteomics investigation in order to highlight some key elements of CSF quality control. Furthermore, we propose a direct assessment of sample quality (DASQ) by applying a fast MALDI‐TOF‐MS methodology to evaluate molecular features of sample degradation and oxidation. We propose DASQ as a fast and simple initial step to be included in large‐scale projects for neurological biomarker studies. In fact, such a procedure will improved the development of standardized protocols in order to have well‐characterized CSF biobanks.

Identification of immunoreactive proteins of Mycobacterium avium subsp. paratuberculosis

Mycobacterium avium subsp. paratuberculosis (MAP) is the cause of a chronic enteritis of ruminants (bovine paratuberculosis (PTB)—Johnes disease) that is associated with enormous worldwide economic losses for the animal production. Diagnosis is based on observation of clinical signs, the detection of antibodies in milk or serum, or evaluation of bacterial culture from feces. The limit of these methods is that they are not able to detect the disease in the subclinical stage and are applicable only when the disease is already advanced. For this reason, the main purpose of this study is to use the MAP proteome to detect novel immunoreactive proteins that may be helpful for PTB diagnoses. 2DE and 2D immunoblotting of MAP proteins were performed using sera of control cattle and PTB‐infected cattle in order to highlight the specific immunoreactive proteins. Among the assigned identifiers to immunoreactive spots it was found that most of them correspond to surface‐located proteins while three of them have never been described before as antigens. The identification of these proteins improves scientific knowledge that could be useful for PTB diagnoses. The sequence of the identified protein can be used for the synthesis of immunoreactive peptides that could be screened for their immunoreaction against bovine sera infected with MAP. All MS data have been deposited in the ProteomeXchange consortium with identifier PXD001159 and DOI 10.6019/PXD001159.

Changes in protein expression profiles in bovine endometrial epithelial cells exposed to E. coli LPS challenge

E. coli is one of the most frequently involved bacteria in uterine diseases. Lipopolysaccharide (LPS) is a component of the outer membrane of Gram-negative bacteria involved in pathogenic processes leading to post-partum metritis and endometritis in cattle. It also causes inflammation of the endometrium. The increase of cell proliferation by LPS is part of the inflammatory process. The aim of this study was to investigate possible changes in protein expression in relation to the proliferative response of bEECs after challenge with E. coli-LPS. In vitro culture of bEECs was performed from cow genital tracts collected at a slaughterhouse. In passage 5, bEECs from each of 9 cows (3 series of 3 cows) were exposed to 0, 8, and 16 μg ml-1 LPS for 72 h. At time 0 and 72 h later, attached cells/living cells were counted and for each time and LPS dosage, cells were frozen for proteomic analyses. All samples from the 3 series were analyzed by 2-D gel electrophoresis coupled to MALDI-TOF/TOF mass spectrometry. The samples from the first series were subjected to shotgun nLC-MS/MS analysis. From the whole differential proteomics analysis, 38 proteins were differentially expressed (p < 0.05 to p < 0.001) following exposure to LPS. Among them, twenty-eight were found to be up-regulated in the LPS groups in comparison to control groups and ten were down-regulated. Differentially expressed proteins were associated with cell proliferation and apoptosis, transcription, destabilization of cell structure, oxidative stress, regulation of histones, allergy and general cell metabolism pathways. The de-regulations induced by LPS were consistent with the proliferative phenotype and indicated strong alterations of several cell functions. In addition, some of the differentially expressed proteins relates to pathways activated at the time of implantation. The specific changes induced through those signals may have negative consequences for the establishment of pregnancy.

Exploring the neural mechanisms of finasteride: a proteomic analysis in the nucleus accumbens

The enzyme 5α-reductase (5αR) catalyzes the conversion of progesterone and testosterone into neuroactive steroids implicated in a wide array of behavioral functions. The prototypical 5αR inhibitor, finasteride (FIN), is clinically approved for the treatment of androgenic alopecia and benign prostatic hyperplasia. Recent evidence has shown that FIN, albeit generally well tolerated, can induce untoward psychological effects in a subset of patients; furthermore, this drug may have therapeutic efficacy for a number of different neuropsychiatric conditions, ranging from Tourette syndrome to schizophrenia. In rat models of these conditions, FIN has been shown to block the effects of dopamine receptors in the nucleus accumbens (NAcc), a key terminal of the dopamine mesolimbic system. The biological underpinnings of these effects, however, remain mostly elusive. To elucidate the neurochemical networks that may be responsible for the behavioral effects of FIN, we evaluated the proteomic profile of the NAcc following acute (100mg/kg, IP) and subchronic (7 days; 100mg/kg/day, IP) treatment with this drug, in comparison with vehicle treatment (n=5/group). Two-dimensional electrophoresis (2-DE) analysis coupled to mass spectrometry revealed significant changes in the expression of nine proteins (CRMP2, PSMD1, STX18, KCNC3, CYP255, GABRP, GABT, PRPS1, CYP2B3), which were further analyzed by ontological classification (PANTHER). These results point to a number of novel potential chemical targets of FIN, and may help elucidate the underpinnings of FINs behavioral effects and therapeutic potential for neuropsychiatric disorders.

Direct Assessment of Plasma/Serum Sample Quality for Proteomics Biomarker Investigation

Blood proteome analysis for biomarker discovery represents one of the most challenging tasks to be achieved through clinical proteomics due to the sample complexity, such as the extreme heterogeneity of proteins in very dynamic concentrations, and to the observation of proper sampling and storage conditions. Quantitative and qualitative proteomics profiling of plasma and serum could be useful both for the early detection of diseases and for the evaluation of pathological status. Two main sources of variability can affect the precision and accuracy of the quantitative experiments designed for biomarker discovery and validation. These sources are divided into two categories, pre-analytical and analytical, and are often ignored; however, they can contribute to consistent errors and misunderstanding in biomarker research. In this chapter, we review critical pre-analytical and analytical variables that can influence quantitative proteomics. According to guidelines accepted by proteomics community, we propose some recommendations and strategies for a proper proteomics analysis addressed to biomarker studies.