Bioinformatics Approaches Applied to the Discovery of Antifungal Peptides.

Antifungal peptides (AFPs) comprise a group of substances with a broad spectrum of activities and complex action mechanisms. They develop in nature via an evolutionary process resulting from the interactions between hosts and pathogens. The AFP database is experimentally verified and curated from research articles, patents, and public databases. In this review, we compile information about the primary databases and bioinformatics tools that have been used in the discovery of AFPs during the last 15 years. We focus on the classification and prediction of AFPs using different physicochemical properties, such as polarity, hydrophobicity, hydrophilicity, mass, acidic, basic, and isoelectric indices, and other structural properties. Another method for discovering AFPs is the implementation of a peptidomic approach and bioinformatics filtering, which gave rise to a new family of peptides that exhibit a broad spectrum of antimicrobial activity against Candida albicans with low hemolytic effects. The application of machine intelligence in the sphere of biological sciences has led to the development of automated tools. The progress made in this area has also paved the way for producing new drugs more quickly and effectively. However, we also identified that further advancements are still needed to complete the AFP libraries.

Quantitative Proteomic Study Unmasks Fibrinogen Pathway in Polycystic Liver Disease.

(1) Background: Polycystic liver disease (PLD) is a heterogeneous group of congenital disorders characterized by bile duct dilatation and cyst development derived from cholangiocytes. Nevertheless, the cystogenesis mechanism is currently unknown and the PLD treatment is limited to liver transplantation. Novel and efficient therapeutic approaches are th6us needed. In this context, the present work has a principal aim to find novel molecular pathways, as well as new therapeutic targets, involved in the hepatic cystogenesis process. (2) Methods: Quantitative proteomics based on SWATH-MS technology were performed comparing hepatic proteomes of Wild Type and mutant/polycystic livers in a polycystic kidney disease (PKD) murine model (Pkd1cond/cond;Tam-Cre-/+). (3) Results: We identified several proteins altered in abundance, with two-fold cut-off up-regulation or down-regulation and an adjusted p-value significantly related to hepatic cystogenesis. Then, we performed enrichment and a protein-protein analysis identifying a cluster focused on hepatic fibrinogens. Finally, we validated a selection of targets by RT-qPCR, Western blotting and immunohistochemistry, finding a high correlation with quantitative proteomics data and validating the fibrinogen complex. (4) Conclusions: This work identified a novel molecular pathway in cystic liver disease, highlighting the fibrinogen complex as a possible new therapeutic target for PLD.

Human obese white adipose tissue sheds depot-specific extracellular vesicles and reveals candidate biomarkers for monitoring obesity and its comorbidities.

Extracellular vesicles (EVs) have been recently postulated as key players in metabolic disorders emerging as an alternative way of paracrine/endocrine communication. However, the nature of EVs shed by adipose tissue (AT) and their role in obesity is still very limited. Here, we isolated human morbid obese visceral (VAT) and subcutaneous (SAT) whole AT shed EVs from donors submitted to bariatric surgery to characterize their protein cargo by qualitative and quantitative/SWATH mass spectrometry analysis. We identified 574 different proteins shed by morbid obese VAT and 401 proteins in those from SAT, establishing the first obese AT EV proteome reference map. Only 50% of identified proteins in VAT vesicles were common to those in SAT; additionally, EVs shed by obese VAT showed more AT and obesity-related adipokines than SAT. Functional classification shows that obese VAT vesicles exhibit an enrichment of proteins implicated in AT inflammation and insulin resistance such as TGFBI, CAVN1, CD14, mimecan, thrombospondin-1, FABP-4 or AHNAK. Selected candidate biomarkers from the quantitative-SWATH analysis were validated in EVs from independent morbid obese and from moderate obese to lean individuals showing that morbid obese VAT vesicles are characterized by a diminution of syntenin 1 and the elevation of TGFBI and mimecan. Interestingly, TGFBI and mimecan containing vesicles could be detected and quantified at circulating level in plasma. Thus, a significant elevation of -TGFBI-EVs was detected on those obese patients with a history of T2D compared to nondiabetic, and an augmentation of mimecan-EVs in obese plasma compared to those in healthy lean individuals. Thus, we conclude that obese AT release functional EVs carrying AT and obesity candidate biomarkers which vary regarding the AT of origin. Our findings suggest that circulating EV-TGFBI may facilitate monitoring T2D status in obese patients, and EV-mimecan may be useful to track adiposity, and more precisely, visceral obesity.

Biomarkers in Glycogen Storage Diseases: An Update.

Glycogen storage diseases (GSDs) are a group of 19 hereditary diseases caused by a lack of one or more enzymes involved in the synthesis or degradation of glycogen and are characterized by deposits or abnormal types of glycogen in tissues. Their frequency is very low and they are considered rare diseases. Except for X-linked type IX, the different types are inherited in an autosomal recessive pattern. In this study we reviewed the literature from 1977 to 2020 concerning GSDs, biomarkers, and metabolic imbalances in the symptoms of some GSDs. Most of the reported studies were performed with very few patients. Classification of emerging biomarkers between different types of diseases (hepatics GSDs, McArdle and PDs and other possible biomarkers) was done for better understanding. Calprotectin for hepatics GSDs and urinary glucose tetrasaccharide for Pompe disease have been approved for clinical use, and most of the markers mentioned in this review only need clinical validation, as a final step for their routine use. Most of the possible biomarkers are implied in hepatocellular adenomas, cardiomyopathies, in malfunction of skeletal muscle, in growth retardation, neutropenia, osteopenia and bowel inflammation. However, a few markers have lost interest due to a great variability of results, which is the case of biotinidase, actin alpha 2, smooth muscle, aorta and fibroblast growth factor receptor 4. This is the first review published on emerging biomarkers with a potential application to GSDs.

Effect of VSL#3 Probiotic in a Patient with Glycogen Storage Disease Type Ia and Irritable Bowel Disease-like Disease.

Gut Inflammatory bowel disease (IBD) is a group of chronic gastrointestinal disorders characterised by relapsing and remitting inflammation of the gastrointestinal tract. The two most common types of IBDs are ulcerative colitis and Crohn's disease. Patients with glycogen storage disease (GSD) type Ia present with gastrointestinal symptoms such as recurrent abdominal pain, bloating and changes in stool form or frequency, which is clinically difficult to distinguish from IBD. We report the case of a 36-year-old man with GSD type Ia and IBD-like disease. A commercial probiotic (VSL#3®) was chosen as a nutritional supplement treatment because of its high content of microbial species and strains. Three different tests were performed: normal-dose, no-dose and half-dose tests. The study periods for the normal-dose, no-dose and half-dose tests were 4 weeks from the treatment initiation, 72 h from the end of the previous period and 4 weeks to 6 months after the end of the 72-h period, respectively. When the probiotic treatment was stopped, he experienced several symptoms similar to those before the start of the treatment. The intestinal symptoms were less severe with the half-dose nutritional supplement treatment than with no treatment. Probiotics may reduce the number of irritable gut episodes and improve the patient's well-being and overall quality of life. More studies are needed to determine whether the improvement in more severe cases of GSD is due mainly to changes in the composition of the gut microbiota, as in this patient.

Biofilms and vulvovaginal candidiasis.

Candida species, including C. albicans, are part of the mucosal flora of most healthy women, and inhabit the gastrointestinal and genitourinary tracts. Under favourable conditions, they can colonize the vulvovaginal mucosa, giving rise to symptomatic vulvovaginal candidiasis (VVC). The mechanism by which Candida spp. produces inflammation is unknown. Both, the blastoconidia and the pseudohyphae are capable of destroying the vaginal epithelium by direct invasion. Although the symptoms are not always related to the fungal burden, in general, VVC is associated with a greater number of yeasts and pseudohyphae. Some years ago, C. albicans was the species most frequently involved in the different forms of VVC. However, infections by different species have emerged during the last two decades producing an increase in causative species of VVC such as C. glabrata, C. parapsilosis, C. krusei and C. tropicalis. Candida species are pathogenic organisms that have two forms of development: planktonic and biofilm. A biofilm is defined as a community of microorganisms attached to a surface and encompassed by an extracellular matrix. This form of presentation gives microorganisms greater resistance to antifungal agents. This review, about Candia spp. with a special emphasis on Candida albicans discusses specific areas such as biofilm structure and development, cell morphology and biofilm formation, biofilm-associated gene expression, the cell surface and adherence, the extracellular matrix, biofilm metabolism, and biofilm drug resistance in vulvovaginitis biofilms as an important virulence factor in fungi.

Recent advances in melanoma research via "omics" platforms.

Melanoma has a high mortality rate and metastatic melanoma is highly resistant to conventional therapies. "Omics" fields such as proteomics and microRNA and exosome studies have provided new knowledge to complement the information generated by genomic studies. This work aimed to review the current status of biomarker discovery for melanoma through multi-"omics" platforms. A few sets of novel microRNAs and proteins are described, some of them with important implications in suppressing melanoma at different stages. Upregulation of genes involved in angiogenesis, immunosuppressive factors, modification of stroma, capture of melanoma cells in lymph nodes and factors responsible for tumour cell recruitment have been identified in exosomes, among molecules with other functions. A remarkable series of proteins involved in epithelial-mesenchymal/mesenchymal-epithelial transitions, inflammation, motility, proliferation and progression processes, centrosome amplification, aneuploidy, inhibition of CD8+ effector T-cells, and metastasis in general were identified. Genomic and protein-protein interactions or metabolome levels were not analysed. Proteomics tools such as Orbitrap shotgun mass spectrometry or deep mining proteomic analysis utilizing high-resolution reversed phase nanoseparation in combination with mass spectrometry are also discussed. The application of these tools together with bioinformatics approaches applied to the clinical setting will enable the implementation of personalized medicine in the near future.

[Application of an obesity treatment protocol for 2 years]. / Aplicación de un protocolo de tratamiento de obesidad durante 2 años.

OBJECTIVE: To evaluate the effectiveness of a clinic protocol used in the Complexo Hospitalario Universitario de Vigo (CHUVI) for obese outpatients. PATIENTS AND METHODS: The study included 47 obese outpatients. All of them were evaluated in clinical department and applied the obesity protocol for a period of 2 years. Variables as weight, BMI and levels of obesity in the initial and final time were evaluated. RESULTS AND DISCUSSION: In obese patients between 26 and 65 years was observed a tendency to reduce their degree of obesity, with significant differences in 2012 compared to 2010. There are differences in behavior between men and women in terms of change in obesity graduation. CONCLUSIONS: In our study we found differences in behavior between men and women in terms of grade change in obesity, in women there is a greater tendency to reduce.

Objetivo: Evaluar la eficacia de un protocolo clínico para pacientes obesos utilizado en la consulta de obesidad del Complexo Hospitalario Universitario de Vigo (CHUVI). Pacientes y métodos: En el estudio participaron 47 pacientes procedentes de la consulta de obesidad del CHUVI. Todos ellos fueron evaluados en consulta y siguieron el protocolo de obesidad durante un periodo de 2 años. Se evaluaron variables como el peso, el IMC y los grados de obesidad en el momento inicial y final. Resultados y discusión: En pacientes obesos entre 26 y 65 años se observa una tendencia a disminuir su grado de obesidad, con diferencias significativas en el 2012 respecto al 2010. Hay diferencias de comportamiento entre hombres y mujeres en cuanto al cambio de graduación en la obesidad. Conclusiones: En nuestro estudio hemos comprobado diferencias de comportamiento entre hombres y mujeres en cuanto al cambio de graduación en la obesidad; en las mujeres hay una mayor tendencia a reducirlo.

Aplicación de un protocolo de tratamiento de obesidad durante 2 años / Application of an obesity treatment protocol for 2 years

Objetivo: Evaluar la eficacia de un protocolo clínico para pacientes obesos utilizado en la consulta de obesidad del Complexo Hospitalario Universitario de Vigo (CHUVI). Pacientes y métodos: En el estudio participaron 47 pacientes procedentes de la consulta de obesidad del CHUVI. Todos ellos fueron evaluados en consulta y siguieron el protocolo de obesidad durante un periodo de 2 años. Se evaluaron variables como el peso, el IMC y los grados de obesidad en el momento inicial y final. Resultados y discusión: En pacientes obesos entre 26 y 65 años se observa una tendencia a disminuir su grado de obesidad, con diferencias significativas en el 2012 respecto al 2010. Hay diferencias de comportamiento entre hombres y mujeres en cuanto al cambio de graduación en la obesidad. Conclusiones: En nuestro estudio hemos comprobado diferencias de comportamiento entre hombres y mujeres en cuanto al cambio de graduación en la obesidad; en las mujeres hay una mayor tendencia a reducirlo (AU)

Objective: To evaluate the effectiveness of a clinic protocol used in the Complexo Hospitalario Universitario de Vigo (CHUVI) for obese outpatients. Patients and methods: The study included 47 obese outpatients. All of them were evaluated in clinical department and applied the obesity protocol for a period of 2 years. Variables as weight, BMI and levels of obesity in the initial and final time were evaluated. Results and discussion: In obese patients between 26 and 65 years was observed a tendency to reduce their degree of obesity, with significant differences in 2012 compared to 2010. There are differences in behavior between men and women in terms of change in obesity graduation. Conclusions: In our study we found differences in behavior between men and women in terms of grade change in obesity, in women there is a greater tendency to reduce (AU)

Clinical application of development of nonantibiotic macrolides that correct inflammation-driven immune dysfunction in inflammatory skin diseases.

BACKGROUND: Inflammation-driven immune dysfunction supports the development of several chronic human disorders including skin diseases. Nonantibiotic macrolides have anti-inflammatory and/or immunomodulatory activity that suggests the exploitation of these in the treatment of skin diseases characterized by inflammatory disorders. MATERIALS AND METHODS: We performed an extensive review of the nonantibiotic macrolide literature published between 2005 and 2012, including cross-references of any retrieved articles. We also included some data from our own experience. RESULTS: Calcineurin antagonists such as tacrolimus and ascomycins (e.g., pimecrolimus) act by inhibiting the activation of the nuclear factor for activated T cells (NFAT). There are new applications for these macrolides that have been available for several years and have been applied to skin and hair disorders such as atopic dermatitis, oral lichen planus, vitiligo, chronic autoimmune urticaria, rosacea, alopecia areata, pyoderma gangrenosum, Behcet's disease, neutrophilic dermatosis, and lupus erythematosus. We also reviewed new macrolides, like rapamycin, everolimus, and temsirolimus. In addition to the literature review, we report a novel class of nonantibiotic 14-member macrocycle with anti-inflammatory and immunomodulatory effects. CONCLUSIONS: This paper summarizes the most important clinical studies and case reports dealing with the potential benefits of nonantibiotic macrolides which have opened new avenues in the development of anti-inflammatory strategies in the treatment of cutaneous disorders.

Unveiling New Molecular Factors Useful for Detection of Pelvic Inflammatory Disease due to Chlamydia trachomatis Infection.

Background. Untreated Chlamydia trachomatis infections in women can result in disease sequelae such as pelvic inflammatory disease (PID), ultimately culminating in tubal occlusion and infertility. While nucleic acid amplification tests can effectively diagnose uncomplicated lower genital tract infections, they are not suitable for diagnosing upper genital tract pathological sequelae. Objective. The purpose of this paper was to provide a comprehensive review of new molecular factors associated with the diagnosis and prognosis of PID. Material and Methods. The literature was searched using the key words "Chlamydia trachomatis infections," "pelvic inflammatory disease," and "molecular factors" in the PubMed database. Relevant articles published between 1996 and 2012 were evaluated. Conclusions. The use of new molecular factors could potentially facilitate earlier diagnosis and prognosis in women with PID due to C. trachomatis infection.

New Perspectives of "omics" Applications in Melanoma Research.

BACKGROUND: Oncoproteomics is the study of proteins and their interactions in a cancer cell by proteomic technologies and has the potential to revolutionize clinical practice, including cancer diagnosis. Recent technological advances in the analysis of the human genome have opened the door to improving our primitive understanding of the gene expression patterns in cancer. The examination of the phenotypic and (epi) genetic changes in cutaneous melanoma has identified several genes deemed central to the development and progression of melanoma. METHODS: A review of the literature was performed to determine the role of epigenetic modifications in human melanoma. The role of array-based high-throughput gene expression analysis in understanding the specific genes involved as well as the pathways and the comparative gene expression patterns of primary and metastatic melanoma. The development and clinical application of selective pharmacologic agents are also discussed. RESULTS: We identified several articles that have extensively studied the role of epigenetics in melanoma, further elucidating the complex processes involved in gene regulation and expression. Other studies utilizing gene microarray analysis and other whole genome approaches reveal a wide array of genes and expression patterns in human melanoma. Several genes have been identified as potential prognostic markers of tumor progression and overall clinical outcome. CONCLUSIONS: High-throughput gene expression analysis has had a major impact in melanoma research. Several gene expression platforms have provided insight into the gene expression patterns in melanoma. Such data will provide foundations for the future development of prognostic markers and improved targeted therapies for patients with melanoma.