Application of PolyPRep tools on HIV protease polyproteins using molecular docking

Abstract In recent years, the development of high-throughput technologies for obtaining sequence data leveraged the possibility of analysis of protein data in silico. However, when it comes to viral polyprotein interaction studies, there is a gap in the representation of those proteins, given their size and length. The prepare for studies using state-of-the-art techniques such as Machine Learning, a good representation of such proteins is a must. We present an alternative to this problem, implementing a fragmentation and modeling protocol to prepare those polyproteins in the form of peptide fragments. Such procedure is made by several scripts, implemented together on the workflow we call PolyPRep, a tool written in Python script and available in GitHub. This software is freely available only for noncommercial users.

Resumo Nos últimos anos, o desenvolvimento de tecnologias de alto rendimento para obtenção de dados sequenciais potencializou a possibilidade de análise de dados proteicos in silico. No entanto, quando se trata de estudos de interação de poliproteínas virais, existe uma lacuna na representação dessas proteínas, devido ao seu tamanho e comprimento. Para estudos utilizando técnicas de ponta como o Aprendizado de Máquina, uma boa representação dessas proteínas é imprescindível. Apresentamos uma alternativa para este problema, implementando um protocolo de fragmentação e modelagem para preparar essas poliproteínas na forma de fragmentos de peptídeos. Tal procedimento é feito por diversos scripts, implementados em conjunto no workflow que chamamos de PolyPRep, uma ferramenta escrita em script Python e disponível no GitHub. Este software está disponível gratuitamente apenas para usuários não comerciais.

Application of PolyPRep tools on HIV protease polyproteins using molecular docking / Aplicação da ferramenta PolyPRep em poliproteínas de protease de HIV usando docking molecular

Abstract In recent years, the development of high-throughput technologies for obtaining sequence data leveraged the possibility of analysis of protein data in silico. However, when it comes to viral polyprotein interaction studies, there is a gap in the representation of those proteins, given their size and length. The prepare for studies using state-of-the-art techniques such as Machine Learning, a good representation of such proteins is a must. We present an alternative to this problem, implementing a fragmentation and modeling protocol to prepare those polyproteins in the form of peptide fragments. Such procedure is made by several scripts, implemented together on the workflow we call PolyPRep, a tool written in Python script and available in GitHub. This software is freely available only for noncommercial users.

Resumo Nos últimos anos, o desenvolvimento de tecnologias de alto rendimento para obtenção de dados sequenciais potencializou a possibilidade de análise de dados proteicos in silico. No entanto, quando se trata de estudos de interação de poliproteínas virais, existe uma lacuna na representação dessas proteínas, devido ao seu tamanho e comprimento. Para estudos utilizando técnicas de ponta como o Aprendizado de Máquina, uma boa representação dessas proteínas é imprescindível. Apresentamos uma alternativa para este problema, implementando um protocolo de fragmentação e modelagem para preparar essas poliproteínas na forma de fragmentos de peptídeos. Tal procedimento é feito por diversos scripts, implementados em conjunto no workflow que chamamos de PolyPRep, uma ferramenta escrita em script Python e disponível no GitHub. Este software está disponível gratuitamente apenas para usuários não comerciais.

Exploring the microbiome, antibiotic resistance genes, mobile genetic element, and potential resistant pathogens in municipal wastewater treatment plants in Brazil.

Wastewater treatment plants (WWTPs) have been widely investigated in Europe, Asia and North America regarding the occurrence and fate of antibiotic resistance (AR) elements, such as antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and antibiotic resistant bacteria and pathogens. However, monitoring data about AR elements in municipal WWTPs in Brazil are scarce. This study investigated the abundance of intI1, five ARGs (sul1, tetA, blaTEM, ermB and qnrB) and 16S rRNA in raw and treated wastewater of three WWTPs, using different sewage treatments named CAS (Conventional activated sludge), UASB/BTF (UASB followed by biological trickling filter) and MAS/UV (modified activated sludge with UV disinfection stage). Bacterial diversity and the presence of potentially pathogenic groups were also evaluated, and associations between genetic markers and the bacterial populations were presented. All WWTPs decreased the loads of genetic markers finally discharged to receiving water bodies and showed no evidence of being hotspots for antimicrobial resistance amplification in wastewater, since the abundances of intI1 and ARGs within the bacterial population were not increased in the treated effluents. UASB/BTF showed a similar performance to that of the CAS and MAS/UV, reinforcing the sanitary and environmental advantages of this biological treatment, widely applied for wastewater treatment in warm climate regions. Bacterial diversity and richness increased after treatments, and bacterial communities in wastewater samples differed due to catchment areas and treatment typologies. Potential pathogenic population underwent considerable decrease after the treatments; however, strong significant correlations with intI1 and ARGs revealed potential multidrug-resistant pathogenic bacteria (Aeromonas, Arcobacter, Enterobacter, Escherichia-Shigella, Stenotrophomonas and Streptococcus) in the treated effluents, although in reduced relative abundances. These are contributive results for understanding the fate of ARGs, MGEs and potential pathogenic bacteria after wastewater treatments, which might support actions to mitigate their release into Brazilian aquatic environments in the near future.

Pseudo-Fringe sign in frontal fibrosing alopecia-like cutaneous lupus erythematosus.

BACKGROUND: Marginal alopecia presents itself frequently in dermatological practice. For patients who present peripheral scalp hair loss, cicatricial and non-cicatricial alopecia should be considered, such as ophiasis, traction alopecia and frontal fibrosing alopecia. In spite of the several types of hair loss that have been described in cutaneous lupus erythematosus, the 'pseudo-fringe sign' had never been observed in such patents. OBJECTIVE: This study aims at including the 'pseudo-fringe sign' as another possibility of clinical manifestation in patients with cutaneous lupus erythematosus. METHODS: A case report of a 67-year-old lady with the diagnosis of lupus erythematosus and peripheral hair loss is shown in this study; the respective differential diagnosis have also been discussed. RESULTS: The diagnosis of a scarring alopecia caused by lupus erythematosus was established with dermoscopy and histopathology. CONCLUSION: Cutaneous lupus erythematosus is another diagnostic possibility for patients who display the 'pseudo-fringe sign'.

Application of PolyPRep tools on HIV protease polyproteins using molecular docking.

In recent years, the development of high-throughput technologies for obtaining sequence data leveraged the possibility of analysis of protein data in silico. However, when it comes to viral polyprotein interaction studies, there is a gap in the representation of those proteins, given their size and length. The prepare for studies using state-of-the-art techniques such as Machine Learning, a good representation of such proteins is a must. We present an alternative to this problem, implementing a fragmentation and modeling protocol to prepare those polyproteins in the form of peptide fragments. Such procedure is made by several scripts, implemented together on the workflow we call PolyPRep, a tool written in Python script and available in GitHub. This software is freely available only for noncommercial users.

Jarisch-Herxheimer reaction among syphilis patients in Rio de Janeiro, Brazil.

The Jarisch-Herxheimer reaction (JHR) is a syndrome observed after antimicrobial treatment of some infectious diseases. The syndrome has clinical characteristics of an inflammatory reaction to antibiotic treatment. A prospective study of patients with a clinical and laboratory diagnosis of syphilis was conducted at a sexually transmitted diseases clinic in Rio de Janeiro, Brazil. Patients were treated with benzathine penicillin and observed for the JHR. A total of 115 patients were included in this study. Fifty-one patients (44%) had secondary syphilis; 37 (32%), primary; 26 (23%), latent; and one (1%), tertiary syphilis. Ten patients (9%) developed the JHR. All JHRs occurred in patients with secondary and latent syphilis. No patients experienced an allergic reaction to penicillin. The JHR occurred less frequently than in previous studies. It is important that health-care professionals recognize the clinical characteristics of the JHR so that it is not misinterpreted as an allergic reaction to penicillin.

Breast cancer patients with micrometastases in sentinel lymph nodes: differences considering additional metastatic lymph nodes.

AIMS: Characterization of breast cancer patients with micrometastases in sentinel lymph node (SLN) and establish differences between micrometastatic breast cancers with additional metastatic lymph nodes (LNS) versus no other lymph node invasion. METHODS: Analysis of 30 breast cancers, N1mi or pN0(i+), diagnosed and treated in our department from July 2000 to July 2008. RESULTS: Micrometastases in SLNs were found in 30 patients. Complete axillary dissection revealed other metastatic LNs in 24%. Concerning breast cancers with additional LN invasion versus no other LN invasion, tumors located in the superior-external quadrant were more frequent in the former group. Other characteristics as clinical presentation, histological subtype, focality, cytonuclear grade, hormone receptors and Her2 expression were not significantly different in either group. Regarding SLN invasion, the presence of at least two micrometastatic foci were significantly more relevant in patients with other metastatic LN invasion (p < 0.01). Micrometastases diagnosed only after immunohistochemistry (IHC) were exclusively found in patients without other LN invasion, reaching statistical significance (p < 0.05). CONCLUSIONS: Complete axillary dissection revealed additional LN invasion in 24% of patients with micrometastases in the SLN. Tumors with additional LN invasion were more frequently found in the superior external quadrant and SLNs harbored at least two micrometastatic foci. Micrometastases diagnosed exclusively by IHC techniques were more relevant in cases without additional lymph node invasion.

The role of HLA antigens in the development of paracoccidioidomycosis.

BACKGROUND: Paracoccidioidomycosis is a systemic granulomatous disease that involves primarily the lungs and may disseminate to other organs and systems. It is caused by Paracoccidioides brasiliensis, a fungus that exhibits reversible thermal dimorphism and whose natural habitat is presently unknown. There are two main clinical forms: the acute (subacute) juvenile form and the chronic adult form. The former runs a more rapid course and is more severe than the latter. This mycosis is found throughout Latin America. Brazil accounts for 80% of reported cases. Presumably P. brasiliensis thrives in humid and hot places, especially near forests or farms. The infection is endemic in certain areas, especially in Brazil, Colombia and Venezuela, where nearly 100% of the population show cutaneous paracoccidioidina positive skin tests, indicating previous contact with the fungus, although a small percentage show clinical manifestations of the disease. METHODS: We compared the expression of HLA class I antigens in a healthy group (control) and in a group of patients with paracoccidioidomycosis (chronic adult form) using the Terasaki lymphocytotoxicity test modified by Amos for HLA antigen analysis. AIMS: To discover indications of whether or not individual susceptibility to P. brasiliensis might depend on some specific immunological defect. RESULTS: There is no evidence of association between a specific HLA antigen and paracoccidioidomycosis in the subjects studied. Further investigations are recommended.

[Comparative study of benign and malignant tumor of the ovary]. / Estudo comparativo de tumores benignos e malignos do ovário.

This study concerns the evaluation of epidemiologic, clinical and laboratory parameters and the comparison of the multiple parameters between benign and malignant tumors of the ovary to establish significant criteria allowing a Malignant Risk Index to be defined. The incidence of ovarian cancer was higher among post-menopausal women with no use of oral contraceptives. There was no correlation between sterility, infertility or nulliparity and ovarian cancer. The age at menarche, menopause or first term delivery showed no influence on the risk of ovarian cancer. The Authors verified significant differences (p < 0.001) in the levels of serum CA 125 between patients with benign ovarian tumors and patients with ovarian cancer. Those differences showed high sensitivity and specificity. Ultrasonographic criteria were difficult to interpret because of their subjectivity. However, there were significant differences concerning the size of the tumors, the bilaterality, the solid component and ascites; all these criteria were more frequent among malignant masses. It is imperative to define a high confidence degree Malignant Risk Index for ovarian tumors allowing the establishment of screening strategies applicable to risk populations.

Pharmacological characterization of Sephadex-induced oedema in rat paws: predominant role of serotonin and platelet-activating factor.

An intravenous injection of Sephadex beads has been used to induce lung inflammation and bronchial hyperreactivity in small animals. In the present study, we injected Sephadex beads (0.3-5.5 mg/paw) into rat paws and followed the resulting inflammation plethysmometrically. Our results show that Sephadex beads induced a significant and dose-dependent increase in the hindpaw volume at 5 min; it was maximal at 30-60 min and declined at 4 h. However, the paw volume remained significantly increased for up to 21 days. The initial 4-hour-oedema was confirmed by histopathology of the paw tissues, but the persistent increase in paw volume was related to a chronic inflammatory (granulomatous) response. The Sephadex-induced oedema was predominantly due to serotonin (5-HT) release since specific antagonists such as methysergide (1 mg/kg) and pizotifen (0.1-2 mg/kg) administered both systemically and locally were able to inhibit the oedema (10-100 microgram/paw) as could pretreatment with compound 48/80. In addition, platelet-activating factor (PAF) was also shown to be involved, since systemic pretreatment using the specific PAF antagonist BN 52021 (1 mg/kg) was able to inhibit the increase in paw volume induced by Sephadex. Effective doses of indomethacin (2 mg/kg), L-NAME (1 mg/kg), pyrilamine (1-2 mg/kg), ondansetron (1 mg/kg) and HOE 140 (1 mg/kg) did not affect the Sephadex-induced oedema, thus ruling out the participation of prostaglandins, nitric oxide, histamine, 5-HT3 receptors and bradykinin in its development. Since the late increases in paw volume induced by Sephadex were reduced by pretreatment of the animals with the immunosuppressive drugs rapamycin and dexamethasone but not cyclosporin, our results also suggested that distinct immunological pathways may be involved in the modulation of the chronic phase of inflammation induced by Sephadex beads in rat paws.

[Mycetoma due to Actinomadura madurae. A report of 2 cases]. / Micetoma por Actinomadura madurae. Relato de dois casos.

Actinomadura madurae mycetoma was diagnosed in two patients by the dermatologic outpatient clinic of the Clementino Fraga Filho University Hospital (UFRJ) and the Antonio Pedro University Hospital (UFF). The first case was a 27-year-old Negro male from the outskirts of Rio de Janeiro, who was injured prior to the onset of the disease in 1988. The affected left foot showed swelling, nodules, sinus tracts, purulent discharge containing grains, and serious bone involvement with lytic lesions. Histological examination showed deeply basophilic stained grains with typical wide-fringed borders. The mycological examination revealed an actinomycete identified as A. madurae by culture. Oral tetracycline for six months did not improve the clinical-radiological picture and the patient was submitted to amputation. The second case was a 70-year-old white male, with previous injury in 1974, which occurred in Pernambuco State. Enlargement of the right foot draining sinuses formation with discharge of pus and grains. In tissue sections the grains were large and surrounded by amorphous eosinophilic clubs radially oriented. There was discrete improvement by tetracycline and sulfonamide. No follow-up.

A test for the evaluation of ingestion by neutrophils.

A rapid, simple and inexpensive technique was developed to evaluate particle ingestion by neutrophils (PMNs) and alternatively investigate the activity of the complement system. Whole blood specimens, obtained in EDTA, were mixed with a suspension of activated Baker's yeast in minimal volumes (3 and 1 drops of each, respectively). The mixture was incubated at 37 degrees C for 1 h and centrifuged at 200 g for 5 min. The sediment was resuspended in FBS and blood films were stained with Giemsa. Two hundred PMNs/film were counted and the percentage of phagocytizing cells and the mean number of ingested particles per cell were determined. Samples from 11 male and 15 female subjects showed mean rates of 80.0 +/- 10.8 (SD) and 83.3 +/- 5.8 of PMNs with phagocytic vacuoles containing 2.9 +/- 0.5 and 3.2 +/- 0.7 ingested particles/cell, respectively. There were no statistically significant differences between sexes.