The impact of transformation zone representation on the frequency of abnormal cervical cytological results.

OBJECTIVE: To compare the frequency of abnormal cervical cytological results with and without representation of the transformation zone (TZ) in a medium-sized city in Brazil according to the Bethesda categorization. METHODS: We performed an analytical observational study evaluating cytological results over 15 years from conventional smears collected within the Public Brazilian Health System in Araçatuba, Brazil. Tests were stratified by age and cytological result according to Brazilian guidelines and the Bethesda System. RESULTS: There were 261,881 examinations, 159,251 with and 102,630 without TZ representation. The global frequency of abnormal results was higher in smears with TZ representation (crude odds ratio [OR] 4.03; 95% confidence interval [CI] [3.71-4.38]). Considering only women between 25 and 64 years (the target of the national guidelines), there were higher results for high-grade squamous intraepithelial lesions (OR 11.54; 95% CI 6.74-19.78), low-grade squamous intraepithelial lesions (OR 2.82; 95% CI 2.17-3.67) atypical squamous cell in which high-grade intraepithelial lesion cannot be excluded (OR 6.90; 95% CI 4.91-9.66) and atypical squamous cell of undetermined significance (OR 3.53; 95% CI 3.11-4.01) among cases with TZ representation. CONCLUSION: Samples with TZ representation were associated with higher rates of abnormal results. Health professionals should be regularly trained to understand the weakness of cytological examinations when the TZ is not represented, especially in developing countries.

Barriers to patient recruitment in a poststroke neurorehabilitation multicenter trial in Brazil.

There is a high demand for stroke rehabilitation in the Brazilian public health system, but most studies that have addressed rehabilitation for unilateral spatial neglect (USN) after stroke have been performed in high-income countries. Therefore, the aim of this study was to analyze USN patient recruitment in a multicenter noninvasive brain stimulation clinical trial performed in Brazil and to provide study design recommendations for future studies. We evaluated the reasons for exclusion of patients from a multicenter, randomized, double-blinded clinical trial of rehabilitation of USN patients after stroke. Clinical and demographic variables were compared between the included and excluded patients. A descriptive statistical analysis was performed. Only 173 of the 1953 potential neglect patients (8.8%) passed the initial screening. After screening evaluation, 87/173 patients (50.3%) were excluded for clinical reasons. Cognitive impairment led to the exclusion of 21/87 patients (24.1%). Low socioeconomic status led to the exclusion of 37/173 patients (21.4%). Difficulty obtaining transportation to access treatment was the most common reason for their exclusion (16/37 patients, 43.3%). The analyzed Brazilian institutions have potential for conducting studies of USN. The recruitment of stroke survivors with USN was restricted by the study design and limited financial support. A history of cognitive impairment, intracranial stenting or craniectomy, and lack of transportation were the most common barriers to participating in a multicenter noninvasive brain stimulation trial among patients with USN after stroke.

Cervical cytology results among pregnant and non-pregnant women in Brazil.

OBJECTIVE: To compare the prevalence of abnormal cervical smear results among pregnant and non-pregnant women with and without representation of the transformation zone (TZ) in a mid-sized city in Brazil. STUDY DESIGN: This observational analytical and retrospective study analyzed cervical smear results from pregnant and non-pregnant women in a mid-sized city in Brazil. Private data were collected at private clinics over seven years and from public services over 16 years. All results were reported according to Bethesda System. Pregnant women were separated from non-pregnant women, and women were stratified into two age groups (25-29 years and 30-34 years) in general analyses. For TZ representation and cytologic-histologic correlation, there was no age stratification. RESULTS: Among public services cervical smears, the frequency of atypical squamous cells of undetermined significance (ASC-US) was higher for pregnant women in the entire group (odds ratio [OR] 1.91; confidence interval [CI] 1.07-3.39) and among women from 30 to 40 years old (OR 2.79; CI 1.38-5.66). The same occurred for low-grade squamous intraepithelial lesion (LSIL) in the total group (OR 3.50; CI 1.44-8.53) and among women 30 to 40 years old (OR 4.57; CI 1.45-14.42). The frequency of ASC-US was higher in pregnant women with TZ representation exams than those without (OR 4.62; CI 2.17-9.84). The same occurred for those with atypical squamous cells, which cannot exclude high-grade squamous intraepithelial lesion (OR 9.81; CI 1.63-59.15) and LSIL (OR 10.47; CI 3.39-32.36). Among pregnant women with abnormal cervical smear results, 85.74% were followed up through cytology, and an average of 26.12% of patients underwent biopsy, of which almost all were positive for dysplasia. CONCLUSION: Pregnant and non-pregnant women did not differ in cervical smears with actual precursor lesions. Nevertheless, considering the opportunistic nature of Brazilian cervical cancer screening, prenatal visits present an opportunity to perform cervical smears in pregnant women. TZ representation correlated with higher rates of abnormal cervical smears, reinforcing the clinical importance of endocervical/metaplastic cell representation, including among pregnant women.

Barriers to patient recruitment in a poststroke neurorehabilitation multicenter trial in Brazil

There is a high demand for stroke rehabilitation in the Brazilian public health system, but most studies that have addressed rehabilitation for unilateral spatial neglect (USN) after stroke have been performed in high-income countries. Therefore, the aim of this study was to analyze USN patient recruitment in a multicenter noninvasive brain stimulation clinical trial performed in Brazil and to provide study design recommendations for future studies. We evaluated the reasons for exclusion of patients from a multicenter, randomized, double-blinded clinical trial of rehabilitation of USN patients after stroke. Clinical and demographic variables were compared between the included and excluded patients. A descriptive statistical analysis was performed. Only 173 of the 1953 potential neglect patients (8.8%) passed the initial screening. After screening evaluation, 87/173 patients (50.3%) were excluded for clinical reasons. Cognitive impairment led to the exclusion of 21/87 patients (24.1%). Low socioeconomic status led to the exclusion of 37/173 patients (21.4%). Difficulty obtaining transportation to access treatment was the most common reason for their exclusion (16/37 patients, 43.3%). The analyzed Brazilian institutions have potential for conducting studies of USN. The recruitment of stroke survivors with USN was restricted by the study design and limited financial support. A history of cognitive impairment, intracranial stenting or craniectomy, and lack of transportation were the most common barriers to participating in a multicenter noninvasive brain stimulation trial among patients with USN after stroke.

Using 14C-glyphosate to investigate the distribution of two formulations in transgenic glyphosate-resistant soybean.

Glyphosate residues in grain can be explained by the concentrations and formulations of glyphosate products. This study aimed to evaluate the residues from glyphosate formulations labeled with 14C-glyphosate applied to leaves of glyphosate-resistant soybean (GRS) in two life cycles by liquid scintillation spectrometry. Different plant tissues were analyzed after the end of the plants' life cycles. The experimental design was four repetitions of three treatments: Roundup® Original, Roundup Ready®, and unformulated glyphosate (control). The application of the dosing solution was 120 µL on the first four trifoliate leaves (10 µL per leaflet) of each plant, deposited manually with a 1-µL dispenser. All treatment solutions were calculated at a 1.2 kg a.e ha-1 of glyphosate. Glyphosate formulations of Roundup® Original and Roundup Ready® increased 14C-glyphosate distribution in GRS compared to the unformulated herbicide, regardless of the experiment (first or second cycle). Overall, the percentages of total radioactivity applied (18.33 kBq) found in grains were less than 5%. Grains, stems, and leaves showed the highest levels of herbicide residues compared to other parts of the plant. Despite the Roundup Ready® formulation having increased residues, the highest value found in grains, 1.95 mg kg-1, was less than 10 mg kg-1, the maximum residue limit (MRL) in Brazil.

Proposal of an iELISA for Mycoplasma bovis diagnosis in dairy cattle and associated risk factors / [Proposta de um iELISA para diagnóstico de Mycoplasma bovis em bovinos leiteiros e fatores de risco associados]

Mycoplasma bovis is a highly contagious agent associated with several pathologies in cattle. The detection of reactive antibodies to M. bovis by Indirect Enzyme-Linked Immunosorbent Assay (iELISA) identifies if there was an exposure to the microorganism. The current study aimed to optimize an iELISA from M. bovis total cell antigen, applying it to bovine serum samples, and to evaluate risk factors. Serum samples were obtained from 400 cows from 17 herds from Southeast Brazil. In the optimization of iELISA, the following was established: 2 µg/mL of antigen, sera dilution 1:300, and conjugate dilution 1:15000. The frequency was 62.3% (249/400) of reactive animals and 100% (17/17) of reactive herds. Risk factors were: herds with more than 100 animals (OR= 3.1; CI= 95%); Holstein breed (OR= 72.5; CI= 95%); cows (OR= 29.7; CI= 95%); intensive breeding system (OR= 3.3; CI= 95%); associated small ruminant production (OR= 4.4; CI= 95%); milk production above 500L (OR= 2.9; CI= 95%); no quarantine (OR= 1.5; CI= 95%); mechanical milking (OR= 5.5; CI= 95%) and cases of mastitis (OR= 5.5; CI= 95%). The proposed iELISA was able to detect antibodies reactive to M. bovis in bovine serum. Knowledge of these risk factors can assist in the implementation of prophylactic measures.(AU)

Mycoplasma bovis é um agente altamente contagioso relacionado a várias patologias em bovinos. A detecção de anticorpos reativos a M. bovis por Ensaio de Imunoadsorção Enzimática Indireto (iELISA) identifica se houve exposição ao microrganismo. O presente estudo teve como objetivo otimizar um iELISA de antígeno celular total de M. bovis, aplicando-o a amostras de soro bovino, bem como avaliar fatores de risco. Amostras de soro foram obtidas de 400 vacas de 17 rebanhos da Região Sudeste do Brasil. Na otimização do iELISA foram obtidos: 2µg/mL de antígeno, diluição dos soros 1:300 e do conjugado 1:15000. A frequência de animais reativos foi de 62,3% (249/400) e de 100% (17/17) para os rebanhos. Os fatores de risco foram: rebanhos com mais de 100 animais (OR= 3,1; IC= 95%); raça Holandesa (OR= 72,5;IC= 95%); vacas (OR= 29,7;IC= 95%); sistema intensivo (OR= 3,3; C= 95%); produção de pequenos ruminantes (OR= 4,4;IC=95%); produção de leite acima de 500L (OR= 2,9;IC= 95%); sem quarentena (OR= 1,5;IC= 95%); ordenha mecânica (OR= 5,5;IC= 95%) e casos de mastite (OR= 5,5;IC= 95%). O iELISA proposto foi capaz de detectar anticorpos reativos a M. bovis no soro bovino. O conhecimento desses fatores de risco pode auxiliar na implementação de medidas profiláticas.(AU)

Cisplatin treatment modulates Annexin A1 and inhibitor of differentiation to DNA 1 expression in cervical cancer cells.

Cisplatin (Cis) is a choice chemotherapy approach to cervical cancer by inducing DNA adducts and subsequent apoptosis. We have investigated the effects of Cis on Annexin A1 (ANXA1) and inhibitor of DNA binding 1 (ID1) proteins expression to elucidate further mechanisms of Cis actions. Human cervical tissue samples from twenty-four patients, with Cervical Intraepithelial Neoplasia (CIN, stage I, II and III), were evaluated to quantified ANXA1 and ID1 expressions. In vitro, human epidermoid carcinoma of the cervix (SiHa cell line) were treated with Annexin A1 peptide (ANXA12-26), Cis or Cis + ANXA12-26 to evaluate cell proliferation and migration, cytotoxicity of treatments as well as ANXA1 and ID1 modulations by mRNA and protein expression. Our findings showed expression of ID1 and ANXA1 proteins in tissue samples from Cervical Intraepithelial Neoplasia (CIN) patients, with intense immunological identification of ID1 in the CIN III stage. In SiHa cells, treatments with Cis alone or Cis + ANXA12-26, increase mRNA expressions of the ANXA1 and reduced the ID1. In agreement, Cis + ANXA12-26 enhanced ANXA1 protein expression and Cis or Cis + ANXA12-26 abolished ID1 protein expression. Cell proliferation was reduced after treatment with ANXA12-26 peptide and more significant after Cis or Cis + ANXA12-26 treatments. These two last treatments reduced cell viability, by inducing late apoptosis, and impaired cell migration. Together, our data highlight endogenous ANXA1 is involved in Cis therapy for cervical cancer.

Association Between DMSO and Sugars in the Sperm Cryopreservation of Pacu.

　　BACKGROUND: The cryopreservation protocol that has been developed exclusively for the preservation of the sperm of the species different. OBJECTIVE: this study was to evaluate the effect of the association of 10% DMSO with trehalose, raffinose, sucrose and lactose concentrations on the sperm cells of Piaractus mesopotamicus. MATERIALS AND METHODS: Sperms were collected from the animals through abdominal massage. The samples were diluted in the Beltsville Thawing Solution without different concentrations of other sugars (test conditions). Sixty days after the cryopreservation, cell movement analysis was performed using CASA. RESULTS: The results revealed that the parameters for total motility and motility period were superior when 100mM raffinose (P <0.05). The lateral displacement of the head was observed to be improved was 100mM lactose, 150mM sucrose and 150mM raffinose (P <0.05) as compared to treatment wherein lactose (0mM) was omitted. CONCLUSION: the results of our study indicated that the ideal parameters for cryopreservation, were obtained when the cryopreservation fluid contained 100mM raffinose in association with DMSO.

Contemporary and historical oceanographic processes explain genetic connectivity in a Southwestern Atlantic coral.

Understanding connectivity patterns has implications for evolutionary and ecological processes, as well as for proper conservation strategies. This study examined population genetic structure and migration patterns of the coral Mussismilia hispida, one of the main reef builders in the Southwestern Atlantic Ocean. For this, 15 sites were sampled along its entire distributional range employing 10 microsatellite loci. M. hispida was divided into five genetically differentiated populations by Structure analysis. Population structure and migration estimates are consistent with present-day oceanographic current patterns, zones of upwelling and historical sea-level changes. The Central Region and Oceanic Islands populations had the highest genetic diversity, were possibly the main sources of migrants for other populations and presented mutual migrant exchange. This mutual exchange and the high diversity of Oceanic Islands, a peripherical population, is highly interesting and unexpected, but can be explained if these sites acted as refugia in past low sea-level stance. This is the first connectivity study in the region using hyper-variable markers and a fine sampling scale along 3,500 km. These results enlighten the population dynamics of an important reef building species and shows how oceanographic processes may act as barriers to dispersal for marine species, providing valuable information for management strategies.

Reduced Glutathione and ATP in the Seminal Cryopreservation of Tambaqui.

BACKGROUND: The aim of this study was to analyze the effect of reduced glutathione (GR) and adenosine triphosphate (ATP) in cryopreserved sperm tambaqui, Colossoma macropomum.. OBJECTIVE: Semen samples were frozen at different concentrations of GR (2, 4, and 6 mM) and ATP (7.5, 15, 30 mM) evaluated separately. MATERIALS AND METHODS: Different concentrations of GR and ATP were added to the diluent Beltsville Thawing Solution 10 % of DMSO (extender control). The thawed sperm was evaluated as the kinetic parameters for Computer Assisted Semen Analysis (CASA) and cell feature parameters by flow cytometry. RESULTS: All concentrations of GR and ATP had gradual reduction in the production of reactive oxygen species, mainly ATP 15; 22.5 mM and 30 mM, which decreased by 50% or more when compared to the control. All concentrations of GR and ATP did not change (P> 0.05) DNA fragmentation and lipid peroxidation. The membrane fluidity GR in concentrations 4 and 6 mM were better than control; and the concentrations of 2 and 4 mM maintained more efficiently to motility period, total and progressive motility. CONCLUSION: Thus, it is indicated the use of BTS extender with 10% DMSO added 4 mM GR thawed sperm Tambaqui C. macropomum.

Crude glycerin levels in sugarcane silage: losses and nutritional value / Níveis de glicerina bruta na ensilagem de cana-de-açúcar: perdas e valor nutricional

The objective was to evaluate the effect and the best level of crude glycerin inclusion in sugarcane ensilage on the parameters of the chemical composition and fermentative losses. The treatments consisted of À ve levels of inclusion of crude glycerin (0, 1, 5, 10 and 15% inclusion in natural matter) during sugarcane silage. A completely randomized design was used, with À ve treatments with six replicates. The silages were manufactured in PVC pipes. The utilization of crude glycerin increased on average 16.3; 54.1; 24.0 and 17.8% of the dry matter, ether extract, non-À brous carbohydrates and total digestible nutrients of sugarcane silage, respectively, in relation to silage control sugarcane (P≤0.05). Increments of 0.56% and 0.18% in the dry matter and ether extract were found in sugarcane silages for each 1% inclusion of glycerin, respectively. Among the inclusion levels, the addition of each percentage unit of glycerin in the natural material reduced by 2.3% and 2.1% to the efÁ uent losses and gases losses, respectively. The addition of 15% of crude glycerin in sugarcane ensilage improves the chemical composition and reduces fermentation losses.

Objetivou - se avaliar o efeito e o melhor nível de inclusão de glicerina bruta na ensilagem de cana-de-açúcar sobre os parâmetros da composição química e perdas fermentativas. Os tratamentos consistiram de cinco níveis de inclusão de glicerina bruta (0, 1, 5, 10 e 15% de inclusão na matéria natural) durante a ensilagem de cana-de-açúcar. Utilizou-se o delineamento inteiramente casualizado sendo cinco tratamentos com seis repetições. As silagens foram confeccionadas em tubos de PVC. A utilização de glicerina bruta aumentou em média 16,3; 54,1; 24,0 e 17,8% os teores de matéria seca, extrato etéreo, carboidratos não À brosos e nutrientes digestíveis totais da silagem de cana em relação à silagem de cana sem aditivo (nível 0%; P≤0,05). Incrementos de 0,56% e 0,18% nos teores de matéria seca e extrato etéreo foram veriÀ cados nas silagens de cana para cada 1% de inclusão de glicerina, respectivamente. Entre os níveis de inclusão, a adição de cada unidade percentual de glicerina na matéria natural reduziu 2,3% e 2,1% às perdas por eÁ uentes e perdas por gases, respectivamente. A adição de glicerina bruta na ensilagem de cana-de-açúcar no nível de 15% na matéria natural melhora a composição bromatológica e reduz perdas fermentativas.

Crude glycerin levels in sugarcane silage: losses and nutritional value / Níveis de glicerina bruta na ensilagem de cana-de-açúcar: perdas e valor nutricional

The objective was to evaluate the effect and the best level of crude glycerin inclusion in sugarcane ensilage on the parameters of the chemical composition and fermentative losses. The treatments consisted of À ve levels of inclusion of crude glycerin (0, 1, 5, 10 and 15% inclusion in natural matter) during sugarcane silage. A completely randomized design was used, with À ve treatments with six replicates. The silages were manufactured in PVC pipes. The utilization of crude glycerin increased on average 16.3; 54.1; 24.0 and 17.8% of the dry matter, ether extract, non-À brous carbohydrates and total digestible nutrients of sugarcane silage, respectively, in relation to silage control sugarcane (P≤0.05). Increments of 0.56% and 0.18% in the dry matter and ether extract were found in sugarcane silages for each 1% inclusion of glycerin, respectively. Among the inclusion levels, the addition of each percentage unit of glycerin in the natural material reduced by 2.3% and 2.1% to the efÁ uent losses and gases losses, respectively. The addition of 15% of crude glycerin in sugarcane ensilage improves the chemical composition and reduces fermentation losses.(AU)

Objetivou - se avaliar o efeito e o melhor nível de inclusão de glicerina bruta na ensilagem de cana-de-açúcar sobre os parâmetros da composição química e perdas fermentativas. Os tratamentos consistiram de cinco níveis de inclusão de glicerina bruta (0, 1, 5, 10 e 15% de inclusão na matéria natural) durante a ensilagem de cana-de-açúcar. Utilizou-se o delineamento inteiramente casualizado sendo cinco tratamentos com seis repetições. As silagens foram confeccionadas em tubos de PVC. A utilização de glicerina bruta aumentou em média 16,3; 54,1; 24,0 e 17,8% os teores de matéria seca, extrato etéreo, carboidratos não À brosos e nutrientes digestíveis totais da silagem de cana em relação à silagem de cana sem aditivo (nível 0%; P≤0,05). Incrementos de 0,56% e 0,18% nos teores de matéria seca e extrato etéreo foram veriÀ cados nas silagens de cana para cada 1% de inclusão de glicerina, respectivamente. Entre os níveis de inclusão, a adição de cada unidade percentual de glicerina na matéria natural reduziu 2,3% e 2,1% às perdas por eÁ uentes e perdas por gases, respectivamente. A adição de glicerina bruta na ensilagem de cana-de-açúcar no nível de 15% na matéria natural melhora a composição bromatológica e reduz perdas fermentativas.(AU)

Expression of a symbiosis-specific gene in Symbiodinium type A1 associated with coral, nudibranch and giant clam larvae.

Symbiodinium are responsible for the majority of primary production in coral reefs and found in a mutualistic symbiosis with multiple animal phyla. However, little is known about the molecular signals involved in the establishment of this symbiosis and whether it initiates during host larval development. To address this question, we monitored the expression of a putative symbiosis-specific gene (H+-ATPase) in Symbiodinium A1 ex hospite and in association with larvae of a scleractinian coral (Mussismilia hispida), a nudibranch (Berghia stephanieae) and a giant clam (Tridacna crocea). We acquired broodstock for each host, induced spawning and cultured the larvae. Symbiodinium cells were offered and larval samples taken for each host during the first 72 h after symbiont addition. In addition, control samples including free-living Symbiodinium and broodstock tissue containing symbionts for each host were collected. RNA extraction and RT-PCR were performed and amplified products cloned and sequenced. Our results show that H+-ATPase was expressed in Symbiodinium associated with coral and giant clam larvae, but not with nudibranch larvae, which digested the symbionts. Broodstock tissue for coral and giant clam also expressed H+-ATPase, but not the nudibranch tissue sample. Our results of the expression of H+-ATPase as a marker gene suggest that symbiosis between Symbiodinium and M. hispida and T. crocea is established during host larval development. Conversely, in the case of B. stephanieae larvae, evidence does not support a mutualistic relationship. Our study supports the utilization of H+-ATPase expression as a marker for assessing Symbiodinium-invertebrate relationships with applications for the differentiation of symbiotic and non-symbiotic associations. At the same time, insights from a single marker gene approach are limited and future studies should direct the identification of additional symbiosis-specific genes, ideally from both symbiont and host.

Genetic relationship between the Nordestino horse and national and international horse breeds.

Knowledge of genetic diversity and relationships between breeds is very important for conservation programs. Hair samples were collected from 393 individual Nordestino horses and genotyped using 14 microsatellite markers in order to investigate the genetic relationship between this breed and 66 international horse breeds. There was high allelic diversity and inbreeding coefficient within population values were not significant, which was probably due to crossbreeding. Despite the Nordestino horse population being in Hardy-Weinberg equilibrium, a global deficit of heterozygotes was observed. This may represent evidence of repeated use of the same stallions for breeding, which is consistent with the high number of castrated males found. Campolina, Mangalarga Marchador, and Mangalarga were the Brazilian horse breeds most closely related to the Nordestino horse, which is a reflection of recent introgressions. Among Iberian horse breeds, the Sorraia breed appears to have had an important influence on the genetics of the Nordestino horse. Those results provide important information that can guide future conservation programs.

Role of parents in the promotion of hand hygiene in the paediatric setting: a systematic literature review.

BACKGROUND: When a child is hospitalized, parents have to share their role to protect the child with the hospital, and establish a partnership with healthcare workers to deliver safe care to the child, including undertaking good hand hygiene practices. AIM: To review the scientific evidence about the participation of parents in the promotion of hand hygiene in paediatric settings. METHODS: A systematic search of MEDLINE, EMBASE and SciELO databases was undertaken using the following terms: ('hand hygiene'[MeSH] OR 'hand hygiene' OR 'hand disinfection'[MeSH] OR hand disinf* OR hand wash* OR handwash* OR hand antisep*) AND (parent OR caregiver OR mother OR father OR family OR families OR relatives). The Integrated Quality Criteria for Review of Multiple Study Designs tool was used for quality assessment. FINDINGS: The literature search yielded 1645 articles, and 11 studies met the inclusion criteria for the final analysis. Most studies were observational, and were based on questionnaires or interviews. Most parents had little knowledge about the indications to perform hand hygiene, but recognized hand hygiene as a relevant tool for the prevention of healthcare-associated infections. Their willingness to remind healthcare workers about a failed opportunity to perform hand hygiene was variable and, overall, rather low. Parents felt more comfortable about reminding healthcare workers about hand hygiene if they had previously been invited to do so. CONCLUSIONS: Literature on the subject is scarce. The promotion of hand hygiene by parents should be further explored by research as a potential intervention for enhancing patient safety in paediatric settings.

Comparison of different protocols for the extraction of microbial DNA from reef corals

This study aimed to test different protocols for the extraction of microbial DNA from the coral Mussismilia harttii. Four different commercial kits were tested, three of them based on methods for DNA extraction from soil (FastDNA SPIN Kit for soil, MP Bio, PowerSoil DNA Isolation Kit, MoBio, and ZR Soil Microbe DNA Kit, Zymo Research) and one kit for DNA extraction from plants (UltraClean Plant DNA Isolation Kit, MoBio). Five polyps of the same colony of M. harttii were macerated and aliquots were submitted to DNA extraction by the different kits. After extraction, the DNA was quantified and PCR-DGGE was used to study the molecular fingerprint of Bacteria and Eukarya. Among the four kits tested, the ZR Soil Microbe DNA Kit was the most efficient with respect to the amount of DNA extracted, yielding about three times more DNA than the other kits. Also, we observed a higher number and intensities of DGGE bands for both Bacteria and Eukarya with the same kit. Considering these results, we suggested that the ZR Soil Microbe DNA Kit is the best adapted for the study of the microbial communities of corals.

Comparison of different protocols for the extraction of microbial DNA from reef corals

This study aimed to test different protocols for the extraction of microbial DNA from the coral Mussismilia harttii. Four different commercial kits were tested, three of them based on methods for DNA extraction from soil (FastDNA SPIN Kit for soil, MP Bio, PowerSoil DNA Isolation Kit, MoBio, and ZR Soil Microbe DNA Kit, Zymo Research) and one kit for DNA extraction from plants (UltraClean Plant DNA Isolation Kit, MoBio). Five polyps of the same colony of M. harttii were macerated and aliquots were submitted to DNA extraction by the different kits. After extraction, the DNA was quantified and PCR-DGGE was used to study the molecular fingerprint of Bacteria and Eukarya. Among the four kits tested, the ZR Soil Microbe DNA Kit was the most efficient with respect to the amount of DNA extracted, yielding about three times more DNA than the other kits. Also, we observed a higher number and intensities of DGGE bands for both Bacteria and Eukarya with the same kit. Considering these results, we suggested that the ZR Soil Microbe DNA Kit is the best adapted for the study of the microbial communities of corals.

HydroPaCe: understanding and predicting cross-inhibition in serine proteases through hydrophobic patch centroids.

MOTIVATION: Protein-protein interfaces contain important information about molecular recognition. The discovery of conserved patterns is essential for understanding how substrates and inhibitors are bound and for predicting molecular binding. When an inhibitor binds to different enzymes (e.g. dissimilar sequences, structures or mechanisms what we call cross-inhibition), identification of invariants is a difficult task for which traditional methods may fail. RESULTS: To clarify how cross-inhibition happens, we model the problem, propose and evaluate a methodology called HydroPaCe to detect conserved patterns. Interfaces are modeled as graphs of atomic apolar interactions and hydrophobic patches are computed and summarized by centroids (HP-centroids), and their conservation is detected. Despite sequence and structure dissimilarity, our method achieves an appropriate level of abstraction to obtain invariant properties in cross-inhibition. We show examples in which HP-centroids successfully predicted enzymes that could be inhibited by the studied inhibitors according to BRENDA database. AVAILABILITY: www.dcc.ufmg.br/~raquelcm/hydropace CONTACT: valdetemg@ufmg.br; raquelcm@dcc.ufmg.br; santoro@icb.ufmg.br SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.