In silico constraint-based strain optimization methods: the quest for optimal cell factories

Shifting from chemical to biotechnological processes is one of the cornerstones of 21st century industry. The production of a great range of chemicals via biotechnological means is a key challenge on the way toward a bio-based economy. However, this shift is occurring at a pace slower than initially expected. The development of efficient cell factories that allow for competitive production yields is of paramount importance for this leap to happen. Constraint-based models of metabolism, together with in silico strain design algorithms, promise to reveal insights into the best genetic design strategies, a step further toward achieving that goal. In this work, a thorough analysis of the main in silico constraint-based strain design strategies and algorithms is presented, their application in real-world case studies is analyzed, and a path for the future is discussed.

Phage therapy: a step forward in the treatment of Pseudomonas aeruginosa infections

Antimicrobial resistance constitutes one of the major worldwide public health concerns. Bacteria are becoming resistant to the vast majority of antibiotics and nowadays, a common infection can be fatal. To revert this situation, the use of phages for the treatment of bacterial infections has been extensively studied as an alternative therapeutic strategy. Since P. aeruginosa is one of the most common causes of healthcare-associated infections, many studies have reported the in vitro and in vivo antibacterial efficacy of phage therapy against this bacterium. This review collects data of all the P. aeruginosa phages sequenced to date, providing a better understanding about their biodiversity. This review will further address the in vitro and in vivo results obtained by using phages to treat or prevent P. aeruginosa infections as well as the major hurdles associated with this therapy.

Analysis of a Local HIV-1 Epidemic in Portugal Highlights Established Transmission of non-B and -G Subtypes

Existing data supports Portugal as the Western Europe country with highest HIV-1 subtype diversity. However, detailed phylogenetic studies of Portuguese HIV-1 epidemics are still scarce. Thus, our main goal was to analyze the phylodynamics of a local HIV-1 infection in the Portuguese region of Minho. Molecular epidemiological analysis was applied to data from 289 HIV-1 infected individuals followed in the reference Hospital of the province of Minho, Portugal, in which isolated viruses had been sequenced between 2000 and 2012. Viruses of the G (29.1%) and B (27.0%) subtypes were the most frequent, followed by recombinant forms (17.6%), C (14.5%), F1 (7.3%) and A1 (4.2%) subtypes. Multinomial logistic regression revealed that the odds of being infected with A1 and F1 subtype increased over the years when compared with B, G, C or recombinant viruses. As expected, polyphyletic patterns suggesting multiple and old introductions of subtypes B and G were found. However, transmission clusters of non-B and -G viruses among native individuals were also found with the dates of the most recent common ancestor estimated to the early 2000s. Our study supports that the HIV-1 subtype diversity in the Portuguese region of Minho is high and has been increasing in a manner that is apparently driven by factors other than immigration and international travel. Infections with A1 and F1 viruses in the region of Minho are becoming established and were mainly found in sexually transmitted clusters, reinforcing the need for more efficacious control measures targeting this infection route.

Monitoramento da biodeterioração da madeira de três espécies amazônicas pela técnica da colorimetria

Objetivou-se avaliar o emprego da colorimetria na caracterização da biodeterioração das madeiras de marupá, jequitibá e cumaru submetidas ao ataque de fungos de podridão branca e parda. Para tanto, corpos de prova de cada espécie amazônica foram submetidos a ensaios de apodrecimento acelerado, de acordo com a American Society for Testing and Materials - ASTM D2017, durante 20 semanas. Os parâmetros colorimétricos L* (luminosidade), a* (coordenada verde-vermelho), b* (coordenada amarelo-azul) e a variação total da cor (∆E) foram determinados semanalmente até a quarta semana, e posteriormente a cada duas semanas até a vigésima semana, com auxílio de um espectrofotocolorímetro. Adicionalmente, foram determinadas as perdas de massa dos corpos de prova. Os resultados permitiram destacar que a colorimetria foi eficaz no monitoramento da biodeterioração da madeira, bem como para diferenciação da podridão branca e parda. As melhores predições da resistência natural aos fungos de podridão branca e parda foram obtidas com os parâmetros b* e L*, respectivamente. Enfatiza-se também, o emprego da ∆E como parâmetro auxiliar na estimativa da biodeterioração da madeira, em razão de suas correlações significativas com a perda de massa.

Influence of the hip joint modeling approaches on the kinematics of human gait

The influence of the hip joint formulation on the kinematic response of the model of human gait is investigated throughout this work. To accomplish this goal, the fundamental issues of the modeling process of a planar hip joint under the framework of multibody systems are revisited. In particular, the formulations for the ideal, dry, and lubricated revolute joints are described and utilized for the interaction of femur head inside acetabulum or the hip bone. In this process, the main kinematic and dynamic aspects of hip joints are analyzed. In a simple manner, the forces that are generated during human gait, for both dry and lubricated hip joint models, are computed in terms of the system’s state variables and subsequently introduced into the dynamics equations of motion of the multibody system as external generalized forces. Moreover, a human multibody model is considered, which incorporates the different approaches for the hip articulation, namely ideal joint, dry, and lubricated models. Finally, several computational simulations based on different approaches are performed, and the main results presented and compared to identify differences among the methodologies and procedures adopted in this work. The input conditions to the models correspond to the experimental data capture from an adult male during normal gait. In general, the obtained results in terms of positions do not differ significantly when the different hip joint models are considered. In sharp contrast, the velocity and acceleration plotted vary significantly. The effect of the hip joint modeling approach is clearly measurable and visible in terms of peaks and oscillations of the velocities and accelerations. In general, with the dry hip model, intra-joint force peaks can be observed, which can be associated with the multiple impacts between the femur head and the cup. In turn, when the lubricant is present, the system’s response tends to be smoother due to the damping effects of the synovial fluid.

Endoscopic retrograde cholangiopancreatography for suspected choledocholithiasis : from guidelines to clinical practice

Endoscopic retrograde cholangiopancreatography for suspected choledocholithiasis: From guidelines to clinical practice.

Lack of the transcription factor hypoxia-inducible factor (HIF)-1α in macrophages accelerates the necrosis of Mycobacterium avium-induced granulomas

Accepted Manuscript

Transmission and progression to disease of Mycobacterium tuberculosis phylogenetic lineages in The Netherlands

The aim of this study was to determine if mycobacterial lineages affect infection risk, clustering, and disease progression among Mycobacterium tuberculosis cases in The Netherlands. Multivariate negative binomial regression models adjusted for patient-related factors and stratified by patient ethnicity were used to determine the association between phylogenetic lineages and infectivity (mean number of positive contacts around each patient) and clustering (as defined by number of secondary cases within 2 years after diagnosis of an index case sharing the same fingerprint) indices. An estimate of progression to disease by each risk factor was calculated as a bootstrapped risk ratio of the clustering index by the infectivity index. Compared to the Euro-American reference, Mycobacterium africanum showed significantly lower infectivity and clustering indices in the foreign-born population, while Mycobacterium bovis showed significantly lower infectivity and clustering indices in the native population. Significantly lower infectivity was also observed for the East African Indian lineage in the foreign-born population. Smear positivity was a significant risk factor for increased infectivity and increased clustering. Estimates of progression to disease were significantly associated with age, sputum-smear status, and behavioral risk factors, such as alcohol and intravenous drug abuse, but not with phylogenetic lineages. In conclusion, we found evidence of a bacteriological factor influencing indicators of a strain's transmissibility, namely, a decreased ability to infect and a lower clustering index in ancient phylogenetic lineages compared to their modern counterparts. Confirmation of these findings via follow-up studies using tuberculin skin test conversion data should have important implications on M. tuberculosis control efforts.

Determination of catalase activity and its inhibition by a simple manometric method

[Excerpt] Introduction: There has been a considerable amount of controversy about the use of manometric methods to measure catalase activity. As Maehly and Chance point out in their excellent review] the advantages of these methods is "... that they can be used for any kind of biological material, and purification of the enzyme is not required. The assay is independent of small amounts of peroxidase activity. It is fairly simple to perform, it is rapid and it can be adapted to continuous reading of the reaction". A variety of drawbacks are also listed by the same authors, viz, the inactivation of the enzyme under the experimental conditions and the time lag before a constant rate of oxygen evolution is reached. [...]

Prospective assessment of different indices of cardiac risk for patients undergoing noncardiac surgeries

OBJECTIVE: To compare the accuracy of 4 different indices of cardiac risk currently used for predicting perioperative cardiac complications. METHODS: We studied 119 patients at a university-affiliated hospital whose cardiac assessment had been required for noncardiac surgery. Predictive factors of high risk for perioperative cardiac complications were assessed through clinical history and physical examination, and the patients were followed up after surgery until the 4th postoperative day to assess the occurrence of cardiac events. All patients were classified according to 4 indices of cardiac risk: the Goldman risk-factor index, Detsky modified risk index, Larsen index, and the American Society of Anesthesiologists' physical status classification and their compared accuracies, examining the areas under their respective receiver operating characteristic (ROC) curves. RESULTS: Cardiac complications occurred in 16% of the patients. The areas under the ROC curves were equal for the Goldman risk-factor index, the Larsen index, and the American Society of Anesthesiologists' physical status classification: 0.48 (SEM ± 0.03). For the Detsky index, the value found was 0.38 (SEM ± 0.03). This difference in the values was not statistically significant. CONCLUSION: The cardiac risk indices currently used did not show a better accuracy than that obtained randomly. None of the indices proved to be significantly better than the others. Studies to improve our ability to predict such complications are still required.

O peptídeo natriurético do tipo B é preditor de eventos em pós-operatório de cirurgia ortopédica

FUNDAMENTO: A avaliação clínica nem sempre é suficiente para predizer complicações cardíacas pós-operatórias (PO). O peptídeo natriurético do tipo B (BNP) tem grande valor prognóstico em pacientes (pts) com insuficiência cardíaca. Seu valor como preditor de eventos em cirurgias ortopédicas ainda não foi testado. OBJETIVO: Avaliar o valor do BNP em predizer complicações cardíacas no PO de cirurgia ortopédica. MÉTODOS: Avaliados de modo prospectivo, 208 pts submetidos à cirurgia para correção de fratura de fêmur e artroplastia de quadril ou de joelho. Foram 149 (71,6%) mulheres e a idade média foi de 72,6 ± 8,8 anos. Os pacientes foram submetidos, no pré-operatório, à avaliação clínica convencional e estimativa do risco cirúrgico pela classificação da American Society of Anesthesiologists (ASA). O BNP foi dosado no pré-operatório e avaliou-se a sua capacidade de predizer eventos cardíacos (morte, infarto agudo do miocárdio, angina instável, fibrilação atrial, taquicardia ventricular ou insuficiência cardíaca) no PO, através de análise multivariada por regressão logística. RESULTADOS: Dezessete (8,0%) pacientes apresentaram eventos cardíacos. A mediana de BNP foi significativamente maior nesses pacientes quando comparada a dos sem eventos cardíacos (93 [variação interquartil 73-424] vs 26,6 [13,2-53,1], p = 0,0001). O BNP foi o principal preditor independente de eventos (p = 0,01). A classificação da ASA não foi preditor independente. A análise de curva ROC demonstrou que para um corte de 60 pg/ml, o BNP apresentou sensibilidade de 76,0% e especificidade de 79,0% para predizer eventos, com área sob a curva de 83,0%. CONCLUSÃO: O BNP é um preditor independente de eventos cardíacos no PO de cirurgias ortopédicas.

Os critérios para classificação da insuficiência mitral não foram adequados na cardiomiopatia dilatada

FUNDAMENTO: A insuficiência mitral (IM) é frequente nos pacientes com cardiomiopatia dilatada. Não se sabe se os critérios para classificação da IM são adequados para pacientes com cardiomiopatia dilatada OBJETIVO: Avaliar a concordância entre os quatro métodos ecocardiográficos mais utilizados para classificação da IM. MÉTODOS: Noventa pacientes com cardiomiopatia dilatada foram incluídos. A IM foi classificada por quatro métodos ecocardiográficos: área do jato regurgitante (AJ), vena contracta (VC), área do orifício regurgitante (AOR) e volume regurgitante (VR). A IM foi classificada em leve, moderada ou importante segundo os critérios da American Society of Echocardiography e também foi dividida em tercis conforme os valores absolutos. O teste de Kappa foi utilizado para avaliar a concordância entre os métodos. O coeficiente de Pearson foi utilizado para avaliar a correlação entre os valores absolutos por cada método. RESULTADOS: A classificação da IM, de acordo com cada método, foi a seguinte: AJ: 26 leve, 44 moderada, 20 importante; VC: 12 leve, 72 moderada, 6 importante; AOR: 70 leve, 15 moderada, 5 importante; VR: 70 leve, 16 moderada, 4 importante. A concordância entre os métodos foi ruim (kappa = 0,11; p < 0,001), porém foi observada uma forte correlação entre os valores absolutos de cada método (0,70 a 0,95; p < 0,01). A concordância foi melhor com a divisão dos valores em tercis (kappa = 0,44; p < 0,01). CONCLUSÃO: Os critérios para classificação da IM não são adequados para os pacientes com cardiomiopatia dilatada. É necessário estabelecer novos valores de corte para classificar a IM nestes pacientes.

Applicability of the Appropriate use Criteria for Myocardial Perfusion Scintigraphy

Background: Appropriateness Criteria for nuclear imaging exams were created by American College of Cardiology (ACC) e American Society of Nuclear Cardiology (ASNC) to allow the rational use of tests. Little is known whether these criteria have been followed in clinical practice. Objective: To evaluate whether the medical applications of myocardial perfusion scintigraphy (MPS) in a private nuclear medicine service of a tertiary cardiology hospital were suitable to the criteria of indications proposed by the American medical societies in 2005 and 2009 and compare the level of indication of both. Methods: We included records of 383 patients that underwent MPS, November 2008 up to February 2009. Demographic characteristics, patient's origin, coronary risk factors, time of medical graduation and appropriateness criteria of medical applications were studied. The criteria were evaluated by two independent physicians and, in doubtful cases, defined by a medical expert in MPS. Results: Mean age was 65 ± 12 years. Of the 367 records reviewed, 236 (64.3%) studies were performed in men and 75 (20.4%) were internee. To ACC 2005, 255 (69.5%) were considered appropriate indication and 13 (3.5%) inappropriate. With ACC 2009, 249 (67.8%) were considered appropriate indications and 13 (5.2%) inappropriate. Conclusions: We observed a high rate of adequacy of medical indications for MPS. Compared to the 2005 version, 2009 did not change the results.

Results of An International Study of Quantitative BCR/ABL Assays Using Defined RNA Samples

Molecular monitoring of BCR/ABL transcripts by real time quantitative reverse transcription PCR (qRT-PCR) is an essential technique for clinical management of patients with BCR/ABL-positive CML and ALL. Though quantitative BCR/ABL assays are performed in hundreds of laboratories worldwide, results among these laboratories cannot be reliably compared due to heterogeneity in test methods, data analysis, reporting, and lack of quantitative standards. Recent efforts towards standardization have been limited in scope. Aliquots of RNA were sent to clinical test centers worldwide in order to evaluate methods and reporting for e1a2, b2a2, and b3a2 transcript levels using their own qRT-PCR assays. Total RNA was isolated from tissue culture cells that expressed each of the different BCR/ABL transcripts. Serial log dilutions were prepared, ranging from 100 to 10-5, in RNA isolated from HL60 cells. Laboratories performed 5 independent qRT-PCR reactions for each sample type at each dilution. In addition, 15 qRT-PCR reactions of the 10-3 b3a2 RNA dilution were run to assess reproducibility within and between laboratories. Participants were asked to run the samples following their standard protocols and to report cycle threshold (Ct), quantitative values for BCR/ABL and housekeeping genes, and ratios of BCR/ABL to housekeeping genes for each sample RNA. Thirty-seven (n=37) participants have submitted qRT-PCR results for analysis (36, 37, and 34 labs generated data for b2a2, b3a2, and e1a2, respectively). The limit of detection for this study was defined as the lowest dilution that a Ct value could be detected for all 5 replicates. For b2a2, 15, 16, 4, and 1 lab(s) showed a limit of detection at the 10-5, 10-4, 10-3, and 10-2 dilutions, respectively. For b3a2, 20, 13, and 4 labs showed a limit of detection at the 10-5, 10-4, and 10-3 dilutions, respectively. For e1a2, 10, 21, 2, and 1 lab(s) showed a limit of detection at the 10-5, 10-4, 10-3, and 10-2 dilutions, respectively. Log %BCR/ABL ratio values provided a method for comparing results between the different laboratories for each BCR/ABL dilution series. Linear regression analysis revealed concordance among the majority of participant data over the 10-1 to 10-4 dilutions. The overall slope values showed comparable results among the majority of b2a2 (mean=0.939; median=0.9627; range (0.399 - 1.1872)), b3a2 (mean=0.925; median=0.922; range (0.625 - 1.140)), and e1a2 (mean=0.897; median=0.909; range (0.5174 - 1.138)) laboratory results (Fig. 1-3)). Thirty-four (n=34) out of the 37 laboratories reported Ct values for all 15 replicates and only those with a complete data set were included in the inter-lab calculations. Eleven laboratories either did not report their copy number data or used other reporting units such as nanograms or cell numbers; therefore, only 26 laboratories were included in the overall analysis of copy numbers. The median copy number was 348.4, with a range from 15.6 to 547,000 copies (approximately a 4.5 log difference); the median intra-lab %CV was 19.2% with a range from 4.2% to 82.6%. While our international performance evaluation using serially diluted RNA samples has reinforced the fact that heterogeneity exists among clinical laboratories, it has also demonstrated that performance within a laboratory is overall very consistent. Accordingly, the availability of defined BCR/ABL RNAs may facilitate the validation of all phases of quantitative BCR/ABL analysis and may be extremely useful as a tool for monitoring assay performance. Ongoing analyses of these materials, along with the development of additional control materials, may solidify consensus around their application in routine laboratory testing and possible integration in worldwide efforts to standardize quantitative BCR/ABL testing.