Estudo in vitro de derivados sintéticos da Isoniazida e da Pirazinamida sobre Leishmania (Viannia) braziliensis

As leishmanioses são um grupo de doenças causadas por protozoários do gênero Leishmania spp que afetam 98 países. No Brasil, no ano de 2013, foram relatados 3.253 casos de leishmaniose visceral e 18.226 casos de Leishmaniose Tegumentar Americana. O tratamento de primeira escolha continua sendo realizado com antimoniais pentavalentes, e em casos de insucessos os fármacos de segunda escolha são a pentamidina e a anfotericina B. Tais medicamentos causam intensos efeitos adversos e ultimamente têm surgido cepas resistentes aos mesmos. Em áreas endêmicas têm sido cada vez mais comum o surgimento da co-infecção Leishmania com Mycobacterium tuberculosis. O tratamento para a tuberculose com pirazinamida (PZA) e isoniazida (INZ), controla a leishmaniose. Esses dados sugerem atividade anti-leishmania da PZA e da INZ. O objetivo deste trabalho foi avaliar a atividade in vitro da INZ e da PZA e seus compostos derivados (série G e série R, respectivamente) sobre Leishmania (Viannia) braziliensis. As moléculas foram testadas em monocamadas de macrófagos peritoneais de camunongos infectados com L. (V) braziliensis durante 48h. Todas as moléculas testadas inibiram o índice de infecção de forma dose dependente em comparação aos controles. As moléculas da série R foram mais ativas do que a PZA, porém o resultado foi significativo somente para a R02 (p < 0,005). Apenas a molécula R05 (76,64M) foi relativamente tóxica para macrófagos. Os compostos mais ativos foram R02, G01 e G02, cujos índices de seletividade foram 14,31, 19 e 30, respectivamente. A dosagem de nitrito foi feita em sobrenadantes de monocamadas de macrófagos peritoniais infectados e tratados com as substâncias nas concentrações 10 e 100M. A G01 e a G02 estimularam a produção de NO2 nas duas concentrações, entretanto o resultado foi estatisticamente significativo para a G02 em 100M (p < 0,0001), a G05 só estimulou óxido nítrico na maior concentração. Todos os compostos da série R estimularam NO2, contudo, o resultado foi estatisticamente significativo para a R03 e R05 a 100M (p < 0,001). Adicionalmente, foi realizado uma análise preditiva in sílico de parâmetros farmacocinéticos das moléculas mais ativas in vitro, utilizando o software admetSAR. Os dados obtidos mostraram que de forma semelhante às suas moléculas originais a G01, G02 e R02 apresentaram alta capacidade de serem absorvidas pelo trato gastrointestinal, baixo potencial hepatotoxico e carcinogênico. Juntos, esses dados demonstram que essas moléculas são seletivamente tóxicas para o parasito com potencial para serem testadas pela via oral em estudos em modelo experimental de infecção.

Alterações da expressão da proteína PHEX na Hanseníase

A hanseníase é uma doença infecciosa causada pelo Mycobacteruim leprae, um bacilo intracelular obrigatório, que prolifera principalmente na pele e nos nervos periféricos no interior de células como macrófagos e células de Schwann. A transmissão ocorre por meio das mucosas das vias respiratórias, provavelmente por aerossóis expelidos por indivíduos infectados. O homem é o seu hospedeiro natural sendo a multiplicação do bacilo muito lenta, com um período de geração estimado de 14 dias. Apesar da mínima variação no genoma do M. leprae, a doença é caracterizada por um espectro de formas clínicas bem definido, decorrente da capacidade de resposta imune do hospedeiro. Em pacientes classificados como multibacilares (MB) a doença é disseminada, com inúmeras lesões de pele e proliferação bacilar considerável. Nesses indivíduos ocorre hiporresponsividade celular ao M. leprae. Nas formas paucibacilares (PB), os pacientes apresentam uma ou poucas lesões, a carga bacilar é pequena e, às vezes não observada por meio da baciloscopia tradicional e ocorre resposta imune patógeno-específica. As incapacidades físicas nos pacientes decorrem da neuropatia e osteopatia e podem ser irreversíveis. Essas deformidades podem avançar mesmo após a diminuição da carga bacilar com o final do tratamento poliquimioterápico. A presente tese teve por objetivo estudar as implicações da proteína PHEX nas alterações fisiopatológicas da hanseníase, em especial as alterações ósseas. A proteína PHEX (Phosphate-regulating gene with Homologies to Endopeptidase on the X chromosome) é expressa em várias células humanas e, no primeiro artigo que compõe essa tese, demonstramos que o M.leprae leva à diminuição da expressão de PHEX em linhagens de células de Schwann e osteoblastos humanos. Este efeito foi igualmente causado por outras espécies de micobactérias. No segundo manuscrito ora submetido, observamos que em leucócitos sanguíneos de pacientes hansenianos também ocorreu modulação negativa de PHEX. Este efeito não se relacionou com a capacidade de produção de citocinas inflamatórias frente ao M. leprae in vitro ou com alterações bioquímicas. O efeito inibidor da mineralização ocasionado pela modulação negativa de PHEX talvez contribua para a doença óssea da hanseníase, auxiliando a explicar a capacidade do M. leprae de penetrar e sobreviver no osso.

7 种蛇毒小肽对临床分离耐(多) 药结核分枝杆菌的体外活性研究

目的　检测7 种从蛇毒分离的小肽是否对临床分离的耐药性结核分枝杆菌菌株具有活性。方法　放射性方法检测蛇毒 小肽对结核分枝杆菌的最小抑制浓度,细菌存活计数确证放射性方法的结果。结果　7 种蛇毒小肽对耐药性结核分枝杆菌菌 株都有活性。其MIC 值分别为(μg·mL - 1) : Opiophagus hannah 5. 4 , Naja at ra 8. 6 , B ungarus f asciatus 6. 4 , Trimeresurus ste2 jnegri 12. 6 , Protobothrops mucrosquamatus 11. 8 , Protobothrops jerdonii 7 , A gksist rodon halys 4. 2 。结论　这些结果是首次报 道,为进一步设计和开发新来源的抗结核病新药提供了依据。

Oligonucleotide ligation assay-based DNA chip for multiplex detection of single nucleotide polymorphism

An oligonucleotide ligation assay-based DNA chip has been developed to detect single nucleotide polymorphism. Synthesized nonamers, complementary to the flanking sequences of the mutation sites in target DNA, were immobilized onto glass slides through disulfide bonds on their 5' terminus. Allele-specific pentamers annealed adjacent to the nonamers on the complementary target DNA, containing 5'-phosphate groups and biotin labeled 3'-ends, were mixed with the target DNA in tube. Ligation reactions between nonamers and pentamers were carried out on chips in the presence of T4 DNA ligase. Ligation products were directly visualized on chips through enzyme-linked assay. The effect of G:T mismatch at different positions of pentamers on the ligation were evaluated. The results showed that any mismatch between pentamer and the target DNA could lead to the decrease of ligation, which can be detected easily. The established approach was further used for multiplex detection of mutations in rpoB gene of rifampin-resistant Mycobacterium tuberculosis clinical isolates. (C) 2003 Elsevier B.V. All rights reserved.

结核分枝杆菌尼克酰胺酶/吡嗪酰胺酶的研究

本研究通过一系列生物学手段系统阐述了结核分枝杆菌尼克酰胺酶/吡嗪酰胺酶（PncA酶）的生物化学特征，并鉴定了酶当中的关键氨基酸。结果表明体外表达的结核分枝杆菌PncA酶是一个分子量为22.4 KDa的单体酶，其最适pH值和温度分别为6.6 ~ 7.4和35 ~ 45 °C。电感耦合等离子原子发射光谱结果表明PncA酶是一种含有Mn2+和Fe2+的蛋白，二者的比率为1:1。通过运用高效液相色谱和耦联氨酶试验的方法对纯化的PncA酶进行了动力学分析，结果表明PncA酶拥有相同的吡嗪酰胺酶和尼克酰胺酶活性。通过定点突变得到了9个突变，圆二色谱数据证明突变并没有引起PncA酶的二级结构的改变。对这9个突变的酶活性和金属离子含量分析的结果表明，D8、K96和C138是PncA酶结合和催化底物的关键氨基酸残基，D49、H51、H57和H71是金属离子结合的关键氨基酸，而Y103和S104则有可能与底物的结合稳定有关。我们的结果也表明，尽管与Pyrococcus horikoshii PncA酶的序列同源性很高，但二者在对金属离子的结合方式上存在明显差异, 并有可能导致两者在催化机制上的差异, 值得进一步研究。 通过筛选抗吡嗪酰胺药物的临床分离结核分枝杆菌19株，并对其pncA基因序列进行测序分析。结果再一次表明结核分枝杆菌PncA酶的突变与吡嗪酰胺耐药性密切相关，检测的准确性为78.9 %，并发现了一个在16位的甘氨酸突变为丝氨酸的新突变。

结核分枝杆菌基因组学及特异检测技术研究

结核分枝杆菌(M.tuberculosis)，俗称结核杆菌，是引起结核病的病原菌。可侵犯全身各器官，但以肺结核为最多见。结核病至今仍为重要的传染病。估计世界人口中1/3感染结核分枝杆菌。据WHO报道，每年约有800万新病例发生，至少有300万人死于该病。我国建国前死亡率达200-300人/10万，居各种疾病死亡原因之首，建国后，随着人民生活水平提高，卫生状态改善，特别是开展了群防群治，儿童普遍接种卡介苗，结核病的发病率和死亡率大为降低。由于耐药结核的出现已及HIV共感染等因素影响，目前发病率又有上升趋势。对于结核病的防治而言，其首要问题是结核病的诊断，而结核病的实验室检查已成为临床医生诊断结核病、判断疗效和评估预后不可缺少的手段。结核病的临床诊断主要根据病史、痰培养、涂片抗酸染色、胸片等结果，其中痰结核检查是诊断肺结核的重要依据之一，检测方法常规采用细菌学检查。痰中细菌学检查主要采用痰涂片和培养方法，涂片虽简单易行，但阳性率低，培养虽为金标准，但周期太长，均难以满足临床需要。细菌对部分患者可造成误诊或漏诊。近年来随着现代科学技术的不断进展，分子生物学技术在结核病诊断方面取得了显著的成绩，实时动态荧光定量(FQ—PCR)技术又是在原有的PCR技术上一次质的飞跃。 尽管许多文献已经报道了结核耐药的分子机理，但耐药的分子机理并没有充分了解。本研究利用全基因组鸟枪法测序和高通量测序技术，测定了两株结核分枝杆菌菌株TFJA和TFJB全基因组序列，分别为药物敏感株和耐多药株。在序列初步拼接后，获得了由189个DNA contigs（DNA序列连接群）组成的基因组框架图。借助10kb左右插入片段克隆的正反向末端序列信息以及PCR扩增技术，确定了全部DNA contigs在基因组上的物理位置，最后补上了所有“间隙(gap)” ，得到了全基因组序列。三种限制性酶切物理图谱证明了序列拼接的正确性。两株结核菌基因组大小为4.4Mbp左右，GC含量都在65.6%左右，其中TFJB株比TFJA株大7kbp，分别具有3591、3648个基因，83.7%的基因位于先导链上。我们比较了两株细菌的949SNPs位点，发现94个在TFJB中不同nsSNPs，这些SNPs位点的碱基在其它的结核分枝杆菌基因组中是相同的。我们去掉了那些代谢途径与毒力代谢无关的基因，最后选择了6个基因的18个SNP，检测这些SNP在277株耐药或者药物敏感结核分枝杆菌中的保守性以及其耐药相关性。用PCR扩增含有SNP的序列，用统计学检验这些SNP是否耐药相关，结果发现，TFJB0109_CDS04405基因的407位点SNP（g->a）和TFJB0109_CDS00149基因上的SNP（720a->c，722插入t，727t->g，729g->t，以及735g->t）可能与SM耐药相关，其P-value分别是0.04128、0.02160和0.01394（见表3）。 结核是一种慢性传染病，其病原体为TB。在全基因组序列分析研究的同时，我们筛选到一套灵敏度较高、特异性较好的REAL TIME-PCR检测引物，并用它对105份不同发病时间的病人标本进行了检测。初步结果表明，应用本方法，样本检出率为98%，这一结果比涂片及分离培养更灵敏。

Atualização em tuberculose bovina.

2009

The rpf gene of Micrococcus luteus encodes an essential secreted growth factor

Galina V. Mukamolova, Obolbek A. Turapov, Konstantin Kazarian, Miroslav Telkov, Arseny S. Kaprelyants, Douglas B. Kell and Michael Young (2002). The rpf gene of Micrococcus luteus encodes an essential secreted growth factor. Molecular Microbiology, 46 (3), 611-621. Sponsorship: BBSRC / Russian Foundation for Basic Research (grant 00-04-48691)/ WHO Global Programme for Vaccines and Immunization / Wellcome Trust RAE2008

Paradoxical worsening of tuberculosis in a heart-lung transplant recipient.

We report on a heart-lung transplant recipient who presented with pulmonary tuberculosis (TB) 2.5 months after transplantation and then developed a paradoxical reaction after 4 months of adequate anti-TB treatment. She eventually recovered with anti-TB and high-dose steroid treatments. METHODS: Using sequential bronchoalveolar lavages, we assessed the inflammatory response in the lung and investigated the alveolar immune response against a Mycobacterium tuberculosis antigen. RESULTS: The paradoxical reaction was characterized by a massive infiltration of the alveolar space by M. tuberculosis antigen-specific CD4(+) T cells and by the presence of a CD4(-)CD8(-) T lymphocyte subpopulation bearing phenotypic markers (CD16(+)/56(+)) classically associated with NK cells. CONCLUSION: This case report illustrates that even solid organ transplant recipients receiving intense triple-drug immune suppression may be able to develop a paradoxical reaction during TB treatment. Transplant physicians should be aware of this phenomenon in order to differentiate it from treatment failure.

Pairing QuantiFERON gold in-tube with opt-out HIV testing in a tuberculosis contact investigation in the Southeastern United States.

Knowing one's HIV status is particularly important in the setting of recent tuberculosis (TB) exposure. Blood tests for assessment of tuberculosis infection, such as the QuantiFERON Gold in-tube test (QFT; Cellestis Limited, Carnegie, Victoria, Australia), offer the possibility of simultaneous screening for TB and HIV with a single blood draw. We performed a cross-sectional analysis of all contacts to a highly infectious TB case in a large meatpacking factory. Twenty-two percent were foreign-born and 73% were black. Contacts were tested with both tuberculin skin testing (TST) and QFT. HIV testing was offered on an opt-out basis. Persons with TST >or=10 mm, positive QFT, and/or positive HIV test were offered latent TB treatment. Three hundred twenty-six contacts were screened: TST results were available for 266 people and an additional 24 reported a prior positive TST for a total of 290 persons with any TST result (89.0%). Adequate QFT specimens were obtained for 312 (95.7%) of persons. Thirty-two persons had QFT results but did not return for TST reading. Twenty-two percent met the criteria for latent TB infection. Eighty-eight percent accepted HIV testing. Two (0.7%) were HIV seropositive; both individuals were already aware of their HIV status, but one had stopped care a year previously. None of the HIV-seropositive persons had latent TB, but all were offered latent TB treatment per standard guidelines. This demonstrates that opt-out HIV testing combined with QFT in a large TB contact investigation was feasible and useful. HIV testing was also widely accepted. Pairing QFT with opt-out HIV testing should be strongly considered when possible.

Mycobacteriosis in Chesapeake Bay Striped Bass (Morone saxatilis): The Interaction of Nutrition and Disease

Field and laboratory studies were conducted from 1998 - 2005 to examine the relationship between nutritional status and mycobacteriosis in Chesapeake Bay striped bass (Morone saxatilis). A review of DNA from archived tissue blocks indicated that the disease has been present since at least 1984. Field surveys and feeding trials were conducted from 1998-1999 to determine the nutritional condition of striped bass and the association with disease state. Proximate composition revealed elevated moisture (~ 80%) and low storage lipids (< 0.5% ww), characteristic of a poorly nourished population. These findings were not consistent with data collected in 1990-1991, or with experimentally fed fish. Mycobacteriosis explained little of the variance in chemical composition (p > 0.2); however elevated moisture and low lipid concentration were associated with fish with ulcerative lesions (p < 0.05). This suggests that age 3 and 4 striped bass were in poor nutritional health in 1998-1999, which may be independent from the disease process. Challenge studies were performed to address the hypothesis that disease progression and severity may be altered by nutritional status of the host. Intraperitoneal inoculation of 104 CFU M. marinum resulted in high mortality, elevated bacterial density, and poor granuloma formation in low ration (0.15% bw/d) groups while adequately fed fish (1% bw/d) followed a normal course of granulomatous inflammation with low mortality to a steady, equilibrium state. Further, we demonstrated that an active inflammatory state could be reactivated in fish through reductions in total diet. The energetic demand of mycobacteriosis, was insignificant in comparison to sham inoculated controls in adequately fed fish (p > 0.05). Declines in total body energy were only apparent during active, inflammatory stages of disease. Overall, these findings suggest that: 1) mycobacteriosis is not a new disease of Chesapeake Bay striped bass, 2) the disease has little energetic demand in the normal, chronic progression, and 3) poor nutritional health can greatly enhance the progression and severity, and reactivation of disease. The implications of this research are that management strategies focused on enhancing the nutritional state of striped bass could potentially alter the disease dynamics in Chesapeake Bay.

Antisense Gene Silencing and Bacteriophages as Novel Disinfection Processes for Engineered Systems

The growth and proliferation of invasive bacteria in engineered systems is an ongoing problem. While there are a variety of physical and chemical processes to remove and inactivate bacterial pathogens, there are many situations in which these tools are no longer effective or appropriate for the treatment of a microbial target. For example, certain strains of bacteria are becoming resistant to commonly used disinfectants, such as chlorine and UV. Additionally, the overuse of antibiotics has contributed to the spread of antibiotic resistance, and there is concern that wastewater treatment processes are contributing to the spread of antibiotic resistant bacteria.

Due to the continually evolving nature of bacteria, it is difficult to develop methods for universal bacterial control in a wide range of engineered systems, as many of our treatment processes are static in nature. Still, invasive bacteria are present in many natural and engineered systems, where the application of broad acting disinfectants is impractical, because their use may inhibit the original desired bioprocesses. Therefore, to better control the growth of treatment resistant bacteria and to address limitations with the current disinfection processes, novel tools that are both specific and adaptable need to be developed and characterized.

In this dissertation, two possible biological disinfection processes were investigated for use in controlling invasive bacteria in engineered systems. First, antisense gene silencing, which is the specific use of oligonucleotides to silence gene expression, was investigated. This work was followed by the investigation of bacteriophages (phages), which are viruses that are specific to bacteria, in engineered systems.


For the antisense gene silencing work, a computational approach was used to quantify the number of off-targets and to determine the effects of off-targets in prokaryotic organisms. For the organisms of Escherichia coli K-12 MG1655 and Mycobacterium tuberculosis H37Rv the mean number of off-targets was found to be 15.0 + 13.2 and 38.2 + 61.4, respectively, which results in a reduction of greater than 90% of the effective oligonucleotide concentration. It was also demonstrated that there was a high variability in the number of off-targets over the length of a gene, but that on average, there was no general gene location that could be targeted to reduce off-targets. Therefore, this analysis needs to be performed for each gene in question. It was also demonstrated that the thermodynamic binding energy between the oligonucleotide and the mRNA accounted for 83% of the variation in the silencing efficiency, compared to the number of off-targets, which explained 43% of the variance of the silencing efficiency. This suggests that optimizing thermodynamic parameters must be prioritized over minimizing the number of off-targets. In conclusion for the antisense work, these results suggest that off-target hybrids can account for a greater than 90% reduction in the concentration of the silencing oligonucleotides, and that the effective concentration can be increased through the rational design of silencing targets by minimizing off-target hybrids.

Regarding the work with phages, the disinfection rates of bacteria in the presence of phages was determined. The disinfection rates of E. coli K12 MG1655 in the presence of coliphage Ec2 ranged up to 2 h-1, and were dependent on both the initial phage and bacterial concentrations. Increasing initial phage concentrations resulted in increasing disinfection rates, and generally, increasing initial bacterial concentrations resulted in increasing disinfection rates. However, disinfection rates were found to plateau at higher bacterial and phage concentrations. A multiple linear regression model was used to predict the disinfection rates as a function of the initial phage and bacterial concentrations, and this model was able to explain 93% of the variance in the disinfection rates. The disinfection rates were also modeled with a particle aggregation model. The results from these model simulations suggested that at lower phage and bacterial concentrations there are not enough collisions to support active disinfection rates, which therefore, limits the conditions and systems where phage based bacterial disinfection is possible. Additionally, the particle aggregation model over predicted the disinfection rates at higher phage and bacterial concentrations of 108 PFU/mL and 108 CFU/mL, suggesting other interactions were occurring at these higher concentrations. Overall, this work highlights the need for the development of alternative models to more accurately describe the dynamics of this system at a variety of phage and bacterial concentrations. Finally, the minimum required hydraulic residence time was calculated for a continuous stirred-tank reactor and a plug flow reactor (PFR) as a function of both the initial phage and bacterial concentrations, which suggested that phage treatment in a PFR is theoretically possible.

In addition to determining disinfection rates, the long-term bacterial growth inhibition potential was determined for a variety of phages with both Gram-negative and Gram-positive bacteria. It was determined, that on average, phages can be used to inhibit bacterial growth for up to 24 h, and that this effect was concentration dependent for various phages at specific time points. Additionally, it was found that a phage cocktail was no more effective at inhibiting bacterial growth over the long-term than the best performing phage in isolation.

Finally, for an industrial application, the use of phages to inhibit invasive Lactobacilli in ethanol fermentations was investigated. It was demonstrated that phage 8014-B2 can achieve a greater than 3-log inactivation of Lactobacillus plantarum during a 48 h fermentation. Additionally, it was shown that phages can be used to protect final product yields and maintain yeast viability. Through modeling the fermentation system with differential equations it was determined that there was a 10 h window in the beginning of the fermentation run, where the addition of phages can be used to protect final product yields, and after 20 h no additional benefit of the phage addition was observed.

In conclusion, this dissertation improved the current methods for designing antisense gene silencing targets for prokaryotic organisms, and characterized phages from an engineering perspective. First, the current design strategy for antisense targets in prokaryotic organisms was improved through the development of an algorithm that minimized the number of off-targets. For the phage work, a framework was developed to predict the disinfection rates in terms of the initial phage and bacterial concentrations. In addition, the long-term bacterial growth inhibition potential of multiple phages was determined for several bacteria. In regard to the phage application, phages were shown to protect both final product yields and yeast concentrations during fermentation. Taken together, this work suggests that the rational design of phage treatment is possible and further work is needed to expand on this foundation.

Interception of host angiogenic signalling limits mycobacterial growth.

Pathogenic mycobacteria induce the formation of complex cellular aggregates called granulomas that are the hallmark of tuberculosis. Here we examine the development and consequences of vascularization of the tuberculous granuloma in the zebrafish-Mycobacterium marinum infection model, which is characterized by organized granulomas with necrotic cores that bear striking resemblance to those of human tuberculosis. Using intravital microscopy in the transparent larval zebrafish, we show that granuloma formation is intimately associated with angiogenesis. The initiation of angiogenesis in turn coincides with the generation of local hypoxia and transcriptional induction of the canonical pro-angiogenic molecule Vegfaa. Pharmacological inhibition of the Vegf pathway suppresses granuloma-associated angiogenesis, reduces infection burden and limits dissemination. Moreover, anti-angiogenic therapies synergize with the first-line anti-tubercular antibiotic rifampicin, as well as with the antibiotic metronidazole, which targets hypoxic bacterial populations. Our data indicate that mycobacteria induce granuloma-associated angiogenesis, which promotes mycobacterial growth and increases spread of infection to new tissue sites. We propose the use of anti-angiogenic agents, now being used in cancer regimens, as a host-targeting tuberculosis therapy, particularly in extensively drug-resistant disease for which current antibiotic regimens are largely ineffective.

The Macrophage-Specific Promoter mfap4 Allows Live, Long-Term Analysis of Macrophage Behavior during Mycobacterial Infection in Zebrafish.

Transgenic labeling of innate immune cell lineages within the larval zebrafish allows for real-time, in vivo analyses of microbial pathogenesis within a vertebrate host. To date, labeling of zebrafish macrophages has been relatively limited, with the most specific expression coming from the mpeg1 promoter. However, mpeg1 transcription at both endogenous and transgenic loci becomes attenuated in the presence of intracellular pathogens, including Salmonella typhimurium and Mycobacterium marinum. Here, we describe mfap4 as a macrophage-specific promoter capable of producing transgenic lines in which transgene expression within larval macrophages remains stable throughout several days of infection. Additionally, we have developed a novel macrophage-specific Cre transgenic line under the control of mfap4, enabling macrophage-specific expression using existing floxed transgenic lines. These tools enrich the repertoire of transgenic lines and promoters available for studying zebrafish macrophage dynamics during infection and inflammation and add flexibility to the design of future macrophage-specific transgenic lines.

A computational analysis of antisense off-targets in prokaryotic organisms

© 2014 .The adoption of antisense gene silencing as a novel disinfectant for prokaryotic organisms is hindered by poor silencing efficiencies. Few studies have considered the effects of off-targets on silencing efficiencies, especially in prokaryotic organisms. In this computational study, a novel algorithm was developed that determined and sorted the number of off-targets as a function of alignment length in Escherichia coli K-12 MG1655 and Mycobacterium tuberculosis H37Rv. The mean number of off-targets per a single location was calculated to be 14.1. ±. 13.3 and 36.1. ±. 58.5 for the genomes of E. coli K-12 MG1655 and M. tuberculosis H37Rv, respectively. Furthermore, when the entire transcriptome was analyzed, it was found that there was no general gene location that could be targeted to minimize or maximize the number of off-targets. In an effort to determine the effects of off-targets on silencing efficiencies, previously published studies were used. Analyses with acpP, ino1, and marORAB revealed a statistically significant relationship between the number of short alignment length off-targets hybrids and the efficacy of the antisense gene silencing, suggesting that the minimization of off-targets may be beneficial for antisense gene silencing in prokaryotic organisms.