Unsupervised deep learning for identifying the O 6-carboxymethyl guanine by nanopore sequencing / 生物医学工程学杂志

O 6-carboxymethyl guanine(O 6-CMG) is a highly mutagenic alkylation product of DNA that causes gastrointestinal cancer in organisms. Existing studies used mutant Mycobacterium smegmatis porin A (MspA) nanopore assisted by Phi29 DNA polymerase to localize it. Recently, machine learning technology has been widely used in the analysis of nanopore sequencing data. But the machine learning always need a large number of data labels that have brought extra work burden to researchers, which greatly affects its practicability. Accordingly, this paper proposes a nano-Unsupervised-Deep-Learning method (nano-UDL) based on an unsupervised clustering algorithm to identify methylation events in nanopore data automatically. Specially, nano-UDL first uses the deep AutoEncoder to extract features from the nanopore dataset and then applies the MeanShift clustering algorithm to classify data. Besides, nano-UDL can extract the optimal features for clustering by joint optimizing the clustering loss and reconstruction loss. Experimental results demonstrate that nano-UDL has relatively accurate recognition accuracy on the O 6-CMG dataset and can accurately identify all sequence segments containing O 6-CMG. In order to further verify the robustness of nano-UDL, hyperparameter sensitivity verification and ablation experiments were carried out in this paper. Using machine learning to analyze nanopore data can effectively reduce the additional cost of manual data analysis, which is significant for many biological studies, including genome sequencing.

Genetic regulation of the ompX porin of Salmonella Typhimurium in response to hydrogen peroxide stress

BACKGROUND: Salmonella Typhimurium is a Gram negative pathogen that causes a systemic disease in mice resembling typhoid fever. During its infective cycle, S. Typhimurium is phagocytized by macrophages and proliferates inside a Salmonella containing vacuole where Salmonella is exposed and survives oxidative stress induced by H2O2 through modulation of gene expression. After exposure of Salmonella to H2O2, the expression of the porin encoding gene ompX increases, as previously shown by microarray analysis. Expression of ompX mRNA is regulated at a post transcriptional level by MicA and CyaR sRNAs in aerobiosis. In addition, sequence analysis predicts a site for OxyS sRNA in ompX mRNA. RESULTS: In this work we sought to evaluate the transcriptional and post transcriptional regulation of ompX under H2O2 stress. We demonstrate that ompX expression is induced at the transcriptional level in S . Typhimurium under such conditions. Unexpectedly, an increase in ompX gene transcript and promoter activity after challenges with H2O2 does not translate into increased protein levels in the wild type strain, suggesting that ompX mRNA is also regulated at a post transcriptional level, at least under oxidative stress. In silico gene sequence analysis predicted that sRNAs CyaR, MicA, and OxyS could regulate ompX mRNA levels. Using rifampicin to inhibit mRNA expression, we show that the sRNAs (MicA, CyaR and OxyS) and the sRNA:mRNA chaperone Hfq positively modulate ompX mRNA levels under H2O2 induced stress in Salmonella during the exponential growth phase in Lennox broth. CONCLUSIONS: Our results demonstrate that ompX mRNA is regulated in response to H2O2 by the sRNAs CyaR, MicA and OxyS is Salmonella Typhimurium.

Polymorphism of P66 in / 生物医学与环境科学（英文）

Objective@#To study the polymorphism in P66 and its human B-cell epitopes of @*Methods@#Polymerase chain reaction (PCR) and sequencing were used to obtain the P66 sequences of 59 Chinese @*Results@#Results showed that genetic and amino acid diversity presented in the 66 kD protein of all 59 Chinese strains, especially in @*Conclusion@#In P66 of 59 Chinese strains, polymorphisms were widely distributed. More importantly, the P66 amino acid sequences of

Resistencia a carbapenemes en aislamientos de pseudomonas aeruginosa: un ejemplo de interacción entre distintos mecanismos / Carbapenem resistance in pseudomonas aeruginosa isolates: an example of interaction between different mechanisms

Objetivo. Identificar la proteína de membrana externa ausente en los aislamientos resistentes y determinar tanto las causas de su ausencia en la membrana, como la presencia de otros mecanismos de resistencia a carbapenemes en aislamientos clínicos de Pseudomonas aeruginosa. Métodos. Se estudió un brote de 20 aislamientos de P. aeruginosa previamente caracterizados como productores de la metalobetalactamasa IMP-13. Estos aislamientos presentaron igual expresión de la enzima IMP-13, pero solo cinco de ellos fueron resistentes acarbapenemes. En esos cinco aislamientos resistentes se confirmó la ausencia de una proteína de membrana externa. Se secuenciaron oprD y ampC; se identificaron las proteínas de membrana externa por desorción/ionización láser asistida por matriz/espectometría de masa tiempo de vuelo (MALDI-TOF); se determinó el nivel de expresión de OprD, de AmpC y de los sistemas de eflujo tipo Mex, por reacción en cadena de polimerasa en tiempo real, y por último, se determinó la contribución del déficit de OprD a la resistencia a carbapenemes. Resultados. La proteína de la membrana externa ausente en el grupo R (resistentes a ambos carbapenemes) fue identificada como OprD-TS, pero no se observaron variaciones en suexpresión. El gen oprD presentó mutaciones en los cinco aislamientos resistentes. Se observó la misma producción de la enzima tipo AmpC PDC-5 y del sistema de eflujo Mex AB-OprM entre los aislamientos sensibles y resistentes a carbapenemes. Se analizó cómo la presencia conjunta de IMP-13 y el déficit de OprD contribuyen al aumento de la resistencia.Conclusiones. Distintos mecanismos contribuyen a la resistencia de aislamientos productores de IMP-13 a carbapenemes. La posibilidad de no detectar estos aislamientos productores de IMP-13 representa un riesgo latente de selección de mutantes con mecanismos de resistencia que se suman para aumentar la resistencia a carbapenemes.

Objective. To identify the outer membrane protein absent in the resistant isolates and to determine both the causes of its absence in the membrane and the presence of othermechanisms of carbapenem resistance in clinical isolates of Pseudomonas aeruginosa. Methods. Twenty isolates from an outbreak of P. aeruginosa previously characterized as metallo-beta-lactamase IMP-13 producers were studied. All the isolates exhibitedequal expression of the IMP-13 enzyme, but only five of them were carbapenemresistant. It was found that the five resistant isolates lacked a outer membrane protein. The oprD and ampC genes were sequenced; the outer membrane proteins were identifiedusing matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry; the OprD and AmpC expressions, as well as the Mex efflux system, were assessed by real-time polymerase chain reaction; and finally, the contribution of reduced OprD to carbapenem resistance was determined. Results. The absent outer membrane protein in group R was identified as OprD-TS; however, no variations in its expression were observed. The oprD gene presentedmutations in the five resistant isolates. The production of AmpC PDC-5-type enzyme and the MexAB-OprM efflux system was the same in both carbapenem-sensitive and‑resistant isolates. The contribution of the combined presence of IMP-13 and reducedOprD to increased resistance was examined. Conclusions. Different mechanisms contribute to carbapenem resistance in IMP-13-producing isolates. The possibility that these IMP-13-producing isolates could go undetected poses a latent risk when selecting mutants with added resistancemechanisms in order to enhance carbapenem resistance.

Prevalencia de infección cervical por Chlamydia trachomatis en mujeres de la Región Metropolitana / Prevalence of cervical infection by Chlamydia trachomatis among Chilean women living in the Metropolitan Región

Background: Chlamydia trachomatis is the most common bacterial sexually transmitted infection (STI) worídwide. In women, chlamydia infections are 75 percent asymptomatic and can lead to pelvic inflammatory disease, infertility, and ectopic pregnancy. Infants exposed to the microorganism at birth also have a high risk to develop conjunctivitis and pneumonía. Aim: To determine the prevalence of C trachomatis in women in the Metropolitan área of Santiago (Chile). Patients and methods: Cervical specimens were collected from 403 women attending three gynecological outpatient settings from Apríl 2003 to June 2005. These included one public hospital (n =100), a prívate medical center (n =268), and a clinic for adolescents (n =35). Mean ages ofeach group of patients were 35.6±8,2, 33.4±8.1 and 16.9±4.2 years, respectively. The diagnosis of C trachomatis was performed by the amplification byPCRofa 517-base pair segment of the cryptic plasmid on specimens extracted by a commercial procedure. Positive specimens were conñrmed by nested PCRs targeting the ompl gene. The presence of vaginal infections and its association with C trachomatis was investigated in a subset of 223 women ofthe prívate center. Residís: C trachomatis was detected in the cervix of 19 out of 403 women, resulting in a prevalence of 4.7 percent. The distribution of positive cases among different age groups was not significantly different. Women presenting with bacterial vaginosis had a significantly higher prevalence of C trachomatis infection (p <0.01). Conclusions: This study found a high prevalence of C trachomatis among gynecologic patients that should prompt preventive strategies.

Determination of asymptomatic Chiamydia trachomatis infections by omp1 gene based-PCR

The objective of this research was to determine the prevalence of genital C. trachomatis infection in asymptomatic women by using highly sensitive nested-polymerase chain reaction [PCR] in urine sample. One hundred-forty asymptomatic women were randomly selected from those who attended gynecology out patient department of Hazraate Rasool Hospital in Tehran. First catch urine specimen were collected from all the participants. DNA extraction was performed by means of High Pure PCR Template Preparation Kit [HPPTP] according to the manufacture's instructions. Extracted DNA was tested by omp1 gene based nested-PCR, using sets of primers to amplify C. trachomatis omp1 gene. Visualization of a 1027 bp fragment from omp1 gene in agarose gel electrophoresis was considered as a positive result. In total, 140 urines were tested for determination of C. trachomatis infection. C. trachomatis omp-1 was detected in 22.1% of cases [31/140]. The overall prevalence rates of C. trachomatis in the urine sample as determined by omp1 based nested-PCR were 4.3% in group I [age, <25 years], 12.1% in group II [age, 25-34 years], 5.0% in group III [age, 35-44 years] and 0.7% in group IV [>44 years]. The highest prevalence of C. trachomatis infection [12.1%] was seen in women aged 25-34 years. This finding was not statistically significant [p=0.710]. Also, there was not relation between C. trachomatis infection and some probable risk factors such as young age [<25 years], STD history and missing use of barrier contraceptive in this study. The prevalence of C. trachomatis infection in the women not seeking health care warrants more comprehensive study using high sensitive omp1 based nested- PCR to identify and treat a large number of infected women in Iran

A hospital based study on the prevalence of conjunctivitis due to Chlamydia trachomatis.

BACKGROUND & OBJECTIVES: Very few studies have been done in India to determine the prevalence of Chlamydia trachomatis causing conjunctivitis using polymerase chain reaction (PCR) methods. Hence the prevalence of primary conjunctivitis due to C. trachomatis among individuals attending ophthalmic hospitals in Chennai was determined and compared with our earlier results. METHODS: A total of 328 conjunctival swabs from 255 (both eyes 73 and one eye 182) patients were investigated by fluorescent antibody test (FAT) on direct smears, culture and PCRs for cryptic plasmid and major outer membrane protein (MOMPI) gene of C. trachomatis. An infant with ophthalmia neonatorum was also included. RESULTS: Among these 328 specimens processed, 16 (4.9%) from 12 (4.7%) patients were positive by cryptic plasmid PCR. Among these, 3 from 2 patients were positive by FAT (direct smear), culture and PCR for MOMP 1 gene. Both eyes of the infant with ophthalmia neonatorum were positive by all the methods. The sensitivity of FAT and culture (18.8%) was lower compared to PCR. INTERPRETATION & CONCLUSION: A significant decrease in the prevalence of adult chlamydial conjunctivitis has occurred in the 10-year period among patients reporting to the ophthalmic hospitals in Chennai. PCR using cryptic plasmid primers was found to be the most sensitive method to detect C. trachomatis in patients with conjunctivitis.