Bacterial classification with convolutional neural networks based on different data reduction layers

Abstract

For high accuracy classification of DNA sequences through Convolutional Neural Networks (CNNs), it is essential to use an efficient sequence representation that can accelerate similarity comparison between DNA sequences. In addition, CNN networks can be improved by avoiding the dimensionality problem associated with multi-layer CNN features. This paper presents a new approach for classification of bacterial DNA sequences based on a custom layer. A CNN is used with Frequency Chaos Game Representation (FCGR) of DNA. The FCGR is adopted as a sequence representation method with a suitable choice of the frequency k-lengthen words occurrence in DNA sequences. The DNA sequence is mapped using FCGR that produces an image of a gene sequence. This sequence displays both local and global patterns. A pre-trained CNN is built for image classification. First, the image is converted to feature maps through convolutional layers. This is sometimes followed by a down-sampling operation that reduces the spatial size of the feature map and removes redundant spatial information using the pooling layers. The Random Projection (RP) with an activation function, which carries data with a decent variety with some randomness, is suggested instead of the pooling layers. The feature reduction is achieved while keeping the high accuracy for classifying bacteria into taxonomic levels. The simulation results show that the proposed CNN based on RP has a trade-off between accuracy score and processing time.     

Synthesis of the Human Insulin Gene: Protein Expression,Scaling Up and Bioactivity

Abstract

Optimized Synthetic human insulin gene was preferred to easy of cloning, plasmid stability, and protein expression away from the native sequence and its rare codons. Two steps to obtain the insulin, so we assembled the gene of 293 bp using a battery of overlapped synthetic oligos, then cloned into pET101directional TOPO expression vector downstream to the T7 promoter. The proinsulin products were produced as inclusion bodies in E. coli at a level of 10%. The batch cultivation of the strain yielded 6 g/L, while the high cell density of fed‐batch cultivation yielded 46 g/L. The proinsulin purification yielded 110 mg/gram cell weight, and 1.3 mg/gram of a bioactive insulin. The native insulin was generated by enzymatic conversion of chemically processed proinsulin. The produced insulin was matched with that of a commercial aqueous version at a level of enzyme immunoassys, SDS‐PAGE, RP‐HPLC, and bioactivity. The present results showed that the produced insulin has a comparable biochemical and potency similar to that of commercial one.     

Screening of Marine Bacterial Producers of Polyunsaturated Fatty Acids and Optimisation of Production

Water samples from three different environments including Mid Atlantic Ridge, Red Sea and Mediterranean Sea were screened in order to isolate new polyunsaturated fatty acids (PUFAs) bacterial producers especially eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). Two hundred and fifty-one isolates were screened for PUFA production and among them the highest number of producers was isolated from the Mid-Atlantic Ridge followed by the Red Sea while no producers were found in the Mediterranean Sea samples. The screening strategy included a simple colourimetric method followed by a confirmation via GC/MS. Among the tested producers, an isolate named 66 was found to be a potentially high PUFA producer producing relatively high levels of EPA in particular. A Plackett–Burman statistical design of experiments was applied to screen a wide number of media components identifying glycerol and whey as components of a production medium. The potential low-cost production medium was optimised by applying a response surface methodology to obtain the highest productivity converting industrial by-products into value-added products. The maximum achieved productivity of EPA was 20 mg/g, 45 mg/l, representing 11 % of the total fatty acids, which is approximately five times more than the amount produced prior to optimisation. The production medium composition was 10.79 g/l whey and 6.87 g/l glycerol. To our knowledge, this is the first investigation of potential bacteria PUFA producers from Mediterranean and Red Seas providing an evaluation of a colourimetric screening method as means of rapid screening of a large number of isolates.     

Thyroid hormone response to thyrotropin releasing hormone after cold treatment during pre- and postnatal development in the domestic fowl

The purpose of the present study was to compare the effect of periodic cooling during the establishment of a functional pituitary-thyroid axis at days 11-14 of incubation and at other developmental stages, on the subsequent thyroid hormone response to thyrotropin releasing hormone (TRH). In the first and second experiment chick embryos were cooled for 6 hr/day to 30 degrees C from day 11 till 14 and from day 15 till 18 respectively, whereas control groups were incubated throughout at 37.8 degrees C. In both experiments the thyroxine (T4) response upon TRH in 19 day-old embryos was higher in the previously cold treated embryos, according to the percentages of increase. However, the higher T4 response in the cold treated animals disappeared in 1 or 7 day-old chicks hatched from the 2nd experiment, but remained present in chicks of the same ages in the 1st experiment. In a third experiment the T4 response to TRH injection immediately and 3 and 8 days after a temperature treatment (25 degrees C or 12 degrees C) for one week on four weeks old broiler chickens was found to be similar in both temperature groups. In all experiments there was a concomitant triiodothyronine (T3) increase after TRH injection, but differences between experimental groups were observed at days 15 and 19 of incubation and immediately after the postnatal temperature treatment. As an overall conclusion the results indicate that cold treatment only during the establishment of the hypothalamo-hypophysial control of thyroid function can have a long lasting effect by enhancing the T4 response to TRH injection.     

Impact of innovative nanoadditives on biodigesters microbiome

Nanoparticles (NPs) supplementation to biodigesters improves the digestibility of biowaste and the generation of biogas. This study investigates the impact of innovative nanoadditives on the microbiome of biodigesters. Fresh cow manure was anaerobically incubated in a water bath under mesophilic conditions for 30 days. Three different NPs (zinc ferrite, zinc ferrite with 10% carbon nanotubes and zinc ferrite with 10% C76 fullerene) were separately supplemented to the biodigesters at the beginning of the incubation period. Methane and hydrogen production were monitored daily. Manure samples were collected from the digesters at different time points and the microbial communities inside the biodigesters were investigated via real-time PCR and 16 S rRNA gene amplicon-sequencing. The results indicate that zinc ferrite NPs enhanced biogas production the most. The microbial community was significantly affected by NPs addition in terms of archaeal and bacterial 16 S rRNAgene copy numbers. The three ZF formulations NPs augmented the abundance of members within the hydrogenotrophic methanogenic phyla Methanobacteriaceae. While Methanomassiliicoccacaea were enriched in ZF/C76 supplemented biodigester due to a significant increase in hydrogen partial pressure, probably caused by the enrichment of Spirochaetaceae (genus Treponema). Overall, NPs supplementation significantly enriched acetate-producing members within Hungateiclostridiaceae in ZF/CNTs, Dysgonomonadaceae in ZF and Spirochaetaceae ZF/C76 biodigesters.     

Impact of the age of Biomphalaria alexandrina snails on Schistosoma mansoni transmission: modulation of the genetic outcome and the internal defence system of the snail

Of the approximately 34 identified Biomphalaria species,Biomphalaria alexandrina represents the intermediate host of Schistosoma mansoni in Egypt. Using parasitological and SOD1 enzyme assay, this study aimed to elucidate the impact of the age of B. alexandrina snails on their genetic variability and internal defence against S. mansoni infection. Susceptible and resistant snails were reared individually for self-reproduction; four subgroups of their progeny were used in experiment. The young susceptible subgroup showed the highest infection rate, the shortest pre-patent period, the highest total cercarial production, the highest mortality rate and the lowest SOD1 activity. Among the young and adult susceptible subgroups, 8% and 26% were found to be resistant, indicating the inheritance of resistance alleles from parents. The adult resistant subgroup, however, contained only resistant snails and showed the highest enzyme activity. The complex interaction between snail age, genetic background and internal defence resulted in great variability in compatibility patterns, with the highest significant difference between young susceptible and adult resistant snails. The results demonstrate that resistance alleles function to a greater degree in adults, with higher SOD1 activity and provide potential implications for Biomphalaria control. The identification of the most susceptible snail age enables determination of the best timing for applying molluscicides. Moreover, adult resistant snails could be beneficial in biological snail control.     

Liraglutide treatment effects on rat ovarian and uterine tissues

Liraglutide is a Glucagon-like peptide-1 (GLP-1) analogue used for the treatment of type II diabetes mellitus and obesity. The present study aimed at investigating the effect of Liraglutide in ovarian and uterine tissues in albino rats. 30 female rats were divided into 3 groups, 10 rats each. Group (I) served as control group, group (II) animals administrated therapeutic doses of liraglutide for 5 weeks and group (III) animals were injected with Liraglutide as the pervious group. Then they were left for 2 weeks after drug termination as a recovery period. The biochemical results showed a decrease in the female reproductive hormones profile, luteinizing hormone (LH), follicle stimulating hormone (FSH), estrogen (ER), progesterone (PR) and an increase in the level of testosterone (T). Liraglutide administration caused a significant decrease in the antioxidant markers, glutathione (GSH), catalase (CAT), and superoxide dismutase (SOD) and a significant increase in the activity of malondialdehyde (MDA). The histopathological examination revealed apoptosis of granulosa cells of different types of follicles with an increase in atretic and disorganized follicles. Vacuolar degenerative changes, and Atrophied muscle with sever inflammatory cell infiltrate in endometrium with congested, dilated blood vessels could be detected in uterine tissues. However, most of the deleterious effects of liraglutide decreased after drug discontinuation. In this study, we clarify the harmful effect of the liraglutide on ovarian and uterine tissues, thus potentially causing reproductive health malfunction and reducing the chances of pregnancy.     

Importance of natural licks for the mammals in Bornean inland tropical rain forests

An intensive camera-trapping study and a nutrient analysis were carried out to understand how natural licks are important for mammals in inland tropical rain forests where soil cations are usually depleted. Using camera traps, we investigated the fauna, food habits, and the frequency of visitation by species at five natural licks in the Deramakot forest reserve, Sabah, Malaysia. All food-habit types of mammals (carnivore, herbivore-frugivore, insectivore, and omnivore), which included 29 (78.4%) of 37 species known in Deramakot, were recorded at the natural licks. The sambar deer, followed by the bearded pig, the lesser mouse-deer, the Malay badger, and the orangutan were the most commonly recorded species and represented 77.5% in terms of the frequency of appearance in all photographs taken throughout the year. These results indicated that, although the proportion of species recorded at the natural licks relative to the whole mammalian fauna of the forest was high, the frequency of visitation greatly varied among the species, and only a few species dominated. The frequency of visitation seemed to reflect both the density of species and the demand for the minerals, because some endangered, low-density species were more frequently recorded by cameras than expected—for example, the orangutan which was one of the top five species among natural-lick users. The natural licks with greater concentrations of minerals in seepage soil water were significantly preferred by the sambar deer and the bearded pig than those with lower concentrations of minerals. This result suggests that the chemical properties of soil water in natural licks determine the frequency of visitation of these herbivorous species that have strong demand for minerals.     

Evaluation of mRNA expression level of the ATP synthase membrane subunit c locus 1 (ATP5G1) gene in patients with schizophrenia

BackgroundSchizophrenia is a serious, complex mental disorder. The impairment of oxidative phosphorylation has a detrimental consequence on CNS function. Different ATP synthase subunits have been involved in the pathological process of various neurodegenerative disorders. Our goal was to evaluate the mRNA expression level of the ATP synthase membrane subunit c locus 1 (ATP5G1, also named ATP5MC1) gene in patients with schizophrenia.MethodsDetermination of the expression levels of ATP5G1 in plasma and peripheral blood mononuclear cells (PBMCs) were performed by real-time PCR in 90 controls and 90 patients with schizophrenia.ResultsPatients had significantly decreased ATP5G1 mRNA expression levels in both plasma and PBMCs compared to controls. The receiver operating characteristic curve was applied to detect a cut-off value of ATP5G1 expression in plasma and PBMCs. The ATP5G1 relative expression in PBMCs had better performance with a cut-off value ≤ 21 (AUC = 0.892, P < 0.001), sensitivity of 94.44%, and specificity of 72.22% in discriminating between schizophrenic patients. ATP5G1 expression in PBMCs was an independent predictor in schizophrenia.ConclusionThis study revealed a down-regulation of ATP5G1 expression in schizophrenia, precisely expression in PBMCs. That might give insight into the role of ATP5G1 gene in the pathogenesis of schizophrenia.     

Putative abrogation impacts of Ajwa seeds on oxidative damage,liver dysfunction and associated complications in rats exposed to carbon tetrachloride

Molecular Biology Reports - Industrial toxicants such as Carbon tetrachloride (CCl4) are known to disrupt the oxidative–antioxidative balance, which generates excessive amounts of free...