Interaction between high-intensity interval training and high-protein diet on gut microbiota composition and body weight in obese male rats

Diet and exercise are two critical factors that regulate gut microbiota, affecting weight management. The present study investigated the effect of 10 weeks of high-intensity interval training (HIIT) and a high-protein diet (HPD) on gut microbiota composition and body weight changes in obese male Wistar rats. Forty obese rats were randomly divided into five groups, including HPD, HIIT + HPD, HIIT + high-fat diet (HFD) (continuing HFD during intervention), obese control 1 (continuing HFD during intervention), obese control 2 (cutting off HFD at the beginning of the intervention and continuing standard diet), and eight non-obese Wistar rats as a non-obese control (NOC) group (standard diet). Microbial community composition and diversity analysis by sequencing 16S rRNA genes derived from the fecal samples, body weight, and Lee index were assessed. The body weight and Lee index in the NOC, HIIT + HFD, HPD, and HIIT + HPD groups were significantly lower than that in the OC1 and OC2 groups along with the lower body weight and Lee index in the HPD and HIIT + HPD groups compared with the HIIT + HFD group. Also, HFD consumption and switching from HFD to a standard diet or HPD increased gut microbiota dysbiosis. Furthermore, HIIT along with HFD increased the adverse effects of HFD on gut microbiota, while the HIIT + HPD increased microbial richness, improved gut microbiota dysbiosis, and changed rats' phenotype to lean. It appears that HFD discontinuation without doing HIIT does not improve gut microbiota dysbiosis. Also, the HIIT + HFD, HPD, and HIIT + HPD slow down HFD-induced weight gain, but HIIT + HPD is a more reliable strategy for weight management due to its beneficial effects on gut microbiota composition.

Rodents as vehicle for delivery of transgenic bacteria to make paratransgenic sand fly vectors of cutaneous leishmaniasis in field condition

Vector-borne diseases, among them leishmaniasis, cause more than 700,000 deaths annually. The lack of an effective vaccination and the increasing resistance of sand flies to insecticides require the urgent development of innovative approaches to contain the disease. The use of engineered bacteria that express anti-parasite molecules (paratransgenesis) shows much promise. However, a challenge for implementation of this strategy is to devise means to introduce modified bacteria into sand flies in the field. In this study, we use rodent food bait as a delivery strategy to introduce two mCherry-fluorescent bacteria, Serratia AS1 and Enterobacter cloacae, into adult sand flies in field settings. Bacteria-infected food was provided to Rhombomys opimus rodents. These bacteria transiently pass through the rodent alimentary tract and are delivered to larval habitats with the rodent feces. The feces are ingested by sand fly larvae and, in the case of Serratia AS1, are trans-stadially transmitted to adults. This is the first report of targeting delivery of Serratia AS1 in a paratransgenic system to control transmission of leishmaniasis under field condition. This novel strategy shows promise for delivering transgenic bacteria to Leishmania vectors in the field.

Bioremediation of a salty petrochemical wastewater containing bisphenol A by a novel indigenous Pseudomonas pseudoalcaligenes

One novel indigenous halotolerant, Pseudomonas sp, with high potential for bisphenol A (BPA) biodegradation was isolated from an outlet of petrochemical wastewater in Iran. The optimal temperature and pH for degradation of BPA by this strain were 30 °C and 7, respectively. This strain was able to decrease COD (chemical oxygen demand) of basal salt medium containing 300 mg L^-1 BPA as sole carbon source and 40 g L^-1 NaCl from 655.2 to 109.2 mg L^-1 (about 83% decrease) after 36 h. The bacterium degraded 56.3 (19%), 202.43 (67%), 288.86 (96%) and 300 mg L^-1 (100%) BPA in basal salt medium containing 300 mg L^-1 BPA and 40 g L^-1 NaCl within 12, 18, 24 and 36 h, respectively. In addition, this strain could degrade phenol (100 mg L^-1) and BPA (300 mg L^-1) in salty petrochemical wastewater within 24 h, completely. In batch fermentation of petrochemical wastewater using this strain higher growth and phenol (100 mg L^-1), BPA (372 mg L^-1) removal within 6 h were achieved. High performance liquid chromatography (HPLC) and gas chromatography mass spectrometry (GC/MS) analysis revealed several intermediates during the BPA degradation process. These intermediates were identified as 4-hydroxybenzaldehyde, 4-hydroxyacetophenone, 4-hydroxyphenylacetate, M-hydroxymandelic acid, 2-phenylpropane-1,2-diol, 2-phenyl-2-propanol and lactic acid. The possible BPA-biodegradation pathway based on the identified metabolites and in agreement with recorded pathway in KEGG database was proposed. Preliminary 16S rDNA sequence analysis and subsequent genetically characterization through comprehensive genomic analysis identified the strain as Pseudomonas pseudoalcaligenes strain YKJ.

Evaluation of anti-malaria potency of wild and genetically modified Enterobacter cloacae expressing effector proteins in Anopheles stephensi

Background

Malaria is one of the most lethal infectious diseases in tropical and subtropical areas of the world. Paratransgenesis using symbiotic bacteria offers a sustainable and environmentally friendly strategy to combat this disease. In the study reported here, we evaluated the disruption of malaria transmission in the Anopheles stephensi-Plasmodium berghei assemblage using the wild-type (WT) and three modified strains of the insect gut bacterium, Enterobacter cloacae.

Methods

The assay was carried out using the E. cloacae dissolvens WT and three engineered strains (expressing green fluorescent protein-defensin (GFP-D), scorpine-HasA (S-HasA) and HasA only, respectively). Cotton wool soaked in a solution of 5% (wt/vol) fructose + red dye (1/50 ml) laced with one of the bacterial strains (1 × 10⁹cells/ml) was placed overnight in cages containing female An. stephensi mosquitoes (age: 3–5 days). Each group of sugar-fed mosquitoes was then starved for 4–6 h, following which time they were allowed to blood-feed on P. berghei–infected mice for 20 min in the dark at 17–20 °C. The blood-fed mosquitoes were kept at 19 ± 1 °C and 80 ± 5% relative humidity, and parasite infection was measured by midgut dissection and oocyst counting 10 days post-infection (dpi).

Results

Exposure to both WT and genetically modified E. cloacae dissolvens strains significantly (P < 0.0001) disrupted P. berghei development in the midgut of An. stephensi, in comparison with the control group. The mean parasite inhibition of E. cloacae^WT, E. cloacae^HasA, E. cloacae^S−HasA and E. cloacae^GFP−D was measured as 72, 86, 92.5 and 92.8 respectively.

Conclusions

The WT and modified strains of E. cloacae have the potential to abolish oocyst development by providing a physical barrier or through the excretion of intrinsic effector molecules. These findings reinforce the case for the use of either WT or genetically modified strains of E. cloacae bacteria as a powerful tool to combat malaria.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-022-05183-0.

Bioinformatics analysis of extracellular subtilisin E from Bacillus subtilis

Bacillus spp. are the main sources of subtilisin E, which has several applications in biotechnology. The 3D structure of subtilisin E has a significant impact on its efficacy. In this study, we evaluated subtilisin E from Bacillus subtilis subsp. subtilis str. 168 by bioinformatic methods. The results revealed that the subtilisin E sequence from B. subtilis contains highly conserved amino acids, including histidine (H), aspartic acid (D) and serine (S). Subtilisin E cleaves the bonds between hydrophobic and polar amino acids in keratin-associated proteins. The effects of point mutations on the crystal structure of subtilisin E (PDB ID: 1SCJ) showed that changes of asparagine 123 (N123) to valine (V) and serine 331 (S331) to leucine (L) respectively, were the most stabilizing. Genomic analysis of the subtilisin E-coding gene (aprE) indicated that this gene and the yhfN gene are expressed through a σA promoter. The analysis of TBFs revealed AbrB, ScoC, DegU, Hpr, σA, SinR, TenA, and DegU as relevant regulators of aprE expression. Phylogenetic analysis showed that subtilisin Es have highly conserved structures among Bacillus spp., sharing a common ancestor, where their coding genes were duplicated and evolved within the Bacillus spp. As the conclusion, our in silico study demonstrated that the overexpression of the aprE gene and stability of the produced subtilisin E can be improved though system biology methods such as point mutations and identifying the involved transcription factors (TFs) or/and TBFs.Communicated by Ramaswamy H. Sarma.

Design, construction, and expression of recombinant human interferon beta gene in CHO-s cell line using EBV-based expression system

Background and purpose

Codon optimization has been considered as a powerful strategy to increase the expression level of protein therapeutics in mammalian cells. As an empirical approach to study the effects of the codon usage and GC content on heterologous gene expression in suspension adapted Chinese hamster ovary (CHO-s) cells, we redesigned the recombinant human interferon beta (rhIFN- β) gene based on the codon preference of the CHO cell in a way to increase the GC content in the third position of each codon.

Experimental approach

The nucleotide sequence of the codon-optimized rhIFN-β was synthesized in parallel with the wild-type and expressed transiently in CHO-s cells using Epstein-Bar virus (EBV)-based expression system. The protein expression of the rhIFN-β by codon-optimized and wild-type genes were quantified using ELISA test.

Findings / Results

The results indicated a 2.8-fold increase in the expression level of the biologically active form of the rhIFN-β by codon-optimized sequence.

Conclusion and implications

These results shed light on the capability of codon optimization to create a stable CHO cell for scaling up the production of recombinant therapeutics such as rhIFN-β.

CD44 Gene rs8193 C Allele Is Significantly Enriched in Gastric Cancer Patients

OBJECTIVE

Gastric cancer is a multifactorial disease. In addition to environmental factors, many genes are involved in this malignancy. One of the genes associated with gastric cancer is CD44 gene and its polymorphisms. CD44 gene plays role in regulating cell survival, growth and mobility. The single nucleotide polymorphism (SNP) rs8193, located in the CD44 gene, has not been studied in gastric cancer patients of the Iranian population. The present study aims to study this polymorphism in 86 gastric cancer patients and 96 healthy individuals.

MATERIALS AND METHODS

In this cross-sectional case-control study, rs8193 polymorphism was genotyped by allele specific primer polymerase chain reaction (ASP-PCR) technique. The obtained data were statistically analyzed. To find the potential mechanism of action, rs8193 was bioinformatically investigated.

RESULTS

rs8193 C allele played a risk factor role for gastric cancer. Patients carrying this allele were more susceptible to have gastric cancer, with lymph node spread. On the other hand, rs8193 T allele, a protective factor, was associated with a higher chance of accumulation in the lower stages of cancer. C allele might impose its effect via destabilizing CD44 and miR-570 interaction.

CONCLUSION

rs8193 is statistically associated with the risk of malignancy, lymph node spread and stage of gastric cancer in Iranian population.

Comprehensive genomic analysis of an indigenous Pseudomonas pseudoalcaligenes degrading phenolic compounds

Environmental contamination with aromatic compounds is a universal challenge. Aromatic-degrading microorganisms isolated from the same or similar polluted environments seem to be more suitable for bioremediation. Moreover, microorganisms adapted to contaminated environments are able to use toxic compounds as the sole sources of carbon and energy. An indigenous strain of Pseudomonas, isolated from the Mahshahr Petrochemical plant in the Khuzestan province, southwest of Iran, was studied genetically. It was characterized as a novel Gram-negative, aerobic, halotolerant, rod-shaped bacterium designated Pseudomonas YKJ, which was resistant to chloramphenicol and ampicillin. Genome of the strain was completely sequenced using Illumina technology to identify its genetic characteristics. MLST analysis revealed that the YKJ strain belongs to the genus Pseudomonas indicating the highest sequence similarity with Pseudomonas pseudoalcaligenes strain CECT 5344 (99% identity). Core- and pan-genome analysis indicated that P. pseudoalcaligenes contains 1,671 core and 3,935 unique genes for coding DNA sequences. The metabolic and degradation pathways for aromatic pollutants were investigated using the NCBI and KEGG databases. Genomic and experimental analyses showed that the YKJ strain is able to degrade certain aromatic compounds including bisphenol A, phenol, benzoate, styrene, xylene, benzene and chlorobenzene. Moreover, antibiotic resistance and chemotaxis properties of the YKJ strain were found to be controlled by two-component regulatory systems.

Cometabolic degradation of bisphenol A by pure culture of Ralstonia eutropha and metabolic pathway analysis

Bisphenol A (BPA) is a toxic compound emitting to the environment mainly by polycarbonate production facilities. In this research, BPA with the initial concentrations in the range of 1-40 mg l^-1 was degraded by Ralstonia eutropha. The bacteria were unable to use BPA as the sole carbon source. Therefore, resting and growing cells of phenol-adapted R. eutropha were used for cometabolic biodegradation of BPA with phenol at the concentration of 100 mg l^-1. The optimum initial concentrations of BPA were 20 mg l^-1 in both approaches of cometabolism. By using resting cells, BPA removal efficiency (RE) reached to 57%, however, RE decreased to 37% by growing cells in the presence of phenol. BPA-degrading activity was inhibited at BPA concentrations >20 mg l^-1. Liquid chromatography-mass spectrometry technique was used to identify some metabolic intermediates generated during BPA degradation process as 1,2-bis(4-hydroxyphenyl)-2-propanol, 4-(2-propanol)-phenol, 4-hydroxyacetophenone, 4-isopropenylphenol, and 4-hydroxybenzoic acid. Finally, metabolic pathways for BPA degradation were proposed in this study.

Practical evaluation of 11 de novo assemblers in metagenome assembly

Next Generation Sequencing (NGS) technologies are revolutionizing the field of biology and metagenomic-based research. Since the volume of metagenomic data is typically very large, De novo metagenomic assembly can be effectively used to reduce the total amount of data and enhance quality of downstream analysis, such as annotation and binning. Although, there are many freely available assemblers, but selecting one suitable for a specific goal can be highly challenging. In this study, the performance of 11 well-known assemblers was evaluated in the assembly of three different metagenomes. The results obtained show that metaSPAdes is the best assembler and Megahit is a good choice for conservative assembly strategy. In addition, this research provides useful information regarding the pros and cons of each assembler and the effect of read length on assembly, thereby helping scholars to select the optimal assembler based on their objectives.

Dynamics of Transgenic Enterobacter cloacae Expressing Green Fluorescent Protein Defensin (GFP-D) in Anopheles stephensi Under Laboratory Condition

BACKGROUND

Enterobacter cloacae bacterium is a known symbiont of the most Anopheles gut microflora and nominated as a good candidate for paratransgenic control of malaria. However, the population dynamics of this bacterium within An. stephensi and its introduction methods to the mosquitoes have not yet been explored.

METHODS

Enterobacter cloacae subsp. dissolvens expressing green fluorescent protein and defensin (GFP-D) was used to study transstadial transmission and the course of time, larval habitat, sugar, and blood meal on dynamics of the bacterium in the mosquito life stages in the laboratory condition. The bacterial quantities were measured by plating samples and counting GFP expressing colonies on the Tet-BHI agar medium.

RESULTS

The E. cloacae population remained stable in sugar bait at least for eleven days whereas it was lowered in the insectary larval habitat where the bacteria inadequately recycled. The bacterium was weakly transmitted transstadially from larval to adult stage. The bacterial populations increased smoothly and then dramatically in the guts of An. stephensi following sugar and blood meal respectively followed by a gradual reduction over the time.

CONCLUSION

Enterobacter cloacae was highly stable in sugar bait and increased tremendously in the gut of female adult An. stephensi within 24h post blood meal. Sugar bait stations can be used for introduction of the transgenic bacteria in a paratransgenic approach. It is recommended to evaluate the attraction of sugar bait in combination with attractive kairomones as well as its stability and survival rate in the semi-field or field conditions.

Enhancement of crystallinity of cellulose produced by Escherichia coli through heterologous expression of bcsD gene from Gluconacetobacter xylinus

OBJECTIVES

To evaluate the crystallinity index of the cellulose produced by Escherichia coli Nissle 1917 after heterologous expression of the cellulose synthase subunit D (bcsD) gene of Gluconacetobacter xylinus BPR2001.

RESULTS

The bcsD gene of G. xylinus BPR2001 was expressed in E. coli and its protein product was visualized using SDS-PAGE. FTIR analysis showed that the crystallinity index of the cellulose produced by the recombinants was 0.84, which is 17% more than that of the wild type strain. The increased crystallinity index was also confirmed by X-ray diffraction analysis. The cellulose content was not changed significantly after over-expressing the bcsD.

CONCLUSION

The bcsD gene can improve the crystalline structure of the bacterial cellulose but there is not any significant difference between the amounts of cellulose produced by the recombinant and wild type E. coli Nissle 1917.

Study the effect of F17S mutation on the chimeric Bacillus thermocatenulatus lipase

Lipases (triacylglycerol acylhydrolase, EC 3.1.1.3) are one of the highest value commercial enzymes as they have potential applications in biotechnology for detergents, food, pharmaceuticals, leather, textiles, cosmetics, and paper industries; and are currently receiving considerable attention because of their potential applications in biotechnology. Bacillus thermocatenulatus Lipase 2 (BTL2) is one of the most important research targets, because of its potential industrial applications. In this study, the effect of substitution Phe17 with Ser in mutated BTL2 lipase, which conserved pentapeptide (112Ala-His-Ser-Gln-Gly116) was replaced with similar sequences (207Gly-Glu-Ser-Ala-Gly211) of Candida rugosa lipase (CLR) at the nucleophilic elbow region. Docking results confirmed the mutated lipase to be better than the chimeric lipase. So, cloning was conducted, and the mutated and chimeric btl2 genes were expressed in Escherichia coli, and then the enzymes were purified by anion exchange chromatography. The mutation increased lipase lipolytic activity against most of the applied substrates, with the exception of tributyrin when compared with chimeric lipase. Further, the mutated lipase exhibited higher activity than the chimeric lipase at all temperatures. Optimum pH of the mutated lipase was obtained at pH 9.5, which was more than the chimeric one. Enzyme activity of the mutated lipase in the presence of organic solvents, detergents, and metal ions was also improved than the chimeric lipase.

Efficient Cadmium Bioaccumulation by Displayed Hybrid CS3 Pili: Effect of Heavy Metal Binding Motif Insertion Site on Adsorption Capacity and Selectivity

The objective of this study was to evaluate the influence of insertion site of the metal binding motif on the bioaccumulation capacity of the hybrid CS3 pili displayed on the surface of Escherichia coli using both computational and experimental methods. Two metal binding motifs (cadmium binding motif (cbm) and cadmium binding beta motif (cbβm)), identified by searching against the PROSITE database, were inserted into five putative permissive sites of CstH protein (CS3 pili subunit) by using SOEing PCR technique. The expression and surface display of the hybrid pili were evaluated using dot and Western blotting methods and also immunofluorescence microscopy. The cadmium binding affinity and selectivity of the recombinant bacteria displaying various hybrid pili were evaluated using atomic absorption procedure. The results showed that the cadmium binding motifs enabled the cells to sequester cadmium 8- to 16-fold higher than the E.coli expressing native pili. The location of the metal binding motifs in the pili subunit had also a significant effect on the metal-binding properties of the hybrid pili. The insertion at positions 107-108 and 92-93 of the mature CstH showed the highest adsorption in comparison to other positions.

Characterization of a farnesyl diphosphate synthase gene from Penicillium brevicompactum MUCL 19011

OBJECTIVES

Farnesyl diphosphate synthase is a critical enzyme in the isoprenoids biosynthesis pathway responsible for ergosterol and secondary metabolites biosynthesis in fungi.

RESULTS

Characterization of fds from Penicillium brevicompactum (Pbfds) was performed using TAIL-PCR and RT-PCR followed by complementation tests in Saccharomyces cerevisiae and determination of its expression profile by semi-quantitative RT-PCR. Promoter analysis suggests some binding sites for transcription factors some of which are involved in fungal growth and response to environmental stress. The Pbfds ORF encodes a cytosolic 39.7 kDa protein with a high conservation among Eurotiomycetes and the highest identity (96 %) with Pen. chrysogenum. Homology-based structural modeling suggests that the PbFDS is formed by the arrangement of 15 core helices around a large central cavity where the catalytic reaction takes place. Superimposition of the predicted 3D structure of the enzyme on its ortholog in human reveals the same folding pattern in the counterparts.

CONCLUSION

The Pbfds expression may be stimulated in response to the environmental stresses and fungal growth and encodes the PBFDS--a cytosolic enzyme which with a key role in ergosterol and secondary metabolites biosynthesis.

A Nested-Splicing by Overlap Extension PCR Improves Specificity of this Standard Method

BACKGROUND

Splicing by overlap extension (SOE) PCR is used to create mutation in the coding sequence of an enzyme in order to study the role of specific residues in protein's structure and function.

OBJECTIVES

We introduced a nested-SOE-PCR (N -SOE-PCR) in order to increase the specificity and generating mutations in a gene by SOE-PCR.

MATERIALS AND METHODS

Genomic DNA from Bacillus thermocatenulatus was extracted. Nested PCR was used to amplify B. thermocatenulatus lipase gene variants, namely wild type and mutant, using gene specific and mutagenic specific primers, followed by cloning in a suitable vector. Briefly in N-SOE-PCR method, instead of two pairs of primers, three pairs of primers are used to amplify a mutagenic fragment. Moreover, the first and second PCR products are slightly longer than PCR products in a conventional SOE. PCR products obtained from the first round of PCR are used for the second PCR by applying the nested and mutated primers. Following to the purification of the amplified fragments, they will be subject of the further purification and will be used as template to perform the third round of PCR using gene specific primers. In the end, the products will be cloned into a suitable vector for subsequent application.

RESULTS

In comparison to the conventional SOE-PCR, the improved method (i.e. N-SOE-PCR) increases the yield and specificity of the products. In addition, the proposed method shows a large reduction in the non-specific products.

CONCLUSIONS

By applying two more primers in the conventional SOE, the specificity of the method will be improved. This would be in part due to annealing of the primers further inside the amplicon that increases both the efficiency and a better attachment of the primers. Positioning of the primer far from both ends of an amplicon leads to an enhanced binding as well as increased affinity in the third round of amplification in SOE.

Aerobic bacterial flora of biotic and abiotic compartments of a hyperendemic Zoonotic Cutaneous Leishmaniasis (ZCL) focus

Background

Identification of the microflora of the sand fly gut and the environmental distribution of these bacteria are important components for paratransgenic control of Leishmania transmission by sand flies.

Methods

Biotic and abiotic bacterial communities of four compartments of a hyper-endemic focus of Zoonotic Cutaneous Leishmaniasis (ZCL) were investigated using 16S ribosomal DNA sequencing and phylogenetic tree construction. These compartments include Phlebotomus papatasi’s gut, skin and intestinal tract of great gerbil Rhombomys opimus, the gerbil nest supplies, and plant food sources of the vectors and reservoirs.

Results

Sequence homology analysis using nine available 16S rDNA data bases revealed 40, 24, 15 and 14 aerobic bacterial species from the vector guts, the gerbil bodies, the gerbil nests, and the plants, respectively. The isolated bacteria belong to wide ranges including aerobic to facultative anaerobic, pathogen to commensals, sand fly oviposition inducers, land to air and ocean habitats, animal and human probiotics, and plant growth-promoting rhizobacteria. Matching data analysis suggested that the adult P. papatasi gut bacteria could be acquired from three routes, adult sugar feeding on the plant saps, adult blood feeding on the animal host, and larval feeding from nest supplies. However, our laboratory experiment showed that none of the bacteria of the reservoir skin was transmitted to female sand fly guts via blood feeding. The microflora of sand fly guts were associated with the sand fly environment in which the predominant bacteria were Microbacterium, Pseudomonas, and Staphylococcus in human dwellings, cattle farms, and rodent colonies, respectively. Staphylococcus aureus was the most common bacterium in sand fly guts. Presence of some sand fly ovipoisition inducers such Bacillus spp. and Staphylococcus saprophyticus support association between gut flora and oviposition induction.

Conclusions

Results of this study showed that Bacillus subtilis and Enterobacter cloacae particularly subsp. dissolvens are circulated among the sand fly guts, the plants, and the sand fly larval breeding places and hence are possible candidates for a paratransgenic approach to reduce Leishmania transmission.

Malpighian tubules are important determinants of Pseudomonas transstadial transmission and longtime persistence in Anopheles stephensi

Background

Pseudomonas is a genus of bacteria commonly found in investigations of gut microbes in malaria mosquitoes. Among those mosquitoes is the dominating malaria vector in Asia, Anopheles stephensi, where Pseudomonas is a prevailing bacterium and natural inhabitant of its breeding places. In order to explore the reason for finding Pseudomonas so frequently, an investigation of its localization and transstadial properties was undertaken.

Methods

A Pseudomonas isolate from An. stephensi was transformed successfully with an endogenous plasmid modified to express green fluorescent protein (GFP). Subsequently, the Pseudomonas-GFP was added to the laboratory larval breeding place of An. stephensi and taken up by the larvae. After 24 hours, the larvae were cleaned and moved to a bath with double-distilled water. Also, female adults were fed sugar solution containing Pseudomonas-GFP. The Pseudomonas-GFP was traced in the alimentary canal of larvae, pupae and adults.

Results

Fluorescent microscopy and PCR assays showed that the Pseudomonas bacteria underwent transstadial transmission from larvae to pupae and then to adults. In blood-fed female mosquitoes, the bacteria increased in numbers and remained in the mosquito body for at least three weeks after eclosion. In addition to the midgut, the Malpighian tubules of both larvae and adult mosquitoes were colonized by the bacteria. Also Pseudomonas-GFP that was distributed through sugar solution was able to colonize the Malpighian tubules of adult females.

Conclusions

Colonization of the Malpighian tubules by Pseudomonas bacteria seems to be important for the transstadial passage from larvae to adult and presumably for the longevity of the bacteria in the adult mosquito. The existence of an entry point in the larval stage, and the long duration in the female gut, opens up for a possible use of Pseudomonas in mosquito paratransgenesis.

Biodegradation of bisphenol A by the newly-isolated Enterobacter gergoviae strain BYK-7 enhanced using genetic manipulation

Endogenous bacterial strains possessing a high bisphenol A (BPA)-tolerance/degradation activity were isolated from different outlets of petrochemical wastewater in Iran using the enrichment cultivation approach.

Cloning and characterization of newly isolated lipase from Enterobacter sp. Bn12

A mesophilic Enterobacter sp. Bn12 producing an alkaline thermostable lipase was isolated from soil in Tehran, Iran. The lipase gene (ELBn12) was identified from a genomic library. Sequence analysis of the DNA fragment revealed an open reading frame of 879 bp encoding a lipase with a molecular mass of 31.3 kDa. The deduced amino acid sequence showed 96% identity with a lipase of Enterobacter sp. Ag1 and the identity of their DNA sequences was 88.9%. ELBn12 belongs to the lipase subfamily I.1 and its catalytic triad consists of Ser82, Asp237 and His259. The lipase was expressed in Escherichia coli (BL21) pLysS and partially purified by anion exchange chromatography. The maximum activity of ELBn12 was obtained at temperature of 60 °C and pH 8.0 towards tricaprylin (C₈) and its specific activity was around 2900 U/mg. ELBn12 was stable within a broad pH range from 6.0 to 11.0. The enzyme showed high stability in both polar and nonpolar organic solvents at 50% (v/v). The lipase activity was enhanced in the presence of 10 mM of Ca²⁺, Mg²⁺ and K⁺, while heavy metals (Fe³⁺ and Zn²⁺) had strong inhibitory effect. ELBn12 showed high activity in the presence of 1% (w/v) nonionic surfactants, however ionic surfactants inhibited the lipolytic activity. ELBn12 characteristics show that it has a potential to be used in various industrial processes.

Aerobic Microbial Community of Insectary Population of Phlebotomus papatasi

BACKGROUND

Microbes particularly bacteria presenting in the gut of haematophagous insects may have an important role in the epidemiology of human infectious disease.

METHODS

The microbial flora of gut and surrounding environmental of a laboratory strain of Phlebotomus papatasi, the main vector of Zoonotic Cutaneous Leishmaniasis (ZCL) in the old world, was investigated. Biochemical reactions and 16s rDNA sequencing of the isolated bacteria against 24 sugars and amino acids were used for bacteria species identification. Common mycological media used for fungi identification as well.

RESULTS

Most isolates belonged to the Enterobacteriaceae, a large, heterogeneous group of gram-negative rods whose natural habitat is the intestinal tract of humans and animals. Enterobacteriaceae groups included Edwardsiella, Enterobacter, Escherichia, Klebsiella, Kluyvera, Leminorella, Pantoea, Proteus, Providencia, Rahnella, Serratia, Shigella, Tatumella, and Yersinia and non Enterobacteriaceae groups included Bacillus, Staphylococcus and Pseudomonas. The most prevalent isolates were Proteus mirabilis and P. vulgaris. These saprophytic and swarming motile bacteria were isolated from all immature, pupae, and mature fed or unfed male or female sand flies as well as from larval and adult food sources. Five fungi species were also isolated from sand flies, their food sources and colonization materials where Candida sp. was common in all mentioned sources.

CONCLUSION

Midgut microbiota are increasingly seen as an important factor for modulating vector competence in insect vectors so their possible effects of the mirobiota on the biology of P. papatasi and their roles in the sandfly-Leishmania interaction are discussed.

Expression Enhancement in Trastuzumab Therapeutic Monoclonal Antibody Production using Genomic Amplification with Methotrexate

BACKGROUND

Trastuzumab (Herceptin) is a humanized monoclonal antibody (mAb) which is used for specific treatment of metastatic breast cancer in patients with overexpression of HER2/neu receptor. In this study, we have attempted to develop a biosimilar version of trastuzumab mAb.

METHODS

According to in silico studies, the heavy and light chains of trastuzumab mAb were designed and constructed. The recombinant constructs were co-transfected in CHO DG44 cell line. Stable transformants were selected on a semi solid medium. Genomic amplification with methotrexate was achieved for heavy chain gene amplification. Biological activity of produced antibody in comparison with Herceptin was tested by flow cytometry method.

RESULTS

Three folds of amplification were obtained after seven rounds of methotrexate treatments. The results indicated the equal expression level of heavy and light chains. The yield of purified mAb was between 50 to 60 mg/l /day. According to the results, the produced mAb had similar affinity to HER2(+) tumor cells to that of Herceptin.

CONCLUSION

High-level recombinant protein expression can be achieved by amplification of the recombinant gene with a selectable marker, such as Dihydrofolate Reductase (DHFR). It is usually accepted that DHFR gene can be amplified in DHFR(－) CHO cells, which consequently leads to amplification of the co-linked target gene, and finally amplification of recombinant protein. In this research, with the aim of producing a biosimilar version of herceptin, the effect of genomic amplification was investigated on the increasing the gene copy number using quantitative real-time PCR.

Cloning and Expression of Gumboro VP2 Antigen in Aspergillus niger

BACKGROUND

Infectious Bursal Disease Virus (IBDV) causes a highly immunosuppressive disease in chickens and is a pathogen of major economic importance to the poultry industry worldwide. The VP2 protein is the major host-protective immunogen of IBDV and has been considered as a potential subunit vaccine against the disease. VP2 coding sequence was cloned in an inducible fungal vector and the protein was expressed in Aspergillus niger (A. niger).

METHODS

Aiming at a high level of expression, a multicopy AMA1-pyrG-based episomal construct driven by a strong inducible promoter, glaA, was prepared and used in transformation of A. niger pyrG-protoplasts. SDS-PAGE and western blot analysis was carried out to confirm the expression of the protein.

RESULTS

A number of pyrG (+) positive transformants were isolated and the presence of expression cassette was confirmed. Western blot analysis of one of these recombinant strains using monospecific anti-VP2 antibodies demonstrated the successful expression of the protein. The recombinant protein was also detected by serum obtained from immunized chicken.

CONCLUSION

In the present study, we have generated a recombinant A. niger strain expressing VP2 protein intracellulary. This recombinant strain of A. niger may have potential applications in oral vaccination against IBDV in poultry industry.

In silico prediction of exposure amino acid sequences of outer inflammatory protein A of Helicobacter pylori for surface display on Eschierchia coli

BACKGROUND:

Outer inflammatory protein A (OipA) is an outer membrane protein of Helicobacter pylori that is involved in inducing IL-8 and intracellular signaling. In this study, we have predicted exposure amino acid sequences of OipA for insertion in permissive sites of CstH subunit of Eschierchia coli CS3 pilli for bacterial surface display.

MATERIALS AND METHODS:

Databases: National Center for Biotechnology Institute and Protein Data Bank. Servers: PHD, SABLE, GOR 4, SignalP3.0, TBBpred, PRODIV-TMHMM, TMRPres2D, CPH Models, PHYRE, GETAREA, VADAR, Pep state and pep window. Software: Swiss PDB viewer and Discovery studio.

RESULTS:

In silico prediction of exposure amino acid sequences of OipA led to detection of six sequences of amino acid, 76-87, 106-112, 170-182, 222-230, 242-258, and 278-290. These sequences inserted between amino acid sequences 66-67, 100-101, and 109-110 of CstH that were predicted by Eskandari et al. as permissive sites of CstH.

CONCLUSION:

OipA has the ability to induce IL-8 from gastric epithelial cells and some papers are mentioned that this outer membrane protein involve to attachment and intracellular signaling. Receptor of OipA and adhesion motifs on this protein is unknown. Detection of exposure motifs aids to recognition of adhesion motifs and receptor of OipA on gastric epithelial cells. In this study, we have predicted exposure amino acid sequences for insert to subunit CstH of CS3 pilli E. coli for surface display.

In silico design, construction and cloning of Trastuzumab humanized monoclonal antibody: A possible biosimilar for Herceptin

Background:

There is a novel hypothesis in that antibodies may have specificity for two distinct antigens that have been named “dual specificity”. This hypothesis was evaluated for some defined therapeutic monoclonal antibodies (mAbs) such as Trastuzumab, Pertuzumab, Bevacizumab, and Cetuximab. In silico design and construction of expression vectors for trastuzumab monoclonal antibody also in this work were performed.

Materials and Methods:

First, in bioinformatics studies the 3D structures of concerned mAbs were obtained from the Protein Data Bank (PDB). Three-dimensional structural alignments were performed with SIM and MUSTANG softwares. AutoDock4.2 software also was used for the docking analysis. Second, the suitable genes for trastuzumab heavy and light chains were designed, synthesized, and cloned in the prokaryotic vector. These fragments individually were PCR amplified and cloned into pcDNA™ 3.3-TOPO^® and pOptiVEC™ TOPO^® shuttle vectors, using standard methods.

Results:

First, many bioinformatics tools and softwares were applied but we did not meet any new dual specificity in the selected antibodies. In the following step, the suitable expression cascade for the heavy and light chains of Trastuzumab therapeutic mAb were designed and constructed. Gene cloning was successfully performed and created constructs were confirmed using gene mapping and sequencing.

Conclusions:

This study was based on a recently developed technology for mAb expression in mammalian cells. The obtained constructs could be successfully used for biosimilar recombinant mAb production in CHO DG44 dihydrofolate reductase (DHFR) gene deficient cell line in the suspension culture medium.

Efficient biodegradation of naphthalene by a newly characterized indigenous Achromobacter sp. FBHYA2 isolated from Tehran Oil Refinery Complex

A bacterial strain, FBHYA2, capable of degrading naphthalene, was isolated from the American Petroleum Institute (API) separator of the Tehran Oil Refinery Complex (TORC). Strain FBHYA2 was identified as Achromobacter sp. based on physiological and biochemical characteristics and also phylogenetic similarity of 16S rRNA gene sequence. The optimal growth conditions for strain FBHYA2 were pH 6.0, 30 °C and 1.0% NaCl. Strain FBHYA2 can utilize naphthalene as the sole source of carbon and energy and was able to degrade naphthalene aerobically very fast, 48 h for 96% removal at 500 mg/L concentration. The physiological response of Achromobacter sp., FBHYA2 to several hydrophobic chemicals (aliphatic and aromatic hydrocarbons) was also investigated. No biosurfactant was detected during bacterial growth on any aliphatic/aromatic hydrocarbons. The results of hydrophobicity measurements showed no significant difference between naphthalene- and LB-grown cells. The capability of the strain FBHYA2 to degrade naphthalene completely and rapidly without the need to secrete biosurfactant may make it an ideal candidate to remediate polycyclic aromatic hydrocarbon (PAH)-contaminated sites.

Biodegradation pathway and detoxification of the diazo dye Reactive Black 5 by Phanerochaete chrysosporium

The in vivo biodegradation of the diazo dye Reactive Black 5 (RB5) by Phanerochaete chrysosporium immobilised on cubes of nylon sponge and on sunflower-seed shells (SS) in laboratory-scale bioreactors was investigated. The SS cultivation led to the best results with a decolouration percentage of 90.3% in 72 h for an initial RB5 concentration of 100 mg/L. It was found that the addition of 0.4 mM veratryl alcohol (VA) into the medium considerably increased the decolouration rate in SS cultivation. However, the addition of VA had no effect in the nylon cultivation. Thin layer chromatography (TLC) revealed that RB5 was transformed into one metabolite after 24 h. UV-vis spectroscopy and Fourier Transform Infrared (FT-IR) also confirmed the biodegradation of RB5. Toxicity of RB5 solutions before and after fungal treatment was assayed using Sinorhizobium meliloti as a sensitive soil microorganism. P. chrysosporium transformed the toxic dye RB5 into a non-toxic product.

The influence of riboflavin and nicotinic acid on Shigella sonnei colony conversion

BACKGROUND AND OBJECTIVES

Shigella, causative of bacillary dysentery, has two colony forms. The loss of large virulence plasmid from virulent Shigella sonnei form I, during cell storage and subculturing, lead to avirulent form II. Environmental factors, e.g. culture media composition, could affect the conversion of the bacterial forms.

MATERIALS AND METHODS

In this study, some components, i.e., B-complex vitamins, nicotinic acid and riboflavin, were added to the bacterial culture medium and their influence on colony conversion were examined.

RESULTS

The findings revealed that colony conversion is temperature independent and growth on the SS agar did not stabilize the bacterium in form I. Also, the findings showed that colonies on the minimal media supplemented with nicotinic acid and riboflavin, were stable in form I. In addition, according to the findings, the active OxyR has potential binding sites upstream of two genes involved in the replication of large virulence plasmid and expression of O-polysaccharide, i.e., repB and wbgT, respectively.

CONCLUSION

Based on the findings of the present study, it is possible that nicotinic acid and riboflavin activate the transcriptional regulatory protein OxyR via dropping off the intracellular reducing power and in this way stabilize the colonies in form I.

Decolouration of azo dyes by Phanerochaete chrysosporium immobilised into alginate beads

BACKGROUND, AIM AND SCOPE

Because of high discharged volumes and effluent composition, wastewater from the textile industry can be considered as the most polluting amongst all industrial sectors, thus greatly requiring appropriate treatment technologies. Although some abiotic methods for the reduction of several dyes exist, these require highly expensive catalysts and reagents. Biotechnological approaches were proven to be potentially effective in the treatment of this pollution source in an eco-efficient manner. The white-rot fungi are, so far, the most efficient microorganisms in degrading synthetic dyes. This white-rot fungi's property is due to the production of extracellular lignin-modifying enzymes, which are able to degrade a wide range of xenobiotic compounds because of their low substrate specificity. In this paper, we studied the ability of the white-rot fungus Phanerochaete chrysosporium immobilised into Ca-alginate beads to decolourise different recalcitrant azo dyes such as Direct Violet 51 (DV), Reactive Black 5 (RB), Ponceau Xylidine (PX) and Bismark Brown R (BB) in successive batch cultures. To the best of our knowledge, this is the first study on the immobilisation of P. chrysosporium into Ca-alginate beads for its application in dye decolouration.

MATERIALS AND METHODS

P. chrysosporium was immobilised into Ca-alginate beads using a method of gel recoating to minimise cellular leaking. The immobilised fungus was transferred to 250-ml Erlenmeyer flasks containing 50 ml of growth medium and incubated on an orbital shaker at 150 rpm and 30 degrees C for 7 days. The ratio of beads/medium used was 10% (w/v). The dyes were added into the culture flasks when MnP production started (50 U l(-1)), which corresponded with the seventh cultivation day. MnP activity and dye decolouration were measured spectrophotometrically.

RESULTS

The dyes DV, RB and PX were almost totally decolourised at the end of each batch during the course of three successive batches. However, the dye BB was more resistant to decolouration and it was not completely decolourised (86.7% in 144 h). Further, the beads were kept in sterilised calcium chloride (2 g l(-1)) for 3 weeks at 4 degrees C. After these three storage weeks, the immobilised P. chrysosporium was again efficiently reused for azo dye decolouration during two successive batches, decolouration being more effective even for BB. Also, the in vitro decolouration of the aforementioned azo dyes by crude MnP from P. chrysosporium was performed. The decolouration levels obtained were lower than those attained with the whole cultures especially for RB and BB dyes, in spite of the fact that dye concentrations used were considerable lower.

DISCUSSION

The good performance of the immobilisation system was likely due to the gel re-coating method utilised to prepare the alginate beads which not only maintained the beads integrity but also avoided cellular leaking. The lower decolouration percentages obtained by the enzyme indicates that the mycelial biomass may supply other intracellular or mycelial-bound enzymes, or other compounds that favour dye decolouration.

CONCLUSIONS

Immobilised P. chrysosporium efficiently decolourised different types of azo dyes. In this decolouration process, the MnP secreted by the fungus played the main role whilst adsorption was found to be negligible except for the dye BB.

RECOMMENDATIONS AND PERSPECTIVES

Efforts should be made to scale up and apply fungal decolouration techniques to real industrial dye-containing wastewater. Further, detailed characterisation of the intermediates and metabolites produced during biodegradation must be done to ensure the safety of the decolourised wastewater.

Assessment of the joint effect of laccase and cellobiose dehydrogenase on the decolouration of different synthetic dyes

In this paper the efficiency of the combined action of laccase and cellobiose dehydrogenase (CDH) to decolourise different synthetic dyes such as Remazol Brilliant Blue R (RBBR), Methyl Green (MG), Direct Violet (DV), Ponceau Xylidine (PX), Bismark Brown (BB) and Poly R-478 (PR) was assessed. It was found that the use of CDH could be a promising alternative to the utilisation of the expensive and poisonous chemical mediators such as HOBT although much research on this topic remains still to be done.

Isolation and identification of a lipase producing Bacillus sp. from soil

Lipase production in an indigenous lipolytic Bacillus sp. was detected in media containing Tributyrin-Tween 80 and Rhodamine B-Olive oil. The statistical Taguchi model was used to predict the optimum experimental conditions for bacterial growth and lipase production. Partial optimization was carried out for selection of salt base, oil, glucose, NH4Cl and yeast extract concentrations, inoculum density, pH and agitation. Maximum lipase activity was detected in the cell free supernatants of cultures grown in a medium containing 10 g L(-1) yeast extract, 15 g L(-1) NH4Cl, 3 g L(-1) K2HPO4, 1 g L(-1) KH2PO4, 0.1 g L(-1) MgSO4 x 7H2O, 2 g L(-1) glucose, 0.6 mM MgCl2 and 15 ml L(-1) olive oil, pH 8.5 at 30 degrees C for 24 h and low agitation. The amount oflipase produced in the designed medium was in agreement with the predicted values by the statistical method. 16S rRNA cloning and sequencing identified the test organism as Bacillus pumilus.