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.

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.

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. cloacaeWT, E. cloacaeHasA, E. cloacaeS-HasA and E. cloacaeGFP-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.

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.

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.

A Cross-section Metagenomics and 16S Ribosomal DNA Based Evaluation of the Bacterial and Archaeal Communities Resident in the Forumad Chromite Mine, Northeastern of Iran.

Background: The Forumad chromite area from Sabzevar ophiolite belt, Northeastern Iran, is an environment with high concentration of heavy metals, particularly chromite and magnesite minerals, containing chromium and magnesium. Objectives: In this study for the first time, we analyzed and report the diversity of microbial (bacterial and archaeal) community inhabiting in Forumad chromite mine environment using metagenomics approach. Materials and Methods: Samples were obtained from different areas of the mine, and total DNA was extracted from water and soil samples. 16S rDNA was amplified using universal primers and the PCR products were cloned in pTz57R/T plasmid. Then, 43% of the positive clones were randomly sequenced. BLAST program in NCBI and EzTaxon databases were used to identify similar 16S rDNA sequences. Phylogenetic analysis was performed using the MEGA5 software and multiple alignments of sequences. Results: In the phylogenetic analyses, proteobacteria, which contains many heavy metals tolerant bacteria especially chromium, were the dominant population in bacterial libraries with Rheinheimera and Cedecaeas the most abundant genuses. Other phyla were Bacteroidetes, Firmicutes, Verrucomicrobia, Chloroflexi, Actinobacteria, Acidobacteria, Cyanobacteria, Gemmatimonadetes, and Planctomycetes. In the archaeal clone library, all the sequences were related to the phylum Thaumarchaeota. Further, 68.6% of the sequences had less than 98.7℅ similarity with the recorded strains which could represent new taxons. Conclusions: The results showed that there was a high microbial diversity in the Forumad chromite area. These results can be used for detoxification and bioremediation of regions contaminated with heavy metals, although more studies are needed.

Production of Mycophenolic Acid by a Newly Isolated Indigenous Penicillium glabrum.

Soil-occupant fungi produce a variety of mycotoxins as secondary metabolites, one of which is mycophenolic acid (MPA), an antibiotic and immunosuppressive agent. MPA is mainly produced by several species of Penicillium, especially Penicillium brevicompactum. Here, we present the first report of MPA production by a local strain belonging to Penicillium glabrum species. We screened ascomycete cultures isolated from moldy food and fruits, as well as soils, collected from different parts of Iran. MPA production of one hundred and forty Penicillium isolates was analyzed using HPLC. Three MPA producer isolates were identified, among which the most producer was subjected to further characterization, based on morphological and microscopic analysis, as well as molecular approach (ITS, rDNA and beta-tubulin gene sequences). The results revealed that the best MPA producer belongs to P. glabrum IBRC-M 30518, and can produce 1079 mg/L MPA in Czapek-Dox medium.

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- ß) 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-ß 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-ß 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-ß 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-ß.

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.

Increased cellulose production by heterologous expression of bcsA and B genes from Gluconacetobacterxylinus in E. coli Nissle 1917.

Based on cellulose biosynthesis pathway of Gluconacetobacterxylinus BPR2001 and E. coli Nissle 1917, bcsA and bcsB genes have been selected and bioinformatics studies done to the analyses of nucleotide and amino acid sequence alignment, stability of RNA, protein, and promotor power. We amplify and clone bcsA, bcsB, and bcsAB genes of G. xylinus BPR2001 in Escherichiacoli Nissle 1917 under the inducible tac promoter. Our results of bioinformatics predictions demonstrate similar active site and three-dimensional structure of BcsA and BcsB proteins in two different bacteria. In addition, our data reveal that BcsA and BcsB proteins of E. coli have weaker promotor power, RNA secondary structure, and protein stability than that of the same proteins in G. xylinus. Some of the reasons of BcsAB protein selection from G. xylinus and its heterologous expression in E. coli is the noted points. Production of the related proteins visualized using SDS-PAGE. We find out that Congo red absorbance at 490 nm has no significant difference in wild-type strain (E. coli Nissle 1917) compared to recombinants bcsA+ or bcsB+, but recombinant bcsAB+ could produce more cellulose than that of the wild-type strain. Furthermore, the measurement of cellulose dry weights of all samples confirms bacterial cellulose production enhancement in recombinant bcsAB+ (1.94 g l-1). The FTIR analysis reveals that the crystallinity indices do not change significantly after over expressing each of genes.

An Efficient Approach for Two Distal Point Site-Directed Mutagenesis from Randomly Ligated PCR Products.

Site-directed mutagenesis is one of the most important tools in molecular biology. The majority of the mutagenesis methods have been developed to mutate one region of target DNA in each cycle of mutagenesis, while in some cases there is a need to mutate several distal points. We used a new method to simultaneously mutate two distal points in the target DNA. Different regions of the target DNA were amplified in three separate PCR reactions. The PCR products were back-to-back and together they made the complete length of the template DNA. Mutations were introduced to PCR products by middle mutagenic primers. PCR products were mixed and ligated with random blunt ligation, and then the desired mutated DNA fragments were selected in two steps by flanking restriction enzyme digestion and size selection. Selected fragments were amplified in another PCR reaction using flanking primers and finally cloned into the plasmid vector. This mutagenesis process is simple, there is no need to use modified primers and long or difficult PCR reactions.

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.

In silico and experimental improvement of bacteriorhodopsin production in Halobacterium salinarum R1 by increasing DNA-binding affinity of Bat through Q661R/Q665R substitutions in HTH motif.

DNA-binding motif of bacterioopsin activator (Bat) protein is a Helix-Turn-Helix motif, which binds to bop promoter and induces bacterioopsin (Bop) expression under light and low oxygen tension. Bacterioopsin is linked to retinal to produce bacteriorhodopsin (BR), which in turn supplies energy source in Halobacterium salinarum. In this study, effect of Bat HTH motif-promoter DNA interaction on bacterioopsin (Bop) expression was investigated using in silico and experimental approaches. Molecular docking showed that the most stable DNA-protein complex was generated by Q661R/Q665R mutant. Based on the in silico analysis, HTH motif was mutated using site-directed mutagenesis and Hbt. salinarum recombinant strains were developed by introduction of mutant bat genes. Double positively charged amino acid substitutions (Q661R/Q665R) in second helix of HTH motif increased whereas deletion of this region decreased BR production. However, other single substitutions (Q665R and Q661H) did not change BR production. These findings represent key role of HTH motif stability for DNA binding and regulation of bacterioopsin (Bop) expression and bacteriorhodopsin (BR) production independent of environmental condition.

Presence of Eisenia fetida enhanced phytoremediation of anthracene by Lolium perenne / Presença de Eisenia fetida aumentou a fitorremediação do antraceno por Lolium perene

The efficiency of co-application of Eisenia fetida and ryegrass was evaluated in a process called earthworm-assisted phytoremediation. Anthracene was used as a model compound for polycyclic aromatic hydrocarbons (PAHs). The experiments were conducted on a loamy soil in greenhouse conditions. At the end of the experiment, the soil samples were analyzed for residual anthracene by HPLC. Results showed that, phytoremediation using ryegrass could remove 81% of anthracene; however, the rate of removal was 92% when E. fetida was applied simultaneously. E. fetida alone could also remove the initial concentration of anthracene by 40%. Although ryegrass itself could remove anthracene significantly, the employment of earthworm, together with plant was more efficient than each of them individually. The application of E. fetida could also enhance the growth parameters of ryegrass significantly. In comparison to the control, the presence of E. fetida increased plant dry weight (7.8%), root length (47%), shoots length (32%), and root volume (12%). The number of live earthworms was also increased in the planted pots, indicating the helpfulness of the plant for survival of the earthworm in the PAH-contaminated soil. Although plant and earthworm use completely different mechanisms for anthracene degradation, they improve efficiency and survival of the three-component-system.

A eficiência da co-aplicação de Eisenia fetida e azevém foi avaliada em um processo denominado fitorremediação assistida por minhocas. O antraceno foi usado como um composto modelo para hidrocarbonetos aromáticos policíclicos (PAHs). Os experimentos foram conduzidos em um solo argiloso em condições de estufa. No final da experiência, as amostras de solo foram analisadas quanto ao antraceno residual por HPLC. Os resultados mostraram que, a fitorremediação com azevém pode remover 81% do antraceno; no entanto, a taxa de remoção foi de 92% quando E. fetida foi aplicada simultaneamente. E. fetida sozinha também foi capaz de remover a concentração inicial de antraceno em 40%. Embora o próprio azevém pudesse remover significativamente o antraceno, o emprego da minhoca, juntamente com a planta, foi mais eficiente do que cada um deles individualmente. A aplicação de E. fetida também pode melhorar significativamente os parâmetros de crescimento do azevém. Em comparação com o controle, a presença de E. fetida aumentou o peso seco da planta (7,8%), o comprimento da raiz (47%), o comprimento da parte aérea (32%) e o volume radicular (12%). O número de minhocas vivas também aumentou nos vasos plantados, indicando a utilidade da planta para a sobrevivência da minhoca no solo contaminado com PAH. Embora plantas e minhocas usem mecanismos completamente diferentes para a degradação do antraceno, eles melhoram a eficiência e a sobrevivência do sistema de três componentes.

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.

Role of Q177A and K173A/Q177A substitutions in thermostability and activity of the ELBn12 lipase.

Thermostable lipases have many applications in detergent industries and in organic synthesis. There are many ways to improve thermal stability of enzymes, for example, higher hydrophobicity, greater structural packing, higher content of the charged residues, and lower thermolabile ones. In this study, thermolabile Gln (sensitive to higher temperatures) was substituted with Ala in native ELBn12 and mutated K173A lipases to examine its effect on thermal stability and activity of the lipases. Single (Q177A) and double mutants (K173A/Q177A) were expressed in Escherichia coli pLysS. The Q177A variant increased both activity and thermostability of the lipase, whereas K173A/Q177A had a negative effect on the lipase activity and only had better thermal stability than the native at 50 °C. pH stability of the double mutant between 9.0 and 11 was also lower than the other variants. Stability analysis in the presence of chemicals showed that Q177A mutant had better activity with 50% (v/v) organic solvents. On the other hand, K173A lipase showed increased activity with 1% (w/v) nonionic surfactant, and finally K173A/Q177A had better stability with 10 mM metal ions compared to the native lipase.

Development of an asporogenic Bacillus cereus strain to improve keratinase production in exponential phase by switching sigmaH on and sigmaF off.

Many bacteria, including the genus Bacillus, are able to produce proteases (keratinase). In Bacillus, proteases are produced in the stationary phase and initial stages of sporulation. Protease production is coordinated with sporulation in which expression of various genes by different sigma factors manages the transition from the exponential to the stationary phase. In the present study the sigma-F gene of an indigenous Bacillus cereus strain, which is involved in transcription of genes maintaining sporulation, was deleted. The sigma-H gene, whose product activates the genes that function in the zero phase of sporulation and inhibits suppression of protease production, and spo0B genes were expressed in the exponential phase under the control of a sucrose-inducible promoter from the Bacillus sacPA operon. For the first time, an asporogenic strain of B. cereus was generated that produced higher keratinase (390 U compared with the 198 U of the wild-type strain) and protease (450 U compared with the 290 U of the wild-type strain) activities in the exponential growth phase by induction with sucrose. The new strain is promising for production of keratinase for degradation of feather waste to produce feather meal for poultry feed and decrease environmental pollution from the poultry industry.

Evaluation of nine popular de novo assemblers in microbial genome assembly.

Next generation sequencing (NGS) technologies are revolutionizing biology, with Illumina being the most popular NGS platform. Short read assembly is a critical part of most genome studies using NGS. Hence, in this study, the performance of nine well-known assemblers was evaluated in the assembly of seven different microbial genomes. Effect of different read coverage and k-mer parameters on the quality of the assembly were also evaluated on both simulated and actual read datasets. Our results show that the performance of assemblers on real and simulated datasets could be significantly different, mainly because of coverage bias. According to outputs on actual read datasets, for all studied read coverages (of 7×, 25× and 100×), SPAdes and IDBA-UD clearly outperformed other assemblers based on NGA50 and accuracy metrics. Velvet is the most conservative assembler with the lowest NGA50 and error rate.

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.