Site-specific gene knock-in and bacterial phytase gene expression in Chlamydomonas reinhardtii via Cas9 RNP-mediated HDR

In the present study, we applied the HDR (homology-directed DNA repair) CRISPR-Cas9-mediated knock-in system to accurately insert an optimized foreign bacterial phytase gene at a specific site of the nitrate reductase (NR) gene (exon 2) to achieve homologous recombination with the stability of the transgene and reduce insertion site effects or gene silencing. To this end, we successfully knocked-in the targeted NR gene of Chlamydomonas reinhardtii using the bacterial phytase gene cassette through direct delivery of the CRISPR/Cas9 system as the ribonucleoprotein (RNP) complex consisting of Cas9 protein and the specific single guide RNAs (sgRNAs). The NR insertion site editing was confirmed by PCR and sequencing of the transgene positive clones. Moreover, 24 clones with correct editing were obtained, where the phytase gene cassette was located in exon 2 of the NR gene, and the editing efficiency was determined to be 14.81%. Additionally, site-specific gene expression was analyzed and confirmed using RT-qPCR. Cultivation of the positive knocked-in colonies on the selective media during 10 generations indicated the stability of the correct editing without gene silencing or negative insertion site effects. Our results demonstrated that CRISPR-Cas9-mediated knock-in could be applied for nuclear expression of the heterologous gene of interest, and also confirmed its efficacy as an effective tool for site-specific gene knock-in, avoiding nuclear positional effects and gene silencing in C. reinhardtii. These findings could also provide a new perspective on the advantageous application of RNP-CRISPR/Cas9 gene-editing to accelerate the commercial production of complex recombinant proteins in the food-grade organism "C. reinhardtii".

Physiological and Biochemical Responses of Commercial Strawberry Cultivars under Optimal and Drought Stress Conditions

Improving the extent of adaptation and the choice of the most tolerant cultivar is the first step to mitigating the adverse effects of limited water, especially in susceptible plants such as strawberries. To address this issue, two commercial strawberry cultivars (Camarosa and Gaviota) were compared when irrigated to match 100, 75, 50, and 25% field capacity (FC) to simulate the control, slight, moderate, and severe drought stress conditions, respectively. Drought stress induced the reduction of total chlorophyll, carotenoid, relative water content, and phenolic content significantly, whereas the activity of antioxidant enzymes, electrolyte leakage, osmolyte accumulation, and oxidative markers upsurged progressively in drought severity-dependent behavior. Gaviota produced more proline, hydrogen peroxide as a marker of membrane lipid peroxidation and disposed of by higher electrolyte leakage, significantly. On the other hand, Camarosa having higher soluble carbohydrates as well as enzymatic and non-enzymatic antioxidants could be considered a drought-tolerant cultivar. Genotypic variation between these cultivars could be used in breeding projects to promote drought-tolerant strawberries in the future.

CRISPR-mediated genome editing in poplar issued by efficient transformation

Background

CRISPR has been increasingly used for plant genetic improvements because of its high efficiency and precision. Recently, the authors have reported the possibility of homology-directed repair (HDR) using CRISPR/Cas9 through woody plants such as poplar. HDR often replaces nucleotides with one donor DNA template (DDT), including homologous sequences.

Methods

CRISPR-Cas9 was recruited, and three variables, Agrobacteria inoculator concentration, pDDT/pgRNA ratio, and homologous arm length, were designed to integrate nptII and 2XCamV 35S into the MKK2 promoter zone.

Results

Here, we showed that recovered poplars on kanamycin-supplemented media exhibited enhanced expression of MKK2 affected by the precise integration of 2XcamV 35S and nptII, improving biochemical and phenotypic properties. Our findings confirmed that Agrobacterium inoculator OD₆₀₀ = 2.5, increased DDT numbers during cell division to 4:1 pDDT/pgRNA, and optimized homologous arms 700 bp caused efficient HDR and increased MKK2 expression.

Conclusion

Efficient transformations resulted from optimized variables, directly affecting the HDR efficiency through woody plants such as poplar.

A simple local expression for the prefactor in transition state theory

We present a simple and accurate computational technique to determine the frequency prefactor in harmonic transition state theory without necessitating full phonon density of states (DOS) calculations. The atoms in the system are partitioned into an "active region," where the kinetic process takes place, and an "environment" surrounding the active region. It is shown that the prefactor can be obtained by a partial phonon DOS calculation of the active region with a simple correction term accounting for the environment, under reasonable assumptions regarding atomic interactions. Convergence with respect to the size of the active region is investigated for different systems, as well as the reduction in computational costs when compared to full phonon DOS calculation. Additionally, we provide an open source implementation of the algorithm that can be added as an extension to Large-scale Atomic/Molecular Massively Parallel Simulator software.

Functional characterization of the gene promoter for an Elaeis guineensis phosphate starvation-inducible, high affinity phosphate transporter in both homologous and heterologous model systems

Oil palm is grown in tropical soils with low bioavailability of Pi. A cDNA clone specifically expressed under phosphate-starvation condition in oil palm roots was identified as a high-affinity phosphate transporter (EgPHT1). The deduced amino acid sequence has 6 transmembrane domains each at the N- and C-termini separated by a hydrophilic linker. Comparison of promoter motifs within 1500 bp upstream of ATG of 10 promoters from high- and low-affinity phosphate transporter from both dicots and monocots including EgPHT1 was performed. The EgPHT1 promoter was fused to β-glucuronidase (GUS) reporter gene and its activity was analysed by histochemical and fluorometric GUS assays in transiently transformed oil palm tissues and T₃ homozygous transgenic Arabidopsis plants. In response to Pi-starvation, no GUS activity was detected in oil palm leaves, but a strong inducible activity was observed in the roots (1.4 times higher than the CaMV35S promoter). GUS was specifically expressed in transgenic Arabidopsis roots under Pi deficiency and starvation of the other macronutrients (N and K) did not induce GUS activity. Eight motifs including ABRERATCAL (abscisic-acid responsive), RHERPATEXPA7 (root hair-specific), SURECOREATSULTR11 (sulfur-deficiency response), LTRECOREATCOR15 (temperature-stress response), MYB2CONSENSUSAT and ACGTATERD1 (water-stress response) as well as two novel motifs, 3 (TAAAAAAA) and 26 (TTTTATGT) identified through pattern discovery, occur at significantly higher frequency (p < 0.05) in the high-than the low-affinity phosphate transporter promoters. The Pi deficiency-responsive elements in EgPHT1 includes the P1BS, W-box, E-box and the G-box. Thus, EgPHT1 is important for improving Pi uptake in oil palm with potential for engineering efficient Pi acquisition.

Kinetic modeling of bacteriocin-like inhibitory substance secretion by Pediococcus acidilactici Kp10 and its stability in food manufacturing conditions

This paper deliberates the modelling and validation of bacteriocin-like inhibitory substance (BLIS) secretion by Pediococcus acidilactici Kp10 at different agitation speeds in a stirred tank bioreactor. A range of models namely the re-parameterised logistic, Luedeking-Piret and maintenance energy were assessed to predict the culture performance of the said bacterium. Growth of P. acidilactici Kp10 was enhanced with increased agitation speed up to 600 rpm while BLIS secretion was maximum at 400 rpm but decreased at higher agitation speed. Growth of P. acidilactici aptly subscribed to the re-parameterised logistic model while BLIS secretion and lactose consumption fitted well with the Luedeking-Piret model. The models revealed a relationship between growth of the bacterium and BLIS secretion. Bacterial growth and BLIS secretion were largely affected by the agitation speed of the stirred tank bioreactor which regulated the oxygen transfer to the culture. BLIS secretion by P. acidilactici Kp10 was however enhanced in oxygen-limited culture. The study also assessed BLIS from the perspective of its stability when subjected to factors such as temperature, pH and detergents. Results showed that BLIS produced by this strain was not affected by heat (at 25-100 °C for 20 min and at 121 °C for 15 min), surfactant (Tween 40, 60 and 80 and urea), detergents (up to 1% SDS), organic solvents (50% each of acetone, methanol and ethanol) and stable in a wide range of pH (2-10). The above information are pertinent with reference to commercial applications of this bacterial product in food manufacturing which invariably involve various sterilization processes and subjected to a wide pH range.

Microtiter miniature shaken bioreactor system as a scale-down model for process development of production of therapeutic alpha-interferon2b by recombinant Escherichia coli

Background

Demand for high-throughput bioprocessing has dramatically increased especially in the biopharmaceutical industry because the technologies are of vital importance to process optimization and media development. This can be efficiently boosted by using microtiter plate (MTP) cultivation setup embedded into an automated liquid-handling system. The objective of this study was to establish an automated microscale method for upstream and downstream bioprocessing of α-IFN2b production by recombinant Escherichia coli. The extraction performance of α-IFN2b by osmotic shock using two different systems, automated microscale platform and manual extraction in MTP was compared.

Results

The amount of α-IFN2b extracted using automated microscale platform (49.2 μg/L) was comparable to manual osmotic shock method (48.8 μg/L), but the standard deviation was 2 times lower as compared to manual osmotic shock method. Fermentation parameters in MTP involving inoculum size, agitation speed, working volume and induction profiling revealed that the fermentation conditions for the highest production of α-IFN2b (85.5 μg/L) was attained at inoculum size of 8%, working volume of 40% and agitation speed of 1000 rpm with induction at 4 h after the inoculation.

Conclusion

Although the findings at MTP scale did not show perfect scalable results as compared to shake flask culture, but microscale technique development would serve as a convenient and low-cost solution in process optimization for recombinant protein.

Multiple overlap extension PCR (MOE-PCR): an effective technical shortcut to high throughput synthetic biology

The current study describes multiple-overlap-extension PCR (MOE-PCR) as a simple and effective approach to assembling multiple DNA fragments with various sizes and features in a single in vitro reaction.

Enhancement of BLIS production by Pediococcus acidilactici kp10 in optimized fermentation conditions using an artificial neural network

The present study was aimed at enhancing the production of BLIS produced byPediococcus acidilacticiKp10 through optimizing the fermentation parameters.

Frequency of Polyomavirus BK Infection in Kidney Transplant Patients Suspected to Nephropathy

BACKGROUND

Polyomavirus BK is a major cause of nephropathy in immunosuppressed transplanted patients. Non-invasive diagnostic protocols such as molecular detection of polyomavirus BK replication are a useful strategy to predict BK virus-associated nephropathy (BKVAN).

OBJECTIVE

To determine the prevalence of polyomavirus BK infection among kidney transplant patients suspected to have BKVAN.

METHODS

In a cross-sectional study 108 kidney transplanted patients whose laboratory and clinical presentation were in favor of nephropathy between 2010 and 2012, were enrolled for analysis. Polyomavirus BK replication was evaluated in plasma and tissue samples of studied patients using a quantitative real-time PCR. Active cytomegalovirus infection was analyzed in studied patients using antigenemia method. A possible association between polyomavirus BK infection with clinical and laboratory risk factors of BKVAN were evaluated.

RESULTS

The polyomavirus BK replication was found in 17 (15.7%) of 108 of plasma and 9 (11%) of 82 tissue samples in kidney transplanted patients. Cytomegalovirus co-infection was found in 3 of 17 and 3 of 9 plasma and tissue samples in polyomavirus BK infected patients, respectively. Significant associations were found between polyomavirus BK infection with tubulointerstitial nephritis and acute cellular rejection, as important pathologic findings of BKVAN.

CONCLUSION

Diagnosis of single and co-infection of polyomavirus BK infection in plasma samples is a useful assay to evaluate the risk of BKVAN in kidney transplant patients. Established threshold values for studied viral infections have beneficial use in screening of kidney transplant patients at risk of BKVAN, need to confirm and standardized in completed further studies.

Enhancement of protein production by microalgae Dunaliella salina under mixotrophic conditions using response surface methodology

Schematic diagram of the upstream and downstream factors affecting transgene expression.