A Simple Method for Encapsulating Single Cells in Alginate Microspheres Allows for Direct PCR and Whole Genome Amplification

Microdroplets are an effective platform for segregating individual cells and amplifying DNA. However, a key challenge is to recover the contents of individual droplets for downstream analysis. This paper offers a method for embedding cells in alginate microspheres and performing multiple serial operations on the isolated cells. Rhodobacter sphaeroides cells were diluted in alginate polymer and sprayed into microdroplets using a fingertip aerosol sprayer. The encapsulated cells were lysed and subjected either to conventional PCR, or whole genome amplification using either multiple displacement amplification (MDA) or a two-step PCR protocol. Microscopic examination after PCR showed that the lumen of the occupied microspheres contained fluorescently stained DNA product, but multiple displacement amplification with phi29 produced only a small number of polymerase colonies. The 2-step WGA protocol was successful in generating fluorescent material, and quantitative PCR from DNA extracted from aliquots of microspheres suggested that the copy number inside the microspheres was amplified up to 3 orders of magnitude. Microspheres containing fluorescent material were sorted by a dilution series and screened with a fluorescent plate reader to identify single microspheres. The DNA was extracted from individual isolates, re-amplified with full-length sequencing adapters, and then a single isolate was sequenced using the Illumina MiSeq platform. After filtering the reads, the only sequences that collectively matched a genome in the NCBI nucleotide database belonged to R. sphaeroides. This demonstrated that sequencing-ready DNA could be generated from the contents of a single microsphere without culturing. However, the 2-step WGA strategy showed limitations in terms of low genome coverage and an uneven frequency distribution of reads across the genome. This paper offers a simple method for embedding cells in alginate microspheres and performing PCR on isolated cells in common bulk reactions, although further work must be done to improve the amplification coverage of single genomes.     

Conformational flexibility of a model protein upon immobilization on self-assembled monolayers

The present study reports on the retention of conformational flexibility of a model allosteric protein upon immobilization on self-assembled monolayers (SAMs) on gold. Organothiolated SAMs of different compositions were utilized for adsorptive and covalent attachment of bovine liver glutamate dehydrogenase (GDH), a well-characterized allosteric enzyme. Sensitive fluorimetric assays were developed to determine immobilization capacity, specific activity, and allosteric properties of the immobilized preparations as well as the potential for repeated use and continuous catalytic transformations. The allosteric response of the free and immobilized forms towards ADP, L-leucine and high concentrations of NAD(+), some of the well-known activators for this enzyme, were determined and compared. The enzyme immobilized by adsorption or chemical binding responded similarly to the activators with a greater degree of activation, as compared to the free form. Also loss of activity involving the two immobilization procedures were similar, suggesting that residues essential for catalytic activity or allosteric properties of GDH remained unchanged in the course of chemical modification. A recently established method was used to predict GDH orientation upon immobilization, which was found to explain some of the experimental results presented. The general significance of these observations in connection with retention of native properties of protein structures upon immobilization on SAMs is discussed.     

Morpho-Physiological and Antioxidant Traits of Marigold cv. ‘Sparse Petal’ and ‘Compact Petal’ as Influenced by Irrigation Intervals

The effect of irrigation intervals was studied on physiological, morphological, and antioxidant traits of two marigold (Calendula officinalis L.) cultivars in Karaj, Iran, in a split-plot experiment based on a randomized complete block design with three replications. The experimental treatments included irrigation at three levels of I1 (irrigation interval of 3 days), I2 (irrigation interval of 5 days), and I3 (irrigation interval of 7 days) as the main plot and cultivar at two levels of V1 (cv. ‘sparse petal’) and V2 (cv. ‘compact petal’) as the sub-plot. The results based on the comparison of the means showed that the increase in irrigation interval from 3 to 7 days decreased the leaf area index, crop growth rate, relative growth rate, and net assimilation rate by 73.53, 85.76, 93.47, and 94.81%, respectively. It also decreased the flower yield, plant height, flower number, and leaf number by 71.92, 41.84, 99.31, and 58.67%, respectively. The interaction between irrigation and cultivar revealed that I3V1 had the highest total phenol content (3013.59 g gallic acid 100 g^?1 tissue) and antioxidant capacity (60.8%). It can be inferred that the treatment of I1 and cv. ‘compact petal’ give the best results for flower yield and physiological and morphological traits, and the treatment of I3 and both cultivars provide the best results for antioxidant traits in the climatic conditions of the Karaj region.

     

Association Study of 167 Candidate Genes for Schizophrenia Selected by a Multi-Domain Evidence-Based Prioritization Algorithm and Neurodevelopmental Hypothesis

Integrating evidence from multiple domains is useful in prioritizing disease candidate genes for subsequent testing. We ranked all known human genes (n = 3819) under linkage peaks in the Irish Study of High-Density Schizophrenia Families using three different evidence domains: 1) a meta-analysis of microarray gene expression results using the Stanley Brain collection, 2) a schizophrenia protein-protein interaction network, and 3) a systematic literature search. Each gene was assigned a domain-specific p-value and ranked after evaluating the evidence within each domain. For comparison to this ranking process, a large-scale candidate gene hypothesis was also tested by including genes with Gene Ontology terms related to neurodevelopment. Subsequently, genotypes of 3725 SNPs in 167 genes from a custom Illumina iSelect array were used to evaluate the top ranked vs. hypothesis selected genes. Seventy-three genes were both highly ranked and involved in neurodevelopment (category 1) while 42 and 52 genes were exclusive to neurodevelopment (category 2) or highly ranked (category 3), respectively. The most significant associations were observed in genes PRKG1, PRKCE, and CNTN4 but no individual SNPs were significant after correction for multiple testing. Comparison of the approaches showed an excess of significant tests using the hypothesis-driven neurodevelopment category. Random selection of similar sized genes from two independent genome-wide association studies (GWAS) of schizophrenia showed the excess was unlikely by chance. In a further meta-analysis of three GWAS datasets, four candidate SNPs reached nominal significance. Although gene ranking using integrated sources of prior information did not enrich for significant results in the current experiment, gene selection using an a priori hypothesis (neurodevelopment) was superior to random selection. As such, further development of gene ranking strategies using more carefully selected sources of information is warranted.     

Adaptation of human embryonic stem cells to feeder-free and matrix-free culture conditions directly on plastic surfaces

Previous studies have shown that cultivation of undifferentiated human embryonic stem (hES) cells requires human fibroblasts (hF) or mouse embryonic fibroblast (mEF) feeders or a coating matrix such as laminin, fibronectin or Matrigel in combination with mEF or hF conditioned medium. We here demonstrate a successful feeder-free and matrix-free culture system in which undifferentiated hES cells can be cultured directly on plastic surfaces without any supportive coating, in a hF conditioned medium. The hES cells cultured directly on plastic surfaces grow as colonies with morphology very similar to cells cultured on Matrigel(TM). Two hES cell lines SA167 and AS034.1 were adapted to matrix-free growth (MFG) and have so far been cultured up to 43 passages and cryopreserved successfully. The lines maintained a normal karyotype and expressed the expected marker profile of undifferentiated hES cells for Oct-4, SSEA-3, SSEA-4, TRA-1-60, TRA-1-81 and SSEA-1. The hES cells formed teratomas in SCID mice and differentiated in vitro into derivates of all three germ layers. Thus, the MFG-adapted hES cells appear to retain pluripotency and to remain undifferentiated. The present culture system has a clear potential to be scaleable up to a manufacturing level and become the preferred culture system for various applications such as cell therapy and toxicity testing.     

Inhibitory Effects of Ephedra major Host on Aspergillus parasiticus Growth and Aflatoxin Production

This study was undertaken to evaluate the effect of Ephedra major Host, an important medicinal plant with various biological activities, on growth and aflatoxin (AF) production by Aspergillus parasiticus NRRL 2999. The fungus was cultured in yeast extract-sucrose (YES) broth, a conductive medium that supports AF production, in the presence of various concentrations of essential oil (EO), hexanic and methanolic extracts of plant aerial parts, fruits, and roots using microbioassay technique. After incubating for 96 h at 28°C in static conditions, mycelial dry weight was determined as an index of fungal growth, and aflatoxin B₁ (AFB₁) was measured using HPLC technique. Based on the obtained results, EO of plant aerial parts significantly inhibited fungal growth at the highest concentration of 1000 μg/ml without any obvious effect on AFB₁ production at all concentrations used. Among plant extracts tested, only methanolic extract of aerial parts and roots were found to inhibit fungal growth and AFB₁ production dose-dependently with an IC₅₀ value of 559.74 and 3.98 μg/ml for AFB₁, respectively. Based on the GC/MS data, the major components of E. major EO were bis (2-ethylhexyl) phthalate (42.48%), pentacosane (20.94%), docosane (14.64%), citronellol (5.15%), heptadecan (4.41%), cis-3-Hexen-1-ol benzoate (4.07%), and 7-Octen-2-ol (3.25%). With respect to the potent inhibition of fungal growth and AF production by E. major, this plant may be useful in protecting crops from both toxigenic fungal growth and AF contamination.     

NH3 on a BC3 nanotube: effect of doping and decoration of aluminum

The adsorption of the NH₃ molecule was investigated on pristine, Al-doped and Al-decorated BC₃ nanotubes (BC₃NT) using density functional theory calculations. It was found that NH₃ prefers to be adsorbed on a B atom of the tube wall, releasing energy of 1.02 eV. Al-doping increases the acidity of the tube surface and, therefore, its reactivity toward NH₃ so that the released energy in this case is about 1.62 eV, while decorating the BC₃NT with Al atom decreases the acidity and reactivity. Although Al-doping has no significant effect on the electronic properties of the BC₃NT, Al-decoration significantly reduces its HOMO/LUMO energy gap from 2.37 to 1.16 eV so that the tube becomes an n-type semiconductor. However, we believe that the acidity of the BC₃NTs may be controlled by doping or decoration of Al atoms.