MADM (Mosaic Analysis with Double Markers) technology offers a genetic approach in mice to visualize and concomitantly manipulate genetically defined cells at clonal level and single cell resolution. MADM employs Cre recombinase/loxP-dependent interchromosomal mitotic recombination to reconstitute two split marker genes—green GFP and red tdTomato — and can label sparse clones of homozygous mutant cells in one color and wild-type cells in the other color in an otherwise unlabeled background. At present, major MADM applications include lineage tracing, single cell labeling, conditional knockouts in small populations of cells and induction of uniparental chromosome disomy to assess effects of genomic imprinting. MADM can be applied universally in the mouse with the sole limitation being the specificity of the promoter controlling Cre recombinase expression. Here I review recent developments and extensions of the MADM technique and give an overview of the major discoveries and progresses enabled by the implementation of the novel genetic MADM tools.

The newly developed next-generation sequencing platforms, in combination with genome-scale amplification methods, provide a powerful tool to study genomics from a single cell. This mini-review summarizes the technologies of single cell genomics and their applications in several areas of biomedical research including stem cells, cancer biology and reproductive medicine. Particularly, it highlights recent advances in single cell exome sequencing, RNA-seq, and genome sequencing. The application of these powerful techniques will shed new light on the fundamental principles of gene transcription and genome organization at single-cell level and improve our understanding of cellular heterogeneity and diversity in multicellular organisms.

Flavonoid biosynthetic genes are often coordinately regulated in a temporal manner during flower or fruit development, resulting in specific accumulation profiles of flavonoid compounds. R2R3-MYB-type transcription factors (TFs) “recruit” a set of biosynthetic genes to produce flavonoids, and, therefore, R2R3-MYBs are responsible for the coordinated expression of structural genes. Although a wealth of information regarding the identified and functionally characterized R2R3-MYBs that are involved in flavonoid accumulation is available to date, this is the first review on the global regulation of MYB factors in the flavonoid pathway. The data presented in this review demonstrate that anthocyanin, flavone/flavonol/3-deoxyflavonoid (FFD), proanthocyanidin (PA), and isoflavonoid are independently regulated by different subgroups of R2R3-MYBs. Furthermore, FFD-specific R2R3-MYBs have a preference for early biosynthetic genes (EBGs) as their target genes; anthocyanin-specific R2R3-MYBs from dicot species essentially regulate late biosynthetic genes (LBGs); the remaining R2R3-MYBs have a wider range of target gene specificity. To elucidate the nature of the differential target gene specificity between R2R3-MYBs, we analyzed the DNA binding domain (also termed the MYB-domain) of R2R3-MYBs and the distribution of the recognition cis-elements. We identified four conserved amino acid residues located in or just before helix-3 of dicot anthocyanin R2R3-MYBs that might account for the different recognition DNA sequence and subsequently the different target gene specificity to the remaining R2R3-MYB TFs.

Sedum alfredii Hance is a terrestrial zinc/cadmium (Zn/Cd)-hyperaccumulating and lead (Pb)-accumulating plant. Previous studies on S. alfredii were mostly focused on its physiological mechanism of heavy metal uptake and the application in phytoextraction of metals from contaminated soils. In this study, we evaluated the application potential of S. alfredii in the cleanup of heavy metals from contaminated lake water. Our research revealed that changing pH in lake water would not make particular difference on the final accumulation amount of heavy metals, because the acidic water environment negatively affected plant growth compared with the neutral and alkaline environments, but was more conducive for heavy metal absorption and accumulation. In addition, S. alfredii showed an increase of approximately 2.2-fold in dry weight (DW) when cultured with lake water for 25 d. At the same time, it accumulated approximately 5.0 mg/kg DW of Cd and 41.4 mg/kg DW of Pb. The absorption of heavy metals was highly effective during the first 10 d of culture. Also, the quality of lake water was greatly improved after only 2-d cleanup by S. alfredii. In general, this hyperaccumulator exhibits great potential for application in the cleanup of heavy metals-polluted waters.

Protocorm-like bodies (PLBs) or thin cell layers (TCLs) derived from PLBs of hybrid Cymbidium Twilight Moon ‘Day Light’ can induce new or neo-PLBs on Teixeira Cymbidium (TC) medium, which contains 0.1 mg/L α-naphthaleneacetic acid, 0.1 mg/L kinetin, 2 g/L tryptone and 20 g/L sucrose, and is solidified with 8 g/L Bacto agar. This study aimed to assess the response of neo-PLB formation to an ethylene-liberating compound (2-chloroethylphosphonic acid (CEPA)), to two ethylene inhibitors (silver nitrate (AgNO₃) and aminoethoxyvinylglycine (AVG)), and to aeration (made possible by using Milliseal^? or autoclaved filter paper). AgNO₃ at 1 or 2 mg/L in TC medium significantly increased the fresh weight of PLBs while 1 mg/L of AgNO₃ also showed a significant increase in the number of neo-PLB from both half-PLBs and from tTCLs. In contrast, AVG and CEPA inhibited neo-PLB formation. Neo-PLB formation from half-PLB or TCL explants in the presence of aeration resulted in significantly lower neo-PLB weight. The use of AgNO₃ and aeration are alternative means to mass produce neo-PLBs for micropropagation purposes.

To improve the fermentation yield of xylanase by optimizing the fermentation conditions for strain Xw2, a Plackett-Burman design was used to evaluate the effects of eight variables on xylanase production by strain Xw2. The steepest ascent (descent) method was used to approach the optimal response surface experimental area. The optimal fermentation conditions were obtained by central composite design and response surface analysis. The results showed that the composition of the optimal fermentation medium was corn cob+ 1.5% wheat bran (1:1), 0.04% MnSO₄, 0.04% K₂HPO₄·3H₂O, and an inoculum size of 6% in 50 mL liquid volume (pH= 6.0). The optimal culture conditions were 28°C at 150 r/min for 54.23 h. The results of this study can serve as the basis for the industrial production and application of xylanase.

In this work, the most detrimental missense mutations of Mad1 protein that cause various types of cancer were identified computationally and the substrate binding efficiencies of those missense mutations were analyzed. Out of 13 missense mutations, I Mutant 2.0, SIFT and PolyPhen programs identified 3 variants that were less stable, deleterious and damaging respectively. Subsequently, modeling of these 3 variants was performed to understand the change in their conformations with respect to the native Mad1 by computing their root mean squared deviation (RMSD). Furthermore, the native protein and the 3 mutants were docked with the binding partner Mad2 to explain the substrate binding efficiencies of those detrimental missense mutations. The docking studies identified that all the 3 mutants caused lower binding affinity for Mad2 than the native protein. Finally, normal mode analysis determined that the loss of binding affinity of these 3 mutants was caused by altered flexibility in the amino acids that bind to Mad2 compared with the native protein. Thus, the present study showed that majority of the substrate binding amino acids in those 3 mutants displayed loss of flexibility, which could be the theoretical explanation of decreased binding affinity between the mutant Mad1 and Mad2.

Sol-gel derived silica has tremendous applications as a biocompatible scaffold for the immobilization of cells. The use of xerogel as a matrix in the blueprint of biosensors is an appealing proposition due to several inimitable characteristics of xerogels, primarily because of their high porous nature, amendable pore size, and exceptionally large internal surface area. Morphological (X-Ray Diffraction and Thermogravimmetric Analysis) and optical (Fourier Transform Infrared and UV-Vis absorption) studies of the silica matrices with entrapped Rhizobial (Rz) structure of the biomaterial has been made. Temporal and concentration dependent studies were conducted for impregnated samples; it showed that the response time for the new biosensor for determining the concentration of Rz is less than 20 min. In this work, first time a novel avenue to create a generic approach for the fabrication of biosensor has been created.

The current work was attempted to isolate and characterize the serratiopeptidase producing Serratia sp. Among the 10 bacterial isolates 7 strains were identified as Serratia sp. Out of 7 strains one showed potent proteolytic activity and selected for further studies. Based on the morphological, biochemical and molecular characterization, the potent isolate (RH03) was identified as Serratia marcescens (GenBank accession number: KC961637) and the strain was designated as Serratia marcescens VITSD2. The production of serratiopeptidase was carried out in trypticase soya broth and the enzyme was partially purified using ammonium sulfate precipitation and dialysis. The specific activity was determined by casein hydrolysis assay and was found to be 12.00, 21.33, and 25.40 units/mg for crude, precipitated and dialysed samples. The molecular weight of the protease was determined by SDS-PAGE and it was found to be 50 kDa. The antibacterial activity of the produced serratiopeptidase showed moderate activity against Pseudomonas aeruginosa MTCC No. 4676 (12 mm) and Escherichia coli MTCC No. 1588 (15 mm).