Stochastic variational variable selection for high-dimensional microbiome data.

Background: The rapid and accurate identification of a minimal-size core set of representative microbial species plays an important role in the clustering of microbial community data and interpretation of clustering results. However, the huge dimensionality of microbial metagenomics datasets is a major challenge for the existing methods such as Dirichlet multinomial mixture (DMM) models. In the approach of the existing methods, the computational burden of identifying a small number of representative species from a large number of observed species remains a challenge.

Phenolic signals for prehaustorium formation in .

is a root parasitic plant that causes considerable crop yield losses. To parasitize host plants, parasitic plants develop a specialized organ called the haustorium that functions in host invasion and nutrient absorption. The initiation of a prehaustorium, the primitive haustorium structure before host invasion, requires the perception of host-derived compounds, collectively called haustorium-inducing factors (HIFs).

High throughput method of 16S rRNA gene sequencing library preparation for plant root microbial community profiling.

Microbiota are a major component of agroecosystems. Root microbiota, which inhabit the inside and surface of plant roots, play a significant role in plant growth and health. As next-generation sequencing technology allows the capture of microbial profiles without culturing the microbes, profiling of plant microbiota has become a staple tool in plant science and agriculture.

The CCR4-NOT complex maintains liver homeostasis through mRNA deadenylation.

The biological significance of deadenylation in global gene expression is not fully understood. Here, we show that the CCR4-NOT deadenylase complex maintains expression of mRNAs, such as those encoding transcription factors, cell cycle regulators, DNA damage response-related proteins, and metabolic enzymes, at appropriate levels in the liver. Liver-specific disruption of , encoding a scaffold subunit of the CCR4-NOT complex, leads to increased levels of mRNAs for transcription factors, cell cycle regulators, and DNA damage response-related proteins because of reduced deadenylation and stabilization of these mRNAs.

The CCR4-NOT Deadenylase Complex Maintains Adipocyte Identity.

Shortening of poly(A) tails triggers mRNA degradation; hence, mRNA deadenylation regulates many biological events. In the present study, we generated mice lacking the gene, which encodes an essential scaffold subunit of the CCR4-NOT deadenylase complex in adipose tissues (-AKO mice) and we examined the role of CCR4-NOT in adipocyte function. -AKO mice showed reduced masses of white adipose tissue (WAT) and brown adipose tissue (BAT), indicating abnormal organization and function of those tissues.

Programmable Artificial Cells Using Histamine-Responsive Synthetic Riboswitch.

Artificial cells that encapsulate DNA-programmable protein expression machinery are emerging as an attractive platform for studying fundamental cellular properties and applications in synthetic biology. However, interfacing these artificial cells with the complex and dynamic chemical environment remains a major and urgent challenge. We demonstrate that the repertoire of molecules that artificial cells respond to can be expanded by synthetic RNA-based gene switches, or riboswitches.

Self-powered RNA nanomachine driven by metastable structure.

Many non-coding and regulatory RNA elements have evolved to exploit transient or metastable structures that emerge during transcription to control complex folding pathways or to encode dynamic functions. However, efforts to engineer synthetic RNA devices have mostly focused on the thermodynamically stable structures. Consequently, significant challenges and opportunities exist in engineering functional RNAs that explicitly take advantage of cotranscriptionally generated transient or metastable structures.

Analyzing and Tuning Ribozyme Activity by Deep Sequencing To Modulate Gene Expression Level in Mammalian Cells.

Self-cleaving ribozymes, in combination with aptamers and various classes of RNAs, have been heavily engineered to create RNA devices to control gene expression. Although understanding of sequence-function relationships of ribozymes is critical for such efforts, our current knowledge of self-cleaving ribozymes is mostly limited to the results from small scale mutational studies performed under different conditions, or qualitative results of mutate-and-select experiments that may contain experimental biases. Here, we applied our strategy based on deep sequencing to comprehensively assay a large number of mutants to systematically examine the effect of the P4 stem sequence on the activity of an HDV-like ribozyme.

Large Scale Mutational and Kinetic Analysis of a Self-Hydrolyzing Deoxyribozyme.

Deoxyribozymes are catalytic DNA sequences whose atomic structures are generally difficult to elucidate. Mutational analysis remains a principal approach for understanding and engineering deoxyribozymes with diverse catalytic activities. However, laborious preparation and biochemical characterization of individual sequences severely limit the number of mutants that can be studied biochemically.

Deep Sequencing Analysis of Aptazyme Variants Based on a Pistol Ribozyme.

Chemically regulated self-cleaving ribozymes, or aptazymes, are emerging as a promising class of genetic devices that allow dynamic control of gene expression in synthetic biology. However, further expansion of the limited repertoire of ribozymes and aptamers, and development of new strategies to couple the RNA elements to engineer functional aptazymes are highly desirable for synthetic biology applications. Here, we report aptazymes based on the recently identified self-cleaving pistol ribozyme class using a guanine aptamer as the molecular sensing element.

High-Throughput Mutational Analysis of a Twister Ribozyme.

Recent discoveries of new classes of self-cleaving ribozymes in diverse organisms have triggered renewed interest in the chemistry and biology of ribozymes. Functional analysis and engineering of ribozymes often involve performing biochemical assays on multiple ribozyme mutants. However, because each ribozyme mutant must be individually prepared and assayed, the number and variety of mutants that can be studied are severely limited.

High-throughput assay and engineering of self-cleaving ribozymes by sequencing.

Self-cleaving ribozymes are found in all domains of life and are believed to play important roles in biology. Additionally, self-cleaving ribozymes have been the subject of extensive engineering efforts for applications in synthetic biology. These studies often involve laborious assays of multiple individual variants that are either designed rationally or discovered through selection or screening.

Simple identification of two causes of noise in an aptazyme system by monitoring cell-free transcription.

Aptazymes are artificially synthesized ribozymes that catalyze reactions in response to ligand binding. Certain types of aptazymes can be utilized as RNA-based regulators of gene expression. These aptazymes contain a sequestered ribosome-binding site (rbs) and release the rbs through self-cleavage in response to ligand binding, inducing the expression of the downstream gene.

A controllable gene expression system in liposomes that includes a positive feedback loop.

We introduced a positive feedback loop into a LacI-dependent gene expression system in lipid vesicles, producing a cell-like system that senses and responds to an external signal with a high signal-to-noise ratio. This fully reconstituted system will be a useful tool in future applications in in vitro synthetic biology.

Kinetic analysis of aptazyme-regulated gene expression in a cell-free translation system: modeling of ligand-dependent and -independent expression.

Aptazymes are useful as RNA-based switches of gene expression responsive to several types of compounds. One of the most important properties of the switching ability is the signal/noise (S/N) ratio, i.e.

A target site for spontaneous insertion of IS10 element in pUC19 DNA located within intrinsically bent DNA.

Residual insertion sequence elements (IS elements) in Escherichia coli strains that are commonly used for DNA cloning are known to cause cloning artifacts by transposing themselves into the recombinant DNA fragments. In such cases, chance insertion of IS elements may occur at integration sites in the cloning targets, which in the case of the IS10 element is a 9-bp consensus sequence. We report here that the integration of IS10-related DNA sequences into the pUC19 cloning vector and its derivative occurred with considerable frequency in E.