R2D ligase: Unveiling a novel DNA ligase with surprising DNA-to-RNA ligation activity.

DNA ligases catalyze bond formation in the backbone of nucleic acids via the formation of a phosphodiester bond between adjacent 5' phosphates and 3' hydroxyl groups on one strand of the duplex. While DNA ligases preferentially ligate single breaks in double-stranded DNA (dsDNA), they are capable of ligating a multitude of other nucleic acid substrates like blunt-ended dsDNA, TA overhangs, short overhangs and various DNA-RNA hybrids. Here we report a novel DNA ligase from Cronobacter phage CR 9 (R2D Ligase) with an unexpected DNA-to-RNA ligation activity. The R2D ligase shows excellent efficiency when ligating DNA to either end of RNA molecules using a DNA template. Furthermore, we show that DNA can be ligated simultaneously to both the 5' and 3' ends of microRNA-like molecules in a single reaction mixture. Abortive adenylated side product formation is suppressed at lower ATP concentrations and the ligase reaction reaches near completion when ligating RNA-to-DNA or DNA-to-RNA. The ligation of a DNA strand to the 5'-PO4 2- end of RNA is unique among the commercially available ligases and may facilitate novel workflows in microRNA analysis, RNA sequencing and the preparation of chimeric guide DNA-RNA for gene editing applications.

Microbial mechanism of biochar addition to reduce N2O emissions from soilless substrate systems.

The soilless peat-based substrate partially solves the global soil problem in greenhouse vegetable production. However, it still produces serious N2O emissions due to the application of nutrient solutions. The pyrolysis biochar is regarded as an effective measure to reduce soil N2O emissions. However, the effect and mechanism of biochar on N2O emissions from the soilless substrate remain unknown. Therefore, this study set up six treatments by adjusting the ratio of biochar addition of peat-based substrate: 0% (0BC), 2% (2BC), 4% (4BC), 6% (6BC), 8% (8BC) and 10% (10BC) (v/v). The results showed that compared to the control treatment, N2O emissions reduced by 81%, 71%, 51%, 61%, and 75% in the 2BC, 4BC, 6BC, 8BC and 10BC treatments, respectively. In addition, lettuce yield increased by 10% and 7% in the 2BC and 4BC treatments and decreased by 0.5%, 4% and 6% in the 6BC, 8BC and 10BC treatments, respectively. Combining stable isotope technology, qPCR analysis and high-throughput sequencing, five microbial pathways of N2O production, including bacterial and archaea nitrification (BN and AN), denitrification performed by fungi, denitrifier bacteria and nitrifier bacteria (FD, DD and ND), were roughly distinguished. In addition, the extent of N2O reduction was obtained by δ18O vs.δ15NSP map. For all treatments, overall, the DD process (over 50%) was the main process of N2O production and reduction, while ND and AN processes were almost negligible (less 5%). In detail, the decrease of N2O emissions was caused by decreasing the contribution of FD in the 6BC, 8BC and 10BC treatments and reducing the contribution of BN in the 0BC and 2BC treatments. In addition, biochar addition increased the extent of N2O reduction to N2. In summary, the 2% biochar addition presented the greatest extent of N2O reduction to N2 (83%) and the lowest N2O emissions as well as the highest lettuce yields and nitrogen utilization efficiency. Therefore, 2% biochar is deemed the most optimal addition to the peat-based substrate.

The impact of expression vector position on transgene transcription allows for rational expression vector design in a targeted integration system.

Site-specific integration (SSI) technology has emerged as an effective approach by the pharmaceutical industry for the development of recombinant Chinese hamster ovary (CHO) cell lines. While SSI systems have been demonstrated to be effective for the development of CHO cell lines, they can be limiting in terms of both transgene expression and in the case of multi-specifics, the ability to generate the correct product of interest. To maximize the performance of Pfizer's dual SSI expression system for expressing monoclonal and multi-specific antibodies, we used a novel approach to investigate the positional effect of transgenes within expression vectors by engineering nucleotide polymorphisms (NP)s to use as biomarkers to track the level of transcript output from each expression vector position. We observed differences in transcript level for two different transgenes across all four expression vector positions interrogated. We then applied these learnings to rationally design expression vectors for six different mAbs and a multi-specific antibody. We showed enhanced productivity and optimal product quality when compared to a conventional expression vector topology. The learnings gained here can potentially aid in the determination of optimal vector topologies for several IgG-like multi-specific formats.

Genetic and Molecular Factors Determining Grain Weight in Rice.

Grain weight is one of the major factors determining single plant yield production of rice and other cereal crops. Research has begun to reveal the regulatory mechanisms underlying grain weight as well as grain size, highlighting the importance of this research for plant molecular biology. The developmental trait of grain weight is affected by multiple molecular and genetic aspects that lead to dynamic changes in cell division, expansion and differentiation. Additionally, several important biological pathways contribute to grain weight, such as ubiquitination, phytohormones, G-proteins, photosynthesis, epigenetic modifications and microRNAs. Our review integrates early and more recent findings, and provides future perspectives for how a more complete understanding of grain weight can optimize strategies for improving yield production. It is surprising that the acquired wealth of knowledge has not revealed more insights into the underlying molecular mechanisms. To accelerating molecular breeding of rice and other cereals is becoming an emergent and critical task for agronomists. Lastly, we highlighted the importance of leveraging gene editing technologies as well as structural studies for future rice breeding applications.

Integrating Bioinformatics Tools Into Inquiry-Based Molecular Biology Laboratory Education Modules.

The accelerating expansion of online bioinformatics tools has profoundly impacted molecular biology, with such tools becoming integral to the modern life sciences. As a result, molecular biology laboratory education must train students to leverage bioinformatics in meaningful ways to be prepared for a spectrum of careers. Institutions of higher learning can benefit from a flexible and dynamic instructional paradigm that blends up-to-date bioinformatics training with best practices in molecular biology laboratory pedagogy. At North Carolina State University, the campus-wide interdisciplinary Biotechnology (BIT) Program has developed cutting-edge, flexible, inquiry-based Molecular Biology Laboratory Education Modules (MBLEMs). MBLEMs incorporate relevant online bioinformatics tools using evidenced-based pedagogical practices and in alignment with national learning frameworks. Students in MBLEMs engage in the most recent experimental developments in modern biology (e.g., CRISPR, metagenomics) through the strategic use of bioinformatics, in combination with wet-lab experiments, to address research questions. MBLEMs are flexible educational units that provide a menu of inquiry-based laboratory exercises that can be used as complete courses or as parts of existing courses. As such, MBLEMs are designed to serve as resources for institutions ranging from community colleges to research-intensive universities, involving a diverse range of learners. Herein, we describe this new paradigm for biology laboratory education that embraces bioinformatics as a critical component of inquiry-based learning for undergraduate and graduate students representing the life sciences, the physical sciences, and engineering.

Plant 3' Regulatory Regions From mRNA-Encoding Genes and Their Uses to Modulate Expression.

Molecular biotechnology has made it possible to explore the potential of plants for different purposes. The 3' regulatory regions have a great diversity of cis-regulatory elements directly involved in polyadenylation, stability, transport and mRNA translation, essential to achieve the desired levels of gene expression. A complex interaction between the cleavage and polyadenylation molecular complex and cis-elements determine the polyadenylation site, which may result in the choice of non-canonical sites, resulting in alternative polyadenylation events, involved in the regulation of more than 80% of the genes expressed in plants. In addition, after transcription, a wide array of RNA-binding proteins interacts with cis-acting elements located mainly in the 3' untranslated region, determining the fate of mRNAs in eukaryotic cells. Although a small number of 3' regulatory regions have been identified and validated so far, many studies have shown that plant 3' regulatory regions have a higher potential to regulate gene expression in plants compared to widely used 3' regulatory regions, such as NOS and OCS from Agrobacterium tumefaciens and 35S from cauliflower mosaic virus. In this review, we discuss the role of 3' regulatory regions in gene expression, and the superior potential that plant 3' regulatory regions have compared to NOS, OCS and 35S 3' regulatory regions.

[Research progress in molecular biology of Lonicerae Japonicae Flos].

Molecular biology is a new subject that clarifies the phenomena and nature of life at the molecular level. Its development provides new biotechnology and methods for the study of traditional pharmacognosy. The formation of molecular biology has brought the development of pharmacognosy into a new era of gene research. Lonicerae Japonicae Flos is a classical Chinese medicine. Many scholars of home and abroad have carried out relevant studies on its molecular biology on the basis of the in-depth study with traditional methods, and have achieved certain results. In order to provide references on the method, technical for promoting the modernization of Lonicerae Japonicae Flos, and the development, protection, and utilization of other traditional Chinese medicine resources. This article summarized the application status of molecular biology methods and techniques on the identification, biosynthesis of active constituents, and molecular mechanism of secondary metabolite under stress conditions of Lonicerae Japonicae Flos in recent years. In hybridization technology of tag(RFLP), molecular markers based on PCR(RAPD, AFLP, SSR and ISSR), based on DNA sequence analysis of SNP and DNA barcode for the variety identification, diagnosis, identification of Lonicerae Japonicae Flos, and so forth in detail. At the same time, it is proposed that multi-omics technology can be used to build systems biology technology and platforms, and establish related models of secondary metabolite biosynthesis, so as to deepen acknowledge the molecular mechanism of the active component biosynthesis of Lonicerae Japonicae Flos and the accumulation of metabolites, life activities of other medicinal plants under adverse environment, then to regulate them.

Research progress in molecular biology of Lonicerae Japonicae Flos / 中国中药杂志

Molecular biology is a new subject that clarifies the phenomena and nature of life at the molecular level. Its development provides new biotechnology and methods for the study of traditional pharmacognosy. The formation of molecular biology has brought the development of pharmacognosy into a new era of gene research. Lonicerae Japonicae Flos is a classical Chinese medicine. Many scholars of home and abroad have carried out relevant studies on its molecular biology on the basis of the in-depth study with traditional methods, and have achieved certain results. In order to provide references on the method, technical for promoting the modernization of Lonicerae Japonicae Flos, and the development, protection, and utilization of other traditional Chinese medicine resources. This article summarized the application status of molecular biology methods and techniques on the identification, biosynthesis of active constituents, and molecular mechanism of secondary metabolite under stress conditions of Lonicerae Japonicae Flos in recent years. In hybridization technology of tag(RFLP), molecular markers based on PCR(RAPD, AFLP, SSR and ISSR), based on DNA sequence analysis of SNP and DNA barcode for the variety identification, diagnosis, identification of Lonicerae Japonicae Flos, and so forth in detail. At the same time, it is proposed that multi-omics technology can be used to build systems biology technology and platforms, and establish related models of secondary metabolite biosynthesis, so as to deepen acknowledge the molecular mechanism of the active component biosynthesis of Lonicerae Japonicae Flos and the accumulation of metabolites, life activities of other medicinal plants under adverse environment, then to regulate them.

Are online prediction tools a valid alternative to genomic profiling in the context of systemic treatment of ER-positive breast cancer?

BACKGROUND: Clinicians use clinical and pathological parameters, such as tumour size, grade and nodal status, to make decisions on adjuvant treatments for breast cancer. However, therapeutic decisions based on these features tend to vary due to their subjectivity. Computational and mathematical algorithms were developed using clinical outcome data from breast cancer registries, such as Adjuvant! Online and NHS PREDICT. More recently, assessments of molecular profiles have been applied in the development of better prognostic tools. METHODS: Based on the available literature on online registry-based tools and genomic assays, we evaluated whether these online tools could be valid and accurate alternatives to genomic and molecular profiling of the individual breast tumour in aiding therapeutic decisions, particularly in patients with early ER-positive breast cancer. RESULTS AND CONCLUSIONS: Early breast cancer is currently considered a systemic disease and a complex ecosystem with behaviour determined by the complex genetic and molecular signatures of the tumour cells, mammary stem cells, microenvironment and host immune system. We anticipate that molecular profiling will continue to evolve, expanding beyond the primary tumour to include the tumour microenvironment, cancer stem cells and host immune system. This should further refine therapeutic decisions and optimise clinical outcome. This article was specially invited by the editors and represents work by leading researchers.

Remediation of phthalates in river sediment by integrated enhanced bioremediation and electrokinetic process.

The objective of this study was to evaluate the feasibility of enhanced bioremediation coupling with electrokinetic process for promoting the growth of intrinsic microorganisms and removing phthalate esters (PAEs) from river sediment by adding an oxygen releasing compound (ORC). Test results are given as follows: Enhanced removal of PAEs was obtained by electrokinetics, through which the electroosmotic flow would render desorption of organic pollutants from sediment particles yielding an increased bioavailability. It was also found that the ORC injected into the sediment compartment not only would alleviate the pH value variation due to acid front and base front, but would be directly utilized as the carbon source and oxygen source for microbial growth resulting in an enhanced degradation of organic pollutants. However, injection of the ORC into the anode compartment could yield a lower degree of microbial growth due to the loss of ORC during the transport by EK. Through the analysis of molecular biotechnology it was found that both addition of an ORC and application of an external electric field can be beneficial to the growth of intrinsic microbial and abundance of microflora. In addition, the sequencing result showed that PAEs could be degraded by the following four strains: Flavobacterium sp., Bacillus sp., Pseudomonas sp., and Rhodococcus sp. The above findings confirm that coupling of enhanced bioremediation and electrokinetic process could be a viable remediation technology to treat PAEs-contaminated river sediment.

[Analysis of hot spots and trend of molecular pharmacognosy research based on project supported by National Natural Science Foundation of 1995-2014].

This study collected 1995-2014 molecular pharmacognosy study, a total of 595 items, funded by Natural Science Foundation of China (NSFC). TDA and Excel software were used to analyze the data of the projects about general situation, hot spots of research with rank analytic and correlation analytic methods. Supported by NSFC molecular pharmacognosy projects and funding a gradual increase in the number of, the proportion of funds for pharmaceutical research funding tends to be stable; mainly supported by molecular biology methods of genuine medicinal materials, secondary metabolism and Germplasm Resources Research; hot drugs including Radix Salviae Miltiorrhizae, Radix Rehmanniae, Cordyceps sinensis, hot contents including tanshinone biosynthesis, Rehmannia glutinosa continuous cropping obstacle.

[Application of molecular biotechnology in Pharmacognosy].

Using the methods of informetrics analysis, articles retrieved from the database of CNKI were statistically analyzed on development course and knowledge system, so as to reflect the overall situation of pharmacognostical studies by molecular biotechnology. The result shows that the research on pharmacognosy by molecular biotechnology is an inter-disciplinary research area, the major research fields can be divided into 7 categories, including molecular identification of Chinese medicinal materials, molecular systematics and genetic diversity analysis of Chinese medicinal materials, biosynthesis and bioregulation of secondary metabolites in medicinal plants, molecular mechanism and genetic basis of Dao-di Herbs, and tissue culture and molecular breeding in medicinal plants. The research on pharmacognosy by molecular have achieved remarkable progress in recent 20 years, and have broad development prospects.

Application of molecular biotechnology in Pharmacognosy / 中国中药杂志

Using the methods of informetrics analysis, articles retrieved from the database of CNKI were statistically analyzed on development course and knowledge system, so as to reflect the overall situation of pharmacognostical studies by molecular biotechnology. The result shows that the research on pharmacognosy by molecular biotechnology is an inter-disciplinary research area, the major research fields can be divided into 7 categories, including molecular identification of Chinese medicinal materials, molecular systematics and genetic diversity analysis of Chinese medicinal materials, biosynthesis and bioregulation of secondary metabolites in medicinal plants, molecular mechanism and genetic basis of Dao-di Herbs, and tissue culture and molecular breeding in medicinal plants. The research on pharmacognosy by molecular have achieved remarkable progress in recent 20 years, and have broad development prospects.

Evaluation of four kinds of rapid identification technologies of microbials in pharmaceutical products / 中国药学杂志

OBJECTIVE: To establish a evaluation method of microbial identification technology by comparing four different microbial identification methods. METHODS: A total of 50 tests by API microbial identification system, VITEK 2 compact system, Riboprinter system, and MicroSeq ID DNA sequencing system were performed against 19 standard strains and 10 wild strains. The accuracy and reproducibility of these methods were evaluated. RESULTS: All the four identification technologies could be used to identify specified micro-organisms, but they had difference in other strains. Molecular biotechnology was better than biochemical identification in accuracy and reproducibility. CONCLUSION: The users should establish suitable acceptance criteria for accuracy and reproducibility, taking into account method capability.

Analysis of hot spots and trend of molecular pharmacognosy research based on project supported by National Natural Science Foundation of 1995-2014 / 中国中药杂志

This study collected 1995-2014 molecular pharmacognosy study, a total of 595 items, funded by Natural Science Foundation of China (NSFC). TDA and Excel software were used to analyze the data of the projects about general situation, hot spots of research with rank analytic and correlation analytic methods. Supported by NSFC molecular pharmacognosy projects and funding a gradual increase in the number of, the proportion of funds for pharmaceutical research funding tends to be stable; mainly supported by molecular biology methods of genuine medicinal materials, secondary metabolism and Germplasm Resources Research; hot drugs including Radix Salviae Miltiorrhizae, Radix Rehmanniae, Cordyceps sinensis, hot contents including tanshinone biosynthesis, Rehmannia glutinosa continuous cropping obstacle.

Construction and Evaluation of an Expression Vector Containing Mtb32C (Rv0125) of Mycobacterium tuberculosis.

Expressions of recombinant proteins for different applications are important objectives in molecular biotechnology; however, expression of some recombinant proteins is difficult. Several methods have been designed for expression of these proteins. The aim of this study was to construct a vector containing Mtb32C fragment of Mycobacterium tuberculosis (M.tuberculosis) as a fusion partner in order to improve the expression of fused recombinant proteins. Mtb32C was amplified by polymerase chain reaction (PCR). The amplified fragment was ligated into pET21b+ vector. Colony-PCR, enzyme digestion and DNA sequencing methods were used to confirm the recombinant vector. Colony-PCR showed a 420 bp fragment in size corresponding to the correct size of our fragment. In addition the recombinant plasmids sequencing showed the accuracy of the cloned fragment. For confirming the expression, reverse transcriptase (RT)-PCR analysis was performed showing a 420 bp fragment in agarose gel electrophoresis using specific primers. The construction of a vector containing Mtb32C fragment is promising as a fusion partner for future studies as it affected the expression of the fused proteins and increased immune responses against the partner.

Transgene Pflanzen als orale Impfstoffe Grüne Revolution in der Medizin?: Grüne Revolution in der Medizin?

With the methods of molecular biotechnology it is possible today to produce therapeutical effectiv proteins in plants. So called edible vaccines can be used for active immunization as well as for passive immunization. For an efficient production of recombinant proteins a procedure was developed, in which only the leaves are treated with genetically modified bacteria instead of the time consuming regeneration of transgenic plants. With an orally applicated vaccine a complete systematic immune response can be induced, but in comparison to a parenteral injection, a 100 times higher dosis of the antigen is necessary. The immunogenity of antigens produced in plants was confirmed in several animal experiments. Clinical studies with recombinant antibodies of transgenic plants against the caries pathogen Streptococcus mutans were successful. Future studies will focus on improved production rates, the search for suitable plant species and the phenomenon of oral tolerance.

Biotechnology in modernization of Chinese materia medica / 中草药

Chinese materia medica (CMM) plays an important role both in the disease prevention and therapy system and also in natural drug screening. Biotechnology exhibits applicable prospects in modern research of CMM with progress of natural science and technologies. Amplification fragment length polymorphism (AFLP), restriction fragment length polymorphism (RFLP), random amplification polymorphism of DNA (RAPD), and microsatellite DNA have been used to discriminate and breed herbal varieties. Genetic transformation and techniques of tissue and cell culture are explored to protect herbal resouces and to produce active components or parts on a commercial scale. High throughput technologies of proteome and biochip are expected to probe molecular targets and routes of CMM with the changes of proteome and gene expression. The results can be helpful to novel drug development and secondary exploitation, so as to promote the modernization process of CMM.