Enzymatic tools for engineering natural product glycosylation

Glycosylated natural products have served as reliable platforms for the development of many existing front-line drugs. In an effort to explore the contribution of the sugar constituents of these compounds, research groups have focused upon the development of chemical and enzymatic tools to diversify natural product glycosylation. Among the complementary routes available, in vivo pathway engineering, also referred to as 'combinatorial biosynthesis', is an emerging method that relies upon the co-expression of sugar biosynthetic gene cassettes and glycosyltransferases in a host organism to generate novel glycosylated natural products. An overview of recent progress in combinatorial biosynthesis is highlighted in this review, emphasizing the elucidation of nucleotide-sugar biosynthetic pathways and recent developments on glycosyltransferases.     

Toward supportive data collection tools for plant metabolomics

Over recent years, a number of initiatives have proposed standard reporting guidelines for functional genomics experiments. Associated with these are data models that may be used as the basis of the design of software tools that store and transmit experiment data in standard formats. Central to the success of such data handling tools is their usability. Successful data handling tools are expected to yield benefits in time saving and in quality assurance. Here, we describe the collection of datasets that conform to the recently proposed data model for plant metabolomics known as ArMet (architecture for metabolomics) and illustrate a number of approaches to robust data collection that have been developed in collaboration between software engineers and biologists. These examples also serve to validate ArMet from the data collection perspective by demonstrating that a range of software tools, supporting data recording and data upload to central databases, can be built using the data model as the basis of their design.     

Mapping biomedical terminologies using natural language processing tools and UMLS: Mapping the Orphanet thesaurus to the MeSH

BackgroundOrphanet aims to provide rare disease information to healthcare professionals, patients, and their relatives.ObjectiveThe objective of this work is to evaluate two methodologies (Unified Medical Languages Systems [UMLS] and manual Orphanet-ICD-10 link-based mapping & string-based matching) used to map Orphanet thesaurus to the MeSH thesaurus.ResultsOn a corpus of 375 mappings, the string-based matching provides significantly better results than the UMLS and manual Orphanet-ICD-10 link-based mapping.ConclusionString-based matching could be applied to any biomedical terminology in French not yet included into UMLS.     

Integrons: natural tools for bacterial genome evolution

Integrons were first identified as the primary mechanism for antibiotic resistance gene capture and dissemination among Gram-negative bacteria. More recently, their role in genome evolution has been extended with the discovery of larger integron structures, the super-integrons, as genuine components of the genomes of many species throughout the gamma-proteobacterial radiation. The functional platforms of these integrons appear to be sedentary, whereas their gene cassette contents are highly variable. Nevertheless, the gene cassettes for which an activity has been experimentally demonstrated encode proteins related to simple adaptive functions and their recruitment is seen as providing the bacterial host with a selective advantage. The widespread occurrence of the integron system among Gram-negative bacteria is discussed, with special focus on the super-integrons. Some of the adaptive functions encoded by these genes are also reviewed, and implications of integron-mediated genome evolution in the emergence of novel bacterial species are highlighted.     

VitaPad: visualization tools for the analysis of pathway data

MOTIVATION: Packages that support the creation of pathway diagrams are limited by their inability to be readily extended to new classes of pathway-related data. RESULTS: VitaPad is a cross-platform application that enables users to create and modify biological pathway diagrams and incorporate microarray data with them. It improves on existing software in the following areas: (i) It can create diagrams dynamically through graph layout algorithms. (ii) It is open-source and uses an open XML format to store data, allowing for easy extension or integration with other tools. (iii) It features a cutting-edge user interface with intuitive controls, high-resolution graphics and fully customizable appearance. AVAILABILITY: http://bioinformatics.med.yale.edu CONTACTS: matthew.holford@yale.edu; hongyu.zhao@yale.edu.     

Smart data collection for CryoEM

This report provides an overview of the discussions, presentations, and consensus thinking from the Workshop on Smart Data Collection for CryoEM held at the New York Structural Biology Center on April 6–7, 2022. The goal of the workshop was to address next generation data collection strategies that integrate machine learning and real-time processing into the workflow to reduce or eliminate the need for operator intervention.     

利用GIS和多变量分析估算青藏高原月降水

随着空间降水信息需求的日益增加,空间降水插值已被广泛应用。降水区域不同,插值方法不同;时间尺度不同,插值方法也不相同。适合于所有地区的通用降水插值模型是不存在的。青藏高原自然地理特征独特,分析高原降水的时空格局意义重要。以青藏高原及其周边地区140个气象站点的月降水信息及其该地区的数字高程数据(DEM)为基础,利用G IS工具,对比分析了五种插值方法在青藏高原不同降水年份(以1998年、1997年分别代表丰水及欠水年份)的干湿季(1998年的干湿季分别以12月份和8月份为代表,1997年的干湿季分别以1月份和7月份为代表)月降水插值中的应用,并对整个高原地区的干季和湿季的月降水进行制图。这5种插值方法分别是:克里金插值法、反距离加权法、样条法、混合插值法Ⅰ和混合插值法Ⅱ,前3种插值方法未考虑海拔高度对降水的影响,而混合插值法则将高程作为降水的重要影响因子。结果表明:①在干季,无论是丰水还是欠水年份,月降水量都比较少,高程对降水量的影响较小,在月降水插值时可不考虑高程的影响,克里金法的月降水插值精度最高。②在湿季,月降水量较多,高程的影响较大,混合插值法比局部插值法及克里金插值法的精度高,尤以混合插值法Ⅱ(多元回归和样条法的综合)的精度最高。③干季,整个高原的月降水很少,西部和北部降水最少,东部和南部相对较多;湿季,高原的月降水较多,空间格局表现为由东南向西北递减。     

Middle ear sample collection in the chinchilla

Use of the chinchilla as a model of middle ear infection in auditory research necessitates accessing the middle ear to collect samples or inoculate bacteria. This column describes a simple technique for middle ear access. The procedure is also useful for investigating and treating middle ear infections in chinchillas.     

Mosquito net barriers for sample collection of zoophilic Culicidae

Mosquito net fences 2.30-2.50 m high placed around cowsheds at their night resting sites have been successfully utilized to obtain large samples of malaria vectors of the Anopheles gambiae complex and of other mosquito species. Collections of blood-fed mosquitoes were carried out during the night by inspecting regularly the net side facing the animal enclosure. This sampling procedure has important advantages over alternative procedures based on direct collection on animal or on the use of animal-baited traps.     

Mapping quantitative trait loci from a single-tail sample of the phenotype distribution including survival data

A new effective Bayesian quantitative trait locus (QTL) mapping approach for the analysis of single-tail selected samples of the phenotype distribution is presented. The approach extends the affected-only tests to single-tail sampling with quantitative traits such as the log-normal survival time or censored/selected traits. A great benefit of the approach is that it enables the utilization of multiple-QTL models, is easy to incorporate into different data designs (experimental and outbred populations), and can potentially be extended to epistatic models. In inbred lines, the method exploits the fact that the parental mating type and the linkage phases (haplotypes) are known by definition. In outbred populations, two-generation data are needed, for example, selected offspring and one of the parents (the sires) in breeding material. The idea is to statistically (computationally) generate a fully complementary, maximally dissimilar, observation for each offspring in the sample. Bayesian data augmentation is then used to sample the space of possible trait values for the pseudoobservations. The benefits of the approach are illustrated using simulated data sets and a real data set on the survival of F₂ mice following infection with Listeria monocytogenes.     

Mapping the energetics of water-protein and water-ligand interactions with the "natural" HINT forcefield: predictive tools for characterizing the roles of water in biomolecules

The energetics and hydrogen bonding pattern of water molecules bound to proteins were mapped by analyzing structural data (resolution better than 2.3A) for sets of uncomplexed and ligand-complexed proteins. Water-protein and water-ligand interactions were evaluated using hydropatic interactions (HINT), a non-Newtonian forcefield based on experimentally determined logP(octanol/water) values. Potential water hydrogen bonding ability was assessed by a new Rank algorithm. The HINT-derived binding energies and Ranks for second shell water molecules were -0.04 kcal mol(-1) and 0.0, respectively, for first shell water molecules -0.38 kcal mol(-1) and 1.6, for active site water molecules -0.45 kcal mol(-1) and 2.3, for cavity water molecules -0.55 kcal mol(-1) and 3.3, and for buried water molecules -0.56 kcal mol(-1) and 4.4. For the last four classes, similar energies indicate that internal and external water molecules interact with protein almost equally, despite different degrees of hydrogen bonding. The binding energies and Ranks for water molecules bridging ligand-protein were -1.13 kcal mol(-1) and 4.5, respectively. This energetic contribution is shared equally between protein and ligand, whereas Rank favors the protein. Lastly, by comparing the uncomplexed and complexed forms of proteins, guidelines were developed for prediction of the roles played by active site water molecules in ligand binding. A water molecule with high Rank and HINT score is unlikely to make further interactions with the ligand and is largely irrelevant to the binding process, while a water molecule with moderate Rank and high HINT score is available for ligand interaction. Water molecule displaced for steric reasons were characterized by lower Rank and HINT score. These guidelines, tested by calculating HINT score and Rank for 50 water molecules bound in the active site of four uncomplexed proteins (for which the structures of the liganded forms were also available), correctly predicted the ultimate roles (in the complex) for 76% of water molecules. Some failures were likely due to ambiguities in the structural data.     

Curcumin: A potential therapeutic natural product for adenocarcinomas

Adenocarcinomas comprise a significant class of cancers that occur in several organs (e.g., lung, pancreas, breast, colon, and endometrium). These highly lethal tumor types are predominantly invasive with metastatic tendency. As a pharmacological option for the treatment of adenocarcinomas, curcumin has been widely used in combination with various therapeutic modalities. However, poor stability and low bioavailability of the curcumin has restricted its application in clinic. Therefore, nanoparticle-based curcumin was produced to fortify the pharmacokinetics of curcumin. Enhanced cytotoxicity and bioavailability of curcumin have been obtained by synthesizing new curcumin analogs via chemical modification. This review article aimed to survey recent findings on the role of curcumin in the treatment of adenocarcinomas in several organs and described key players of underlying molecular pathways such as the anti-proliferative, anti-apoptosis, anti-metastasis, anti-inflammatory, and immunomodulatory mechanisms. We also described new approaches to producing curcumin-loaded nanoparticles and combinatorial regimens. A comprehensive literature search has been carried out on PubMed for obtaining the information related to the therapeutic activities of curcumin for adenocarcinomas therapy. The literature search resulted in many in vitro and some in vivo studies that evidenced the effectiveness of curcumin in modulating antitumor signaling pathways to treat adenocarcinomas. In addition, curcumin-loaded nanoplatforms can improve the efficacy against tumor cells. The present review provides a comprehensive view of the therapeutic aspects of curcumin as a treatment for multiple human adenocarcinomas, which warrants further investigation in clinical settings.     

Biological sample collection and processing for molecular epidemiological studies

Molecular epidemiology uses biomarkers and advanced technology to refine the investigation of the relationship between environmental exposures and diseases in humans. It requires careful handling and storage of precious biological samples with the goals of obtaining a large amount of information from limited samples, and minimizing future research costs by use of banked samples. Many factors, such as tissue type, time of collection, containers used, preservatives and other additives, transport means and length of transit time, affect the quality of the samples and the stability of biomarkers and must be considered at the initial collection stage. An efficient study design includes provisions for further processing of the original samples, such as cryopreservation of isolated cells, purification of DNA and RNA, and preparation of specimens for cytogenetic, immunological and biochemical analyses. Given the multiple uses of the samples in molecular epidemiology studies, appropriate informed consent must be obtained from the study subjects prior to sample collection. Use of barcoding and electronic databases allow more efficient management of large sample banks. Development of standard operating procedures and quality control plans is a safeguard of the samples' quality and of the validity of the analyses results. Finally, specific state, federal and international regulations are in place regarding research with human samples, governing areas including custody, safety of handling, and transport of human samples, as well as communication of study results.Here, we focus on the factors affecting the quality and the potential future use of biological samples and some of the provisions that must be made during collection, processing, and storage of samples, based on our experience in the Superfund Basic Research Program and Children's Environmental Health Center, at the University of California, Berkeley.     

Microbial genomics for the improvement of natural product discovery

The quest for the discovery of novel natural products has entered a new chapter with the enormous wealth of genetic data that is now available. This information has been exploited by using whole-genome sequence mining to uncover cryptic pathways, or biosynthetic pathways for previously undetected metabolites. Alternatively, using known paradigms for secondary metabolite biosynthesis, genetic information has been 'fished out' of DNA libraries resulting in the discovery of new natural products and isolation of gene clusters for known metabolites. Novel natural products have been discovered by expressing genetic data from uncultured organisms or difficult-to-manipulate strains in heterologous hosts. Furthermore, improvements in heterologous expression have not only helped to identify gene clusters but have also made it easier to manipulate these genes in order to generate new compounds. Finally, and perhaps the most crucial aspect of the efficient and prosperous use of the abundance of genetic information, novel enzyme chemistry continues to be discovered, which has aided our understanding of how natural products are biosynthesized de novo, and enabled us to rework the current paradigms for natural product biosynthesis.     

Molecular recording: transcriptional data collection into the genome

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Comparison of sample collection methods for the PCR detection of oral anaerobic pathogens

AIMS: To provide evidence that DNA-PCR diagnostics of oral pathogens based on standard sample collection by paper point insertion from the depth of the periodontal pocket can be replaced by a novel non-invasive collection method based on swab technique from the gingiva. METHODS AND RESULTS: In this study we compared the results from two collection methods performed in 35 patients with chronic adult periodontitis. Statistical analysis showed a highly significant association of diagnostic results between both collection techniques. CONCLUSIONS: The Pocket-out method represents a reliable alternative to the standard collection technique for PCR diagnosis of oral pathogens. SIGNIFICANCE AND IMPACT OF THE STUDY: Due to its simplicity and non-invasiveness, the Pocket-out collection could be performed in any physician office, or even by the patient himself. With respect to the putative association between periodontal disease and various systemic illnesses, this method could be integrated with various screening programs of oral pathogens.