The Science of the Modern Kitchen.

The kitchen offers chemists an opportunity to cook up chemistry using everyday ingredients. This is the inspiration behind 'The Science of the Modern Kitchen', a chemistry course offered to non-science undergraduates.

Biochemical studies highlight determinants for metal selectivity in the Escherichia coli periplasmic solute binding protein NikA.

Nickel is an essential micronutrient for the survival of many microbes. On account of the toxicity of nickel and its scarcity in the environment, microbes have evolved specific systems for uptaking and delivering nickel to enzymes. NikA, the solute binding protein for the ATP-binding cassette (ABC) importer NikABCDE, plays a vital role in the nickel homeostasis of Escherichia coli by selectively binding nickel over other metals in the metabolically complex periplasm. While the endogenous ligand for NikA is known to be the Ni(II)-(L-His)2 complex, the molecular basis by which NikA selectively binds Ni(II)-(L-His)2 is unclear, especially considering that NikA can bind multiple metal-based ligands with comparable affinity. Here we show that, regardless of its promiscuous binding activity, NikA preferentially interacts with Ni(II)-(L-His)2, even over other metal-amino acid ligands with an identical coordination geometry for the metal. Replacing both the Ni(II) and the L-His residues in Ni(II)-(L-His)2 compromises binding of the ligand to NikA, in part because these alterations affect the degree by which NikA closes around the ligand. Replacing H416, the only NikA residue that ligates the Ni(II), with other potential metal-coordinating amino acids decreases the binding affinity of NikA for Ni(II)-(L-His)2 and compromises uptake of Ni(II) into E. coli cells, likely due to altered metal selectivity of the NikA mutants. Together, the biochemical and in vivo studies presented here define key aspects of how NikA selects for Ni(II)-(L-His)2 over other metal complexes, and can be used as a reference for studies into the metal selectivity of other microbial solute binding proteins.

Identifying Phytochemicals from Biomedical Literature Utilizing Semantic Knowledge Sources.

Chemicals derived from plants (phytochemicals) are major concepts of interest in the study of medicinal plants. To date, efforts to catalogue and organize phytochemical knowledge have resorted to manual approaches. This study explored the potential to leverage publicly accessible semantic knowledge sources for identifying possible phytochemicals. Within the context of this feasibility study, putative phytochemicals were identified for more than 4,000 plants from the Medical Subject Headings Supplementary Concept Records and the Semantic MEDLINE Database. An examination of phytochemicals identified for five selected plant species using the method developed here reveals that there is a disparity in electronically catalogued phytochemical knowledge compared to information from Dr. Duke's Phytochemical and Ethnobotanical Databases maintained by the United States Department of Agriculture. The results therefore suggest that semantic knowledge sources for biomedicine can be utilized as a source for identifying potential phytochemicals and thus contribute to the overall curation of plant phytochemical knowledge.

Harnessing Biomedical Natural Language Processing Tools to Identify Medicinal Plant Knowledge from Historical Texts.

The growing amount of data describing historical medicinal uses of plants from digitization efforts provides the opportunity to develop systematic approaches for identifying potential plant-based therapies. However, the task of cataloguing plant use information from natural language text is a challenging task for ethnobotanists. To date, there have been only limited adoption of informatics approaches used for supporting the identification of ethnobotanical information associated with medicinal uses. This study explored the feasibility of using biomedical terminologies and natural language processing approaches for extracting relevant plant-associated therapeutic use information from historical biodiversity literature collection available from the Biodiversity Heritage Library. The results from this preliminary study suggest that there is potential utility of informatics methods to identify medicinal plant knowledge from digitized resources as well as highlight opportunities for improvement.

Identifying Plant-Human Disease Associations in Biomedical Literature: A Case Study.

The impact of ethnobotanical data from surveys of traditional medicinal uses ofplants can be enhanced through the validation of biomedical knowledge that may be embedded in literature. This study aimed to explore the use of informatics approaches, including natural language processing and terminology resources, for extracting and comparing ethnobotanical leads from biomedical literature indexed in MEDLINE. Using ethnobotanical data for plant species described in Primary Health Care Manuals of the Micronesian islands of Palau and Pohnpei, the results of this study were done relative to disease concepts from the "Mental, Behavioral And Neurodevelopmental Disorders " ICD-9-CM category. The results from this feasibility study suggest that informatics methods can be used to extract and prioritize relevant ethnobotanical information from biomedical knowledge literature.

Human-induced dwarfing of Himalayan snow lotus, Saussurea laniceps (Asteraceae).

Because evolutionary processes such as genetic drift and natural selection play a crucial role in determining the response that species will have to human-induced disturbances, there is increasing interest in the evolutionary aspects of conservation biology. Harvesting select individuals in natural plant populations can bring about unforeseen impacts that may negatively affect fitness. We analyzed how human harvesting affects two congeners known as snow lotus. Over a period of 100 years, there was a negative trend in plant height (r2= 0.4361, P < 0.001) for the intensely collected and rare species, Saussurea laniceps, but not in the less intensely collected species, Saussurea medusa. Additionally, S. laniceps were significantly smaller in areas of high harvest than in areas with low harvest (Z = 4.91, P < 0.0001), but this was not so for S. medusa. Humans can unconsciously drive evolution and must be considered when managing threatened species.