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The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center for the open-access PDB archive. As wwPDB-designated Archive Keeper, RCSB PDB is also responsible for PDB data security. Annually, RCSB PDB serves >10 000 depositors of three-dimensional (3D) biostructures working on all permanently inhabited continents. RCSB PDB delivers data from its research-focused RCSB.org web portal to many millions of PDB data consumers based in virtually every United Nations-recognized country, territory, etc. This Database Issue contribution describes upgrades to the research-focused RCSB.org web portal that created a one-stop-shop for open access to ∼200 000 experimentally-determined PDB structures of biological macromolecules alongside >1 000 000 incorporated Computed Structure Models (CSMs) predicted using artificial intelligence/machine learning methods. RCSB.org is a ‘living data resource.’ Every PDB structure and CSM is integrated weekly with related functional annotations from external biodata resources, providing up-to-date information for the entire corpus of 3D biostructure data freely available from RCSB.org with no usage limitations. Within RCSB.org, PDB structures and the CSMs are clearly identified as to their provenance and reliability. Both are fully searchable, and can be analyzed and visualized using the full complement of RCSB.org web portal capabilities.

There has been substantial interest in the use of saliva as a diagnostic medium for drugs of abuse because it can be obtained noninvasively. Although drugs of abuse have been investigated in saliva for more than a decade, the role of saliva remains uncertain. A clear picture is difficult to obtain because of variations in (1) the analytical methods used; (2) the dose regimen of subjects, which was either unknown or differed between studies; and (3) the elapsed time between drug intake and sample collection. This communication summarizes the studies on the quantitative determination of different drugs of abuse in saliva to elucidate the current status in this area. Marijuana, cocaine, phencyclidine, opiates, barbiturates, amphetamines, and diazepines (or their metabolites) have all been detected in saliva by various analytical methods, including immunoassay, gas chromatography/mass spectrometry, and thin layer chromatography. Initial studies with cocaine and phencyclidine suggest a correlation between saliva and plasma concentrations of these drugs, indicating a dynamic equilibrium between saliva and blood. Tetrahydrocannabinol, the active component in marijuana, on the other hand, does not appear to be transferred from plasma to saliva. However, tetrahydrocannabinol is sequestered in the buccal cavity during smoking and can be detected in saliva. These findings point to the potential role of saliva in the analysis of many illicit drugs. To clearly identify the role of saliva as a diagnostic medium for drugs of abuse, research efforts should be directed towards (1) performing systematic studies on correlations between saliva, blood, and urine and (2) determining the concentrations of drugs and their metabolites in saliva as a function of dose and time after intake.

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It will always remain a goal of an undergraduate biochemistry laboratory course to engage students hands-on in a wide range of biochemistry laboratory experiences. In 2006, our research group initiated a project for in silico prediction of enzyme function based only on the 3D coordinates of the more than 3800 proteins "of unknown function" in the Protein Data Bank, many of which resulted from the Protein Structure Initiative. Students have used the ProMOL plugin to the PyMOL molecular graphics environment along with BLAST, Pfam, and Dali to predict protein functions. As young scientists, these undergraduate research students wanted to see if their predictions were correct and so they developed an approach for in vitro testing of predicted enzyme function that included literature exploration, selection of a suitable assay and the search for commercially available substrates. Over the past two years, a team of faculty members from seven different campuses (California Polytechnic San Luis Obispo, Hope College, Oral Roberts University, Rochester Institute of Technology, St. Mary's University, Ursinus College, and Purdue University) have transferred this approach to the undergraduate biochemistry teaching laboratory as a Course-based Undergraduate Research Experience. A series of ten course modules and eight instructional videos have been created (www.promol.org/home/basil-modules-1) and the group is now expanding these resources, creating assessments and evaluating how this approach helps student to grow as scientists. The focus of this manuscript will be the logistical implications of this transition on campuses that have different cultures, expectations, schedules, and student populations. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(5):426-436, 2017.

A project-oriented laboratory course has been designed to introduce students to the study of biochemistry as it is practiced. The course is designed to be a capstone experience for students enrolled in a variety of majors at the Rochester Institute of Technology, including those who enter our new B.S. Biochemistry program. The experiments in this course enable the students to explore the protein chemistry, enzymology, and molecular biology of a single enzyme, threonine dehydrogenase, in a series of integrated experiments. The laboratory incorporates both traditional methods (centrifugation, UV-vis spectroscopy, gel electrophoresis, and chromatography) and more recent developments in the field (polymerase chain reaction). Students use a small computer network to prepare for experiments (using simulation software developed at RIT), to evaluate data, to access sequence homology databases over the Internet, and to visualize and model proteins and nucleic acids. The change in the biochemistry teaching lab from a sequence of unrelated experiments to an integrated series of experiments is a model that can be readily adapted by other educators, who can change their courses to focus on a single enzyme with which they are most familiar.

The 5th generation wireless system (5G) will support Internet of Things (IoT) by increasing the interconnectivity of electronic devices to support a variety of new and promising networked applications such as the home of the future, environmental monitoring networks, and infrastructure management systems. The potential benefits of the IoT are as profound as they are diverse. However, the benefits of the IoT come with some significant challenges. Not the least of these is that the increased interconnectivity integral to an IoT network increases its vulnerability to malevolent attacks. There is still no proven methodology for the design of security frameworks with device authentication and access control. This paper attempts to address this problem through the development of a prototype security framework with robust and transparent security protection. This includes an investigation into the security requirements of three different characteristic IoT scenarios (concretely, body IoT, home IoT, and hotel IoT), a design of new authentication mechanisms, and an access control subsystem with fine‐grained roles and risk indicators. Our prototype security framework gives us an insight into some of the major difficulties of IoT security as well as providing some feasible solutions. Copyright © 2015 John Wiley & Sons, Ltd.

As biochemists, one of our most captivating teaching tools is the use of molecular visualization. It is a compelling medium that can be used to communicate structural information much more effectively with interactive animations than with static figures. We have conducted a survey to begin a systematic evaluation of the current classroom usage of molecular visualization. Participants (n = 116) were asked to complete 11 multiple choice and 3 open ended questions. To provide more depth to these results, interviews were conducted with 12 of the participants. Many common themes arose in the survey and the interviews: a shared passion for the use of molecular visualization in teaching, broad diversity in software preference, the lack of uniform standards for assessment, a desire for more quality resources, and the challenge of enabling students to incorporate visualization in their learning. The majority of respondents had used molecular visualization for more than 5 years and mentioned 32 different visualization tools used, with Jmol and PyMOL clearly standing out as the most frequently used programs at the present time. The most common uses of molecular visualization in teaching were lecture and lab illustrations, followed by exam questions, in-class or in-laboratory exercises, and student projects, which frequently included presentations. While a minority of instructors used a grading rubric/scoring matrix for assessment of student learning with molecular visualization, many expressed a desire for common use assessment tools.