Annotation and Curation of the Protein Data Bank

The Protein Data Bank (PDB) is the worldwide repository for experimentally determined 3D structures of biological macromolecules. Established in 1971 with just seven structures, it presently includes more than 56,000 entries. To maintain the highest standards in curation and processing, the members of the worldwide Protein Data Bank (wwPDB) collaborate in data annotation and the development of procedures, tools, and resources. Annotation-related issues, particularly those impacted by new developments
in structural biology, are critically reviewed at in-person and virtual meetings regularly and frequently. Comprehensive documentation of the procedures, formats, and related data dictionaries used in data annotation are available at the wwPDB website(www.wwpdb.org).

Mindful of the impact that changes in annotation procedures or data format may have on users, changes are carefully managed and communicated in a timely fashion. In cases involving complex scientific or policy issues, input is sought from advisory committees, standing task forces, experimental method developers, and community experts. This is exemplified by creation of the recently-released version of the PDB archive which updates and further standardizes database references, small molecule chemistry, biological assemblies, and active sites

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education.

The RCSB Protein Data Bank (RCSB PDB, http://www.rcsb.org) provides access to 3D structures of biological macromolecules and is one of the leading resources in biology and biomedicine worldwide. Our efforts over the past 2 years focused on enabling a deeper understanding of structural biology and providing new structural views of biology that support both basic and applied research and education. Herein, we describe recently introduced data annotations including integration with external biological resources, such as gene and drug databases, new visualization tools and improved support for the mobile web. We also describe access to data files, web services and open access software components to enable software developers to more effectively mine the PDB archive and related annotations. Our efforts are aimed at expanding the role of 3D structure in understanding biology and medicine

Developing an Asthma Self-management Intervention Through a Web-Based Design Workshop for People With Limited Health Literacy:User-Centered Design Approach

BACKGROUND: Technology, including mobile apps, has the potential to support self-management of long-term conditions and can be tailored to enhance adoption. We developed an app to support asthma self-management among people with limited health literacy in a web-based workshop (to ensure physical distancing during the COVID-19 pandemic). OBJECTIVE: The aim of this study is to develop and test a prototype asthma self-management mobile app tailored to the needs of people with limited health literacy through a web-based workshop. METHODS: We recruited participants from a primary care center in Malaysia. We adapted a design sprint methodology to a web-based workshop in five stages over 1 week. Patients with asthma and limited health literacy provided insights into real-life self-management issues in stage 1, which informed mobile app development in stages 2-4. We recruited additional patients to test the prototype in stage 5 using a qualitative research design. Participants gave feedback through a concurrent thinking-aloud process moderated by a researcher. Each interview lasted approximately 1 hour. Screen recordings of app browsing activities were performed. Interviews were audio-recorded and analyzed using a thematic approach to identify utility and usability issues. RESULTS: The stakeholder discussion identified four themes: individual, family, friends, and society and system levels. Five patients tested the prototype. Participants described 4 ways in which the app influenced or supported self-management (utility): offering information, providing access to an asthma action plan, motivating control of asthma through support for medication adherence, and supporting behavior change through a reward system. Specific usability issues addressed navigation, comprehension, and layout. CONCLUSIONS: This study proved that it was possible to adapt the design sprint workshop to a web-based format with the added advantage that it allowed the development and the testing process to be done efficiently through various programs. The resultant app incorporated advice from stakeholders, including sources for information about asthma, medication and appointment reminders, accessible asthma action plans, and sources for social support. The app is now ready to move to feasibility testing

Pemanfaatan Limbah Cair Industri Tahu Harapan Maju, Cimanggis, Depok sebagai Media Kultur Spirulina sp.

Industrial waste in Depok still a problem raised because its contents were not following the government’s quality standards. Contaminants were considered pollutant are Chemical Oxygen Demand (COD), Biochemical Oxygen Demand (BOD), and Total Suspended Solids (TSS) were quite high. One of these wastes was tofu wastewater which produced a foul odor and pollutes the environment when discharged directly into water bodies. Lack of industrial owners' education of the economic value of the waste caused direct disposal without being utilized first. Therefore, this Community Service activity aims to determine the feasibility of tofu industrial wastewater as a Spirulina sp. culture medium and provided education to the tofu factory owners, to utilize their liquid waste. In the implementation several stages are carried out, namely literature studies, sampling, implementing wastewater assessments, counseling also training. The result of this activity is tofu industrial wastewater can be utilized as a medium for cultivating Spirulina sp. which added economic value while reducing the environmental pollution. This can be seen from the results of Spirulina cultivation on the 10th day where the Optical Density (OD) continues to increase and harvested for further use.Industrial waste in Depok still a problem raised because its contents were not following the government’s quality standards. Contaminants were considered pollutant are Chemical Oxygen Demand (COD), Biochemical Oxygen Demand (BOD), and Total Suspended Solids (TSS) were quite high. One of these wastes was tofu wastewater which produced a foul odor and pollutes the environment when discharged directly into water bodies. Lack of industrial owners' education of the economic value of the waste caused direct disposal without being utilized first. Therefore, this Community Service activity aims to determine the feasibility of tofu industrial wastewater as a Spirulina sp. culture medium and provided education to the tofu factory owners, to utilize their liquid waste. In the implementation several stages are carried out, namely literature studies, sampling, implementing wastewater assessments, counseling also training. The result of this activity is tofu industrial wastewater can be utilized as a medium for cultivating Spirulina sp. which added economic value while reducing the environmental pollution. This can be seen from the results of Spirulina cultivation on the 10th day where the Optical Density (OD) continues to increase and harvested for further use

The use of joints of meat as phantoms for ultrasound-guided needling skills : a prospective blinded study

Background -- Needle visualisation during ultrasound-guided procedures is a skill that can be difficult to practise, with commercially available phantoms being expensive and often unrealistic. Our aim was to find an inexpensive, reproducible model that could be used to assist in developing this skill. Methods -- Pork shoulder, beef brisket, and lamb shoulder joints were compared to a standard blue ultrasound phantom. Five ‘chunky’ yarn pieces were twisted together and threaded through each joint to simulate hyperechoic nerves. Participants were instructed to ultrasound each specimen and insert a needle close to a nerve like structure. Using a visual analogue scale, specimens were scored based on realism of appearances of ultrasound images and ‘feel’ of needling. Results -- 38 people participated. All specimens of meat scored significantly higher than the blue phantom (p = 0.01). There was no significant difference between the different types of meat. Conclusions -- Pork, beef and lamb joints are an effective model to use for simulation training for needling skills. They have limited lifespan, but due to its relatively low cost, it is feasible to discard the meat after each training workshop. We hope the use of inexpensive meat products will make ultrasound simulation training simpler to organise and more effective

Structures of complexes comprised of Fischerella transcription factor HetR with Anabaena DNA targets

HetR is an essential regulator of heterocyst development in cyanobacteria. Many mutations in HetR render Anabaena incapable of nitrogen fixation. The protein binds to a DNA palindrome upstream of hetP and other genes. We have determined the crystal structures of HetR complexed with palindromic DNA targets, 21, 23, and 29 bp at 2.50-, 3.00-, and 3.25-Å resolution, respectively. The highest-resolution structure shows fine details of specific protein–DNA interactions. The lower-resolution structures with longer DNA duplexes have similar interaction patterns and show how the flap domains interact with DNA in a sequence nonspecific fashion. Fifteen of 15 protein–DNA contacts predicted on the basis of the structure were confirmed by single amino acid mutations that abolished binding in vitro and complementation in vivo. A striking feature of the structure is the association of glutamate 71 from each subunit of the HetR dimer with three successive cytosines in each arm of the palindromic target, a feature that is conserved among all known heterocyst-forming cyanobacteria sequenced to date

The trpE Gene Negatively Regulates Differentiation of Heterocysts at the Level of Induction in Anabaena sp. Strain PCC 7120

Levels of 2-oxoglutarate (2-OG) reflect nitrogen status in many bacteria. In heterocystous cyanobacteria, a spike in the 2-OG level occurs shortly after the removal of combined nitrogen from cultures and is an integral part of the induction of heterocyst differentiation. In this work, deletion of one of the two annotated trpE genes in Anabaena sp. strain PCC 7120 resulted in a spike in the 2-OG level and subsequent differentiation of a wild-type pattern of heterocysts when filaments of the mutant were transferred from growth on ammonia to growth on nitrate. In contrast, 2-OG levels were unaffected in the wild type, which did not differentiate under the same conditions. An inverted-repeat sequence located upstream of trpE bound a central regulator of differentiation, HetR, in vitro and was necessary for HetR-dependent transcription of a reporter fusion and complementation of the mutant phenotype in vivo. Functional complementation of the mutant phenotype with the addition of tryptophan suggested that levels of tryptophan, rather than the demonstrated anthranilate synthase activity of TrpE, mediated the developmental response of the wild type to nitrate. A model is presented for the observed increase in 2-OG in the trpE mutant