A to Z of polymorphs related by proton transfer

The occurrence of tautomeric polymorphism in the Cambridge Structural Database (CSD) was established to be very rare in a previous study by A. J. Cruz-Cabeza and C. R. Groom (CrystEngComm, 2011, 13, 93). A decade has now elapsed and the CSD has seen a significant increase in its total number of crystal structures, useful CSD subsets have been introduced and the CSD Python API has been developed to allow for complex data mining. Given this, we wanted to revisit tautomeric polymorphs in the CSD alongside other polymorphs related by proton transfer and compare these results with those from an in-house pharmaceutical database in order to assess their prevalence and significance for pharmaceuticals. From A (amine–imine tautomeric polymorphs) to Z (zwitterionic polymorphs), here we study different types of polymorphs related by proton-transfer in the CSD, the CSD drug subset (DrugCSD), the single component drug subset of the CSD (SDrugCSD), and the GSK small molecule crystal structure database (GSD). First, we assess the potential of compounds to exist as tautomers. Whilst 51% of compounds in the CSD are capable of tautomerism, this number increases to 73% and 70% for the SDrugCSD and the GSD respectively. Tautomerism potential is, thus, more prevalent in pharmaceuticals than in common organic compounds in the CSD. Second, in mining the CSD we identify a total of 95 families of polymorphs related by proton transfer which can then be classified into six different categories depending on the type of proton transfer observed and the ionisation of species involved. The most common of such category is that of tautomeric polymorphs followed by zwitterionic polymorphs. The rarest type of proton transfer polymorphs is that of multi-zwitterionic polymorphs where two different zwitterions of the same compound are found in two different crystal structures. Overall, 3% of polymorphic compositions in the DrugCSD are found to be related by proton transfer which, although not very common, is of relevance to pharmaceuticals and drug development due to the potential impact on physical properties. Specific examples of each of the categories are discussed with calculations of lattice energies presented and consideration of ΔpKa values and likelihood of proton transfer and ionisation

Whole genome sequencing-based mapping and candidate identification of mutations from fixed zebrafish tissue

As forward genetic screens in zebrafish become more common, the number of mutants that cannot be identified by gross morphology or through transgenic approaches, such as many nervous system defects, has also increased. Screening for these difficult-to-visualize phenotypes demands techniques such as whole-mount in situ hybridization (WISH) or antibody staining, which require tissue fixation. To date, fixed tissue has not been amenable for generating libraries for whole genome sequencing (WGS). Here, we describe a method for using genomic DNA from fixed tissue and a bioinformatics suite for WGS-based mapping of zebrafish mutants. We tested our protocol using two known zebrafish mutant alleles, gpr126st49 and egr2bfh227, both of which cause myelin defects. As further proof of concept we mapped a novel mutation, stl64, identified in a zebrafish WISH screen for myelination defects. We linked stl64 to chromosome 1 and identified a candidate nonsense mutation in the F-box and WD repeat domain containing 7 (fbxw7) gene. Importantly, stl64 mutants phenocopy previously described fbxw7vu56 mutants, and knockdown of fbxw7 in wild-type animals produced similar defects, demonstrating that stl64 disrupts fbxw7. Together, these data show that our mapping protocol can map and identify causative lesions in mutant screens that require tissue fixation for phenotypic analysis

Automated web-based request mechanism for workflow enhancement in an academic customer-focused biorepository

Informatics systems, particularly those that provide capabilities for data storage, specimen tracking, retrieval, and order fulfillment, are critical to the success of biorepositories and other laboratories engaged in translational medical research. A crucial item—one easily overlooked—is an efficient way to receive and process investigator-initiated requests. A successful electronic ordering system should allow request processing in a maximally efficient manner, while also allowing streamlined tracking and mining of request data such as turnaround times and numerical categorizations (user groups, funding sources, protocols, and so on). Ideally, an electronic ordering system also facilitates the initial contact between the laboratory and customers, while still allowing for downstream communications and other steps toward scientific partnerships. We describe here the recently established Web-based ordering system for the biorepository at Washington University Medical Center, along with its benefits for workflow, tracking, and customer service. Because of the system's numerous value-added impacts, we think our experience can serve as a good model for other customer-focused biorepositories, especially those currently using manual or non-Web–based request systems. Our lessons learned also apply to the informatics developers who serve such biobanks

Multicenter Evaluation of the QIAstat-Dx Respiratory Panel for the Detection of Viruses and Bacteria in Nasopharyngeal Swab Specimens

The QIAstat-Dx Respiratory Panel (QIAstat-Dx RP) is a multiplex in vitro diagnostic test for the qualitative detection of 20 pathogens directly from nasopharyngeal swab (NPS) specimens. The assay is performed using a simple sample-to-answer platform with results available in approximately 69 min. The pathogens identified are adenovirus, coronavirus 229E, coronavirus HKU1, coronavirus NL63, coronavirus OC43, human metapneumovirus A and B, influenza A, influenza A H1, influenza A H3, influenza A H1N1/2009, influenza B, parainfluenza virus 1, parainfluenza virus 2, parainfluenza virus 3, parainfluenza virus 4, rhinovirus/enterovirus, respiratory syncytial virus A and B, Bordetella pertussis, Chlamydophila pneumoniae, and Mycoplasma pneumoniae. This multicenter evaluation provides data obtained from 1,994 prospectively collected and 310 retrospectively collected (archived) NPS specimens with performance compared to that of the BioFire FilmArray Respiratory Panel, version 1.7. The overall percent agreement between QIAstat-Dx RP and the comparator testing was 99.5%. In the prospective cohort, the QIAstat-Dx RP demonstrated a positive percent agreement of 94.0% or greater for the detection of all but four analytes: coronaviruses 229E, NL63, and OC43 and rhinovirus/enterovirus. The test also demonstrated a negative percent agreement of ≥97.9% for all analytes. The QIAstat-Dx RP is a robust and accurate assay for rapid, comprehensive testing for respiratory pathogens

Weight Gain and Decreased Sleep Duration in First-Year College Students: A Longitudinal Study

Poster from the 2017 Food & Nutrition Conference & Expo. Poster Session: Professional Skills; Nutrition Assessment & Diagnosis; Medical Nutrition Therapy

Delayed Matching to Sample: Reinforcement has Opposite Effects on Resistance to Change in Two Related Procedures

The effects of reinforcement on delayed matching to sample (DMTS) have been studied in two within-subjects procedures. In one, reinforcer magnitudes or probabilities vary from trial to trial and are signaled within trials (designated signaled DMTS trials). In the other, reinforcer probabilities are consistent for a series of trials produced by responding on variable-interval (VI) schedules within multiple-schedule components (designated multiple VI DMTS). In both procedures, forgetting functions in rich trials or components are higher than and roughly parallel to those in lean trials or components. However, during disruption, accuracy has been found to decrease more in rich than in lean signaled DMTS trials and, conversely, to decrease more in lean than in rich multiple VI DMTS components. In the present study, we compared these procedures in two groups of pigeons. In baseline, forgetting functions in rich trials or components were higher than and roughly parallel to those in lean trials or components, and were similar between the procedures. During disruption by prefeeding or extinction, accuracy decreased more in rich signaled DMTS trials, whereas accuracy decreased more in lean multiple VI DMTS components. These results replicate earlier studies and are predicted by a model of DMTS from Nevin, Davison, Odum, and Shahan (2007)

Non-myeloid Cell Phagocytosis

As professional phagocytes, myeloid cells, including macrophages, dendritic cells, and neutrophils, are often the targets for investigation and analysis of phagocytosis. Phagocytosis, however, has also been observed in nonmyeloid cells, including epithelium, mesenchymal, and smooth muscle cells. Colloquially known as nonprofessional phagocytes, these nonmyeloid cells are capable of phagocytosis of pathogenic material and efferocytosis of apoptotic bodies. Cells, such as those found in the epithelium, are often the primary site for viral and bacterial infection and have evolved to possess strong anti-pathogenic machinery of their own. The processes by which nonmyeloid cells can engage in phagocytic functions have wide implications for tissue homeostasis and disease pathogenesis, including infection and colonization. This chapter will review the phagocytosis capabilities in these nonmyeloid cells

Complainant behavioral tone, ambivalent sexism, and perceptions of sexual harassment

Previous research has examined the impact of the law on decisions made about social sexual interactions in the workplace in the context of a variety of individual difference variables including gender of the observer and sexist attitudes, as well as situational factors including legal standard and prior exposure to aggressive and submissive complainants. The current study continued this line of inquiry by testing whether hostile or benevolent sexist attitudes behaved differently under manipulated exposure to aggressive and submissive complainants. Full-time workers watched 1 videotape in which aggressive, submissive, or neutral (i.e., businesslike) women complained that male coworkers sexually harassed them; then, participants viewed a second complainant who always acted in a neutral behavioral tone. In the first case, participants high in hostile sexism who took a reasonable person perspective (but not those with a reasonable woman point of view) and all men who viewed an aggressive complainant found less evidence of harassment. With the second set of allegations, female workers who were exposed to a submissive complainant in the first case found less evidence of harassment against the neutral complainant, suggesting that exposure to a submissive complainant triggered some type of victim blaming in female workers. Policy and training implications are discussed