OTU deubiquitinases reveal mechanisms of linkage specificity and enable ubiquitin chain restriction analysis

Sixteen ovarian tumor (OTU) family deubiquitinases (DUBs) exist in humans, and most members regulate cell-signaling cascades. Several OTU DUBs were reported to be ubiquitin (Ub) chain linkage specific, but comprehensive analyses are missing, and the underlying mechanisms of linkage specificity are unclear. Using Ub chains of all eight linkage types, we reveal that most human OTU enzymes are linkage specific, preferring one, two, or a defined subset of linkage types, including unstudied atypical Ub chains. Biochemical analysis and five crystal structures of OTU DUBs with or without Ub substrates reveal four mechanisms of linkage specificity. Additional Ub-binding domains, the ubiquitinated sequence in the substrate, and defined S1’ and S2 Ub-binding sites on the OTU domain enable OTU DUBs to distinguish linkage types. We introduce Ub chain restriction analysis, in which OTU DUBs are used as restriction enzymes to reveal linkage type and the relative abundance of Ub chains on substrates

Pressure drop and holdup predictions in horizontal oil-water flows for curved and wavy interfaces

In this work a modified two-fluid model was developed based on experimental observations of the interface configuration in stratified liquid-liquid flows. The experimental data were obtained in a horizontal 14. mmID acrylic pipe, for test oil and water superficial velocities ranging from 0.02. m/s to 0.51. m/s and from 0.05. m/s to 0.62. m/s, respectively. Using conductance probes, average interface heights were obtained at the pipe centre and close to the pipe wall, which revealed a concave interface shape in all cases studied. A correlation between the two heights was developed that was used in the two-fluid model. In addition, from the time series of the probe signal at the pipe centre, the average wave amplitude was calculated to be 0.0005. m and was used as an equivalent roughness in the interfacial shear stress model. Both the interface shape and roughness were considered in the two-fluid model together with literature interfacial shear stress correlations. Results showed that the inclusion of both the interface curvature and the equivalent roughness in the two-fluid model improved its predictions of pressure drop and interface height over the range of studied superficial oil and water velocities. Compared to the two-fluid model with other interfacial shear stress correlations, the modified model performed better particularly for predicting pressure drop

Why Do the Police Reject Counseling? An Examination of Necessary Changes to Police Subculture.

Abstract This paper reviews the concept of police subculture and examines its role in the management and acceptance of treatment for stress-related injury. In particular, we examine the impact of stigma that attaches to treatment within this subculture. The persistence of the dominant police subculture remains a significant obstacle to officers seeking treatment for stress-related illnesses. The subculture has historically resisted acknowledging the need for treatment in response to the occupational and/or organizational stress-related injury that results from frequent exposure to work-related trauma. Many police administrators are still embedded within and resist changes to the subculture, which results in an atmosphere that is unwelcoming to officers seeking or accepting treatment. This study draws on both qualitative and quantitative studies and modifies labeling theory to determine the sources of stigma involved in the police subculture. The paper reviews the reasons why officers refuse treatment, discusses the issue of stigmatization and labeling, and argues for the need to change police subculture, at least in part by ensuring that administrators support treatment and good health for officers. It is revealed that the stigmatization of officers who seek and receive treatment directly results in others’ refusal/rejection of it. The study recommends that departments address the subcultural processes of labeling and stigmatization associated with stress counseling at the individual, management, and organizational levels to bring about a shift in police subculture and improve the level of occupational health and safety for officers on the force

Student Evaluations of Teaching Are Mostly Awfully Wrong

Student evaluations of teaching (SETs) have been used, researched, and debated for many decades. It is a common practice in higher education institutions, with the supposed purpose of improving course quality and effectiveness, but with unintended consequences of encouraging and motivating poor teaching and causing grade inflation. There is strong evidence that SET “effectiveness” does not measure teaching effectiveness. This paper reviews empirical research examining common concerns about the usefulness (positive and negative) and accuracy of SETs. The findings reveal that student satisfaction relates to their anticipated/expected grades in their courses; hence, they want to get good grades and their instructors want to get a good rating of SET, and this results in grade inflation. The key points are that SETs (1) allow students to speak their “mind”, (2) have no compelling correlation between quality of teaching and learning effectiveness, (3) reward easy, less demanding, and lazy teachers with a positive rating, (4) are biased against gender, attractiveness, ethnicity, race, etc., (5) are weaponized against “some” faculty members, and (6) are like asking convicts awaiting sentencing to evaluate the judge or jurors who convicted them

Why Do the Police Reject Counseling? An Examination of Necessary Changes to Police Subculture. Necessary Changes to Police Subculture.

This paper reviews the concept of police subculture and examines its role in the management and acceptance of treatment for stress-related injury. In particular, we examine the impact of stigma that attaches to treatment within this subculture. The persistence of the dominant police subculture remains a significant obstacle to officers seeking treatment for stress-related illnesses. The subculture has historically resisted acknowledging the need for treatment in response to the occupational and/or organizational stress-related injury that results from frequent exposure to work-related trauma. Many police administrators are still embedded within and resist changes to the subculture, which results in an atmosphere that is unwelcoming to officers seeking or accepting treatment. This study draws on both qualitative and quantitative studies and modifies labeling theory to determine the sources of stigma involved in the police subculture. The paper reviews the reasons why officers refuse treatment, discusses the issue of stigmatization and labeling, and argues for the need to change police subculture, at least in part by ensuring that administrators support treatment and good health for officers. It is revealed that the stigmatization of officers who seek and receive treatment directly results in others’ refusal/rejection of it. The study recommends that departments address the subcultural processes of labeling and stigmatization associated with stress counseling at the individual, management, and organizational levels to bring about a shift in police subculture and improve the level of occupational health and safety for officers on the force

Prediction of peptides binding to MHC class I alleles by partial periodic pattern mining

MHC (Major Histocompatibility Complex) is a key player in the immune response of an organism. It is important to be able to predict which antigenic peptides will bind to a specific MHC allele and which will not, creating possibilities for controlling immune response and for the applications of immunotherapy. However, a problem for MHC class I is the presence of bulges and loops in the peptides, changing the total length. Most machine learning methods in use today require the sequences to be of same length to successfully mine the binding motifs. We propose the use of time-based data mining methods in motif mining to be able to mine motifs position-independently. Also, the information for both binding and non-binding peptides is used on the contrary to the other methods which only rely on binding peptides. The prediction results are between 60-95% for the tested alleles

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences

We present a performance-optimized algorithm, subsampled open-reference OTU picking, for assigning marker gene (e.g., 16S rRNA) sequences generated on next-generation sequencing platforms to operational taxonomic units (OTUs) for microbial community analysis. This algorithm provides benefits over de novo OTU picking (clustering can be performed largely in parallel, reducing runtime) and closed-reference OTU picking (all reads are clustered, not only those that match a reference database sequence with high similarity). Because more of our algorithm can be run in parallel relative to “classic” open-reference OTU picking, it makes open-reference OTU picking tractable on massive amplicon sequence data sets (though on smaller data sets, “classic” open-reference OTU clustering is often faster). We illustrate that here by applying it to the first 15,000 samples sequenced for the Earth Microbiome Project (1.3 billion V4 16S rRNA amplicons). To the best of our knowledge, this is the largest OTU picking run ever performed, and we estimate that our new algorithm runs in less than 1/5 the time than would be required of “classic” open reference OTU picking. We show that subsampled open-reference OTU picking yields results that are highly correlated with those generated by “classic” open-reference OTU picking through comparisons on three well-studied datasets. An implementation of this algorithm is provided in the popular QIIME software package, which uses uclust for read clustering. All analyses were performed using QIIME’s uclust wrappers, though we provide details (aided by the open-source code in our GitHub repository) that will allow implementation of subsampled open-reference OTU picking independently of QIIME (e.g., in a compiled programming language, where runtimes should be further reduced). Our analyses should generalize to other implementations of these OTU picking algorithms. Finally, we present a comparison of parameter settings in QIIME’s OTU picking workflows and make recommendations on settings for these free parameters to optimize runtime without reducing the quality of the results. These optimized parameters can vastly decrease the runtime of uclust-based OTU picking in QIIME

Phylogenetic analysis of faecal microbiota from captive cheetahs reveals underrepresentation of Bacteroidetes and Bifidobacteriaceae

Background: Imbalanced feeding regimes may initiate gastrointestinal and metabolic diseases in endangered felids kept in captivity such as cheetahs. Given the crucial role of the host's intestinal microbiota in feed fermentation and health maintenance, a better understanding of the cheetah's intestinal ecosystem is essential for improvement of current feeding strategies. We determined the phylogenetic diversity of the faecal microbiota of the only two cheetahs housed in an EAZA associated zoo in Flanders, Belgium, to gain first insights in the relative distribution, identity and potential role of the major community members. Results: Taxonomic analysis of 16S rRNA gene clone libraries (702 clones) revealed a microbiota dominated by Firmicutes (94.7%), followed by a minority of Actinobacteria (4.3%), Proteobacteria (0.4%) and Fusobacteria (0.6%). In the Firmicutes, the majority of the phylotypes within the Clostridiales were assigned to Clostridium clusters XIVa (43%), XI (38%) and I (13%). Members of the Bacteroidetes phylum and Bifidobacteriaceae, two groups that can positively contribute in maintaining intestinal homeostasis, were absent in the clone libraries and detected in only marginal to low levels in real-time PCR analyses. Conclusions: This marked underrepresentation is in contrast to data previously reported in domestic cats where Bacteroidetes and Bifidobacteriaceae are common residents of the faecal microbiota. Next to methodological differences, these findings may also reflect the apparent differences in dietary habits of both felid species. Thus, our results question the role of the domestic cat as the best available model for nutritional intervention studies in endangered exotic felids