bluuebunny/crossref_metadata_2025 huggingface dataset:
Cas3-stimulated runaway replication of modified ColE1 plasmids in Escherichia coli is temperature dependent
Authors: Radovčić Marin , Čulo Anja , Ivančić-Baće Ivana
Published: May 2019

The clustered regularly interspersed short palindromic repeats (CRISPR)-Cas system constitutes an adaptive immunity system of prokaryotes against mobile genetic elements using a CRISPR RNA (crRNA)-mediated interference mechanism. In Type I CRISPR-Cas systems, crRNA guided by a Cascade complex recognises the matching target DNA and promotes an R-loop formation, RNA-DNA hybrid. The helicase-nuclease Cas3 protein is then recruited to the Cascade/R-loop complex where it nicks and degrades DNA. The Cas3 activity in CRISPR-Cas immunity is reduced in Δhns cells at 37°C for unknown reasons. Cas3 can also influence regulation of plasmid replication and promote uncontrolled (‘runaway’) replication of ColE1 plasmids independently of other CRISPR-Cas components, requiring only its helicase activity. In this work we wanted to test whether Cas3-stimulated uncontrolled plasmid replication is affected by the temperature in Δhns and/or ΔhtpG mutants. We found that Cas3-stimulated uncontrolled plasmid replication occurs only at 37°C, irrespective of the genotype of the analysed mutants, and dependent on Cas3 helicase function. We also found that plasmid replication was strongly reduced by the hns mutation at 30°C and that Cas3 could interfere with T4 phage replication at both incubation temperatures.
Prevalence, Incidence, and Risk Factors for Overall, Physical, and Cognitive Independence Among Those From Exceptionally Long-Lived Families: The Long Life Family Study
Authors: Santanasto Adam J , Marron Megan M , Boudreau Robert M , Feitosa Mary F , Wojczynski Mary K , Arbeev Konstantin G , Thyagarajan Bharat , Schupf Nicole , Stallard Eric , Sebastiani Paola , Cosentino Stephanie , Christensen Kaare , Newman Anne B
Published: May 2019

Background

The Long Life Family Study (LLFS) enrolled families exhibiting exceptional longevity. The goal of this article was to determine the prevalence and predictors of remaining independent after 7 years in the oldest generation.

Methods

We examined 7-year change in physical (free of activities of daily living difficulty), cognitive (Mini-Mental State Examination score ≥ 24), and overall independence (physically/cognitively independent) in adults aged 90.3 ± 6.3 from LLFS’s oldest generation. Potential predictors (n = 28) of remaining independent included demographics, diseases, biomarkers, anthropometrics, and physical and cognitive performance tasks and were determined using generalized estimating equations (α: p < .05). This was a discovery/exploratory analysis, so no multiple testing correction was employed and the results require independent replication.

Results

At baseline (n = 1442), 67.3%, 83.8%, and 79.7% were overall, physically, and cognitively independent, respectively. After 7 years, 66% died, 7.5% were lost to follow-up, and the prevalence of overall independence decreased to 59.1% in survivors (−8.2%, 95% confidence interval: −14.1%, 2.2%). Of those with baseline independence, 156/226 (69.0%) remained independent. Predictors of remaining physically independent included younger age, better Short Physical Performance Battery score and lung function, smaller waist circumference, and lower soluble receptor for advanced glycation end-product levels (p < .05). Predictors of remaining cognitively independent included no cancer history, better Digit Symbol Substitution Test performance, and higher body weight (p < .05).

Conclusions

The prevalence of independence decreased by only 8.2% after 7 years, demonstrating the close correspondence between disability and mortality. Further, despite a mean baseline age of 90 years, a large proportion of survivors remained independent, suggesting this exceptional subgroup may harbor protective mechanisms.
NMR-based insight into galectin-3 binding to endothelial cell adhesion molecule CD146: Evidence for noncanonical interactions with the lectin’s CRD β-sandwich F-face
Authors: Zhang Zhongyu , Miller Michelle C , Xu Xuejiao , Song Chengcheng , Zhang Fan , Zheng Yi , Zhou Yifa , Tai Guihua , Mayo Kevin H
Published: May 2019

Galectin-3 (Gal-3) binds to cell adhesion glycoprotein CD146 to promote cytokine secretion and mediate endothelial cell migration. Here, we used Nuclear Magnetic Resonance (NMR) 15N-Heteronuclear Single Quantum Coherence (HSQC) spectroscopy to investigate binding between 15N-labeled Gal-3 and the extracellular domain (eFL) of purified CD146 (five Ig-like ectodomains D1–D5) and a shorter, D5-deleted version of CD146 (D1–D4). Binding of Gal-3 and its carbohydrate recognition domain (CRD) to CD146 D1–D4 is greatly reduced vis-à-vis CD146 eFL, supporting the proposal of a larger number of glycosylation sites on D5. Even though the canonical sugar-binding β-sheet S-face (β-strands 1, 10, 3, 4, 5, 6) of the Gal-3 β-sandwich is involved in interactions with CD146 (e.g. N-linked glycosylation sites), equivalent HSQC spectral perturbations at residues on the opposing Gal-3 F-face β-sheet (β-strands 11, 2, 7, 8, 9) indicate involvement of the Gal-3 F-face in binding CD146. This is supported by the observation that addition of lactose, while significantly attenuating Gal-3 binding (primarily with the S-face) to CD146 eFL, does not abolish it. Bio-Layer Interferometry studies with Gal-3 F-face mutants yield KD values to demonstrate a significant decrease (L203A) or increase (V204A, L218A, T243A) in net binding to CD146 eFL compared to wild type Gal-3. However, HSQC lactose titrations show no highly significant effects on sugar binding to the Gal-3 CRD S-face. Overall, our findings indicate that Gal-3 binding to CD146 is more involved than simple interactions with β-galactoside epitopes on the cell receptor, and that there is a direct role for the lectin’s CRD F-face in the CD146 binding process.
Computational Modeling of Anthocyanin Pathway Evolution: Biases, Hotspots, and Trade-offs
Authors: Wheeler L C , Smith S D
Published: May 2019

The alteration of metabolic pathways is a common mechanism underlying the evolution of new phenotypes. Flower color is a striking example of the importance of metabolic evolution in a complex phenotype, wherein shifts in the activity of the underlying pathway lead to a wide range of pigments. Although experimental work has identified common classes of mutations responsible for transitions among colors, we lack a unifying model that relates pathway function and activity to the evolution of distinct pigment phenotypes. One challenge in creating such a model is the branching structure of pigment pathways, which may lead to evolutionary trade-offs due to competition for shared substrates. In order to predict the effects of shifts in enzyme function and activity on pigment production, we created a simple kinetic model of a major plant pigmentation pathway: the anthocyanin pathway. This model describes the production of the three classes of blue, purple, and red anthocyanin pigments, and accordingly, includes multiple branches and substrate competition. We first studied the general behavior of this model using a naïve set of parameters. We then stochastically evolved the pathway toward a defined optimum and analyzed the patterns of fixed mutations. This approach allowed us to quantify the probability density of trajectories through pathway state space and identify the types and number of changes. Finally, we examined whether our simulated results qualitatively align with experimental observations, i.e., the predominance of mutations which change color by altering the function of branching genes in the pathway. These analyses provide a theoretical framework that can be used to predict the consequences of new mutations in terms of both pigment phenotypes and pleiotropic effects.
Social Media and Change in Psychological Distress Over Time: The Role of Social Causation
Authors: Hampton Keith N
Published: May 2019

This article tests the relationship between information and communication technologies (ICT), such as the Internet, cell phones, and social media, and change over time in psychological distress (PD) and risk of serious psychological distress (SPD) associated with depression and anxiety disorders. Using a longitudinal panel design, survey data from a representative sample of American adults, findings revealed that home Internet and social network site (SNS) use are associated with decreased PD over time. Having extended family who are also Internet users further decreases PD. PD increased or decreased in relation to change in the PD of extended family who also use SNSs. For most people, ICT substantively reduce PD; in rare cases, an extreme spike in PD of extended family also on SNSs, there was a trivial increase to the risk of SPD. PD did not change when extended family not on social media experienced a change in their PD.
Head Lice Recognize and Prefer Head Odor Over Foot and Forearms Odors
Authors: Galassi Federico , Gonzalez-Audino Paola , Picollo María I
Published: May 2019

Human head lice, Pediculus humanus capitis De Geer (Phthiraptera: Pediculidae), are hematophagous parasites that infest human heads. They are extreme host specialists suggesting a strict selection behavior towards the human head by the parasites. Despite the public health relevance of P. humanus capitis, the role of chemical clues to select the human head is not well known. In the present study, we attempted to find out whether head lice recognize and select the odor of the head over the odor of other parts of the human body. Our results using a two-choice olfactometer demonstrated that head lice were highly attracted by the volatile compounds of the human odor air, but they did not show preference for the volatiles of head compared to the volatiles of other parts of the body (forearm or foot). Conversely, when head lice were exposed in an experimental arena to the whole human odor of different parts of the body, they showed a preferential response to the whole head odor compared with the whole foot or forearm odors. These results suggest that head lice can at short distance of the host, be oriented towards the head odor of the human host in the selection of the scalp environment.
How to claim what is mine: Negotiating professional roles in inter-organizational projects
Authors: Bos-de Vos Marina , Lieftink Bente M , Lauche Kristina
Published: May 2019

Professional roles within inter-organizational projects have become increasingly diverse and contested, yet little is known about how professionals react to such threats of marginalization. Drawing on empirical data from interviews with architects, a profession in which historically established role boundaries have become particularly blurred, we analyse how professionals negotiate their roles in inter-organizational projects. We identified three types of boundary work—reinstating, bending, and pioneering role boundaries—and illustrate their antecedents and effects for project collaboration. These categories exemplify different responses to the threat of marginalization depending upon professionals’ perceptions of what the specific project called for. Our study provides important insights into boundary work practices emerging in the context of inter-organizational projects and how professionals adjust their claims-making to perceived opportunities, thereby triggering incremental as well as more radical changes in the professional role structures.
Using failed supernovae to constrain the Galactic r-process element production
Authors: Wehmeyer B , Fröhlich C , Côté B , Pignatari M , Thielemann F-K
Published: May 2019

Rapid neutron capture process (r-process) elements have been detected in a large fraction of metal-poor halo stars, with abundances relative to iron (Fe) that vary by over two orders of magnitude. This scatter is reduced to less than a factor of 3 in younger Galactic disc stars. The large scatter of r-process elements in the early Galaxy suggests that the r-process is made by rare events, like compact binary mergers and rare sub-classes of supernovae. Although being rare, neutron star mergers alone have difficulties to explain the observed enhancement of r-process elements in the lowest metallicity stars compared to Fe. The supernovae producing the two neutron stars already provide a substantial Fe abundance where the r-process ejecta from the merger would be injected. In this work we investigate another complementary scenario, where the r-process occurs in neutron star-black hole mergers in addition to neutron star mergers. Neutron star-black hole mergers would eject similar amounts of r-process matter as neutron star mergers, but only the neutron star progenitor would have produced Fe. Furthermore, a reduced efficiency of Fe production from single stars significantly alters the age–metallicity relation, which shifts the onset of r-process production to lower metallicities. We use the high-resolution [(20 pc)3/cell] inhomogeneous chemical evolution tool ‘ICE’ to study the outcomes of these effects. In our simulations, an adequate combination of neutron star mergers and neutron star-black hole mergers qualitatively reproduces the observed r-process abundances in the Galaxy.
Validation of a temperate fourth planet in the K2-133 multiplanet system
Authors: Wells R , Poppenhaeger K , Watson C A
Published: May 2019

We present follow-up observations of the K2-133 multiplanet system. Previously, we announced that K2-133 contained three super-Earths orbiting an M1.5V host star – with tentative evidence of a fourth outer-planet orbiting at the edge of the temperate zone. Here, we report on the validation of the presence of the fourth planet, determining a radius of $1.73_{-0.13}^{+0.14}$ R⊕. The four planets span the radius gap of the exoplanet population, meaning further follow-up would be worthwhile to obtain masses and test theories of the origin of the gap. In particular, the trend of increasing planetary radius with decreasing incident flux in the K2-133 system supports the claim that the gap is caused by photo-evaporation of exoplanet atmospheres. Finally, we note that K2-133 e orbits on the edge of the star's temperate zone, and that our radius measurement allows for the possibility that this is a rocky world. Additional mass measurements are required to confirm or refute this scenario.
Protein interactions in T7 DNA replisome inhibit the bypass of abasic site by DNA polymerase
Authors: Zou Zhenyu , Liang Tingting , Xu Zhongyan , Xie Jiayu , Zhang Shuming , Chen Weina , Wan Siqi , Ling Yihui , Zhang Huidong
Published: May 2019

Abasic site as a common DNA lesion blocks DNA replication and is highly mutagenic. Protein interactions in T7 DNA replisome facilitate DNA replication and translesion DNA synthesis. However, bypass of an abasic site by T7 DNA replisome has never been investigated. In this work, we used T7 DNA replisome and T7 DNA polymerase alone as two models to study DNA replication on encountering an abasic site. Relative to unmodified DNA, abasic site strongly inhibited primer extension and completely blocked strand-displacement DNA synthesis, due to the decreased fraction of enzyme–DNA productive complex and the reduced average extension rates. Moreover, abasic site at DNA fork inhibited the binding of DNA polymerase or helicase onto fork and the binding between polymerase and helicase at fork. Notably and unexpectedly, we found DNA polymerase alone bypassed an abasic site on primer/template (P/T) substrate more efficiently than did polymerase and helicase complex bypass it at fork. The presence of gp2.5 further inhibited the abasic site bypass at DNA fork. Kinetic analysis showed that this inhibition at fork relative to that on P/T was due to the decreased fraction of productive complex instead of the average extension rates. Therefore, we found that protein interactions in T7 DNA replisome inhibited the bypass of DNA lesion, different from all the traditional concept that protein interactions or accessory proteins always promote DNA replication and DNA damage bypass, providing new insights in translesion DNA synthesis performed by DNA replisome.
sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression
Authors: Aparicio-Puerta Ernesto , Lebrón Ricardo , Rueda Antonio , Gómez-Martín Cristina , Giannoukakos Stavros , Jaspez David , Medina José María , Zubkovic Andreja , Jurak Igor , Fromm Bastian , Marchal Juan Antonio , Oliver José , Hackenberg Michael
Published: May 2019

Since the original publication of sRNAtoolbox in 2015, small RNA research experienced notable advances in different directions. New protocols for small RNA sequencing have become available to address important issues such as adapter ligation bias, PCR amplification artefacts or to include internal controls such as spike-in sequences. New microRNA reference databases were developed with different foci, either prioritizing accuracy (low number of false positives) or completeness (low number of false negatives). Additionally, other small RNA molecules as well as microRNA sequence and length variants (isomiRs) have continued to gain importance. Finally, the number of microRNA sequencing studies deposited in GEO nearly triplicated from 2014 (280) to 2018 (764). These developments imply that fast and easy-to-use tools for expression profiling and subsequent downstream analysis of miRNA-seq data are essential to many researchers. Key features in this sRNAtoolbox release include addition of all major RNA library preparation protocols to sRNAbench and improvements in sRNAde, a tool that summarizes several aspects of small RNA sequencing studies including the detection of consensus differential expression. A special emphasis was put on the user-friendliness of the tools, for instance sRNAbench now supports parallel launching of several jobs to improve reproducibility and user time efficiency.
Thermodynamically stable and genetically unstable G-quadruplexes are depleted in genomes across species
Authors: Puig Lombardi Emilia , Holmes Allyson , Verga Daniela , Teulade-Fichou Marie-Paule , Nicolas Alain , Londoño-Vallejo Arturo
Published: May 2019

G-quadruplexes play various roles in multiple biological processes, which can be positive when a G4 is involved in the regulation of gene expression or detrimental when the folding of a stable G4 impairs DNA replication promoting genome instability. This duality interrogates the significance of their presence within genomes. To address the potential biased evolution of G4 motifs, we analyzed their occurrence, features and polymorphisms in a large spectrum of species. We found extreme bias of the short-looped G4 motifs, which are the most thermodynamically stable in vitro and thus carry the highest folding potential in vivo. In the human genome, there is an over-representation of single-nucleotide-loop G4 motifs (G4-L1), which are highly conserved among humans and show a striking excess of the thermodynamically least stable G4-L1A (G3AG3AG3AG3) sequences. Functional assays in yeast showed that G4-L1A caused the lowest levels of both spontaneous and G4-ligand-induced instability. Analyses across 600 species revealed the depletion of the most stable G4-L1C/T quadruplexes in most genomes in favor of G4-L1A in vertebrates or G4-L1G in other eukaryotes. We discuss how these trends might be the result of species-specific mutagenic processes associated to a negative selection against the most stable motifs, thus neutralizing their detrimental effects on genome stability while preserving positive G4-associated biological roles.
A survey of molecular cores in M 17 SWex
Authors: Shimoikura Tomomi , Dobashi Kazuhito , Hirose Asha , Nakamura Fumitaka , Shimajiri Yoshito , Sugitani Koji
Published: May 2019

A survey of molecular cores covering the infrared dark cloud known as the M 17 southwest extension (M 17 SWex) has been carried out with the 45 m Nobeyama Radio Telescope. Based on the N2H+ (J = 1–0) data obtained, we have identified 46 individual cores whose masses are in the range from 43 to $3026\, {M}_{\odot }$. We examined the relationship between the physical parameters of the cores and those of young stellar objects (YSOs) associated with the cores found in the literature. The comparison of the virial mass and the core mass indicates that most of the cores can be gravitationally stable if we assume a large external pressure. Among the 46 cores, we found four massive cores with YSOs. They have large masses of $\gtrsim 1000\, M_{\odot }$ and line widths of $\gtrsim 2.5\:$km s−1 which are similar to those of clumps forming high-mass stars. However, previous studies have shown that there is no active massive star formation in this region. Recent measurements of near-infrared polarization imply that the magnetic field around M 17 SWex is likely to be strong enough to support the cores against self-gravity. We therefore suggest that the magnetic field may prevent the cores from collapsing, causing the low level of massive star formation in M 17 SWex.
A Functional Alternative Oxidase Modulates Plant Salt Tolerance in Physcomitrella patens
Authors: Wu Guochun , Li Sha , Li Xiaochuan , Liu Yunhong , Zhao Shuangshuang , Liu Baohui , Zhou Huapeng , Lin Honghui
Published: May 2019

Alternative oxidase (AOX) has been reported to be involved in mitochondrial function and redox homeostasis, thus playing an essential role in plant growth as well as stress responses. However, its biological functions in nonseed plants have not been well characterized. Here, we report that AOX participates in plant salt tolerance regulation in moss Physcomitrella patens (P. patens). AOX is highly conserved and localizes to mitochondria in P. patens. We observed that PpAOX rescued the impaired cyanide (CN)-resistant alternative (Alt) respiratory pathway in Arabidopsis thaliana (Arabidopsis) aox1a mutant. PpAOX transcription and Alt respiration were induced upon salt stress in P. patens. Using homologous recombination, we generated PpAOX-overexpressing lines (PpAOX OX). PpAOX OX plants exhibited higher Alt respiration and lower total reactive oxygen species accumulation under salt stress condition. Strikingly, we observed that PpAOX OX plants displayed decreased salt tolerance. Overexpression of PpAOX disturbed redox homeostasis in chloroplasts. Meanwhile, chloroplast structure was adversely affected in PpAOX OX plants in contrast to wild-type (WT) P. patens. We found that photosynthetic activity in PpAOX OX plants was also lower compared with that in WT. Together, our work revealed that AOX participates in plant salt tolerance in P. patens and there is a functional link between mitochondria and chloroplast under challenging conditions.
Reading for Evidence of Faith in Herbert’s Poems
Authors: Lyne Raphael
Published: May 2019

In this essay George Herbert’s representations of inward life are seen in the context of (i) the recommendations for self-examination made by theologians of his own time, and (ii) critical terms derived from modern psychological accounts of ‘Theory of Mind’. Lisa Zunshine’s emphasis on ‘embodied transparency’ and ‘metapresentation’ helps capture the way that Herbert exposes his readers to difficult but salutary self-analysis. This is not just a matter of trapping the unwary: the poems are designed for re-reading, re-voicing, and re-thinking, for considering especially the timing of discoveries about one’s own faith, and the origins of the voices that console and cajole the speakers of the poems. In Herbert’s hands, lyric form and the practice of self-scrutiny both respond dynamically to the pressures that resulted from the religious and cultural environment.
Measuring shared responses across subjects using intersubject correlation
Authors: Nastase Samuel A , Gazzola Valeria , Hasson Uri , Keysers Christian
Published: May 2019

Our capacity to jointly represent information about the world underpins our social experience. By leveraging one individual’s brain activity to model another’s, we can measure shared information across brains—even in dynamic, naturalistic scenarios where an explicit response model may be unobtainable. Introducing experimental manipulations allows us to measure, for example, shared responses between speakers and listeners or between perception and recall. In this tutorial, we develop the logic of intersubject correlation (ISC) analysis and discuss the family of neuroscientific questions that stem from this approach. We also extend this logic to spatially distributed response patterns and functional network estimation. We provide a thorough and accessible treatment of methodological considerations specific to ISC analysis and outline best practices.
The TGFβ1 Receptor Antagonist GW788388 Reduces JNK Activation and Protects Against Acetaminophen Hepatotoxicity in Mice
Authors: McMillin Matthew , Grant Stephanie , Frampton Gabriel , Petrescu Anca D , Williams Elaina , Jefferson Brandi , DeMorrow Sharon
Published: May 2019

Acute liver failure is a serious consequence of acetaminophen (APAP)-induced hepatotoxic liver injury with high rates of morbidity and mortality. Transforming growth factor beta 1 (TGFβ1) is elevated during liver injury and influences hepatocyte senescence during APAP-induced hepatotoxicity. This study investigated TGFβ1 signaling in the context of inflammation, necrotic cell death, and oxidative stress during APAP-induced liver injury. Male C57Bl/6 mice were injected with 600 mg/kg APAP to generate liver injury in the presence or absence of the TGFβ receptor 1 inhibitor, GW788388, 1 h prior to APAP administration. Acetaminophen-induced liver injury was characterized using histological and biochemical measures. Transforming growth factor beta 1 expression and signal transduction were assessed using immunohistochemistry, Western blotting and ELISA assays. Hepatic necrosis, liver injury, cell proliferation, hepatic inflammation, and oxidative stress were assessed in all mice. Acetaminophen administration significantly induced necrosis and elevated serum transaminases compared with control mice. Transforming growth factor beta 1 staining was observed in and around areas of necrosis with phosphorylation of SMAD3 observed in hepatocytes neighboring necrotic areas in APAP-treated mice. Pretreatment with GW788388 prior to APAP administration in mice reduced hepatocyte cell death and stimulated regeneration. Phosphorylation of SMAD3 was reduced in APAP mice pretreated with GW788388 and this correlated with reduced hepatic cytokine production and oxidative stress. These results support that TGFβ1 signaling plays a significant role in APAP-induced liver injury by influencing necrotic cell death, inflammation, oxidative stress, and hepatocyte regeneration. In conclusion, targeting TGFβ1 or downstream signaling may be a possible therapeutic target for the management of APAP-induced liver injury.
Aneugen Molecular Mechanism Assay: Proof-of-Concept With 27 Reference Chemicals
Authors: Bernacki Derek T , Bryce Steven M , Bemis Jeffrey C , Dertinger Stephen D
Published: May 2019

A tiered bioassay and data analysis scheme is described for elucidating the most common molecular targets responsible for chemical-induced in vitro aneugenicity: tubulin destabilization, tubulin stabilization, and inhibition of mitotic kinase(s). To evaluate this strategy, TK6 cells were first exposed to each of 27 presumed aneugens over a range of concentrations. After 4 and 24 h of treatment, γH2AX, p53, phospho-histone H3 (p-H3), and polyploidization biomarkers were evaluated using the MultiFlow DNA Damage Assay Kit. The assay identified 27 of 27 chemicals as genotoxic, with 25 exhibiting aneugenic signatures, 1 aneugenic and clastogenic, and 1 clastogenic. Subsequently, a newly described follow-up assay was employed to investigate the aneugenic agents’ molecular targets. For these experiments, TK6 cells were exposed to each of 26 chemicals in the presence of 488 Taxol. After 4 h, cells were lysed and the liberated nuclei and mitotic chromosomes were stained with a nucleic acid dye and labeled with fluorescent antibodies against p-H3 and Ki-67. Flow cytometric analyses revealed that alterations to 488 Taxol-associated fluorescence were only observed with tubulin binders—increases in the case of tubulin stabilizers, decreases with destabilizers. Mitotic kinase inhibitors with known Aurora kinase B inhibiting activity were the only aneugens that dramatically decreased the ratio of p-H3-positive to Ki-67-positive nuclei. Unsupervised hierarchical clustering based on 488 Taxol fluorescence and p-H3: Ki-67 ratios clearly distinguished compounds with these disparate molecular mechanisms. Furthermore, a classification algorithm based on an artificial neural network was found to effectively predict molecular target, as leave-one-out cross-validation resulted in 25/26 agreement with a priori expectations. These results are encouraging, as they suggest that an adequate number of training set chemicals, in conjunction with a machine learning algorithm based on 488 Taxol, p-H3, and Ki-67 responses, can reliably elucidate the most commonly encountered aneugenic molecular targets.
Cytomegalovirus distribution and evolution in hominines
Authors: Murthy Sripriya , O’Brien Kathryn , Agbor Anthony , Angedakin Samuel , Arandjelovic Mimi , Ayimisin Emmanuel Ayuk , Bailey Emma , Bergl Richard A , Brazzola Gregory , Dieguez Paula , Eno-Nku Manasseh , Eshuis Henk , Fruth Barbara , Gillespie Thomas R , Ginath Yisa , Gray Maryke , Herbinger Ilka , Jones Sorrel , Kehoe Laura , Kühl Hjalmar , Kujirakwinja Deo , Lee Kevin , Madinda Nadège F , Mitamba Guillain , Muhindo Emmanuel , Nishuli Radar , Ormsby Lucy J , Petrzelkova Klara J , Plumptre Andrew J , Robbins Martha M , Sommer Volker , Ter Heegde Martijn , Todd Angelique , Tokunda Raymond , Wessling Erin , Jarvis Michael A , Leendertz Fabian H , Ehlers Bernhard , Calvignac-Spencer Sébastien
Published: May 2019

Herpesviruses are thought to have evolved in very close association with their hosts. This is notably the case for cytomegaloviruses (CMVs; genus Cytomegalovirus) infecting primates, which exhibit a strong signal of co-divergence with their hosts. Some herpesviruses are however known to have crossed species barriers. Based on a limited sampling of CMV diversity in the hominine (African great ape and human) lineage, we hypothesized that chimpanzees and gorillas might have mutually exchanged CMVs in the past. Here, we performed a comprehensive molecular screening of all 9 African great ape species/subspecies, using 675 fecal samples collected from wild animals. We identified CMVs in eight species/subspecies, notably generating the first CMV sequences from bonobos. We used this extended dataset to test competing hypotheses with various degrees of co-divergence/number of host switches while simultaneously estimating the dates of these events in a Bayesian framework. The model best supported by the data involved the transmission of a gorilla CMV to the panine (chimpanzee and bonobo) lineage and the transmission of a panine CMV to the gorilla lineage prior to the divergence of chimpanzees and bonobos, more than 800,000 years ago. Panine CMVs then co-diverged with their hosts. These results add to a growing body of evidence suggesting that viruses with a double-stranded DNA genome (including other herpesviruses, adenoviruses, and papillomaviruses) often jumped between hominine lineages over the last few million years.
VON HIPPEL–LINDAU DISEASE
Authors: Aronow Mary E. , Wiley Henry E. , Gaudric Alain , Krivosic Valerie , Gorin Michael B. , Shields Carol L. , Shields Jerry A. , Jonasch Eric W. , Singh Arun D. , Chew Emily Y.
Published: May 2019

Purpose:

To provide an update summarizing the biologic pathways governing von Hippel–Lindau (VHL) disease pathogenesis and to provide an overview of systemic manifestations as well as screening recommendations.

Methods:

A PubMed search of the English language literature was reviewed using the following search terms: von Hippel–Lindau, von Hippel–Lindau disease, and VHL. Of 6,696 publications, the most current and pertinent information related to the pathogenesis and systemic aspects of VHL disease were included in this review.

Results:

von Hippel–Lindau disease is one of the most frequently occurring multisystem familial cancer syndromes. The disease results from germline mutation in the VHL tumor suppressor gene on the short arm of chromosome 3. Mutation in the VHL gene affects multiple cellular processes including transcriptional regulation, extracellular matrix formation, apoptosis, and, in particular, the cellular adaptive response to hypoxia. As a result, there is widespread development of vascular tumors affecting the retina, brain, and spine, as well as a spectrum of benign and malignant tumors and/or cysts in visceral organs.

Conclusion:

The ophthalmologist plays a key role in VHL disease diagnosis, as retinal hemangioblastoma is frequently the first disease manifestation. Screening guidelines for individuals with known VHL disease, and those at risk of VHL disease, help to ensure early detection of potentially vision-threatening and life-threatening disease.
Stability and Sterility of Extemporaneously Prepared Nonpreserved Cefazolin, Ceftazidime, Vancomycin, Amphotericin B, and Methylprednisolone Eye Drops
Authors: Ratprasatporn Nitee , Wittayalertpanya Supeecha , Khemsri Wondee , Chatsuwan Tanittha , Chongpison Yuda , Chamsai Tasanee , Wattanakijkarn Mayura , Chansangpetch Sunee
Published: May 2019

Purpose:

To determine in-use stability and sterility of fortified cefazolin, ceftazidime, vancomycin, amphotericin B, and methylprednisolone eye drops in a simulated inpatient setting with and without a mobile refrigerated container (MR).

Methods:

Each drug was prepared and divided into 4 groups: 1) simulated patient use with the MR group: stored at 4°C and kept in the MR during drug administration, 2) simulated patient use without the MR (NoMR) group: stored at 4°C and no MR, 3) refrigerated control group: stored at 4°C, and 4) room temperature control group: stored at room temperature. Stability and sterility data were evaluated at days 0, 4, 7, 14, 21, and 28. Linear mixed-effects model and survival analysis were performed.

Results:

Median time to 10% loss of concentration for in-use medications (MR/NoMR groups) was >28/27.9, 22.2/22.2, 19.4/19.4, 10.18/<4, and >28/>28 days for cefazolin, ceftazidime, vancomycin, amphotericin B, and methylprednisolone, respectively. There was no significant difference in the predicted concentration loss per day among all groups for vancomycin and methylprednisolone (all P > 0.05). For the other study medications, all room temperature control groups, the cefazolin NoMR group, and the ceftazidime NoMR group had significantly greater predicted concentration loss per day compared with the refrigerated control groups (all P ≤ 0.02). Culture results were negative for all drugs throughout the study.

Conclusions:

The NoMR group showed that the drug significantly degraded rapidly for cefazolin, ceftazidime, and amphotericin B. Implementation of MR could decrease the predicted loss of concentration per day for cefazolin and ceftazidime. In vitro antimicrobial activity and sterility were retained for 28 days.
The Challenge of Autoimmune Pancreatitis
Authors: Pagliari Danilo , Cianci Rossella , Rigante Donato
Published: May 2019

Autoimmune pancreatitis (AIP) is a rare disorder characterized by prompt clinical response to corticosteroids. Lost tolerance to a variety of pancreatic antigens and subsequent development of autoantibodies are presumably involved in the initiation of AIP. Even pediatric patients have been reported with features of AIP, and awareness of this disorder is increasing among different clinicians. The terms lymphoplasmacytic sclerosing pancreatitis and idiopathic duct-centric pancreatitis refer to the different histologic patterns of AIP, named type 1 and type 2, respectively. A combination of serologic, radiologic, and histologic investigations is needed to assess diagnosis of AIP and rule out neoplastic disorders. In addition, type 1 AIP can be distinguished by raised levels of serum immunoglobulin G4 and should be considered as part of systemic immunoglobulin G4–related disease. Conversely, type 2 AIP is frequently reported in younger patients and has less clear immune-mediated pathogenetic mechanisms. The natural history of pediatric AIP is obscure, and the diagnostic usefulness of different autoimmune abnormalities found in adults with AIP is limited for children. Tips to manage pediatric patients with AIP have been recently drafted through a set of recommendation statements. This review describes the current data about AIP and the pathogenic contribution of specific autoantibodies expressly in the pediatric population.
An Integrative Literature Review of Psychiatric Rapid Response Teams and Their Implementation for De-escalating Behavioral Crises in Nonpsychiatric Hospital Settings
Authors: Choi Kristen R. , Omery Anna K. , Watkins Anne Marie
Published: May 2019

OBJECTIVE

To synthesize articles exploring the implementation of psychiatric rapid response teams (RRTs) for behavioral crises in hospital settings.

BACKGROUND

Psychiatric/behavioral crises in nonpsychiatric hospital settings can lead to restraint use, staff injuries, and poor patient outcomes. Psychiatric RRTs may provide a solution, but they are a new, understudied intervention, and their implementation varies across institutions.

METHODS

A systematic, integrative literature review of nursing and biomedical literature yielded 7 articles about psychiatric RRTs. Data were extracted on RRT structure, processes, outcomes, and implementation.

RESULTS

Psychiatric RRTs were structured as a nurse-led, interdisciplinary intervention. When implemented using evidence-based models, they reduced security calls, restraint use, and staff injuries while moderately improving staff knowledge and self-efficacy. RRTs that included education, debriefing, and role modeling appeared to increase staff behavioral management skills and eventually reduced the need for RRTs.

CONCLUSIONS

Psychiatric RRTs have demonstrated promise in quality improvement projects for reducing adverse outcomes related to behavioral health in hospitals.
Nurse Manager Succession Planning
Authors: LaCross Erin , Hall Norma , Boerger Judith A.
Published: May 2019

OBJECTIVE

Perceived readiness to transition to nurse manager roles and demonstrated leadership behaviors were evaluated among participants in a nurse manager succession planning pilot cohort.

BACKGROUND

Equipping nurses within an organization with the leadership competencies to transition to the next role is essential as we face an impending nurse and nurse leader shortage.

METHODS

Quasi-experimental and correlational design methods were used to measure changes in readiness of nurses to enter nurse manager roles over a 90-day pilot.

RESULTS

Participants' perceived readiness to transition to nurse manager roles and demonstrated leadership behaviors increased between days 1 and 90 of the program. Statistically significant increases were attributed to their participation in the nurse manager succession planning pilot cohort.

CONCLUSIONS

This study contributes to the literature regarding nurse manager succession planning. Further research should be conducted so that succession planning for nurse managers becomes not only achievable but also expected.
Severe Trauma and Hemorrhage Leads to Platelet Dysfunction and Changes in Cyclic Nucleotides in The Rat
Authors: Darlington Daniel N. , Wu Xiaowu , Keesee Jeffrey D. , Cap Andrew P.
Published: May 2019

Introduction:

Rats subjected to polytrauma and hemorrhage develop a coagulopathy that is similar to acute coagulopathy of trauma in humans, and is associated with a rise in prothrombin time and a fall in clot strength. Because platelet aggregation accounts for a major proportion of clot strength, we set out to characterize the effects of polytrauma on platelet function.

Methods:

Sprague-Dawley rats were anesthetized with isoflurane. Polytrauma included laparotomy and damage to 10 cm of the small intestines, right and medial liver lobes, right leg skeletal muscle, femur fracture, and hemorrhage (40% of blood volume). No resuscitation was given. Blood samples were taken before and after trauma for the measurement of impedance electrode aggregometry, and intracellular levels of cyclic adenosine and guanosine monophosphate (cAMP, cGMP), inositol trisphosphate (IP3), and adenosine and guanosine triphosphates (ATP, GTP).

Results:

Polytrauma significantly increased the response of collagen (24%) and thrombin (12%) to stimulate platelet aggregation. However, aggregation to adenosine diphosphate (ADP) or arachidonic acid (AA) was significantly decreased at 2 (52% and 46%, respectively) and 4 h (45% and 39%). Polytrauma and hemorrhage also led to a significant early rise in cAMP (101 ± 11 to 202 ± 29 pg/mL per 1,000 platelets), mirrored by a decrease in cGMP (7.8 ± 0.9 to 0.6 ± 0.5). In addition, there was a late fall in ATP (8.1 ± 0.7 to 2.2 ± 0.6 ng/mL per 1,000 platelets) and GTP (1.5 ± 0.2 to 0.3 ± 0.1). IP3 rose initially, and then fell back to baseline.

Conclusions:

Polytrauma and hemorrhage led to a deficit in the platelet aggregation response to ADP and AA after trauma, likely due to the early rise in cAMP, and a later fall in energy substrates, and may explain the decrease in clot strength and impaired hemostasis observed after severe trauma.
Content tuning in the medial temporal lobe cortex: Voxels that perceive, retrieve
Authors: Schultz Heidrun , Tibon Roni , LaRocque Karen F. , Gagnon Stephanie A. , Wagner Anthony D. , Staresina Bernhard P.
Published: May 2019

How do we recall vivid details from our past based only on sparse cues? Research suggests that the phenomenological reinstatement of past experiences is accompanied by neural reinstatement of the original percept. This process critically depends on the medial temporal lobe (MTL). Within the MTL, perirhinal cortex (PRC) and parahippocampal cortex (PHC) are thought to support encoding and recall of objects and scenes, respectively, with the hippocampus (HC) serving as a content-independent hub. If the fidelity of recall indeed arises from neural reinstatement of perceptual activity, then successful recall should preferentially draw upon those neural populations within content-sensitive MTL cortex that are tuned to the same content during perception. We tested this hypothesis by having eighteen human participants undergo functional magnetic resonance imaging (fMRI) while they encoded and recalled objects and scenes paired with words. Critically, recall was cued with the words only. While HC distinguished successful from unsuccessful recall of both objects and scenes, PRC and PHC were preferentially engaged during successful vs. unsuccessful object and scene recall, respectively. Importantly, within PRC and PHC, this content-sensitive recall was predicted by content tuning during perception: Across PRC voxels, we observed a positive linear relationship between object tuning during perception and successful object recall, while across PHC voxels, we observed a positive linear relationship between scene tuning during perception and successful scene recall. Our results thus highlight content-based roles of MTL cortical regions for episodic memory and reveal a direct mapping between content-specific tuning during perception and successful recall.
Integrated Metabolomic and Transcriptomic Profiling Reveals Novel Activation-Induced Metabolic Networks in Human T cells
Authors: Hiemer S. , Jatav S. , Jussif J. , Alley J. , Lathwal S. , Piotrowski M. , Janiszewski J. , Kibbey R. , Alves T. , Dumlao D. , Jha A. , Bandukwala H.
Published: May 2019

The targeting of metabolic pathways is emerging as an exciting new approach for modulating immune cell function and polarization states. In this study, carbon tracing and systems biology approaches integrating metabolomic and transcriptomic profiling data were used to identify adaptations in human T cell metabolism important for fueling pro-inflammatory T cell function. Results of this study demonstrate that T cell receptor (TCR) stimulation leads to a significant increase in glucose and amino acid metabolism that trigger downstream biosynthetic processes. Specifically, increased expression of several enzymes such as CTPS1, IL4I1, and ASL results in the reprogramming of amino acid metabolism. Additionally, the strength of TCR signaling resulted in different metabolic enzymes utilized by T cells to facilitate similar biochemical endpoints. Furthermore, this study shows that cyclosporine represses the pathways involved in amino acid and glucose metabolism, providing novel insights on the immunosuppressive mechanisms of this drug. To explore the implications of the findings of this study in clinical settings, conventional immunosuppressants were tested in combination with drugs that target metabolic pathways. Results showed that such combinations increased efficacy of conventional immunosuppressants. Overall, the results of this study provide a comprehensive resource for identifying metabolic targets for novel combinatorial regimens in the treatment of intractable immune diseases.
Structural basis for ligand-induced inactivation of protein tyrosine receptor type Z (PTPRZ): Physiological relevance of head-to-toe RPTP dimerization
Authors: Fujikawa Akihiro , Sugawara Hajime , Tanga Naomi , Ishii Kentaro , Kuboyama Kazuya , Uchiyama Susumu , Suzuki Ryoko , Noda Masaharu
Published: May 2019

Protein tyrosine phosphatase receptor type Z (PTPRZ) has two receptor isoforms (PTPRZ-A and -B) containing tandem PTP-D1 and -D2 domains intracellularly, with only D1 being active. Pleiotrophin (PTN) binding to the extracellular region of PTPRZ leads to the inactivation of PTPase, thereby inducing oligodendrocyte precursor cell (OPC) differentiation and myelination in the CNS. However, the mechanisms responsible for the ligand-induced inactivation of PTPRZ remain unclear. We herein revealed that the crystal structure of the intracellular region of PTPRZ (PTPRZ-ICR) showed the “head-to-toe”-type dimer conformation, with D2 masking the catalytic site of D1. Mass spectrometry (MS) revealed that PTPRZ-ICR proteins remained in monomer-dimer equilibrium in aqueous solution, and a substrate-derived inhibitory peptide or competitive inhibitor (SCB4380) specifically bound to the monomer form in a 1:1 stoichiometric ratio, supporting the “head-to-toe dimerization” model for inactivation. A D2 deletion (ΔD2) or dimer interface mutation (DDKK) disrupted dimer formation, while the binding of SCB4380 was maintained. Similar to wild-type PTPRZ-B, monomer-biased PTPRZ-B-ΔD2 and PTPRZ-B-DDKK mutants efficiently dephosphorylated p190RhoGAP at Tyr-1105 when co-expressed in BHK-21 cells. The catalytic activities of these mutants were not suppressed by a treatment with PTN, but were inhibited by the cell-permeable PTPase inhibitor NAZ2329. The PTN treatment did not enhance OPC differentiation in primary cultured glial cells prepared from ΔD2 or catalytically-inactive CS mutant knock-in mice. Our results indicate that PTN-induced PTPRZ inactivation is attained by dimer formation of the intracellular tandem PTP domains in the head-to-toe configuration, which is physiologically relevant to the control of OPC differentiation in vivo.