Binding of the small-molecule kinase inhibitor ruxolitinib to membranes does not disturb membrane integrity

Ruxolitinib is a small-molecule protein kinase inhibitor, which is used as a therapeutic agent against several diseases. Due to its anti-inflammatory impact, ruxolitinib has also been considered recently for usage in the treatment of Covid-19. While the specific effects of ruxolitinib on Janus kinases (JAK) is comparatively well investigated, its (unspecific) impact on membranes has not been studied in detail so far. Therefore, we characterized the interaction of this drug with lipid membranes employing different biophysical approaches. Ruxolitinib incorporates into the glycerol region of lipid membranes causing an increase in disorder of the lipid chains. This binding, however, has only marginal influence on the structure and integrity of membranes as found by leakage and permeation assays.     

The structural and dynamic response of MAGI-1 PDZ1 with noncanonical domain boundaries to the binding of human papillomavirus E6

PDZ domains are protein interaction domains that are found in cytoplasmic proteins involved in signaling pathways and subcellular transport. Their roles in the control of cell growth, cell polarity, and cell adhesion in response to cell contact render this family of proteins targets during the development of cancer. Targeting of these network hubs by the oncoprotein E6 of “high-risk” human papillomaviruses (HPVs) serves to effect the efficient disruption of cellular processes. Using NMR, we have solved the three-dimensional solution structure of an extended construct of the second PDZ domain of MAGI-1 (MAGI-1 PDZ1) alone and bound to a peptide derived from the C-terminus of HPV16 E6, and we have characterized the changes in backbone dynamics and hydrogen bonding that occur upon binding. The binding event induces quenching of high-frequency motions in the C-terminal tail of the PDZ domain, which contacts the peptide upstream of the canonical X-[T/S]-X-[L/V] binding motif. Mutations designed in the C-terminal flanking region of the PDZ domain resulted in a significant decrease in binding affinity for E6 peptides. This detailed analysis supports the notion of a global response of the PDZ domain to the binding event, with effects propagated to distal sites, and reveals unexpected roles for the sequences flanking the canonical PDZ domain boundaries.     

Tolerance of forced air emergence by a fish with a broad vertical distribution, the rockpool blenny, Hypsoblennius gilberti (Blenniidae)

Many intertidal fishes, particularly among the Blenniidae and Cottidae, possess amphibious adaptations, including the ability to breathe in air and to avoid desiccation in terrestrial conditions. These traits are absent in subtidal species of blennies and cottids. Hypsoblennius gilberti, the rockpool blenny, is found in shallow rockpools in the mid to high intertidal areas of Southern California, and deeper to 18 m in the subtidal zone. This broad vertical distribution could indicate that this blenny is adapted for tidal air emergence, although H. gilberti has not been observed out of water in its natural habitat. H. gilberti does not emerge voluntarily from hypoxic sea water in the laboratory, but it easily withstands 3 h out of water. The aerial respiratory exchange ratio (CO2 released compared to O2 consumed) is 0.70, similar to that of amphibious intertidal fishes in air, indicating sufficient release of metabolically produced CO2 while emerged. There is no increase in aquatic respiration following emergence. However, unlike other amphibious fishes that maintain aerial oxygen consumption at a level similar to aquatic oxygen consumption, H. gilberti has an aerial oxygen consumption rate one-third that in water. H. gilberti can recover rapidly from terrestrial water loss, and shows no change in evaporative water loss rates at 93% and 77% relative humidities. The amphibious capabilities in H. gilberti, even if rarely used, permit survival in air during tidal emergence. These findings suggest that H. gilberti may demonstrate an intermediate condition between the amphibious species of intertidal fishes that regularly emerge from water, and the subtidal fishes that do not survive air emergence and are completely restricted to an aquatic habitat.     

THE EFFECT OF VALENCE OF IONS ON CELLULAR PERMEABILITY TO WATER

1. Permeability to water in unfertilized eggs of the sea urchin, Arbacia punctulata, was studied by measuring the rate of swelling in hypotonic dextrose solution. 2. Permeability is greatly affected by addition of electrolytes in low concentration. 3. A decrease in permeability to water was found with increasing valence of the cation, using a series of cobaltammine chlorides in which the valence of the cation ranged from 1 to 6. 4. Conversely, an increase in permeability to water was found with increasing valence of the anion, using two series of potassium salts in which the valence of the anion ranged from 1 to 4, and 1 to 3, respectively. 5. It is concluded that the effect of electrolytes on permeability to water depends chiefly on the sign and the number of charges on the ion, in the sense that positive ions decrease permeability to water, while negative ions increase permeability to water; and the effectiveness of the ion is greater the higher its valence. 6. Antagonism has been demonstrated between cations and anions in their effect on permeability, and the method employed permits quantitative study of such antagonism.     

Flexion and extension structural properties and strengths for male cervical spine segments

New vehicle safety standards are designed to limit the amount of neck tension and extension seen by out-of-position motor vehicle occupants during airbag deployments. The criteria used to assess airbag injury risk are currently based on volunteer data and animal studies due to a lack of bending tolerance data for the adult cervical spine. This study provides quantitative data on the flexion-extension bending properties and strength on the male cervical spine, and tests the hypothesis that the male is stronger than the female in pure bending. An additional objective is to determine if there are significant differences in stiffness and strength between the male upper and lower cervical spine. Pure-moment flexibility and failure testing was conducted on 41 male spinal segments (O-C2, C4-C5, C6-C7) in a pure-moment test frame and the results were compared with a previous study of females. Failures were conducted at approximately 90 N-m/s. In extension, the male upper cervical spine (O-C2) fails at a moment of 49.5 (s.d. 17.6)N-m and at an angle of 42.4 degrees (s.d. 8.0 degrees). In flexion, the mean moment at failure is 39.0 (s.d. 6.3 degrees) N-m and an angle of 58.7 degrees (s.d. 5.1 degrees). The difference in strength between flexion and extension is not statistically significant. The difference in the angles is statistically significant. The upper cervical spine was significantly stronger than the lower cervical spine in both flexion and extension. The male upper cervical spine was significantly stiffer than the female and significantly stronger than the female in flexion. Odontoid fractures were the most common injury produced in extension, suggesting a tensile mechanism due to tensile loads in the odontoid ligamentous complex.     

Survey of brown soft scale Coccus hesperidum L. parasitoids in southern California citrus

The parasitoid complex of brown soft scale, Coccus hesperidum L., a multivoltine soft scale, was determined in southern California citrus over the period February 2004–March 2006. The survey was conducted by placing brown soft scale-infested yucca leaves in the canopy of citrus trees and subsequently rearing individually isolated parasitized scales in the laboratory. A total of 14 species parasitized brown soft scale in the field, the most abundant ones belonging to the genus Metaphycus Mercet (75%). The most abundant parasitoid species was Metaphycus angustifrons Compere (38% parasitism), and this is a new record of establishment for this species in California. Coccophagus species accounted for only 11% parasitism. There were important spatio-temporal differences across the parasitoid complex survey locations. We also found that the five most abundant encyrtid parasitoid species showed preferences for scales of different sizes. Our results have implications for biological control of citricola scale, Coccus pseudomagnoliarum (Kuwana), an important pest of citrus in the San Joaquin Valley of central California. Notably, this species is nearly absent in southern California. Brown soft scale is considered to be an alternate host for parasitoids of citricola scale, a univoltine soft scale, at times when the latter species is unavailable for parasitism.     

Expression and localization of trefoil factor family genes in rat submandibular glands

The trefoil factor (TFF) family, which comprises TFF1, TFF2 and TFF3, plays an essential role in epithelial regeneration within the gastrointestinal tract. All three TFFs are present in human saliva; TFF3 is the predominant trefoil peptide. Little is known about the expression and tissue distribution of TFFs in rats, which are commonly used as a model system for human studies. We investigated the localization of the TFF genes that encode secretory peptides in rat submandibular glands (SMG). All three TFFs were expressed in rat SMG, although their location varied. Substantial amounts of TFF1 were detected only in the cytoplasm of epithelial cells in the SMG granular convoluted tubules (GCT), while TFF2 and TFF3 were widely distributed in the cytoplasm of epithelial cells of intercalated ducts (ID), striated ducts (SD) and interlobular ducts (ILD). The three TFFs also were detected especially in the lumens of the SD and ILD. Semi-quantitative RT-PCR and in situ hybridization experiments confirmed TFF1, TFF2 and TFF3 mRNA expressions in the SMG. Greater expression of TFF peptides and mRNA was observed in male rats than in females. The broad expression of TFFs in rat SMG cells and lumens suggests that TFFs function in this organ by their secretion into the duct lumens. We also found differences in TFF expression profiles between rat and human SMG; therefore, caution should be exercised when using rats as a model for human TFF studies.     

Spatial and temporal variation in pollinator community structure relative to a woodland–almond plantation edge

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tigaR: integrative significance analysis of temporal differential gene expression induced by genomic abnormalities

Background

To determine which changes in the host cell genome are crucial for cervical carcinogenesis, a longitudinal in vitro model system of HPV-transformed keratinocytes was profiled in a genome-wide manner. Four cell lines affected with either HPV16 or HPV18 were assayed at 8 sequential time points for gene expression (mRNA) and gene copy number (DNA) using high-resolution microarrays. Available methods for temporal differential expression analysis are not designed for integrative genomic studies.

Results

Here, we present a method that allows for the identification of differential gene expression associated with DNA copy number changes over time. The temporal variation in gene expression is described by a generalized linear mixed model employing low-rank thin-plate splines. Model parameters are estimated with an empirical Bayes procedure, which exploits integrated nested Laplace approximation for fast computation. Iteratively, posteriors of hyperparameters and model parameters are estimated. The empirical Bayes procedure shrinks multiple dispersion-related parameters. Shrinkage leads to more stable estimates of the model parameters, better control of false positives and improvement of reproducibility. In addition, to make estimates of the DNA copy number more stable, model parameters are also estimated in a multivariate way using triplets of features, imposing a spatial prior for the copy number effect.

Conclusion

With the proposed method for analysis of time-course multilevel molecular data, more profound insight may be gained through the identification of temporal differential expression induced by DNA copy number abnormalities. In particular, in the analysis of an integrative oncogenomics study with a time-course set-up our method finds genes previously reported to be involved in cervical carcinogenesis. Furthermore, the proposed method yields improvements in sensitivity, specificity and reproducibility compared to existing methods. Finally, the proposed method is able to handle count (RNAseq) data from time course experiments as is shown on a real data set.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-327) contains supplementary material, which is available to authorized users.     

Combination Effects of Peramivir and Favipiravir against Oseltamivir-Resistant 2009 Pandemic Influenza A(H1N1) Infection in Mice

Antiviral drugs are being used for therapeutic purposes against influenza illness in humans. However, antiviral-resistant variants often nullify the effectiveness of antivirals. Combined medications, as seen in the treatment of cancers and other infectious diseases, have been suggested as an option for the control of antiviral-resistant influenza viruses. Here, we evaluated the therapeutic value of combination therapy against oseltamivir-resistant 2009 pandemic influenza H1N1 virus infection in DBA/2 mice. Mice were treated for five days with favipiravir and peramivir starting 4 hours after lethal challenge. Compared with either monotherapy, combination therapy saved more mice from viral lethality and resulted in increased antiviral efficacy in the lungs of infected mice. Furthermore, the synergism between the two antivirals, which was consistent with the survival outcomes of combination therapy, indicated that favipiravir could serve as a critical agent of combination therapy for the control of oseltamivir-resistant strains. Our results provide new insight into the feasibility of favipiravir in combination therapy against oseltamivir-resistant influenza virus infection.