Amiloride does not alter NaCl avoidance in Fischer-344 rats

Fischer-344 (F-344) rats differ from other common rat strains in that they fail to show any preference for NaCl at any concentration in two- bottle preference tests. Because 100 microM amiloride partially blocks the NaCl-evoked chorda tympani (CT) response in electrophysiological studies, we tested NaCl preference (0.068-0.273 M) in F-344 rats with and without 100 microM amiloride solution as the solvent. A third group was tested with unadulterated NaCl solutions following CT transection. Amiloride had no significant effect on the NaCl preference-aversion function, whereas CT transection significantly reduced NaCl avoidance. These results suggest that the amiloride-sensitive component of the NaCl response is not necessary for F-344 rats to display avoidance of NaCl, but the entire CT input is.      

Diaphragm adaptations in patients with COPD

Inspiratory muscle weakness in patients with COPD is of major clinical relevance. For instance, maximum inspiratory pressure generation is an independent determinant of survival in severe COPD. Traditionally, inspiratory muscle weakness has been ascribed to hyperinflation-induced diaphragm shortening. However, more recently, invasive evaluation of diaphragm contractile function, structure, and biochemistry demonstrated that cellular and molecular alterations occur, of which several can be considered pathologic of nature. Whereas the fiber type shift towards oxidative type I fibers in COPD diaphragm is regarded beneficial, rendering the overloaded diaphragm more resistant to fatigue, the reduction of diaphragm fiber force generation in vitro likely contributes to diaphragm weakness. The reduced diaphragm force generation at single fiber level is associated with loss of myosin content in these fibers. Moreover, the diaphragm in COPD is exposed to oxidative stress and sarcomeric injury. This review postulates that the oxidative stress and sarcomeric injury activate proteolytic machinery, leading to contractile protein wasting and, consequently, loss of force generating capacity of diaphragm fibers in patients with COPD. Interestingly, several of these presumed pathologic alterations are already present early in the course of the disease (GOLD I/II), although these patients appear not limited in their daily life activities. Treatment of diaphragm dysfunction in COPD is complex since its etiology is unclear, but recent findings indicate the ubiquitin-proteasome pathway as a prime target to attenuate diaphragm wasting in COPD.     

Determining the quality and complexity of next-generation sequencing data without a reference genome

We describe an open-source kPAL package that facilitates an alignment-free assessment of the quality and comparability of sequencing datasets by analyzing k-mer frequencies. We show that kPAL can detect technical artefacts such as high duplication rates, library chimeras, contamination and differences in library preparation protocols. kPAL also successfully captures the complexity and diversity of microbiomes and provides a powerful means to study changes in microbial communities. Together, these features make kPAL an attractive and broadly applicable tool to determine the quality and comparability of sequence libraries even in the absence of a reference sequence. kPAL is freely available at https://github.com/LUMC/kPAL.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0555-3) contains supplementary material, which is available to authorized users.     

Sensitization to heat by X-rays

1. Paramecium caudatum is sensitized to heat by sublethal dosages of x-rays. Thus if paramecia are irradiated, then exposed to a sublethal dosage of heat they are killed, but if the same heat exposure precedes the same dosage of radiations, they are not. 2. Sensitivity to both heat and x-rays is much greater in paramecia from the log growth phase than in those from the stationary phase of a culture. 3. Recovery from heat sensitization in animals from the stationary phase of a culture is slow, requiring several days. 4. Division is readily retarded and even temporarily inhibited by sublethal dosage of x-rays. Recovery of the division rate is fairly slow requiring several days. 5. Paramecia can be killed by a dosage of 1,200,000 r (of which about one-half reach the animal) units of x-radiation alone. Smaller dosages are not lethal if the paramecia are transferred to fresh medium immediately upon completion of irradiation. 6. The possibility of utilization of heat sensitization in treatment of malignant growths is discussed.     

The effect of ultraviolet light on the sodium and potassium composition of resting yeast cells

The Na⁺ and K⁺ content of non-metabolizing yeast cells was determined before and after monochromatic ultraviolet (UV) irradiation. UV facilitated the uptake of Na⁺ into and the loss of K⁺ from the cells (net ion flux); the effect is greatest for the shortest wavelength employed (239 mµ) and is partly dependent upon the presence of oxygen. The UV effect on net ion flux persists for at least 90 minutes during which tests were made and it occurs following dosages which are without measurable effect on colony formation. The UV effect on net ion flux is decreased by acidity and promoted by alkalinity. Addition of calcium ions in sufficient amount prevents the usual net ion flux changes observed in irradiated yeast. Increase in concentration gradient between the inside and the outside of the cell increases the net ion flux of irradiated yeast, Na⁺ uptake leading K⁺ loss in all cases. UV appears to act by disorganizing the constituents of the cell surface, permitting K⁺ to leave the cell in exchange for Na⁺. At low intensities of UV this ionic exchange approaches equivalence, but at higher intensities more Na⁺ is taken up than K⁺ is lost. Some evidence suggests that the Na⁺ in excess over that exchanged for K⁺ is adsorbed to charged groups produced by the photochemical effect of UV on the cell surface.     

Evidence for thermal reactions following exposure of Didinium to intermittent ultraviolet radiations

1. The nature of ultraviolet injury and its variation with the same dose given at different intensities and wave lengths have been investigated in the protozoan Didinium nasutum, using time to the fourth division as a measure of injury. 2. The injury has been found to consist of a "slowdown" of division rate, which always occurs, and a "stasis," usually at the second division after irradiation, which appears in varying degrees among more severely injured samples. 3. Injury was found to be almost independent of intensity at three wave lengths out of four studied over a wide range of intermediate and high intensities, but was found to rise sharply with lower intensity at all except the longest wave length. 4. Flashed UV of high intensity is much more effective than the same dose of continuous radiation at high intensity and shorter total time of treatment. It is also more effective than the same dose at low intensity and equal time of treatment, though only slightly so. 5. An increase of injury with rise of temperature and with increase of dark period clearly indicates that injury depends on thermochemical reactions following the absorption of UV in Didinium. 6. The most reasonable assumption is that a similar conclusion applies to other organisms as well, and that its general application may be useful in the investigation of UV effects on protoplasm.     

Increased photoreversal of ultraviolet injury by flashing light

1. Photoreversal of ultraviolet (UV) injury was studied in the ciliate protozoan Tetrahymena pyriformis (geleii) strain W, cultured in the absence of other living organisms. The division pattern of progeny of single animals was followed in hanging drop preparations. 2. A sublethal dose of 450 ergs/mm.² of monochromatic UV of wave length 2654 A produces a lag before the first division followed by a period of cessation of fission after the second division. This cessation sometimes lasts as long as 6 weeks, during which time the animals become smaller and rounder and more opaque. Organisms about to resume division increase in size and transparency; after a few divisions the animals regain their normal division rate. 3. The effect of UV ranging in intensity from 5 to 15 ergs/mm.²/sec. was found to obey the reciprocity law quite well for the UV effect on the division pattern of T. pyriformis. However, the same dose at lower and at higher intensities was less effective. 4. The effect of a dose of UV delivered at high intensity (19 ergs/mm.²/sec.) could be increased by flashing the light, indicating that the system became saturated in the continuous light. 5. A photoreversing dose of monochromatic blue light of wave length 4350 A was found to be more effective when delivered as continuous light at a low intensity, or as intermittent light at a high intensity, rather than as continuous light at the high intensity—indicating that a dark mechanism participates in photoreversal. 6. The time for the dark reaction was determined to be of the order of a few hundredths of a second in experiments in which different lengths of dark period were used while maintaining a constant light period of 0.0025 second. 7. For Colpidium colpoda the efficiency of a given dose of photoreversing light was increased by flashing the light. 8. The present experiments are interpreted in terms of data available in the literature.     

Surprising negative association between IgG1 allotype disparity and anti-adalimumab formation: a cohort study

Introduction

The human monoclonal antibody adalimumab is known to induce an anti-globulin response in some adalimumab-treated patients. Antibodies against adalimumab (AAA) are associated with non-response to treatment. Immunoglobulins, such as adalimumab, carry allotypes which represent slight differences in the amino acid sequences of the constant chains of an IgG molecule. Immunoglobulins with particular IgG (Gm) allotypes are racially distributed and could be immunogenic for individuals who do not express these allotypes. Therefore, we investigated whether a mismatch in IgG allotypes between adalimumab and IgG in adalimumab-treated patients is associated with the development of AAA.

Methods

This cohort study consisted of 250 adalimumab-treated rheumatoid arthritis (RA) patients. IgG allotypes were determined for adalimumab and for all patients. Anti-idiotype antibodies against adalimumab were measured with a regular radio immunoassay (RIA), and a newly developed bridging enzyme linked immunosorbent assay (ELISA) was used to measure anti-allotype antibodies against adalimumab. The association between AAA and the G1m3 and the G1m17 allotypes was determined. For differences between groups we used the independent or paired samples t-test, Mann-Whitney test or Chi square/Fisher's exact test as appropriate. To investigate the influence of confounders on the presence or absence of AAA a multiple logistic regression-analysis was used.

Results

Adalimumab carries the G1m17 allotype. No anti-allotype antibodies against adalimumab were detected. Thirty-nine out of 249 patients had anti-idiotype antibodies against adalimumab (16%). IgG allotypes of RA patients were associated with the frequency of AAA: patients homozygous for G1m17 had the highest frequency of AAA (41%), patients homozygous for G1m3 the lowest frequency (10%), and heterozygous patients' AAA frequency was 14% (P = 0.0001).

Conclusions

An allotype mismatch between adalimumab and IgG in adalimumab-treated patients did not lead to a higher frequency of AAA. On the contrary, patients who carried the same IgG allotype as present on the adalimumab IgG molecule, had the highest frequency of anti-adalimumab antibodies compared to patients whose IgG allotype differed from adalimumab. This suggests that the allotype of adalimumab may not be highly immunogenic. Furthermore, patients carrying the G1m17-allotype might be more prone to antibody responses.     

Exploiting the full power of temporal gene expression profiling through a new statistical test: Application to the analysis of muscular dystrophy data

Background  

The identification of biologically interesting genes in a temporal expression profiling dataset is challenging and complicated by high levels of experimental noise. Most statistical methods used in the literature do not fully exploit the temporal ordering in the dataset and are not suited to the case where temporal profiles are measured for a number of different biological conditions. We present a statistical test that makes explicit use of the temporal order in the data by fitting polynomial functions to the temporal profile of each gene and for each biological condition. A Hotelling T ²-statistic is derived to detect the genes for which the parameters of these polynomials are significantly different from each other.