MRX protects fork integrity at protein–DNA barriers,and its absence causes checkpoint activation dependent on chromatin context

To address how eukaryotic replication forks respond to fork stalling caused by strong non-covalent protein–DNA barriers, we engineered the controllable Fob-block system in Saccharomyces cerevisiae. This system allows us to strongly induce and control replication fork barriers (RFB) at their natural location within the rDNA. We discover a pivotal role for the MRX (Mre11, Rad50, Xrs2) complex for fork integrity at RFBs, which differs from its acknowledged function in double-strand break processing. Consequently, in the absence of the MRX complex, single-stranded DNA (ssDNA) accumulates at the rDNA. Based on this, we propose a model where the MRX complex specifically protects stalled forks at protein–DNA barriers, and its absence leads to processing resulting in ssDNA. To our surprise, this ssDNA does not trigger a checkpoint response. Intriguingly, however, placing RFBs ectopically on chromosome VI provokes a strong Rad53 checkpoint activation in the absence of Mre11. We demonstrate that proper checkpoint signalling within the rDNA is restored on deletion of SIR2. This suggests the surprising and novel concept that chromatin is an important player in checkpoint signalling.     

Human palatal saliva: Adsorption behaviour and the role of low-molecular weight proteins

In situ ellipsometry was employed to study adsorption from human palatal saliva (HPalS) in terms of dependence on surface wettability and saliva concentration ( ? 1%). Adsorbed amounts, kinetics, and elutability with buffer and sodium dodecyl sulphate (SDS) were determined. The low-molecular weight protein content of bulk HPalS was also investigated using two-dimensional gel electrophoresis, and this revealed the presence of a large group of proteins < 100 kDa in size. Adsorption to pure (hydrophilic) and methylated (hydrophobized) silica surfaces revealed that the total adsorbed amounts were greater on hydrophobized silica. Below concentrations of 0.5 and 0.25% saliva, adsorption was concentration dependent on hydrophobized and hydrophilic surfaces, respectively. The initial adsorption ( ? 30 min) was faster on hydrophobized surfaces. Addition of SDS removed more material than buffer rinsing on both surfaces. Analysis of the adsorption kinetics indicated that the presence of low-molecular weight proteins plays a role in adsorption from HPalS.     

Heterometallic [AgFe3S4] ferredoxin variants: synthesis, characterization, and the first crystal structure of an engineered heterometallic iron–sulfur protein

Heterometallic [AgFe₃S₄] iron–sulfur clusters assembled in wild-type Pyrococcus furiosus ferredoxin and two variants, D14C and D14H, are characterized. The crystal structure of the [AgFe₃S₄] D14C variant shows that the silver(I) ion is indeed part of the cluster and is coordinated to the thiolate group of residue 14. Cyclic voltammetry shows one redox pair with a reduction potential of +220 mV versus the standard hydrogen electrode which is assigned to the [AgFe₃S₄]^2+/+ couple. The oxidized form of the [AgFe₃S₄] D14C variant is stable in the presence of dioxygen, whereas the oxidized forms of the [AgFe₃S₄] wild type and D14H variants convert to the [Fe₃S₄] ferredoxin form. The monovalent d ¹⁰ silver(I) ion stabilizes the [Fe₃S₄]^+/0 cluster fragment, as opposed to divalent d ¹⁰ metal ions, resulting in more than 0.4 V difference in reduction potentials between the silver(I) and, e.g., zinc(II) heterometallic [MFe₃S₄] ferredoxins. The trend in reduction potentials for the variants containing the [AgFe₃S₄] cluster is wild type ≤ D14C < D14H and shows the same trend as reported for the variants containing the [Fe₃S₄] cluster, but is different from the D14C < D14H < wild type trend reported for the [Fe₄S₄] ferredoxin. The similarity in the reduction potential trend for the variants containing the heterometallic [AgFe₃S₄] cluster and the [Fe₃S₄] cluster can be rationalized in terms of the electrostatic influence of the residue 14 side chains, rather than the dissociation constant of this residue, as is the case for [Fe₄S₄] ferredoxins. The trends in reduction potentials are in line with there being no electronic coupling between the silver(I) ion and the Fe₃S₄ fragment.     

Studies on Respiratory Enzymes in Rice Kernel

Rice embryo peroxidase 556 was purified to the extent as indicated by the absorbance ratio, RZ greater than 4.0. The enzyme was found to be major basic component among isoenzymes of rice embryo. The preparation was homogeneous as examined by sedimentation analysis, and the sedimentation coefficient, s°_20,w, was 3.76 S. The prosthetic group of the enzyme was identified as protohematin and its content was 1.36%. The minimum molecular weight was calculated to be 46,700. From the typical spectra of ligand-enzyme compounds, peroxidase 556 was found to react with carbon monoxide, cyanide, fluoride, and azide. However, at neutral pH, neither fluoride nor azide reacted with the enzyme. The high affinity of the enzyme to ammonia was one of the most remarkable characteristics of the enzyme. The hydrogen peroxide compounds I and II have been observed in the enzymic reaction, and therefore rice embryo peroxidase 556 is also concluded to follow the common reaction mechanism of plant peroxidases. Overall results show the close resemblance of rice embryo peroxidase 556 with wheat germ peroxidase 556 and hemoprotein 550.     

Impact of Robotic Assistance on Precision of Vitreoretinal Surgical Procedures

Purpose

To elucidate the merits of robotic application for vitreoretinal maneuver in comparison to conventional manual performance using an in-vitro eye model constructed for the present study.

Methods

Capability to accurately approach the target on the fundus, to stabilize the manipulator tip just above the fundus, and to perceive the contact of the manipulator tip with the fundus were tested. The accuracies were compared between the robotic and manual control, as well as between ophthalmologists and engineering students.

Results

In case of manual control, ophthalmologists were superior to engineering students in all the 3 test procedures. Robotic assistance significantly improved accuracy of all the test procedures performed by engineering students. For the ophthalmologists including a specialist of vitreoretinal surgery, robotic assistance enhanced the accuracy in the stabilization of manipulator tip (from 90.9 µm to 14.9 µm, P = 0.0006) and the perception of contact with the fundus (from 20.0 mN to 7.84 mN, P = 0.046), while robotic assistance did not improve pointing accuracy.

Conclusions

It was confirmed that telerobotic assistance has a potential to significantly improve precision in vitreoretinal procedures in both experienced and inexperienced hands.     

Storage Temperature Alters the Expression of Differentiation-Related Genes in Cultured Oral Keratinocytes

Purpose

Storage of cultured human oral keratinocytes (HOK) allows for transportation of cultured transplants to eye clinics worldwide. In a previous study, one-week storage of cultured HOK was found to be superior with regard to viability and morphology at 12°C compared to 4°C and 37°C. To understand more of how storage temperature affects cell phenotype, gene expression of HOK before and after storage at 4°C, 12°C, and 37°C was assessed.

Materials and Methods

Cultured HOK were stored in HEPES- and sodium bicarbonate-buffered Minimum Essential Medium at 4°C, 12°C, and 37°C for one week. Total RNA was isolated and the gene expression profile was determined using DNA microarrays and analyzed with Partek Genomics Suite software and Ingenuity Pathway Analysis. Differentially expressed genes (fold change > 1.5 and P < 0.05) were identified by one-way ANOVA. Key genes were validated using qPCR.

Results

Gene expression of cultures stored at 4°C and 12°C clustered close to the unstored control cultures. Cultures stored at 37°C displayed substantial change in gene expression compared to the other groups. In comparison with 12°C, 2,981 genes were differentially expressed at 37°C. In contrast, only 67 genes were differentially expressed between the unstored control and the cells stored at 12°C. The 12°C and 37°C culture groups differed most significantly with regard to the expression of differentiation markers. The Hedgehog signaling pathway was significantly downregulated at 37°C compared to 12°C.

Conclusion

HOK cultures stored at 37°C showed considerably larger changes in gene expression compared to unstored cells than cultured HOK stored at 4°C and 12°C. The changes observed at 37°C consisted of differentiation of the cells towards a squamous epithelium-specific phenotype. Storing cultured ocular surface transplants at 37°C is therefore not recommended. This is particularly interesting as 37°C is the standard incubation temperature used for cell culture.