The proteome microenvironment determines the protective effect of preconditioning in cisplatin-induced acute kidney injury

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Contents Volume 32 No. 1 (2000) Section One: International Urology and Nephrology

Table of Contents

Contents Volume 32 No. 1 (2000) Section One: International Urology and Nephrology     

A proposed unified interphase nucleus chromosome structure: Preliminary preponderance of evidence

Cryoelectron tomography of the cell nucleus using scanning transmission electron microscopy and deconvolution processing technology has highlighted a large-scale, 100- to 300-nm interphase chromosome structure, which is present throughout the nucleus. This study further documents and analyzes these chromosome structures. The paper is divided into four parts: 1) evidence (preliminary) for a unified interphase chromosome structure; 2) a proposed unified interphase chromosome architecture; 3) organization as chromosome territories (e.g., fitting the 46 human chromosomes into a 10-μm-diameter nucleus); and 4) structure unification into a polytene chromosome architecture and lampbrush chromosomes. Finally, the paper concludes with a living light microscopy cell study showing that the G1 nucleus contains very similar structures throughout. The main finding is that this chromosome structure appears to coil the 11-nm nucleosome fiber into a defined hollow structure, analogous to a Slinky helical spring [https://en.wikipedia.org/wiki/Slinky; motif used in Bowerman et al., eLife 10, e65587 (2021)]. This Slinky architecture can be used to build chromosome territories, extended to the polytene chromosome structure, as well as to the structure of lampbrush chromosomes.

A recent publication introduced iterative deconvolution for scanning transmission electron microscopy (TEM) tomograms of cryopreserved cellular structures (ref. 1 and references therein). Micron-thick areas of the vitrified cells were accessible without prior cryosectioning or lamella preparation. The deconvolution computation simplified interpretation of the tomograms by substantially filling the missing wedges of information that result from incomplete tilts. The effect was a substantial improvement in resolution along the depth (Z) direction. This technology made it possible to assess a tomogram from an area of the nucleus intact, in which large-scale interphase chromosome structures were noted (1).Here, the chromosome structures observed in these nuclear tomograms are further documented and analyzed. This paper is divided into four parts. The first part presents the evidence, preliminary but compelling, for a unified interphase chromosome structure. The second part presents the proposed unified interphase chromosome architecture. The third part shows that this interphase chromosome structure could be further organized as chromosome territories: for example, by fitting the 46 human chromosomes into a 10-μm-diameter nucleus. The fourth part unifies this structure into a polytene chromosome architecture and lampbrush chromosomes. The paper concludes with a living light microscopy cell study showing that the G1 nucleus has very similar structures throughout this organelle.The interphase nucleus encloses the genomic DNA, as well as the machinery for regulation of gene expression, RNA synthesis, and DNA replication (2). DNA is packaged into chromatin, the in vivo structure of which remains unclear. While mitotic chromosomes are highly condensed, interphase chromosomes decondense but remain in distinct territories with little overlap. Interphase chromatin is organized in a number of ways, including immutable gene-rich and -poor domains in the primary sequence and expression-promoting or -suppressing regions that may vary during the cell cycle or reflect cell differentiation (2). A classic distinction is drawn between euchromatin and heterochromatin, with the former more “open” and prone to expression, while the latter is more “closed” and prone to silencing (but see ref. 3). However, different methods, such as fluorescence and electron microscopy (EM), or posttranslational histone modifications, are sensitive to different parameters and do not necessarily agree in their identification.The predominant model to describe the path of the DNA strand in the interphase nucleus is the constrained random walk (4) or fractal globule (5, 6). At prophase, the dispersed polymers must recondense without entangling. During mitosis, the space-filling interphase chromatin condenses into a compact micrometer-sized structure. The degree of order in these structures remains undefined.The double-stranded DNA polymer itself, which in isolation appears as a semiflexible, right-hand helix 2 nm in diameter, winds tightly around core histones to form nucleosomes. Each nucleosome has a DNA footprint of 146 base pairs and a geometric diameter of ∼11 nm (7–9). Nucleosomes appear as beads on a string, but the density and spacing of nucleosomes along the DNA sequence may be highly variable (10). In the next stage, the nucleosomes are supposed to coil up into a 30-nm filament, possibly as a tight solenoid or alternatively with a zig-zag structure (11, 12). Today, the 30-nm filament is largely considered an artifact (13, 14). It has been observed in vitro, in isolated or ruptured nuclei, and in cases of deliberate manipulation of divalent cation concentration, but not in intact nuclei (13–15).Current insights into chromatin structure arise primarily from methods based on sequencing. With a number of significant variations, chromatin is cross-linked, cleaved, captured, and sequenced in order to determine which sequences lie in close proximity (5, 16). These methods have revealed a genetic structure of chromosome territories at the largest scale, active and inactive compartments at the multimega base level, followed by topologically associated domains (also known as TADs) whose regulation is controlled concomitantly even if they appear to be distant in sequence (16, 17). An overall, three-dimensional (3D) spatial map of the genome can be generated from the proximity constraints. Extension of the methods to analysis of individual cells revealed a strong heterogeneity, however, making it difficult to connect proximity data to local structure.Microscopy offers the most direct observations of structure, but specimen preparation may be disruptive. Classic EM requires fixation, followed by solvent-based dehydration and impregnation with a hardening polymer. Heavy metal salts are added to generate image contrast based on electron scattering; the indirect nature makes it difficult to interpret apparent density in terms of molecular composition (18). This limitation was circumvented by electron spectroscopic imaging, which distinguishes protein from nucleic acid on the basis of nitrogen and phosphorus concentrations (19). A recent advance used a DNA-binding dye to induce a localized polymerization of diaminobenzidine, which in turn binds an osmium stain (15). A modest density difference between euchromatin and heterochromatin was found, but no evidence was seen for long-range order (15). Fluorescence microscopy has made great advances with the introduction of superresolution methods. The combination with in situ hybridization permits even a degree of sequencing in situ. Still, long exposures and biochemical manipulations require strong cross-linking, which necessarily influences local structure. Cryoelectron tomography offers the most direct and pristine view of cellular structure, including chromatin, but conventional TEM requires thin sectioning or lamella fabrication using the focused ion beam microscope.Cryoscanning transmission electron tomography is a new addition to the toolkit of cellular imaging techniques. The most obvious advantages in relation to conventional defocus phase-contrast TEM are the ability to accommodate thicker specimens and the quantitative contrast based on electron scattering cross-sections. As implemented for cellular tomography, it provides: 1) a unipolar optical transfer function with the specimen in focus, 2) a long depth of field, and most importantly, 3) strong contrast for low spatial frequencies (20). We have recently demonstrated the application of cryoscanning transmission electron tomography in combination with 3D iterative deconvolution processing to whole-cell tomography and obtained a view of the cell nucleus that revealed unexpected large-scale structures (1).Data Considerations and Their Complexity.The primary data for this paper have considerably different attributes, such as the close-spaced 3D pixels with subtle gray level differences and textures, requiring new ways to display its details and architecture. This is a common problem for various imaging technologies (e.g., cellular cryoelectron tomography and MRI). The usual methods to visualize 3D data, such as moving up and down in the Z-dimension through two-dimensional (2D) slices, do not adequately show 3D relationships. Therefore, we propose the extensive use of stereo with extensions to circumvent this problem. Evidence for the chromosome structure is presented primarily in 3D stereo movies of various kinds (Movie S1 and rocking angular stereo pairs A to C′ presented in Movies S2–S8). Visualization guidance and challenges for the stereo movies are also discussed in depth in SI Appendix.     

Haploidentical Hematopoietic Stem Cell Transplantation in Leukemia’s: Experience from a Cancer Center in India

There has been a surge in haploidentical hematopoietic stem cell transplantation (HSCT) in India recently. However, there is a paucity of data on haploidentical HSCT from India. The report is an analysis of data of haploidentical HSCT performed at our center. Analysis of patients with acute leukemia or chronic myeloid leukemia who underwent haploidentical HSCT during 2014–2019 was performed. The graft versus host disease (GVHD) prophylaxis was post-transplant Cyclophosphamide with Mycophenolate-mofetil and Cyclosporine. All patients were transfused peripheral blood stem cells from donors. Overall survival (OS) was calculated using the Kaplan–Meier method. Twenty-one patients underwent haploidentical HSCT. Fourteen-patients were males. The median age of patients was 15 years. Fludarabine with total body irradiation was the most common conditioning regimen (n = 15, 71.4%). The median duration for neutrophil and platelet engraftment was 14 days. Cumulative incidence of acute and chronic GVHD was 19%, and 38% respectively. The median follow-up was 26 months and the two-year OS was 38%. Twelve (57%) patients died during the study period, 8 patients (38%) died from transplant-related mortality (TRM), and 4 from disease relapse. Sepsis was the cause of death in six of the eight TRM. Nine out of 21 patients (42.8%) are leukemia-free on follow-up. Haploidentical HSCT is a promising modality of treatment in patients who have no suitable matched donors. Though the TRM remains high, good disease control was achieved in 42.8% of patients. Multi-drug resistant bacterial infection remains a challenge in performing haploidentical HSCT in developing countries.     

Harnessing hyperuricemia to atherosclerosis and understanding its mechanistic dependence

Atherosclerosis is regarded as the disease of the arterial vasculature. The main characteristics of atherosclerosis are the abnormal accumulation of lipids, increased inflammatory cells, matrix deposits, and proliferation of smooth muscle cells. Diabetes mellitus, obesity, and hyperlipidemia are the most studied risk factors of atherosclerosis. One least studied risk factor is the uric acid (UA), a high UA in circulation is interlinked with many pathological processes. Several epidemiological studies suggest elevated UA levels as an essential biomarker in the forecast of several cardiovascular diseases. Available evidence claims that UA upholds the atherosclerosis process via disturbing lipid metabolism, reducing the nitric oxide synthesis in endothelial cells, promoting the proliferation of vascular smooth muscle cells, and overwhelms inflammation. In endothelial dysfunction and coronary artery lesions, UA is considered as an independent predictor. The updated studies on the involvement of hyperuricemia in atherosclerosis prove that treatment with xanthine oxidase (XO) inhibitors not just benefits the treatment of hyperuricemia but also reduces the burden of atherosclerosis to a greater extent. In this review, we highlight how the hyperuricemia affects vascular integrity, causes atherosclerosis, and the mechanism of action of XO inhibitors on atherosclerosis.     

Green synthesis of titanium dioxide nanoparticles using Psidium guajava extract and its antibacterial and antioxidant properties

Objective:To determine the efficacies of antibacterial and antioxidant activities of aqueous leaf extract of Psidium guajava mediated biosynthesis of titanium dioxide nanoparticles(TiO_2,NPs).Methods:Synthesized TiO_2 NPs were tested by disc diffusion method against against human pathogenic bacteria.The total antioxidant activity and phenolic content(Folin—Ciocalteau method) of synthesized TiO_2 NTs and aqueous plant extract were determined.The scavenging radicals were estimated hv DPPH method.The synthesized TiO_2 NPs were characterized by XRD,FTIR.FESEM and EDX,Results:FTIR spectra of synthesized TiO_2 NPs exhibited prominent peaks at 3410 cm~(-1)(alkynes),1 578 cm~(-1).1 451 cm~(-1)(alkanes),and 1 123 cm~(-1)(C-O absorption).The morphological characterization of synthesized TiO_2 NPs was analysed by FESEM which showed spherical shape and clusters with an average size of 32.58 nm.The maximum zone of inhibition was observed in the synthesized TiO_2 NPs(20 μg/mL) against Staphylococcus aureus(25 mm) and Escherichia coli(23 mm).The synthesized TiO_2 NPs showed more antibacterial activity than the standard antibiotic disk,tetracycline which drastically reduces the chances for the development of antibiotics resistance of bacterial species.The plant aqueous extract and synthesized TiO_2NPs were found to possess maximum antioxidant activity when compared with ascorbic acid.The content of phenolic compounds(mg/g) in Leaf aqueous extract and synthesized TiO_2 NPs were found to be 85.4 and 18.3 mgTA/g,respectively.Conclusions:Green synthesized TiO_2 NPs provides a promising approach can satisfy the requirement of large-scale industrial production hearing the advantage of low—cost,eco—friendly and reproducible.     

Spectroscopic and Microscopic Characterisation of Parotid and Submandibular Ductal Sialoliths: A Comparative Preliminary Study

Proceedings of the National Academy of Sciences, India Section B: Biological Sciences - Sialoliths, the calcified structures that develop within the salivary gland parenchyma and its ductal system,...     

Cherubism Combined with Epilepsy,Mental Retardation and Gingival Fibromatosis (Ramon Syndrome): A Case Report

Cherubism is an inherited, autosomal dominant disorder that characteristically affects the jaws of children. The disease typically manifest as a bilateral swelling with associated submandibular lymph node enlargements and usually regresses as age advances. The disease is microscopically indistinguishable from other giant cell lesions and is essentially a clinical diagnosis. The association of cherubism with gingival fibromatosis, epilepsy, mental retardation, stunted growth, and hypertrichosis is referred as Ramon syndrome. We report a case of Ramon syndrome in an 8 year old girl.     

Plasma protein adsorption to surfaces grafted with dense homopolymer and copolymer brushes containing poly(N-isopropylacrylamide)

Growing polymer chains from surface initiators in principle allows much more dense polymer surface layers to be created than can be produced by grafting of whole (self-excluding) chains. We have utilized aqueous atom transfer radical polymerization to graft a series of cleavable hydrophilic poly(N-isopropylacrylamide) (PNIPAM) homopolymers and block copolymers of substituted acrylamides from polystyrene latex to give brushes of controlled MW and surface density. Average chain separations much less than their free solution radii of gyration have been achieved. Exposure to radiolabeled single proteins or to whole plasma and subsequent analysis by SDS-PAGE shows that PNIPAM brushes decrease protein adsorption relative to the latex surface or other substituted polyacrylamides. The PNIPAM brushes exhibit a second-order phase transition around 30 degrees C as reflected by a decrease in the hydrodynamic thickness of the brush at higher temperatures. Total plasma protein adsorption is increased at 40 degrees C compared to 20 degrees C but there is significant differential adsorption behavior among the proteins detected by gel-electrophoresis analysis.