Calcium ions function as a booster of chromosome condensation

Effect of Modified Bioceramic Mineral Trioxide Aggregate Cement with Mesoporous Nanoparticles on Human Gingival Fibroblasts

The ion doping of mesoporous silica nanoparticles (MSNs) has played an important role in revolutionizing several materials applied in medicine and dentistry by enhancing their antibacterial and regenerative properties. Mineral trioxide aggregate (MTA) is a dental material widely used in vital pulp therapies with high success rates. The aim of this study was to investigate the effect of the modification of MTA with cerium (Ce)- or calcium (Ca)-doped MSNs on the biological behavior of human gingival fibroblasts (hGFs). MSNs were synthesized via sol-gel, doped with Ce and Ca ions, and mixed with MTA at three ratios each. Powder specimens were characterized using Fourier-transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), and scanning electron microscopy (SEM). Biocompatibility was evaluated using a 3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide (MTT) assay following hGFs' incubation in serial dilutions of material eluates. Antioxidant status was evaluated using Cayman's antioxidant assay after incubating hGFs with material disc specimens, and cell attachment following dehydration fixation was observed through SEM. Material characterization confirmed the presence of mesoporous structures. Biological behavior and antioxidant capacity were enhanced in all cases with a statistically significant increase in CeMTA 50.50. The application of modified MTA with cerium-doped MSNs offers a promising strategy for vital pulp therapies.

Astroglial calcium signaling and homeostasis in tuberous sclerosis complex

Tuberous Sclerosis Complex (TSC) is a multisystem genetic disorder characterized by the development of benign tumors in various organs, including the brain, and is often accompanied by epilepsy, neurodevelopmental comorbidities including intellectual disability and autism. A key hallmark of TSC is the hyperactivation of the mechanistic target of rapamycin (mTOR) signaling pathway, which induces alterations in cortical development and metabolic processes in astrocytes, among other cellular functions. These changes could modulate seizure susceptibility, contributing to the progression of epilepsy and its associated comorbidities. Epilepsy is characterized by dysregulation of calcium (Ca2+) channels and intracellular Ca2+ dynamics. These factors contribute to hyperexcitability, disrupted synaptogenesis, and altered synchronization of neuronal networks, all of which contribute to seizure activity. This study investigates the intricate interplay between altered Ca2+ dynamics, mTOR pathway dysregulation, and cellular metabolism in astrocytes. The transcriptional profile of TSC patients revealed significant alterations in pathways associated with cellular respiration, ER and mitochondria, and Ca2+ regulation. TSC astrocytes exhibited lack of responsiveness to various stimuli, compromised oxygen consumption rate and reserve respiratory capacity underscoring their reduced capacity to react to environmental changes or cellular stress. Furthermore, our study revealed significant reduction of store operated calcium entry (SOCE) along with strong decrease of basal mitochondrial Ca2+ concentration and Ca2+ influx in TSC astrocytes. In addition, we observed alteration in mitochondrial membrane potential, characterized by increased depolarization in TSC astrocytes. Lastly, we provide initial evidence of structural abnormalities in mitochondria within TSC patient-derived astrocytes, suggesting a potential link between disrupted Ca2+ signaling and mitochondrial dysfunction. Our findings underscore the complexity of the relationship between Ca2+ signaling, mitochondria dynamics, apoptosis, and mTOR hyperactivation. Further exploration is required to shed light on the pathophysiology of TSC and on TSC associated neuropsychiatric disorders offering further potential avenues for therapeutic development.

The role of Ca2+-signaling in the regulation of epigenetic mechanisms

Epigenetic mechanisms regulate multiple cell functions like gene expression and chromatin conformation and stability, and its misregulation could lead to several diseases including cancer. Epigenetic drugs are currently under investigation in a broad range of diseases, but the cellular processes involved in regulating epigenetic mechanisms are not fully understood. Calcium (Ca2+) signaling regulates several cellular mechanisms such as proliferation, gene expression, and metabolism, among others. Moreover, Ca2+ signaling is also involved in diseases such as neurological disorders, cardiac, and cancer. Evidence indicates that Ca2+ signaling and epigenetics are involved in the same cellular functions, which suggests a possible interplay between both mechanisms. Ca2+-activated transcription factors regulate the recruitment of chromatin remodeling complexes into their target genes, and Ca2+-sensing proteins modulate their activity and intracellular localization. Thus, Ca2+ signaling is an important regulator of epigenetic mechanisms. Moreover, Ca2+ signaling activates epigenetic mechanisms that in turn regulate genes involved in Ca2+ signaling, suggesting possible feedback between both mechanisms. The understanding of how epigenetics are regulated could lead to developing better therapeutical approaches.

Physiology of intracellular calcium buffering

Calcium signaling underlies much of physiology. Almost all the Ca2+ in the cytoplasm is bound to buffers, with typically only ∼1% being freely ionized at resting levels in most cells. Physiological Ca2+ buffers include small molecules and proteins, and experimentally Ca2+ indicators will also buffer calcium. The chemistry of interactions between Ca2+ and buffers determines the extent and speed of Ca2+ binding. The physiological effects of Ca2+ buffers are determined by the kinetics with which they bind Ca2+ and their mobility within the cell. The degree of buffering depends on factors such as the affinity for Ca2+, the Ca2+ concentration, and whether Ca2+ ions bind cooperatively. Buffering affects both the amplitude and time course of cytoplasmic Ca2+ signals as well as changes of Ca2+ concentration in organelles. It can also facilitate Ca2+ diffusion inside the cell. Ca2+ buffering affects synaptic transmission, muscle contraction, Ca2+ transport across epithelia, and the killing of bacteria. Saturation of buffers leads to synaptic facilitation and tetanic contraction in skeletal muscle and may play a role in inotropy in the heart. This review focuses on the link between buffer chemistry and function and how Ca2+ buffering affects normal physiology and the consequences of changes in disease. As well as summarizing what is known, we point out the many areas where further work is required.

The restriction of calcium influx in metaphase and post-metaphase stages of cell division revealed by imaging secondary ion mass spectrometry (SIMS)

A secondary ion mass spectrometry (SIMS)-based isotopic imaging technique of ion microscopy was used for observing calcium influx in single renal epithelial LLC-PK₁ cells. The CAMECA IMS-3f SIMS instrument, used in the study, is capable of producing isotopic images of single cells at 500 nm spatial resolution. Due to the high-vacuum requirements of the instrument the cells were prepared cryogenically with a freeze-fracture method and frozen freeze-dried cells were used for SIMS analysis. The influx of calcium was imaged directly by exposure of cells to ⁴⁴ Ca stable isotope in the extracellular buffer for 10 min. The ⁴⁴ Ca influx was measured at mass 44 and the distribution of endogenous calcium at mass 40 (⁴⁰ Ca) in the same cell. A direct comparison of interphase cells to cells undergoing division revealed that calcium influx is restricted in metaphase and post-metaphase stages of cell division. This restriction is lifted in late cytokinesis. The net influx of ⁴⁴ Ca in 10 min was approximately half under calcium influx restriction in comparison to interphase cells. Under calcium influx restriction the ⁴⁴ Ca concentration was the same between the mitotic chromosome and the cytoplasm. These observations indicate that the endoplasmic reticulum (ER) calcium uptake is compromised under calcium influx restriction in cells undergoing division.

Making Mitotic Chromosomes in a Test Tube

Mitotic chromosome assembly is an essential preparatory step for accurate transmission of the genome during cell division. During the past decades, biochemical approaches have uncovered the molecular basis of mitotic chromosomes. For example, by using cell-free assays of frog egg extracts, the condensin I complex central for the chromosome assembly process was first identified, and its functions have been intensively studied. A list of chromosome-associated proteins has been almost completed, and it is now possible to reconstitute structures resembling mitotic chromosomes with a limited number of purified factors. In this review, I introduce how far we have come in understanding the mechanism of chromosome assembly using cell-free assays and reconstitution assays, and I discuss their potential applications to solve open questions.

Twisting DNA by salt

The structure and properties of DNA depend on the environment, in particular the ion atmosphere. Here, we investigate how DNA twist -one of the central properties of DNA- changes with concentration and identity of the surrounding ions. To resolve how cations influence the twist, we combine single-molecule magnetic tweezer experiments and extensive all-atom molecular dynamics simulations. Two interconnected trends are observed for monovalent alkali and divalent alkaline earth cations. First, DNA twist increases monotonously with increasing concentration for all ions investigated. Second, for a given salt concentration, DNA twist strongly depends on cation identity. At 100 mM concentration, DNA twist increases as Na+ < K+ < Rb+ < Ba2+ < Li+ ≈ Cs+ < Sr2+ < Mg2+ < Ca2+. Our molecular dynamics simulations reveal that preferential binding of the cations to the DNA backbone or the nucleobases has opposing effects on DNA twist and provides the microscopic explanation of the observed ion specificity. However, the simulations also reveal shortcomings of existing force field parameters for Cs+ and Sr2+. The comprehensive view gained from our combined approach provides a foundation for understanding and predicting cation-induced structural changes both in nature and in DNA nanotechnology.

Function and regulation of transcription factors during mitosis-to-G1 transition

During cell division, drastic cellular changes characteristic of mitosis result in the inactivation of the transcriptional machinery, and global downregulation of transcription. Sequence-specific transcription factors (TFs) have thus been considered mere bystanders, devoid of any regulatory function during mitosis. This view changed significantly in recent years, upon the conclusion that many TFs associate with condensed chromosomes during cell division, even occupying a fraction of their genomic target sites in mitotic chromatin. This finding was at the origin of the concept of mitotic bookmarking by TFs, proposed as a mechanism to propagate gene regulatory information across cell divisions, by facilitating the reactivation of specific bookmarked genes. While the underlying mechanisms and biological significance of this model remain elusive, recent developments in this fast-moving field have cast new light into TF activity during mitosis, beyond a bookmarking role. Here, we start by reviewing the most recent findings on the complex nature of TF-chromatin interactions during mitosis, and on mechanisms that may regulate them. Next, and in light of recent reports describing how transcription is reinitiated in temporally distinct waves during mitosis-to-G1 transition, we explore how TFs may contribute to defining this hierarchical gene expression process. Finally, we discuss how TF activity during mitotic exit may impact the acquisition of cell identity upon cell division, and propose a model that integrates dynamic changes in TF-chromatin interactions during this cell-cycle period, with the execution of cell-fate decisions.

In vivo and in vitro performances of chitosan-coated Mg-Zn-Zr-Gd-Ca alloys as bone biodegradable materials in rat models

Mg alloys have attracted significant attention as promising biomedical materials, specifically as fixation materials for promoting fracture healing. However, their unsatisfactory corrosion resistances hinder further clinical applications and thus require attention. This study aims to determine the performance of novel chitosan-coated Mg-1Zn-0.3Zr-2Gd-1Ca alloy and its ability to promote the healing of osteoporotic fractures. Moreover, its corrosion resistance and biocompatibility were assessed. Performance degradations of the samples were measured via electrochemical tests, weight loss test and morphological analysis, and the uncoated and chitosan-coated fixations were compared based on their effects on biocompatibility via the cytotoxicity test, X-rays, and hematoxylin and eosin staining. The effect of bone growth and healing was investigated via immunohistochemical test. Results of the electrochemical tests indicated that compared with the bare body, chitosan-coated Mg-Zn-Ca-Zr-Gd alloys improved by one order of magnitude. Additionally, scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), and weight loss test demonstrated that the corrosion resistance of the chitosan-coated Mg alloy is better than that of the uncoated alloy. In addition, cytotoxicity analysis indicated that the viability and morphology of the chitosan-coated alloy groups were superior to the uncoated groups in vitro. During in vivo analysis, chitosan-coated and uncoated Mg-1Zn-0.3Zr-2Gd-1Ca alloys were implanted into ovariectomized SD female rats with osteoporotic fractures for 1, 2, and 3 weeks. No displacement and shedding were observed through X-rays, and pathological analyses proved that the material was not harmful for liver and kidney tissues. Immunohistochemistry revealed that the chitosan-coated Mg-Zn-Ca-Zr-Gd alloy material contributed to the healing of osteoporotic fractures in the SD rat models. In conclusion, this study demonstrated the chitosan-coated Mg-Zn-Ca-Zr-Gd alloys have improved corrosion resistance and biocompatibility. Moreover, the alloy was found to accelerate the healing of osteoporotic fractures in SD rat models. Therefore, it has significant potential as a fixation material for osteoporotic fractures.

ATR prevents Ca2+ overload-induced necrotic cell death through phosphorylation-mediated inactivation of PARP1 without DNA damage signaling

Hyperactivation of PARP1 is known to be a major cause of necrotic cell death by depleting NAD⁺/ATP pools during Ca²⁺ overload which is associated with many ischemic diseases. However, little is known about how PARP1 hyperactivity is regulated during calcium overload. In this study we show that ATR kinase, well known for its role in DNA damage responses, suppresses ionomycin, glutamate, or quinolinic acid‐induced necrotic death of cells including SH‐SY5Y neuronal cells. We found that the inhibition of necrosis requires the kinase activity of ATR. Specifically, ATR binds to and phosphorylates PARP1 at Ser179 after the ionophore treatments. This site‐specific phosphorylation inactivates PARP1, inhibiting ionophore‐induced necrosis. Strikingly, all of this occurs in the absence of detectable DNA damage and signaling up to 8 hours after ionophore treatment. Furthermore, little AIF was released from mitochondria/cytoplasm for nuclear import, supporting the necrotic type of cell death in the early period of the treatments. Our results reveal a novel ATR‐mediated anti‐necrotic mechanism in the cellular stress response to calcium influx without DNA damage signaling.

Sarco/endoplasmic reticulum Ca2+-ATPase (SERCA) activity is required for V(D)J recombination

A whole-genome CRISPR/Cas9 screen identified ATP2A2, the gene encoding the Sarco/endoplasmic reticulum Ca²⁺-ATPase (SERCA) 2 protein, as being important for V(D)J recombination. SERCAs are ER transmembrane proteins that pump Ca²⁺ from the cytosol into the ER lumen to maintain the ER Ca²⁺ reservoir and regulate cytosolic Ca²⁺-dependent processes. In preB cells, loss of SERCA2 leads to reduced V(D)J recombination kinetics due to diminished RAG-mediated DNA cleavage. SERCA2 deficiency in B cells leads to increased expression of SERCA3, and combined loss of SERCA2 and SERCA3 results in decreased ER Ca²⁺ levels, increased cytosolic Ca²⁺ levels, reduction in RAG1 and RAG2 gene expression, and a profound block in V(D)J recombination. Mice with B cells deficient in SERCA2 and humans with Darier disease, caused by heterozygous ATP2A2 mutations, have reduced numbers of mature B cells. We conclude that SERCA proteins modulate intracellular Ca²⁺ levels to regulate RAG1 and RAG2 gene expression and V(D)J recombination and that defects in SERCA functions cause lymphopenia.

Mitotic chromosomes

Our understanding of the structure and function of mitotic chromosomes has come a long way since these iconic objects were first recognized more than 140 years ago, though many details remain to be elucidated. In this chapter, we start with the early history of chromosome studies and then describe the path that led to our current understanding of the formation and structure of mitotic chromosomes. We also discuss some of the remaining questions. It is now well established that each mitotic chromatid consists of a central organizing region containing a so-called "chromosome scaffold" from which loops of DNA project radially. Only a few key non-histone proteins and protein complexes are required to form the chromosome: topoisomerase IIα, cohesin, condensin I and condensin II, and the chromokinesin KIF4A. These proteins are concentrated along the axis of the chromatid. Condensins I and II are primarily responsible for shaping the chromosome and the scaffold, and they produce the loops of DNA by an ATP-dependent process known as loop extrusion. Modelling of Hi-C data suggests that condensin II adopts a spiral staircase arrangement with an extruded loop extending out from each step in a roughly helical pattern. Condensin I then forms loops nested within these larger condensin II loops, thereby giving rise to the final compaction of the mitotic chromosome in a process that requires Topo IIα.

Calcium ion significance on the maintenance of barley (Hordeum vulgare) chromosome compaction

Cations, especially calcium ions (Ca²⁺), is one of the major factors responsible for the chromosome higher-order structure formation. The effects of cations on the human chromosomes have already been evaluated, however, whether the presence of similar effects on plant chromosomes has not been reported to date. Thus, in this study, we investigated the role of Ca²⁺ on the barley (Hordeum vulgare L.) chromosome structure. Barley chromosomes were isolated from the meristematic tissue within the germinated roots. The roots were subjected to enzymatic treatment, fixed, and drop on the cover glass to spread the chromosomes out. Some chromosomes were treated with BAPTA (1,2-Bis(2-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid) to chelate Ca²⁺. Chromosome samples were then observed by fluorescence microscopy and scanning electron microscopy (SEM). The disperse structure of the chromosome was observed after BAPTA treatment. Chromosomes showed less condensed structure due to Ca²⁺ chelation. The high-resolution of SEM provided a more detailed visualization of chromosome ultrastructure under different calcium ion conditions. This study revealed the calcium ion effect on chromosome structure is important regardless of the organisms, suggesting a similar mechanism of chromosome condensation through humans and plants.

Contribution of advanced fluorescence nano microscopy towards revealing mitotic chromosome structure

The organization of chromatin into higher-order structures and its condensation process represent one of the key challenges in structural biology. This is important for elucidating several disease states. To address this long-standing problem, development of advanced imaging methods has played an essential role in providing understanding into mitotic chromosome structure and compaction. Amongst these are two fast evolving fluorescence imaging technologies, specifically fluorescence lifetime imaging (FLIM) and super-resolution microscopy (SRM). FLIM in particular has been lacking in the application of chromosome research while SRM has been successfully applied although not widely. Both these techniques are capable of providing fluorescence imaging with nanometer information. SRM or "nanoscopy" is capable of generating images of DNA with less than 50 nm resolution while FLIM when coupled with energy transfer may provide less than 20 nm information. Here, we discuss the advantages and limitations of both methods followed by their contribution to mitotic chromosome studies. Furthermore, we highlight the future prospects of how advancements in new technologies can contribute in the field of chromosome science.

Imaging the inner structure of chromosomes: contribution of focused ion beam/scanning electron microscopy to chromosome research

Visualization of the chromosome ultrastructure has revealed new insights into its structural and functional properties. The use of new methods for revealing not only the surface but also the inner structure of the chromosome has been emerged. Some methods have long been used, such as conventional transmission electron microscopy (TEM). Although it has indispensably contributed to the revelation of the ultrastructure of the various biological samples, including chromosomes, some challenges have also been encountered, such as laborious sample preparation, limited view areas, and loss of information on some parts due to ultramicrotome sectioning. Therefore, a more advanced method is needed. Scanning electron microscopy (SEM) is also advantageous in the surface visualization of chromosome samples. However, it is limited by accessibility to gain the inner structure information. Focused ion beam/scanning electron microscopy (FIB/SEM) provides a way to investigate the inner structure of the samples in a direct slice-and-view manner to observe the ultrastructure of the inner part of the sample continuously and further construct a three-dimensional image. This method has long been used in the material science field, and recently, it has also been applied to biological research, such as in showing the inner structure of chromosomes. This review article presents the contributions of this new method to chromosome research and its recent developments in the inner structure of chromosome and discusses its current and potential applications to the high-resolution imaging of chromosomes.

Cold-induced chromatin compaction and nuclear retention of clock mRNAs resets the circadian rhythm

Cooling patients to sub‐physiological temperatures is an integral part of modern medicine. We show that cold exposure induces temperature‐specific changes to the higher‐order chromatin and gene expression profiles of human cells. These changes are particularly dramatic at 18°C, a temperature synonymous with that experienced by patients undergoing controlled deep hypothermia during surgery. Cells exposed to 18°C exhibit largely nuclear‐restricted transcriptome changes. These include the nuclear accumulation of mRNAs encoding components of the negative limbs of the core circadian clock, most notably REV‐ERBα. This response is accompanied by compaction of higher‐order chromatin and hindrance of mRNPs from engaging nuclear pores. Rewarming reverses chromatin compaction and releases the transcripts into the cytoplasm, triggering a pulse of negative limb gene proteins that reset the circadian clock. We show that cold‐induced upregulation of REV‐ERBα is sufficient to trigger this reset. Our findings uncover principles of the cellular cold response that must be considered for current and future applications involving therapeutic deep hypothermia.

Application of the Chromosome Image Analyzing System (CHIAS) for Straightening Cation-treated Bent Chromosomes

Divalent cations, mainly calcium and magnesium ions, are known to play a major role in the maintenance of chromosomes. The depletion of both ions using ethylenediaminetetraacetic acid (EDTA) results in a bent chromosome structure with extended arms and dispersed chromatin fibers. The importance of divalent cations for the maintenance of chromosome structure has been reported previously; nevertheless, previous studies were limited to qualitative data only. Straightening the bent image of the chromosome would provide quantitative data. Thus, this study aimed to evaluate the effects of cation depletion by the application of the Chromosome Image Analyzing System (CHIAS) to straighten bent chromosomes. Human HeLa chromosomes were treated with EDTA as a known chelating agent in order to investigate the importance of divalent cations on the maintenance of chromosome structure. Chromosomes were stained and directly observed with a fluorescence microscope. Images were then analyzed using CHIAS. The results revealed that EDTA-treated chromosomes showed longer arms than those without EDTA treatment, and most of them tended to bend-out. By straightening the image using CHIAS, the bent chromosomes were successfully straightened. The average lengths of the chromosomes treated with and without EDTA were 4.97 and 0.96 μm, respectively. These results signify the advantages of CHIAS for chromosome analysis and highlight the fundamental effects of cations on chromosome condensation.

A potent antagonist antibody targeting connexin hemichannels alleviates Clouston syndrome symptoms in mutant mice

BACKGROUND

Numerous currently incurable human diseases have been causally linked to mutations in connexin (Cx) genes. In several instances, pathological mutations generate abnormally active Cx hemichannels, referred to also as "leaky" hemichannels. The goal of this study was to assay the in vivo efficacy of a potent antagonist antibody targeting Cx hemichannels.

METHODS

We employed the antibody to treat Cx30A88V/A88V adult mutant mice, the only available animal model of Clouston syndrome, a rare orphan disease caused by Cx30 p.A88V leaky hemichannels. To gain mechanistic insight into antibody action, we also performed patch clamp recordings, Ca2+ imaging and ATP release assay in vitro.

FINDINGS

Two weeks of antibody treatment sufficed to repress cell hyperproliferation in skin and reduce hypertrophic sebaceous glands (SGs) to wild type (wt) levels. These effects were obtained whether mutant mice were treated topically, by application of an antibody cream formulation, or systemically, by intraperitoneal antibody injection. Experiments with mouse primary keratinocytes and HaCaT cells revealed the antibody blocked Ca2+ influx and diminished ATP release through leaky Cx30 p.A88V hemichannels.

INTERPRETATION

Our results show anti-Cx antibody treatment was effective in vivo and sufficient to counteract the effects of pathological connexin expression in Cx30A88V/A88V mice. In vitro experiments suggest antibodies gained control over leaky hemichannels and contributed to restoring epidermal homeostasis. Therefore, regulating cell physiology by antibodies targeting the extracellular domain of Cxs may enforce an entirely new therapeutic strategy. These findings support the further development of antibodies as drugs to address unmet medical needs for Cx-related diseases. FUND: Fondazione Telethon, GGP19148; University of Padova, SID/BIRD187130; Consiglio Nazionale delle Ricerche, DSB.AD008.370.003\TERABIO-IBCN; National Science Foundation of China, 31770776; Science and Technology Commission of Shanghai Municipality, 16DZ1910200.

The Winner Takes It All: Auxin-The Main Player during Plant Embryogenesis

In plants, the first asymmetrical division of a zygote leads to the formation of two cells with different developmental fates. The establishment of various patterns relies on spatial and temporal gene expression, however the precise mechanism responsible for embryonic patterning still needs elucidation. Auxin seems to be the main player which regulates embryo development and controls expression of various genes in a dose-dependent manner. Thus, local auxin maxima and minima which are provided by polar auxin transport underlie cell fate specification. Diverse auxin concentrations in various regions of an embryo would easily explain distinct cell identities, however the question about the mechanism of cellular patterning in cells exposed to similar auxin concentrations still remains open. Thus, specification of cell fate might result not only from the cell position within an embryo but also from events occurring before and during mitosis. This review presents the impact of auxin on the orientation of the cell division plane and discusses the mechanism of auxin-dependent cytoskeleton alignment. Furthermore, close attention is paid to auxin-induced calcium fluxes, which regulate the activity of MAPKs during postembryonic development and which possibly might also underlie cellular patterning during embryogenesis.

Cellular dynamics of mammalian red blood cell production in the erythroblastic island niche

Red blood cells, or erythrocytes, make up approximately a quarter of all cells in the human body with over 2 billion new erythrocytes made each day in a healthy adult human. This massive cellular production system is coupled with a set of cell biological processes unique to mammals, in particular, the elimination of all organelles, and the expulsion and destruction of the condensed erythroid nucleus. Erythrocytes from birds, reptiles, amphibians and fish possess nuclei, mitochondria and other organelles: erythrocytes from mammals lack all of these intracellular components. This review will focus on the dynamic changes that take place in developing erythroid cells that are interacting with specialized macrophages in multicellular clusters termed erythroblastic islands. Proerythroblasts enter the erythroblastic niche as large cells with active nuclei, mitochondria producing heme and energy, and attach to the central macrophage via a range of adhesion molecules. Proerythroblasts then mature into erythroblasts and, following enucleation, in reticulocytes. When reticulocytes exit the erythroblastic island, they are smaller cells, without nuclei and with few mitochondria, possess some polyribosomes and have a profoundly different surface molecule phenotype. Here, we will review, step-by-step, the biophysical mechanisms that regulate the remarkable process of erythropoiesis with a particular focus on the events taking place in the erythroblastic island niche. This is presented from the biological perspective to offer insight into the elements of red blood cell development in the erythroblastic island niche which could be further explored with biophysical modelling systems.

First proteomic analysis of diestrus and anestrus canine oocytes at the germinal vesicle reveals candidate proteins involved in oocyte meiotic competence

In domestic dogs, oocyte maturation rates are low and the percentage of oocytes that remain in the stage of germinal vesicle (GV) regardless of culture conditions is high. The present study was conducted to characterize the proteome of canine oocyte at the germinal vesicle stage using label-free mass spectrometry. Ovaries were collected from 415 adult domestic dogs and oocytes were divided anestrus and diestrus group. Protein lysates were subjected to quantitative proteomic analysis to identify differentially expressed proteins in different status reproductive. All runs for each sample were performed on an Easy nLC1000 nano-LC chromatograph system directly connected to a quadrupole-type Orbitrap mass spectrometer. For identification of peptides and proteins, raw data of the spectra were loaded into MaxQuant software version 1.5.2.8. Proteomic data were analysed according to gene ontology and a protein-protein interaction network. 312 proteins were identified and grouped according to their biological processes, molecular functions and cellular component. Forty-six differentially expressed proteins among diestrus and control group were associated with at least one GO term in the biological process database. Several proteins involved in the cell cycle, fertilization, regulation of transcription and signalling pathways that are essential for the full development of oocytes and fertilization were expressed. This study identified proteins that were absent, and more or less expressed in different status reproductive. These differentially expressed proteins revealed a framework of molecular reorganization within a GV that renders its competency. This knowledge will enable the identification of target competence biomarkers and thus the establishment of more adequate means of cultivation to improve the M-I and II indexes in this species and also to better understand the physiology of the domestic dog, promoting the development of new reproduction biotechniques.

Spermidine strongly increases the fidelity of Escherichia coli CRISPR Cas1-Cas2 integrase

Site-selective CRISPR array expansion at the origin of bacterial adaptive immunity relies on recognition of sequence-dependent DNA structures by the conserved Cas1-Cas2 integrase. Off-target integration of a new spacer sequence outside canonical CRISPR arrays has been described in vitro However, this nonspecific integration activity is rare in vivo Here, we designed gel assays to monitor fluorescently labeled protospacer insertion in a supercoiled 3-kb plasmid harboring a minimal CRISPR locus derived from the Escherichia coli type I-E system. This assay enabled us to distinguish and quantify target and off-target insertion events catalyzed by E. coli Cas1-Cas2 integrase. We show that addition of the ubiquitous polyamine spermidine or of another polyamine, spermine, significantly alters the ratio between target and off-target insertions. Notably, addition of 2 mm spermidine quenched the off-target spacer insertion rate by a factor of 20-fold, and, in the presence of integration host factor, spermidine also increased insertion at the CRISPR locus 1.5-fold. The observation made in our in vitro system that spermidine strongly decreases nonspecific activity of Cas1-Cas2 integrase outside the leader-proximal region of a CRISPR array suggests that this polyamine plays a potential role in the fidelity of the spacer integration also in vivo.

Reversible Changes of Chromosome Structure upon Different Concentrations of Divalent Cations

The structural details of chromosomes have been of interest to researchers for many years, but how the metaphase chromosome is constructed remains unsolved. Divalent cations have been suggested to be required for the organization of chromosomes. However, detailed information about the role of these cations in chromosome organization is still limited. In the current study, we investigated the effects of Ca2+ and Mg2+ depletion and the reversibility upon re-addition of one of the two ions. Human chromosomes were treated with different concentrations of Ca2+and Mg2+. Depletion of Ca2+ and both Ca2+ and Mg2+ were carried out using 1, 2-bis(2-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid and ethylenediaminetetraacetic acid (EDTA), respectively. Chromosome structure was examined by fluorescence microscopy and scanning electron microscopy. The results indicated that chromosome structures after treatment with a buffer without Mg2+, after Ca2+ depletion, as well as after depletion of both Mg2+, and Ca2+, yielded fewer compact structures with fibrous chromatin than those without cation depletion. Interestingly, the chromatin of EDTA-treated chromosomes reversed to their original granular diameters after re-addition of either Mg2+ or Ca2+ only. These findings signify the importance of divalent cations on the chromosome structure and suggest the interchangeable role of Ca2+ and Mg2+.

Reorganisation of chromatin during erythroid differentiation

A totipotent zygote has unlimited potential for differentiation into all cell types found in an adult organism. During ontogenesis proliferating and maturing cells gradually lose their differentiation potential, limiting the spectrum of possible developmental transitions to a specific cell type. Following the initiation of the developmental program cells acquire specific morphological and functional properties. Deciphering the mechanisms that coordinate shifts in gene expression revealed a critical role of three-dimensional chromatin structure in the regulation of gene activity during lineage commitment. Several levels of DNA packaging have been recently identified using chromosome conformation capture based techniques such a Hi-C. It is now clear that chromatin regions with high transcriptional activity assemble into Mb-scale compartments in the nuclear space, distinct from transcriptionally silent regions. More locally chromatin is organized into topological domains, serving as functionally insulated units with cell type – specific regulatory loop interactions. However, molecular mechanisms establishing and maintaining such 3D organization are yet to be investigated. Recent focus on studying chromatin reorganization accompanying cell cycle progression and cellular differentiation partially explained some aspects of 3D genome folding. Throughout erythropoiesis cells undergo a dramatic reorganization of the chromatin landscape leading to global nuclear condensation and transcriptional silencing, followed by nuclear extrusion at the final stage of mammalian erythropoiesis. Drastic changes of genome architecture and function accompanying erythroid differentiation seem to be an informative model for studying the ways of how genome organization and dynamic gene activity are connected. Here we summarize current views on the role of global rearrangement of 3D chromatin structure in erythroid differentiation.

Cdk1-dependent phosphorylation of KIF4A at S1186 triggers lateral chromosome compaction during early mitosis

Chromosome organization during cell division is achieved through the timely association of proteins with chromatin and is regulated by protein phosphorylation. Kinesin family member 4A (KIF4A) plays an important role in the chromosome organization through the formation of the chromosome scaffold structure. However, the relationship between the function of KIF4A and its phosphorylation remains unclear. Here, we demonstrate that Cdk1-dependent phosphorylation of KIF4A at S1186 is required for chromosome binding and chromosome scaffold formation. The KIF4A mutant, which is not phosphorylated at S1186, was found to localize to the nucleus during interphase but did not accumulate in the chromosome scaffold after nuclear envelope breakdown. In addition, defects in KIF4A phosphorylation were found to disrupt the interaction of KIF4A with the condensin I complex. As a result, the morphology of the chromosomes was observed to be laterally decondensed, without condensin I in the chromosome scaffold. Additionally, a defect in chromosome segregation, chromosome bridge formation, was often observed. Although both KIF4A and condensin I disappeared from the chromosomes, the chromosomal localization of condensin II was not affected. Collectively, our novel results revealed that Cdk1-dependent KIF4A phosphorylation at S1186 is a trigger for chromosomal organization during early mitosis.

The effect of linker DNA on the structure and interaction of nucleosome core particles

In eukaryotes, the compaction of chromatin fibers composed of nucleosome core particles (NCPs) connected by a linker DNA into chromosomes is highly efficient; however, the underlying folding mechanisms remain elusive. We used small angle X-ray scattering (SAXS) to investigate the influence of linker DNA length on the local structure and the interparticle interactions of the NCPs. In the presence of the linker DNA of 30 bp or less in length, the results suggest partial unwrapping of nucleosomal DNA on the NCP irrespective of the linker DNA length. Moreover, the presence of 15 bp linker DNA alleviated the electrostatic repulsion between the NCPs and prevented the formation of an ordered columnar hexagonal phase, demonstrating that the linker DNA plays an active role in chromatin folding.

Epigenome Interactions with Patterned Neuronal Activity

The temporal coding of action potential activity is fundamental to nervous system function. Here we consider how gene expression in neurons is regulated by specific patterns of action potential firing, with an emphasis on new information on epigenetic regulation of gene expression. Patterned action potential activity activates intracellular signaling networks selectively in accordance with the kinetics of activation and inactivation of second messengers, phosphorylation and dephosphorylation of protein kinases, and cytoplasmic and nuclear calcium dynamics, which differentially activate specific transcription factors. Increasing evidence also implicates activity-dependent regulation of epigenetic mechanisms to alter chromatin architecture. Changes in three-dimensional chromatin structure, including chromatin compaction, looping, double-stranded DNA breaks, histone and DNA modification, are altered by action potential activity to selectively inhibit or promote transcription of specific genes. These mechanisms of activity-dependent regulation of gene expression are important in neural development, plasticity, and in neurological and psychological disorders.

Use of 3D imaging for providing insights into high-order structure of mitotic chromosomes

The high-order structure of metaphase chromosomes remains still under investigation, especially the 30-nm structure that is still controversial. Advanced 3D imaging has provided useful information for our understanding of this detailed structure. It is evident that new technologies together with improved sample preparations and image analyses should be adequately combined. This mini review highlights 3D imaging used for chromosome analysis so far with future imaging directions also highlighted.

The interplay of nanointerface curvature and calcium binding in weak polyelectrolyte-coated nanoparticles

When engineering nanomaterials for application in biological systems, it is important to understand how multivalent ions, such as calcium, affect the structural and chemical properties of polymer-modified nanoconstructs. In this work, a recently developed molecular theory was employed to study the effect of surface curvature on the calcium-induced collapse of end-tethered weak polyelectrolytes. In particular, we focused on cylindrical and spherical nanoparticles coated with poly(acrylic acid) in the presence of different amounts of Ca2+ ions. We describe the structural changes that grafted polyelectrolytes undergo as a function of calcium concentration, surface curvature, and morphology. The polymer layers collapse in aqueous solutions that contain sufficient amounts of Ca2+ ions. This collapse, due to the formation of calcium bridges, is not only controlled by the calcium ion concentration but also strongly influenced by the curvature of the tethering surface. The transition from a swollen to a collapsed layer as a function of calcium concentration broadens and shifts to lower amounts of calcium ions as a function of the radius of cylindrical and spherical nanoparticles. The results show how the interplay between calcium binding and surface curvature governs the structural and functional properties of the polymer molecules. This would directly impact the fate of weak polyelectrolyte-coated nanoparticles in biological environments, in which calcium levels are tightly regulated. Understanding such interplay would also contribute to the rational design and optimization of smart interfaces with applications in, e.g., salt-sensitive and ion-responsive materials and devices.

Nucleosome-level 3D organization of the genome

Nucleosomes are the unitary structures of chromosome folding, and their arrangements are intimately coupled to the regulation of genome activities. Conventionally, structural analyses using electron microscopy and X-ray crystallography have been used to study such spatial nucleosome arrangements. In contrast, recent improvements in the resolution of sequencing-based methods allowed investigation of nucleosome arrangements separately at each genomic locus, enabling exploration of gene-dependent regulation mechanisms. Here, we review recent studies on nucleosome folding in chromosomes from these two methodological perspectives: conventional structural analyses and DNA sequencing, and discuss their implications for future research.

Calcium Dynamics as a Machine for Decoding Signals

Calcium (Ca²⁺) is considered one of the most-important biological cations, because it is implicated in cell physiopathology and cell fate through a finely tuned signaling system. In support of this notion, Ca²⁺ is the primary driver of cell proliferation and cell growth; however, it is also intimately linked to cell death. Functional abnormalities or mutations in proteins that mediate Ca²⁺ homeostasis usually lead to a plethora of diseases and pathogenic states, including cancer, heart failure, diabetes, and neurodegenerative disease. In this review, we examine recent discoveries in the highly localized nature of Ca²⁺-dependent signal transduction and its roles in cell fate, inflammasome activation, and synaptic transmission.

A Transient Rise in Free Mg2+ Ions Released from ATP-Mg Hydrolysis Contributes to Mitotic Chromosome Condensation

For cell division, negatively charged chromatin, in which nucleosome fibers (10 nm fibers) are irregularly folded [1-5], must be condensed into chromosomes and segregated. While condensin and other proteins are critical for organizing chromatin into the appropriate chromosome shape [6-17], free divalent cations such as Mg²⁺ and Ca²⁺, which condense chromatin or chromosomes in vitro [18-28], have long been considered important, especially for local condensation, because the nucleosome fiber has a net negative charge and is by itself stretched like "beads on a string" by electrostatic repulsion. For further folding, other positively charged factors are required to decrease the charge and repulsion [29]. However, technical limitations to measure intracellular free divalent cations, but not total cations [30], especially Mg²⁺, have prevented us from elucidating their function. Here, we developed a Förster resonance energy transfer (FRET)-based Mg²⁺ indicator that monitors free Mg²⁺ dynamics throughout the cell cycle. By combining this indicator with Ca²⁺ [31] and adenosine triphosphate (ATP) [32] indicators, we demonstrate that the levels of free Mg²⁺, but not Ca²⁺, increase during mitosis. The Mg²⁺ increase is coupled with a decrease in ATP, which is normally bound to Mg²⁺ in the cell [33]. ATP inhibited Mg²⁺-dependent chromatin condensation in vitro. Chelating Mg²⁺ induced mitotic cell arrest and chromosome decondensation, while ATP reduction had the opposite effect. Our results suggest that ATP-bound Mg²⁺ is released by ATP hydrolysis and contributes to mitotic chromosome condensation with increased rigidity, suggesting a novel regulatory mechanism for higher-order chromatin organization by the intracellular Mg²⁺-ATP balance.

Mitotic Chromosome Assembly In Vitro: Functional Cross Talk between Nucleosomes and Condensins

The mitotic chromosome is a macromolecular assembly that ensures error-free transmission of the genome during cell division. It has long been a big mystery how long stretches of DNA might be folded into rod-shaped chromosomes or how such an elaborate process might be accomplished at a mechanistic level. Cell-free extracts made from frog eggs offer a unique opportunity to address these questions by enabling mitotic chromosomes to be assembled in a test tube. Moreover, the core part of the chromosome assembly reaction can now be reconstituted with a limited number of purified factors. A combination of these in vitro assays makes it possible not only to prepare a complete list of proteins required for chromosome assembly but also to dissect functions of individual proteins and their cooperation with unparalleled clarity. Emerging lines of evidence underscore the paramount importance of condensins in building mitotic chromosomes and shed new light on the functional cross talk between nucleosomes and condensins in this process.

Condensin II plays an essential role in reversible assembly of mitotic chromosomes in situ

A modified protocol for inducing reversible assembly of mitotic chromosomes in situ is developed. As judged by this assay, which is combined with quantitative morphological analyses using a supervised machine-learning algorithm, condensin II plays a crucial role in both the recovery of chromatin shapes and the reorganization of chromosome axes.

Condensins I and II are multisubunit complexes that play a central role in mitotic chromosome assembly. Although both complexes become concentrated along the axial region of each chromatid by metaphase, it remains unclear exactly how such axes might assemble and contribute to chromosome shaping. To address these questions from a physico-chemical point of view, we have established a set of two-step protocols for inducing reversible assembly of chromosome structure in situ, namely within a whole cell. In this assay, mitotic chromosomes are first expanded in a hypotonic buffer containing a Mg²⁺-chelating agent and then converted into different shapes in a NaCl concentration-dependent manner. Both chromatin and condensin-positive chromosome axes are converted into near-original shapes at 100 mM NaCl. This assay combined with small interfering RNA depletion demonstrates that the recovery of chromatin shapes and the reorganization of axes are highly sensitive to depletion of condensin II but less sensitive to depletion of condensin I or topoisomerase IIα. Furthermore, quantitative morphological analyses using the machine-learning algorithm wndchrm support the notion that chromosome shaping is tightly coupled to the reorganization of condensin II-based axes. We propose that condensin II makes a primary contribution to mitotic chromosome architecture and maintenance in human cells.

Calcium depletion destabilises kinetochore fibres by the removal of CENP-F from the kinetochore

The attachment of spindle fibres to the kinetochore is an important process that ensures successful completion of the cell division. The Ca²⁺ concentration increases during the mitotic phase and contributes microtubule stability. However, its role in the spindle organisation in mitotic cells remains controversial. Here, we investigated the role of Ca²⁺ on kinetochore fibres in living cells. We found that depletion of Ca²⁺ during mitosis reduced kinetochore fibre stability. Reduction of kinetochore fibre stability was not due to direct inhibition of microtubule polymerisation by Ca²⁺-depletion but due to elimination of one dynamic component of kinetochore, CENP-F from the kinetochore. This compromised the attachment of kinetochore fibres to the kinetochore which possibly causes mitotic defects induced by the depletion of Ca²⁺.