Pre-spermiogenic initiation of flagellar growth and correlative ultrastructural observations on nuage, nuclear and mitochondrial developmental morphology in the zebrafish Danio rerio.

The microstructural and ultrastructural changes of germ cells during spermatogenesis of zebrafish (Danio rerio) were examined using light microscopy (LM) and transmission electron microscopy (TEM). Generally the process of spermatogenesis in zebrafish is similar to that of other teleosts, however, here we describe some peculiar features of zebrafish spermatogenic cells which have a limited report in this species. (1) The basic events of spermiogenesis are asynchronous, location of flagellum finished in initial stage, while chromatin condensation sharply occurred in intermediate stage and elimination of excess cytoplasm mainly taken place in final stages. (2) Surprisingly, the cilia or initial flagellae are created in spermatocytes, approach toward the nucleus of early stage spermatids, and then the centrioles depress into nuclear fossa and change their orientation to each other from right angle to obtuse angle about 125°. (3) During spermatogenesis, the chromatin compaction performs in a distinctive pattern, condensed heterogeneously from granular into chromatin clumps with central electron-lucent areas, round or long, which diminished to small nuclear vacuoles in spermatozoa. This finding demonstrates the origin of nuclear vacuoles in zebrafish spermatozoa for the first time. (4) Nuages are observed in both spermatogonia and spermatocytes. They are connected with the mitochondria and nuclear membrane, and are even located in the perinuclear spaces of spermatogonia nuclei. (5) Mitochondrial morphology and distribution shows diversity in different germ cells. The condensed mitochondria appear in pachytene spermatocytes, and mitochondria including membrane conglomerate exist in both spermatocytes and spermatids. This study was undertaken in order to disclose specific spermatogenic cells features in zebrafish that could be helpful for understanding the correlative function in this model species.

The influence of spatial variation in chromatin density determined by X-ray tomograms on the time to find DNA binding sites.

In this work, we examine how volume exclusion caused by regions of high chromatin density might influence the time required for proteins to find specific DNA binding sites. The spatial variation of chromatin density within mouse olfactory sensory neurons is determined from soft X-ray tomography reconstructions of five nuclei. We show that there is a division of the nuclear space into regions of low-density euchromatin and high-density heterochromatin. Volume exclusion experienced by a diffusing protein caused by this varying density of chromatin is modeled by a repulsive potential. The value of the potential at a given point in space is chosen to be proportional to the density of chromatin at that location. The constant of proportionality, called the volume exclusivity, provides a model parameter that determines the strength of volume exclusion. Numerical simulations demonstrate that the mean time for a protein to locate a binding site localized in euchromatin is minimized for a finite, nonzero volume exclusivity. For binding sites in heterochromatin, the mean time is minimized when the volume exclusivity is zero (the protein experiences no volume exclusion). An analytical theory is developed to explain these results. The theory suggests that for binding sites in euchromatin there is an optimal level of volume exclusivity that balances a reduction in the volume searched in finding the binding site, with the height of effective potential barriers the protein must cross during the search process.

Programmable genetic switches to control transcriptional machinery of pluripotency.

Transcriptional activators play a central role in the regulation of gene expression and have the ability to manipulate the specification of cell fate. Pluripotency is a transient state where a cell has the potential to develop into more than one type of mature cell. The induction of pluripotency in differentiated cells requires extensive chromatin reorganization regulated by core transcriptional machinery. Several small molecules have been shown to enhance the efficiency of somatic cell reprogramming into pluripotent stem cells. However, entirely chemical-based reprogramming remains elusive. Recently, we reported that selective DNA-binding hairpin pyrrole-imidazole polyamides conjugated with histone deacetylase inhibitor could mimic natural transcription factors and epigenetically activate certain pluripotency-associated genes. Here, we review the need to develop selective chromatin-modifying transcriptional activators for somatic genome reprogramming.

Analysis of DNA double-strand break response and chromatin structure in mitosis using laser microirradiation.

In this study the femtosecond near-IR and nanosecond green lasers are used to induce alterations in mitotic chromosomes. The subsequent double-strand break responses are studied. We show that both lasers are capable of creating comparable chromosomal alterations and that a phase paling observed within 1-2 s of laser exposure is associated with an alteration of chromatin as confirmed by serial section electron microscopy, DAPI, γH2AX and phospho-H3 staining. Additionally, the accumulation of dark material observed using phase contrast light microscopy (indicative of a change in refractive index of the chromatin) ∼ 34 s post-laser exposure corresponds spatially to the accumulation of Nbs1, Ku and ubiquitin. This study demonstrates that chromosomes selectively altered in mitosis initiate the DNA damage response within 30 s and that the accumulation of proteins are visually represented by phase-dark material at the irradiation site, allowing us to determine the fate of the damage as cells enter G1. These results occur with two widely different laser systems, making this approach to study DNA damage responses in the mitotic phase generally available to many different labs. Additionally, we present a summary of most of the published laser studies on chromosomes in order to provide a general guide of the lasers and operating parameters used by other laboratories.

Sperm chromatin structure is associated with the quality of spermatogenesis in infertile patients.

OBJECTIVE: To establish the diagnostic value of sperm chromatin structure assessment for the evaluation of male factor infertility, in addition to conventional andrological workup. DESIGN: Cross-sectional controlled study. SETTING: A tertiary referral andrology clinic. PATIENT(S): Two hundred seventy-nine male partners of infertile couples. INTERVENTION(S): None. MAIN OUTCOME MEASURE(S): The DNA fragmentation index (DFI) determined by the sperm chromatin structure assay (SCSA), semen parameters, serum levels of reproductive hormones, and World Health Organization (WHO) classification of male factor subfertility. RESULT(S): In all patient categories, except those including patients with hypogonadotrophic hypogonadism, sperm antibodies, or normospermia, DFI was significantly higher compared with in proven fertile controls. After classification of the quality of spermatogenesis based on mean testicular volume (<10 ml vs. >15 ml), follicle stimulating hormone (FSH; > 10 U/L vs. <5 U/L), and inhibin-B (<100 nmol/L vs. >150 nmol/L), the DFI was significantly higher in patients with poor spermatogenesis (35.9%) than in patients with normal spermatogenesis (25.9%). In a multiple regression analysis, the teratozoospermia index, sperm vitality, and FSH were significant determinants of the DFI level. Male age was associated with DFI, but leukocytospermia, body mass index, and smoking were not confounders of DFI. CONCLUSION(S): Impaired spermatogenesis, irrespective of the WHO classification of male factor subfertility, is generally associated with an increase of sperm DNA damage.

Tackling the epigenome in the pluripotent stem cells.

Embryonic stem cells are unique in their abilities of self-renewal and to differentiate into many, if not all, cellular lineages. Transcriptional regulation, epigenetic modifications and chromatin structures are the key modulators in controlling such pluripotency nature of embryonic stem cell genomes, particularly in the developmental decisions and the maintenance of cell fates. Among them, epigenetic regulation of gene expression is mediated partly by covalent modifications of core histone proteins including methylation, phosphorylation and acetylation. Moreover, the chromatins in stem cell genome appear as a highly organized structure containing distinct functional domains. Recent rapid progress of new technologies enables us to take a global, unbiased and comprehensive view of the epigenetic modifications and chromatin structures that contribute to gene expression regulation and cell identity during diverse developmental stages. Here, we summarized the latest advances made by high throughput approaches in profiling epigenetic modifications and chromatin conformations, with an emphasis on genome-wide analysis of histone modifications and their implications in pluripotency nature of embryonic stem cells.

Mitochondrial involvement in Atuna racemosa induced toxicity.

Our group has developed a system to extract information regarding potential novel pharmaceuticals from historic herbal texts. We have shown that one of the plants identified through this technique has the purported antibacterial properties suggested by the text. Here, the toxicity of this antibacterial extract was examined. Using a Jurkat cell model, a therapeutic window between the minimal inhibitory concentration for Gram-positive bacteria and the dose-dependent toxicity of the Atuna racemosa extract was established. Using cells with a mutated caspase 8, it was shown that the toxicity does not involve caspase 8. However, by transmission electron microscopy and a potentiometric dye, the toxicity was shown to involve the mitochondria. This toxicity also resulted in DNA cleavage and activation of caspase 3. This work suggests that the extract, originally reported as an antimicrobial therapeutic in a 400-year-old Dutch herbal text, may maintain a therapeutic window as an antibiotic. Furthermore, this work shows toxicity would occur in a mitochondrial dependent fashion.

Comparison between nuclear chromatin patterns of digitalized images of cells of the mammalian testicular and renal tissues: an imaging segmentation study.

Testicular and renal tissue, obtained from adult cattle, pigs, rats, and human was processed by image digital segmentation and pixel texture analytical techniques for comparative evaluation of nuclear chromatin pattern of testicular primary spermatocytes and renal glomerular endothelial cells. The post mortem performed for the animals and the human subject were for reasons not related with either testicular or renal conditions. The objective was to establish a benchmark for identification of rapidly multiplying cells in images of sections of normal, as well as abnormal mammalian tissue. Based on the observed morphological and texture pattern of the nuclear chromatin of the testicular primary spermatocytes, it was determined that the renal glomerular endothelial cells exhibit similar nuclear chromatin morphology consistent with an ongoing rapid multiplication process. The nuclear chromatin of both cell types manifest identical mitotic figures which are strongly indicative of cellular proliferation.

Protamines and male infertility.

Protamines are the major nuclear sperm proteins. The human sperm nucleus contains two types of protamine: protamine 1 (P1) encoded by a single-copy gene and the family of protamine 2 (P2) proteins (P2, P3 and P4), all also encoded by a single gene that is transcribed and translated into a precursor protein. The protamines were discovered more than a century ago, but their function is not yet fully understood. In fact, different hypotheses have been proposed: condensation of the sperm nucleus into a compact hydrodynamic shape, protection of the genetic message delivered by the spermatozoa, involvement in the processes maintaining the integrity and repair of DNA during or after the nucleohistone-nucleoprotamine transition and involvement in the epigenetic imprinting of the spermatozoa. Protamines are also one of the most variable proteins found in nature, with data supporting a positive Darwinian selection. Changes in the expression of P1 and P2 protamines have been found to be associated with infertility in man. Mutations in the protamine genes have also been found in some infertile patients. Transgenic mice defective in the expression of protamines also present several structural defects in the sperm nucleus and have variable degrees of infertility. There is also evidence that altered levels of protamines may result in an increased susceptibility to injury in the spermatozoan DNA causing infertility or poor outcomes in assisted reproduction. The present work reviews the articles published to date on the relationship between protamines and infertility.

[Structural rearrangements of the chromatin during the adaptive response in two genetically close djungarian hamster fibroblast cell lines with different radiosensitivity].

The capacity of cell for the adaptive response (AR) induction after gamma-irradiation using micronuclear test was investigated. Our model consists of the parental djungarian hamster embryonic fibroblast cell line DH-TK- and its radioresistant progeny (PIC-20). We demonstrated that AR for the more radiosensitive parental cell line was shifted to the lower adaptive and to the challenge doses. The maximal AR for DH-TK- cells was induced at 0.3 Gy adaptive dose and 1.5 Gy challenge dose (adaptive response coefficient (ARC) was 0.4+/- 0.1), whereas for PIC-20 cells these means were 0.5 Gy and 3.0 Gy correspondingly (ARC = 0.45+/-0.1). Using the method of anomalous viscosity time dependence (AVTD) we demonstrated the chromatin rearrangements in both cell lines during 3-5 h after adaptive dose application. The rearrangement degree evaluated by the relative maximal reduced viscosity was considerably higher in PIC-20 cell line than that in DH-TK cells (2.4+/-0.3 vs 1.4+/-0. 1). Interestingly, the time of chromatin rearrangement did not depend neither on the dose nor on the cell type and was similar in both cell lines after 5 h of adaptive dose application. It was also shown that during the AR chromatin relaxation was lower after exposure to both the adaptive and challenge doses than after challenge dose only. In contrast, in the degree of AR chromatin relaxation was higher for both cell lines.

Fertilization failure from a sperm chromatin defect in couples with unexplained infertility.

OBJECTIVE: To investigate the relationship between unexplained infertility and fertilization failure from nucleoprotein defects in ejaculated human sperm and to study the usefulness of sperm chromatin assays, using AO fluorescence dye, to evaluate patients with unexplained infertility before treatment. STUDY DESIGN: From January 1999 to January 2000, 513 infertile couples had the clinical causes of their infertility assessed. During the next investigative period (February 2000-February 2001), 137 cases of unexplained infertility (n = 80) were chosen for this study, as were cases of tubal factor infertility (n = 57) as controls. The status of nuclear chromatin in ejaculated sperm was examined using acridine orange staining, followed by a conventional in vitro fertilization procedure. RESULTS: The number of patients with immature ejaculated sperm was 16 of 30 (53.3%) unexplained infertility cases involving fertilization failure, 8 of 50 (16.0%) unexplained infertility cases without fertilization failure and 5 of 57 (8.8%) tubal factor infertility cases. A significant difference was observed between unexplained infertility cases with fertilization failure and the other groups (P < .0001). CONCLUSION: These results suggest that the nuclear immaturity of ejaculated human sperm may be 1 of the primary factors underlying unexplained infertility.

Chromatin (dis)organization and cancer: BUR-binding proteins as biomarkers for cancer.

Malignant transformation of cells is associated with changes in gene expression. Gross alterations in chromatin organization may be involved in such gene dysregulation, as well as the involvement of specific transcription factors. Specialized genomic DNA segments that exhibit high affinity to the nuclear matrix in vitro have been designated as matrix/scaffold attachment regions (MARs/SARs). MARs are postulated to anchor chromatin onto the nuclear matrix, thereby organizing genomic DNA into topologically distinct loop domains that are important in replication and transcription. In support of this notion, MARs often colocalize or exist in close proximity to regulatory sequences including enhancers. Base unpairing regions (BURs) are typically 100-150 bp regions within MARs, possess an intrinsic propensity to unwind under negative superhelical strain, and are considered to be hallmark of MARs. To investigate a potential mechanism that could lead to significant alterations in gene expression in cancer cells, this review focuses on a group of chromatin-associated proteins that specifically recognize double stranded BURs. Several important proteins have been identified from cancer cells as BUR-binding proteins, including poly (ADP-ribose) polymerase (PARP-1), Ku autoantigen, SAF-A, HMG-I(Y), nucleolin and p53. Many of these proteins are dramatically upregulated in malignancy of the breast. Increase in the amount of these BUR-binding proteins, some of which are known to interact with each other, may not only provide an architectural core but also recruit functional multi-molecular complexes at the base of chromatin loops to affect multiple distant genes. Experimental strategies by which these proteins can be exploited as carcinoma-specific diagnostic markers and as targets for antineoplastic therapy are discussed.

[Chromosome aberrations, chromatin diminution and their significance in understanding the molecular genetic organization of eukaryotic chromosomes]. / Aberratsii khromosom, diminutsiia khromatina i ikh znachenie v ponimanii molekuliarno-geneticheskoi organizatsii khromosom éukariot.

The paper analyzes the significance of new data obtained in the study of mechanism of formation of radiation-induced chromosome aberrations and in the investigation of chromatin diminution for understanding of the principles of the molecular genetical organization of eucaryotic chromosome. It is concluded that the structure of eucaryotic chromosome follows a certain plan. For its formation, a large number of various innovations were necessary, which could not been prepared simultaneously under the directed action of natural selection based upon the stochastic mutation process.