Index. B Bcl 2 family, abortive apoptosis, 299

Transcription

1 Index A Abortive apoptosis DNA damage, 301 germ cell apoptosis, genes regulation Bcl 2 family, 299 caspases, 300 c-kit, 300 CREM, 300 p53, 300 hormonal regulation, 301 vs. necrosis, 296 programmed cell death, testicular dysfunction conditions aging, obstructive azoospermia, 304 spermiogenesis failure, varicocele, testicular germ cells, Acridine orange test (AOT) chromatin anomalies, critical and troubleshooting points, 193 flow cytometry, 193 mechanism, principle, 191 sperm chromatin denaturation, 189, 190 technique, Aging abortive apoptosis, testicular dysfunction conditions, epididymis, 339 IVF/ICSI treatment, 338 male fertility (see Fertility) morphological characteristics, 339 oxidative stress, semen analysis, testicular sclerosis, 339 Aniline blue (AB), 238 APO-DIRECT kit, Apoptosis, See also Abortive apoptosis Aromatase and estrogen receptors, ART. See Assisted reproductive technology (ART) Assisted reproductive technology (ART), 96, 102 electrophoresis, 427 fertility potential density gradient centrifugation, 442 laboratory tests, sperm function, 443 integrity testing comet assay, 443 cryopreserved sperm usage, DFI, 449 infertile vs. fertile men, 444 IUI, 444 IVF vs. ICSI, 450 pre-implantation development, 449 raw vs. prepared semen, 448 SCD test, 443 SCSA, 443 sorting techniques, 449 sperm DNA damage, testicular vs. ejaculated sperm, 448 TUNEL assay, 443 in vitro fertilization and ICSI, 444 laboratory, SCD test, sperm epigenetic profile, defects clinical importance, imprinting errors, male infertility, imprinting syndromes, children, treatment, 442 Azoospermia, 162 B Bcl 2 family, abortive apoptosis, 299 C Cancer in males chemotherapy (see Chemotherapy) fertility after cancer therapy, fertility restoration, germ-cell transplantation, impact of, surgical management, 353 pharmacological strategies, 356 radiation therapy, 354 reproductive health before cancer treatment, 353 sperm cryopreservation, 356 sperm chromatin structure assay (SCSA ), A. Zini and A. Agarwal (eds.), Sperm Chromatin: Biological and Clinical Applications in Male Infertility and Assisted Reproduction, DOI / , Springer Science+Business Media, LLC

2 506 Index Candida albicans, Capacitation and acrosome reaction, Caput epididymis, 38 Caspases, 300 Chemiluminescence, Chemotherapy animal studies, impact of, clinical studies, impact of, 355 factors, 354 Chlamydia trachomatis, Chromatin and DNA integrity, testicular sperm biological significance, clinical significance, mature sperm, 7 8 packaging density, 183 proteins, 183 structure vs. DNA damage, spermatozoa active sperm chromatin, DNA loop domains organization, histone-bound sperm chromatin, protamine condensation, sperm DNA, 62, Chromatin remodeling spermatids nuclear proteins transition, 309 posttranslational modifications, specific histones and histone variants, 308 spermatogenesis, 29 and spermatogenesis, RNA expression, Chromomycin A3 (CMA3). See Sperm chromatin maturity; Sperm chromomycin A3 assay Chromomycin, sperm nuclear proteins, 237 Chromosome architecture. See Chromosome positioning, spermatozoa Chromosome positioning, spermatozoa fertilization and early development, fluorescence in situ hybridization (FISH), interphase cells, longitude and radial positioning, movement, spermatogenesis, sperm chromocenter, 73 subfertile males, 75 Chromosome territories, Chytochemical tests, sperm chromatin maturity. See Sperm chromatin maturity Computer-assisted semen analysis (CASA), 340 CpG islands, 96 Cryoinjury abortive apoptosis, infertile male sperm, 400 mechanisms of, Cryopreservation, sperm DNA. See Sperm cryopreservation Cyclic adenosine monophosphate responsive element modulator (CREM), 300 D Density-gradient centrifugation (DGC), 398 Diabetes and insulin resistance, SCSA, 146 Displacement (D)-Loop, 82 DNA and environment. See Environment, sperm chromatin DNA breaks detection and characterization, 309 and DNA packaging, origins, 309 type II topoisomerases, 310 DNA damage mammalian spermatozoa (see Chromatin) measurement, spermatozoa (see TUNEL assay) in men (see Sperm chromatin damage) in sperm (see Sperm DNA damage) testing, 459 DNA fragmentation, SCSA, 142 DNA methylation enzymes involution, 97 patterns, germ cells, 98 role, sperm epigenome, SCD test, 156 spermatogenesis, 32 sperm epigenetic profile, sperm nucleoproteins, imprinting, 50 DNA methyltransferases expression, male germ line, DNA protamine complex structure, 9 10 DNA repair mechanisms, spermatids, 312 DNMT enzymes, 99, 248 E Electrophoretic sperm separation clinical applications, development of, sperm sorting, equipment set-up and parameters cleaning, 426 current and voltage settings, 426 separation cartridges and sample handling, temperature settings and buffers, 426 principles of, 423 properties of, spermatozoa, 424 sample recovery and purity, 427 sperm morphology and DNA integrity, 427 sperm vitality and motility, 427 Environment, sperm chromatin air pollution, animal experience, 365 biological and clinical relevance, 362 epidemiological indications, human data, 365 insecticides and pesticides, 369 lifestyle impact, occupational exposure, 367 persistent organohalogen pollutants (POPs), phthalates, 369 SCSA, 145 tobacco and other lifestyle factors, Escherichia coli,

3 Index F Fertility aging male autosomal dominant diseases, genetic risks, 341 natural conception, 341 numerical chromosome disorders, structural chromosomal anomalies, 342 assessment, SCD test, and cancer in men (see Cancer) Fluorescence in situ hybridization (FISH), 71 Fluorochromes, sperm chromomycin A3 assay, G Gene expression, sperm epigenetic profile, 243 Genitourinary infections, SCD test, Genomic integrity. See Spermiogenesis, genetic integrity Germ cell transcriptome. See RNA expression, male germ cells g-rays, sperm chromatin damage, H Hepatitis B and C viruses, Histones modifications, sperm epigenetic profile, sperm nuclear proteins description, isolation and purification, 237 to protamine ratio, 237 Human immunodeficiency virus (HIV) type 1, Human mitochondrial DNA. See Sperm mitochondrial DNA Human sperm chromatin structure attributes, 412 inverse correlation, 412 maturation, sperm HA-binding (see Sperm-hyaluronic acid binding) Human sperm DNA integrity. See Acridine orange test (AOT) Hypothalamic pituitary axis, spermatogenesis, 21 I ICR syndrome, 100 ICSI. See Intracytoplasmic sperm injection (ICSI) Immunocytochemistry, sperm nuclear proteins, Imprinting, spermatogenesis, 46 Infection, male accessory gland. See Male accessory gland infection (MAGI) Infertility, men. See Male subfertility In situ death detection kit, TUNEL assay, , 208 Interferon-g (IFNg), Interleukin 1 (IL 1), 387 Interleukin 6 (IL 6), 387 Interleukin 8 (IL 8), 387 Intracytoplasmic sperm injection (ICSI), Intranuclear positioning, chromosomes. See Chromosome positioning, spermatozoa Intrauterine insemination (IUI), 444. See also Sperm DNA integrity tests In vitro fertilization (IVF). See Pregnancy loss after IVF IUI. See Intrauterine insemination (IUI) L Leydig cells, spermatogenesis, 21 Lifestyle factors in sperm chromatin. See Environment, sperm chromatin Loop domains, Low sperm counts, SCD test, M Macrophage migration inhibitory factor (MIF), 388 Male accessory gland infection (MAGI) anatomopathology, chronic inflammation, characteristics, 375 classification, 376 mechanisms, 377 microorganisms and virus effects Candida albicans, Chlamydia trachomatis, Escherichia coli, Hepatitis B virus and Hepatitis C virus, human immunodeficiency virus (HIV) type 1, Mycoplasma hominis, 382 Neisseria gonorrhoeae, 379 papillomavirus, Trichomonas vaginalis, 383 Ureaplasma urealyticum, oxidative stress, proinflammatory cytokine effects IL 1, IL 6, IL 8, 387 interferon-g (IFNg), macrophage migration inhibitory factor (MIF), 388 tumor necrosis factor-a ( TNFa), ROS and cytokines, 377 ultrasonographic criteria, inflammatory involvement, WHO diagnosis, Male factor infertility. See Sperm nuclear proteins Male gamete. See Spermatogenesis Male germ cell development. See RNA expression, male germ cells Male germ cell epigenetics. See Sperm epigenome Male infertility, sperm histone-protamine ratio, 459 WHO sperm parameters, 444 Male subfertility. See also Sperm chromatin damage cause-related therapy, 329 couple assisted reproductive technology, 322 definition, 321 diagnosis, genetic abnormalities, 322

4 508 Index Mammalian protamines, 8 9 Matrix attachment regions, Mitochondrial DNA (mtdna). See Sperm mitochondrial DNA mrna, spermatozoa. See Sperm RNA Mycoplasma hominis, 382 N Neisseria gonorrhoeae, 379 Nucleoprotein assays, sperm nuclear proteins, 235 O Obstructive azoospermia, 304 Oxidative phosphorylation (OXPHOS), Oxidative stress and aging, role (see Sperm DNA damage) sperm DNA damage, 432 P Papillomavirus, Persistent organohalogen pollutants (POPs), PICSI dish-mediated sperm selection. See Human sperm chromatin structure Planar ionic dyes, sperm chromatin maturity, Polymerase gamma (POLG), Postnatal effects, sperm chromatin damage chemical and environmental factors, 468 freeze-drying, freeze thawing, cryoprotectants absence, g-rays, whole-body exposure, in humans, 475 radiation, paternal exposure, 468 scrotal heat stress, 472 sperm preincubation conditions, transgenerational consequences, Posttranscriptional gene silencing. See RNA interference (RNAi) Pregnancy loss after IVF definitions, 458 etiologies, 458 sperm DNA damage impact, Programmed cell death. See Abortive apoptosis Prostate pathogens, 377, 378 Protamines condensation, sperm DNA, 62, spermatogenesis, sperm nuclear proteins description, 235 isolation and purification, 236 P1-P2 ratio generation, 237 quantification, 237 R Radiation therapy, 354 Replication, mtdna, 85 RNA expression, male germ cells alternative splicing, 113 antisense transcription, biological findings and implications, cdna library to HTS, chromatin-related transcriptional regulations, chromatin remodeling and spermatogenesis, germ cell transcriptome informatics, 114 resources, studies, 110 noncoding RNAs (ncrnas), 114 spermatogenesis, RNA interference (RNAi), 263 Round spermatids, 34 RT-PCR, infertile patients, 261, 262 S SCD test. See Sperm chromatin dispersion (SCD) test Scrotal heat stress, sperm chromatin damage, 472 SCSA. See Sperm chromatin structure assay (SCSA ) Semen analysis, Semen quality, Seminiferous tubules, Sertoli cells. See Seminiferous tubules Sperm and accessory gland infection. See Male accessory gland infection (MAGI) Sperm apoptosis, spermatogenesis, Spermatid differentiation, chromatin remodeling, 6 7 Spermatocytogenesis meiosis, mitosis, 26 Spermatogenesis. See also Abortive apoptosis; RNA expression, male germ cells chromatin remodeling, 29 described, 24 disturbances, 37 DNA methylation, 32 efficiency of, epididymal sperm storage, 38 and etiology, DNA damage, 34 extrinsic influences, 37 intrinsic regulation, 37 Leydig cells, 21 neurological pathways, 20 nuclear protein transitions, postspermiation events, 35 protamines, seminiferous epithelium, seminiferous tubules and sertoli cells, sperm apoptosis, capacitation and acrosome reaction, cervical mucus, entry, 38 transport, in epididymis, spermatocytogenesis meiosis, mitosis, 26

5 Index spermatogonia types, spermatozoa acrosome, endpiece, head, 35 neck, 36 tail, 36 spermiation, 28 spermiogenesis, sperm nuclear DNA strand breaks, steroid hormone interaction, terminal differentiation, 4 5 testes immune status, 37 organization, 21 oxidative stress, 34 transition proteins role, Spermatogonia. See Sperm epigenetic profile Spermatozoa. See also Chromosome positioning, spermatozoa; Sperm mitochondrial DNA; TUNEL assay acrosome, and DNA damage (see Chromatin) endpiece, head, 35 neck, 36 tail, 36 Sperm chromatin. See also Chromosome positioning, spermatozoa; TUNEL assay active, ART (see Assisted reproductive technology (ART)) and chemotoxic therapy (see Chemotherapy) and environmental factors (see Environment, sperm chromatin) gene-environment interaction, 370 histone-bound, chromatin structure vs. DNA damage, and imprinting, laboratory evaluation (see TUNEL assay) maturation, nuclear and cytoplasmic aspects, practical applications, remodeling, reorganization of, fertilization, research, origin, 3 4 and sperm cellular maturity, structure (see Human sperm chromatin structure) variability, in composition, 5 6 Sperm chromatin damage. See also Abortive apoptosis; Postnatal effects, sperm chromatin damage assessment of, 323 factors, 325 general population, impact of, 327 genesis of, intraindividual variation, parameters vs. DNA integrity, subfertile men, impact of, Sperm chromatin denaturation, 189, 190 Sperm chromatin dispersion (SCD) test andrology laboratory 509 azoospermia, 162 genitourinary infections, sperm DNA damage and cancer, 162 toxicogenetics, varicocele, 161 assisted reproductive technology (ART) laboratory, and low sperm counts, methodological versatility chromosomal abnormalities, DNA damage intensity, 155 DNA methylation, 156 oxidative DNA base damage, 156 sperm protein matrix, sperm DNA fragmentation, , technical basis, validation, 155 value of, versatility of, 153 Sperm chromatin maturity planar ionic dyes, structural probes acidic aniline blue (AAB), Chromomycin A3 assay, toluidine blue (TB) stain assay, Sperm chromatin structure assay (SCSA ), 443. See also Acridine orange test (AOT) age, 142 animal fertility, 139 boars, 140 bulls, 139 cancer, cell preparation collection and handling, 489 freezing, chromomycin A3 (CMA3) staining, HDS sperm, 132 clinical utility, 147 development, %DFI and %HDS determination, diabetes and insulin resistance, 146 disulfide bonding, chromatin, DNA fragmentation, 142 environmental heat, 145 fever, 145 flow cytometer setup alignment, 490 gating and debris exclusion, 492 reference samples, sample measurement, workstation, 490 genetics, human fertility, 140 materials, 487 medications, methodology, 128 natural conception, parameters of, protocol steps, 487 raw and computer reoriented data, 128, 129 repeatability,

6 510 Index Sperm chromatin structure assay (SCSA ), 443. See also Acridine orange test (AOT) (continued) RNA staining artifacts, 136 sperm DNA fragmentation test, 126 sperm population s identification, 128, staining solutions and buffers, TESA, Test and ART clinics, 141 vs. TUNEL assays, validation, flow cytometry DNA fragmentation test, genotoxicant exposure, 134 human, mouse, varicoceles, 143, 144 Sperm chromocenter, 73 Sperm chromomycin A3 assay and DNA damage, fluorochromes, semen quality, vs. sperm DNA, Sperm comet assay clinical usefulness, 225 diagnostic and prognostic tests, disadvantage of, DNA adducts measurement, 223 fragmentation measurement, protection, prognostic test, 225 risks, sperm DNA damage, sperm DNA damage, causes, standardized methodology, strengths of, 220 Sperm cryopreservation, 356 antioxidant supplements, 404 conventional sperm parameters, impact of, DNA oxidation, 402 efficacy, cryoprotectants, 403 freezing, 402 human sperm DNA, impact of, 400 repeated freezing and thawing effects, Sperm DNA damage. See also Chromatin; Electrophoretic sperm separation antioxidant depletion, protection, apoptosis, and cancer, SCD test, 162 dietary antioxidant effect idiopathic infertility, 433 sperm DNA integrity, testicular function and spermatogenesis, 433 DNA strand breaks, 286 etiology, 432, 459 fertilization, 447 germ line diagnosis, origin, human sperm and chromatin structure, ICSI and IVF, 344 impaired spermiogenesis, leukocytic infiltration, lipid peroxidation, male infertility, measurement, spermatozoa, 284 normalcy of, 343 oxidative DNA damage, 280 oxidative stress, 432 and aging, chemiluminescence, chemistry, reactive oxygen species (ROS), 279 DHE and Mitosox Red, leukocyte contamination, confounding effect, measurement, spermatozoa, pre-embryo development, 447 pregnancy loss after IVF and ICSI, pregnancy outcome, risks, sperm comet assay, seminal antioxidant capacity male infertility, 433 ROS scavenging enzymes, 432 sperm comet assay, tests of, 459 TUNEL assay measurement, , 206, 210 mechanisms, 202 reference ranges, 211 in vitro antioxidant effect cryopreservation and thawing, 436, 437 exogenous ROS, sperm DNA protection, 435 oxidative injury, 434 semen processing, sperm DNA protection, 436 Sperm DNA fragmentation (SDF), , Sperm DNA integrity tests. See also Acridine orange test (AOT); Sperm cryopreservation; Sperm processing clinical utility, guidelines, 502 IUI, mild male-factor infertility, IVF/ICSI candidates pregnancy loss, 502 severe male-factor infertility, pregnancy planners, screening test, 500 Sperm DNA processing. See Sperm processing Sperm enzymes, 66 Sperm epigenetic profile chromatin organization, sperm nucleus, 249 defects, in assisted reproduction techniques (ART) clinical importance, imprinting errors, male infertility, imprinting syndromes, children, DNA methylation, DNA methyltransferases expression, male germ line, genomic imprinting mechanism, mammals, histone modifications, methods, 252 paternal imprints establishment, male germ line, 247 regulation, gene expression, 243 Sperm epigenome

7 Index DNA methylation enzymes involution, 97 patterns, germ cells, 98 role, epigenetics, 96 germ cell expression, 97 histone modifications and epigenetic memory, 99 male reproductive function animal models, drug targeting, human infertility, Sperm-hyaluronic acid binding cytoplasmic retention, 417 DNA chain integrity prediction, 418 sperm chromatin and sperm cellular maturity, sperm plasma membrane remodeling, 417 Tygerberg morphology, 418 Spermiation, 28 Spermiogenesis, failure, abortive apoptosis, genetic integrity definition, 307 detection and characterization, DNA breaks, 309 DNA breaks and DNA packaging, DNA damage response, 311 DNA repair, haploid cell, 313 DNA repair mechanisms, 312 highly conserved process, 313 impact of, impairment, male gamete, nonhomologous end joining, nuclear proteins transition, 309 oocyte, fertilization, 315 origins of, DNA breaks, 309 posttranslational modifications, specific histones and histone variants, 308 topoisomerases, type II topoisomerases, 310 Spermiogenic RNA retention, 261 Sperm mitochondrial DNA mitochondrial nucleoid, 85 mtdna description, 81 D-Loop, 82 electron transfer chain (ETC), 82 haplotype, 90 inheritance, MELAS syndrome, 84 nucleo-mitochondrial interactions, 83 replication, 85, 87 OXPHOS and sperm function, POLG gene, TFAM, variants, Sperm nuclear proteins acid gel preparation, 237 histones description, isolation and purification, 237 to protamine ratio, isolation techniques, 236 mature sperm nucleus, DNA organisation, nucleohistone to nucleoprotamine transition, nucleoprotein assays, 235 protamines amino-acid sequences, 46, 47 anomalies, infertile patients, description, 235 extraction and electrophoretic separation, 46 isolation and purification, 236 P1-P2 ratio generation, 237 quantification, 237 staining techniques aniline blue (AB), 238 chromomycin, 237 immunocytochemistry, Sperm processing antioxidants, freeze-drying, 405 hazards of, seminal plasma removal, 398 seminal plasma components, testicular sperm, 399 vitrification, 405 Sperm RNA aromatase and estrogen receptors, delivery of, ovocyte, effect on, embryo, 265 embryo development, 264 enos and nnos transcripts, 267 genes coexpressed, somatic and male germ cells, 260 interfering RNA, mature spermatozoa, localization, sperm cells, male germ-cell-specific homologous genes, 260 multiple origins, sperm transcripts, 260 paternal genome packaging, 263 spermatozoal transcripts classes, spermiogenic RNA retention, 261 sperm transcriptome, testis-specific genes, 261 transcript variants, Sperm selection, PICSI. See Human sperm chromatin structure Sperm separation. See Electrophoretic sperm separation Sperm washing, 383, 385 Steroid hormone interaction, spermatogenesis, T Terminal deoxynucleotidyltransferase dutp nick end labeling (TUNEL) assay. See TUNEL assay Testicular sperm DNA damage. See Chromatin Testis-specific genes, 261 Topoisomerases II DNA breaks, 310 DNA damage response, Toxicogenetics, SCD test, Transition nuclear proteins (TPs), Trichomonas vaginalis, 383 Tumor necrosis factor-a ( TNFa), TUNEL assay,

8 512 Index TUNEL assay (continued) APO-DIRECT kit, DNA damage measurement, spermatozoa, equipment and reagents, 496 factors affecting, labelling, 154, 155 principle, 495 sample preparation, 496 in situ death detection kit, , 208 specimen collection, 496 sperm DNA damage measurement, , 206, 210 mechanisms, 202 reference ranges, 211 staining protocol, U Ureaplasma urealyticum, V Varicocele abortive apoptosis, testicular dysfunction conditions, SCD test, 161 sperm chromatin structure assay (SCSA ), 143, 144 Vitamin deficiency, 433 Z Zinc, 13