High-throughput gene expression profiling has become an important tool for investigating transcriptional activity in a variety of biological samples. To date, the vast majority of these experiments have focused on specific biological processes and perturbations. Here, we have generated and analyzed gene expression from a set of samples spanning a broad range of biological conditions. Specifically, we profiled gene expression from 91 human and mouse samples across a diverse array of tissues, organs, and cell lines. Because these samples predominantly come from the normal physiological state in the human and mouse, this dataset represents a preliminary, but substantial, description of the normal mammalian transcriptome. We have used this dataset to illustrate methods of mining these data, and to reveal insights into molecular and physiological gene function, mechanisms of transcriptional regulation, disease etiology, and comparative genomics. Finally, to allow the scientific community to use this resource, we have built a free and publicly accessible website (http://expression.gnf.org) that integrates data visualization and curation of current gene annotations.

/pdf/large-scale-analysis-of-the-human-and-mouse-transcriptomes-3xbhi8cyfk.pdf

Large-scale analysis of the human and mouse transcriptomes

G protein-coupled receptor kinases (GRKs) constitute a family of six mammalian serine/threonine protein kinases that phosphorylate agonist-bound, or activated, G protein-coupled receptors (GPCRs) as their primary substrates. GRK-mediated receptor phosphorylation rapidly initiates profound impairment of receptor signaling, or desensitization. This review focuses on the regulation of GRK activity by a variety of allosteric and other factors: agonist-stimulated GPCRs, beta gamma subunits of heterotrimeric GTP-binding proteins, phospholipid cofactors, the calcium-binding proteins calmodulin and recoverin, posttranslational isoprenylation and palmitoylation, autophosphorylation, and protein kinase C-mediated GRK phosphorylation. Studies employing recombinant, purified proteins, cell culture, and transgenic animal models attest to the general importance of GRKs in regulating a vast array of GPCRs both in vitro and in vivo.

G protein-coupled receptor kinases.

Oxidative stress occurs when the production of potentially destructive reactive oxygen species (ROS) exceeds the bodies own natural antioxidant defenses, resulting in cellular damage. Oxidative stress is a common pathology seen in approximately half of all infertile men. ROS, defined as including oxygen ions, free radicals and peroxides are generated by sperm and seminal leukocytes within semen and produce infertility by two key mechanisms. First, they damage the sperm membrane, decreasing sperm motility and its ability to fuse with the oocyte. Second, ROS can alter the sperm DNA, resulting in the passage of defective paternal DNA on to the conceptus. This review will provide an overview of oxidative biochemistry related to sperm health and will identify which men are most at risk of oxidative infertility. Finally, the review will outline methods available for diagnosing oxidative stress and the various treatments available.

/pdf/oxidative-stress-and-male-infertility-a-clinical-perspective-2nu3kdi0jn.pdf

Oxidative stress and male infertility—a clinical perspective

Intraflagellar transport (IFT) is a rapid movement of multi-subunit protein particles along flagellar microtubules and is required for assembly and maintenance of eukaryotic flagella. We cloned and sequenced a Chlamydomonas cDNA encoding the IFT88 subunit of the IFT particle and identified a Chlamydomonas insertional mutant that is missing this gene. The phenotype of this mutant is normal except for the complete absence of flagella. IFT88 is homologous to mouse and human genes called Tg737. Mice with defects in Tg737 die shortly after birth from polycystic kidney disease. We show that the primary cilia in the kidney of Tg737 mutant mice are shorter than normal. This indicates that IFT is important for primary cilia assembly in mammals. It is likely that primary cilia have an important function in the kidney and that defects in their assembly can lead to polycystic kidney disease.

/pdf/chlamydomonas-ift88-and-its-mouse-homologue-polycystic-33g9hb20w3.pdf

Chlamydomonas IFT88 and Its Mouse Homologue, Polycystic Kidney Disease Gene Tg737, Are Required for Assembly of Cilia and Flagella

https://onlinelibrary.wiley.com/doi/pdf/10.1002/j.1939-4640.2002.tb02599.x

Sperm chromatin structure assay: its clinical use for detecting sperm DNA fragmentation in male infertility and comparisons with other techniques.

In this work we apply the Hoechst 33258 DNA staining, the TUNEL procedure and conventional electron microscopy to study the ejaculate of fertile and infertile men, in order to detect apoptosis in human sperm cells. We have observed that apoptosis is abnormally frequent in the sperm cells of the ejaculate of sterile men, and that it shows the classical biochemical and ultrastructural pattern in spermatozoa, spermatids and apoptotic bodies. These characteristics, involving the chromatin, the nuclear envelope, the plasma membrane, the presence of cytoplasmic vacuoles and the status of mitochondria, are consistent whatever the pathology of the patient is. What is varying is the percentage of the apoptotic sperm cells, that is about 0.1% in fertile controls, and increases up to about 10% in varicocele, infected (including AIDS), "round headed' patients, to 20% in cryptorchid men, to 25% in immature patients, and to 50% in testicular seminoma carriers. Obviously in each category the frequence of apoptotic cells increases concomitantly with the degree of the affection. The present demonstration not only extends to human spermiogenetic epithelium the natural presence of apoptosis, which starts in the testis and is revealed in the ejaculate, but also explains many abnormal ultrastructural sperum patterns hitherto unexplained in fertile and infertile individuals.

Apoptosis in human ejaculated sperm cells (notulae seminologicae 9).

To verify the prevalence of semen bacterial contamination and whether the contamination could decrease sperm quality. Spermiogram, semen culture, and sperm transmission electron microscopy (TEM) analysis were performed. TEM data were elaborated using a mathematical formula that calculates a fertility index (FI)—able to define patients as fertile or infertile—and the percentage of sperm apoptosis, immaturity and necrosis. We aligned the amino acid sequence of beta-tubulin with protein of the most frequent species isolated from semen. Patients were divided according to the contaminating species; in each group, we observed fertile individuals, in whom the semen quality was similar to that of controls and infertile men whose sperm quality was significantly decreased, in terms of motility, FI, apoptosis and necrosis. Partial homology between β-tubulin and bacterial proteins was observed. Sperm bacterial contamination is quite frequent and could contribute to the deterioration of the sperm quality of infertile men.

The presence of bacteria species in semen and sperm quality.

By immunocytochemistry and in situ hybridization at the electron microscopy level, and by the PCR technique, we have shown that HIV-1 binds and enters normal sperm; that viral particles, their antigens, and nucleic acid are present in sperm from HIV-1 infected men; and that such sperm can transfer HIV-1 like particles to normal human oocytes. We also present evidence that a galactosylceramide-like compound is present on the sperm membrane and could function as an alternative receptor for HIV.

/pdf/hiv-particles-in-spermatozoa-of-patients-with-aids-and-their-55x9z9nlbk.pdf

HIV-particles in spermatozoa of patients with AIDS and their transfer into the oocyte

The aim of the present study was to demonstrate the mitogenic and differentiating properties of platelet-rich plasma releasates (PRPr) on human chondrocytes in mono- and three-dimensional cultures. In order to assess if PRPr supplementation could maintain the chondrocyte phenotype or at least inhibit the cell de-differentiation even after several days in culture, we performed a proteomic study on several cell cultures independently grown, for different periods of time, in culture medium with FCS, human serum (HS), and releasates obtained from PRP and platelet-poor plasma (PPP). We found that PRP treatment actually induced in chondrocytes the expression of proteins (some of which novel) involved in differentiation.

Biochemical investigation of the effects of human platelet releasates on human articular chondrocytes.

BACKGROUND: Asthenozoospermia may sometimes be related to genetic structural defects of the sperm tail detectable by transmission electron microscopy. Dysplasia of the fibrous sheath (DFS) is a genetic sperm defect, characterized by dysplastic development of the axonemal and periaxonemal cytoskeleton. We report the case of an infertile man with normal sperm count and total sperm immotility in which dysplasia of the fibrous sheath, Akap3, Akap4 gene deletions, meiotic segregation of chromosomes 18, X and Y and Y microdeletions were investigated. METHODS: A 32-year-old man with a 3-year history of primary infertility presented at our Regional Referral Center for Male Infertility. Family medical history, lymphocyte karyotype, PCR analysis, physical examination, hormone assays and semen analysis were performed. RESULTS: Ultrastructural sperm evaluation showed dysplasia of the fibrous sheath. Immunostaining of AKAP4 protein was negative in sperm tails. PCR analysis revealed intragenic deletions of the Akap3 and Akap4 genes. Fluorescence in situ hybridization on sperm showed a high frequency of XY disomy. CONCLUSION: In this infertile patient, our results suggest a possible relationship between dysplasia of the fibrous sheath, partial deletions in the Akap3 and Akap4 genes and absence of AKAP4 protein in the fibrous sheath. These findings, however, were not detected in another four patients with dysplasia of the fibrous sheath. Our results require future confirmatory molecular analyses.

/pdf/gene-deletions-in-an-infertile-man-with-sperm-fibrous-sheath-2ios9ttntj.pdf

Giulia Collodel

Papers

Apoptosis in human ejaculated sperm cells (notulae seminologicae 9).

The presence of bacteria species in semen and sperm quality.

HIV-particles in spermatozoa of patients with AIDS and their transfer into the oocyte

Biochemical investigation of the effects of human platelet releasates on human articular chondrocytes.

Gene deletions in an infertile man with sperm fibrous sheath dysplasia